null User manual

null  User manual
ROBERT K. COLWELL
University of Connecticut
2ULJLQDOO\3XEOLVKHG%\Sinauer AssocLDWHV
Sunderland, MA
ABOUT THE COVER
The cover illustration, by Shahid Naeem, is an original digital painting, created on a
Macintosh computer. © 2004 Shahid Naeem. Used with the artist’s permission.
Biota 2: The Biodiversity Database Manager
© 2004DQG Robert K. Colwell
6HHWKHQH[WSDJHIRUFRS\ULJKWDQGOLFHQVLQJLQIRUPDWLRQ
For information:
Sinauer Associates, Inc.
P.O. Box 407
23 Plumtree Road
Sunderland, MA 01375-0407
U.S.A.
Biota 2: The Biodiversity Database Manager is not in any way affiliated with the U.S. Department of
Agriculture Systematic Entomology Laboratory’s Biosystematic Information on Terrestrial Arthropods
(BIOTA) nomenclatorial database.
All products mentioned herein are trademarks or registered trademarks of their respective owners.
Copyright (2004 and 2011) Robert K. Colwell Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with the Invariant Sections being the Dedication, the Preface, and Chapter 2 (“Biodiversity Data and Relational Databases”), with the Front-­‐Cover Text, being “Biota: The Biodiversity Database Manager, Robert K. Colwell, University of Connecticut, Originally Published by Sinauer Associates, Sunderland, Massachusetts.” A copy of the license is included in the section entitled "GNU Free Documentation License" that begins on the next page. GNU Free Documentation License Version 1.3, 3 November 2008 Copyright (C) 2000, 2001, 2002, 2007, 2008 Free Software Foundation, Inc. <http://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. 0. PREAMBLE The purpose of this License is to make a manual, textbook, or other functional and useful document "free" in the sense of freedom: to assure everyone the effective freedom to copy and redistribute it, with or without modifying it, either commercially or noncommercially. Secondarily, this License preserves for the author and publisher a way to get credit for their work, while not being considered responsible for modifications made by others. This License is a kind of "copyleft", which means that derivative works of the document must themselves be free in the same sense. It complements the GNU General Public License, which is a copyleft license designed for free software. We have designed this License in order to use it for manuals for free software, because free software needs free documentation: a free program should come with manuals providing the same freedoms that the software does. But this License is not limited to software manuals; it can be used for any textual work, regardless of subject matter or whether it is published as a printed book. We recommend this License principally for works whose purpose is instruction or reference. 1. APPLICABILITY AND DEFINITIONS This License applies to any manual or other work, in any medium, that contains a notice placed by the copyright holder saying it can be distributed under the terms of this License. Such a notice grants a world-­‐wide, royalty-­‐free license, unlimited in duration, to use that work under the conditions stated herein. The "Document", below, refers to any such manual or work. Any member of the public is a licensee, and is addressed as "you". You accept the license if you copy, modify or distribute the work in a way requiring permission under copyright law. A "Modified Version" of the Document means any work containing the Document or a portion of it, either copied verbatim, or with modifications and/or translated into another language. A "Secondary Section" is a named appendix or a front-­‐matter section of the Document that deals exclusively with the relationship of the publishers or authors of the Document to the Document's overall subject (or to related matters) and contains nothing that could fall directly within that overall subject. (Thus, if the Document is in part a textbook of mathematics, a Secondary Section may not explain any mathematics.) The relationship could be a matter of historical connection with the subject or with related matters, or of legal, commercial, philosophical, ethical or political position regarding them. The "Invariant Sections" are certain Secondary Sections whose titles are designated, as being those of Invariant Sections, in the notice that says that the Document is released under this License. If a section does not fit the above definition of Secondary then it is not allowed to be designated as Invariant. The Document may contain zero Invariant Sections. If the Document does not identify any Invariant Sections then there are none. The "Cover Texts" are certain short passages of text that are listed, as Front-­‐Cover Texts or Back-­‐Cover Texts, in the notice that says that the Document is released under this License. A Front-­‐Cover Text may be at most 5 words, and a Back-­‐Cover Text may be at most 25 words. A "Transparent" copy of the Document means a machine-­‐readable copy, represented in a format whose specification is available to the general public, that is suitable for revising the document straightforwardly with generic text editors or (for images composed of pixels) generic paint programs or (for drawings) some widely available drawing editor, and that is suitable for input to text formatters or for automatic translation to a variety of formats suitable for input to text formatters. A copy made in an otherwise Transparent file format whose markup, or absence of markup, has been arranged to thwart or discourage subsequent modification by readers is not Transparent. An image format is not Transparent if used for any substantial amount of text. A copy that is not "Transparent" is called "Opaque". Examples of suitable formats for Transparent copies include plain ASCII without markup, Texinfo input format, LaTeX input format, SGML or XML using a publicly available DTD, and standard-­‐conforming simple HTML, PostScript or PDF designed for human modification. Examples of transparent image formats include PNG, XCF and JPG. Opaque formats include proprietary formats that can be read and edited only by proprietary word processors, SGML or XML for which the DTD and/or processing tools are not generally available, and the machine-­‐
generated HTML, PostScript or PDF produced by some word processors for output purposes only. The "Title Page" means, for a printed book, the title page itself, plus such following pages as are needed to hold, legibly, the material this License requires to appear in the title page. For works in formats which do not have any title page as such, "Title Page" means the text near the most prominent appearance of the work's title, preceding the beginning of the body of the text. The "publisher" means any person or entity that distributes copies of the Document to the public. A section "Entitled XYZ" means a named subunit of the Document whose title either is precisely XYZ or contains XYZ in parentheses following text that translates XYZ in another language. (Here XYZ stands for a specific section name mentioned below, such as "Acknowledgements", "Dedications", "Endorsements", or "History".) To "Preserve the Title" of such a section when you modify the Document means that it remains a section "Entitled XYZ" according to this definition. The Document may include Warranty Disclaimers next to the notice which states that this License applies to the Document. These Warranty Disclaimers are considered to be included by reference in this License, but only as regards disclaiming warranties: any other implication that these Warranty Disclaimers may have is void and has no effect on the meaning of this License. 2. VERBATIM COPYING You may copy and distribute the Document in any medium, either commercially or noncommercially, provided that this License, the copyright notices, and the license notice saying this License applies to the Document are reproduced in all copies, and that you add no other conditions whatsoever to those of this License. You may not use technical measures to obstruct or control the reading or further copying of the copies you make or distribute. However, you may accept compensation in exchange for copies. If you distribute a large enough number of copies you must also follow the conditions in section 3. You may also lend copies, under the same conditions stated above, and you may publicly display copies. 3. COPYING IN QUANTITY If you publish printed copies (or copies in media that commonly have printed covers) of the Document, numbering more than 100, and the Document's license notice requires Cover Texts, you must enclose the copies in covers that carry, clearly and legibly, all these Cover Texts: Front-­‐Cover Texts on the front cover, and Back-­‐Cover Texts on the back cover. Both covers must also clearly and legibly identify you as the publisher of these copies. The front cover must present the full title with all words of the title equally prominent and visible. You may add other material on the covers in addition. Copying with changes limited to the covers, as long as they preserve the title of the Document and satisfy these conditions, can be treated as verbatim copying in other respects. If the required texts for either cover are too voluminous to fit legibly, you should put the first ones listed (as many as fit reasonably) on the actual cover, and continue the rest onto adjacent pages. If you publish or distribute Opaque copies of the Document numbering more than 100, you must either include a machine-­‐readable Transparent copy along with each Opaque copy, or state in or with each Opaque copy a computer-­‐network location from which the general network-­‐using public has access to download using public-­‐standard network protocols a complete Transparent copy of the Document, free of added material. If you use the latter option, you must take reasonably prudent steps, when you begin distribution of Opaque copies in quantity, to ensure that this Transparent copy will remain thus accessible at the stated location until at least one year after the last time you distribute an Opaque copy (directly or through your agents or retailers) of that edition to the public. It is requested, but not required, that you contact the authors of the Document well before redistributing any large number of copies, to give them a chance to provide you with an updated version of the Document. 4. MODIFICATIONS You may copy and distribute a Modified Version of the Document under the conditions of sections 2 and 3 above, provided that you release the Modified Version under precisely this License, with the Modified Version filling the role of the Document, thus licensing distribution and modification of the Modified Version to whoever possesses a copy of it. In addition, you must do these things in the Modified Version: A. Use in the Title Page (and on the covers, if any) a title distinct from that of the Document, and from those of previous versions (which should, if there were any, be listed in the History section of the Document). You may use the same title as a previous version if the original publisher of that version gives permission. B. List on the Title Page, as authors, one or more persons or entities responsible for authorship of the modifications in the Modified Version, together with at least five of the principal authors of the Document (all of its principal authors, if it has fewer than five), unless they release you from this requirement. C. State on the Title page the name of the publisher of the Modified Version, as the publisher. D. Preserve all the copyright notices of the Document. E. Add an appropriate copyright notice for your modifications adjacent to the other copyright notices. F. Include, immediately after the copyright notices, a license notice giving the public permission to use the Modified Version under the terms of this License, in the form shown in the Addendum below. G. Preserve in that license notice the full lists of Invariant Sections and required Cover Texts given in the Document's license notice. H. Include an unaltered copy of this License. I. Preserve the section Entitled "History", Preserve its Title, and add to it an item stating at least the title, year, new authors, and publisher of the Modified Version as given on the Title Page. If there is no section Entitled "History" in the Document, create one stating the title, year, authors, and publisher of the Document as given on its Title Page, then add an item describing the Modified Version as stated in the previous sentence. J. Preserve the network location, if any, given in the Document for public access to a Transparent copy of the Document, and likewise the network locations given in the Document for previous versions it was based on. These may be placed in the "History" section. You may omit a network location for a work that was published at least four years before the Document itself, or if the original publisher of the version it refers to gives permission. K. For any section Entitled "Acknowledgements" or "Dedications", Preserve the Title of the section, and preserve in the section all the substance and tone of each of the contributor acknowledgements and/or dedications given therein. L. Preserve all the Invariant Sections of the Document, unaltered in their text and in their titles. Section numbers or the equivalent are not considered part of the section titles. M. Delete any section Entitled "Endorsements". Such a section may not be included in the Modified Version. N. Do not retitle any existing section to be Entitled "Endorsements" or to conflict in title with any Invariant Section. O. Preserve any Warranty Disclaimers. If the Modified Version includes new front-­‐matter sections or appendices that qualify as Secondary Sections and contain no material copied from the Document, you may at your option designate some or all of these sections as invariant. To do this, add their titles to the list of Invariant Sections in the Modified Version's license notice. These titles must be distinct from any other section titles. You may add a section Entitled "Endorsements", provided it contains nothing but endorsements of your Modified Version by various parties-­‐-­‐for example, statements of peer review or that the text has been approved by an organization as the authoritative definition of a standard. You may add a passage of up to five words as a Front-­‐Cover Text, and a passage of up to 25 words as a Back-­‐Cover Text, to the end of the list of Cover Texts in the Modified Version. Only one passage of Front-­‐Cover Text and one of Back-­‐Cover Text may be added by (or through arrangements made by) any one entity. If the Document already includes a cover text for the same cover, previously added by you or by arrangement made by the same entity you are acting on behalf of, you may not add another; but you may replace the old one, on explicit permission from the previous publisher that added the old one. The author(s) and publisher(s) of the Document do not by this License give permission to use their names for publicity for or to assert or imply endorsement of any Modified Version. 5. COMBINING DOCUMENTS You may combine the Document with other documents released under this License, under the terms defined in section 4 above for modified versions, provided that you include in the combination all of the Invariant Sections of all of the original documents, unmodified, and list them all as Invariant Sections of your combined work in its license notice, and that you preserve all their Warranty Disclaimers. The combined work need only contain one copy of this License, and multiple identical Invariant Sections may be replaced with a single copy. If there are multiple Invariant Sections with the same name but different contents, make the title of each such section unique by adding at the end of it, in parentheses, the name of the original author or publisher of that section if known, or else a unique number. Make the same adjustment to the section titles in the list of Invariant Sections in the license notice of the combined work. In the combination, you must combine any sections Entitled "History" in the various original documents, forming one section Entitled "History"; likewise combine any sections Entitled "Acknowledgements", and any sections Entitled "Dedications". You must delete all sections Entitled "Endorsements". 6. COLLECTIONS OF DOCUMENTS You may make a collection consisting of the Document and other documents released under this License, and replace the individual copies of this License in the various documents with a single copy that is included in the collection, provided that you follow the rules of this License for verbatim copying of each of the documents in all other respects. You may extract a single document from such a collection, and distribute it individually under this License, provided you insert a copy of this License into the extracted document, and follow this License in all other respects regarding verbatim copying of that document. 7. AGGREGATION WITH INDEPENDENT WORKS A compilation of the Document or its derivatives with other separate and independent documents or works, in or on a volume of a storage or distribution medium, is called an "aggregate" if the copyright resulting from the compilation is not used to limit the legal rights of the compilation's users beyond what the individual works permit. When the Document is included in an aggregate, this License does not apply to the other works in the aggregate which are not themselves derivative works of the Document. If the Cover Text requirement of section 3 is applicable to these copies of the Document, then if the Document is less than one half of the entire aggregate, the Document's Cover Texts may be placed on covers that bracket the Document within the aggregate, or the electronic equivalent of covers if the Document is in electronic form. Otherwise they must appear on printed covers that bracket the whole aggregate. 8. TRANSLATION Translation is considered a kind of modification, so you may distribute translations of the Document under the terms of section 4. Replacing Invariant Sections with translations requires special permission from their copyright holders, but you may include translations of some or all Invariant Sections in addition to the original versions of these Invariant Sections. You may include a translation of this License, and all the license notices in the Document, and any Warranty Disclaimers, provided that you also include the original English version of this License and the original versions of those notices and disclaimers. In case of a disagreement between the translation and the original version of this License or a notice or disclaimer, the original version will prevail. If a section in the Document is Entitled "Acknowledgements", "Dedications", or "History", the requirement (section 4) to Preserve its Title (section 1) will typically require changing the actual title. 9. TERMINATION You may not copy, modify, sublicense, or distribute the Document except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense, or distribute it is void, and will automatically terminate your rights under this License. However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation. Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice. Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, receipt of a copy of some or all of the same material does not give you any rights to use it. 10. FUTURE REVISIONS OF THIS LICENSE The Free Software Foundation may publish new, revised versions of the GNU Free Documentation License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. See http://www.gnu.org/copyleft/. Each version of the License is given a distinguishing version number. If the Document specifies that a particular numbered version of this License "or any later version" applies to it, you have the option of following the terms and conditions either of that specified version or of any later version that has been published (not as a draft) by the Free Software Foundation. If the Document does not specify a version number of this License, you may choose any version ever published (not as a draft) by the Free Software Foundation. If the Document specifies that a proxy can decide which future versions of this License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Document. 11. RELICENSING "Massive Multiauthor Collaboration Site" (or "MMC Site") means any World Wide Web server that publishes copyrightable works and also provides prominent facilities for anybody to edit those works. A public wiki that anybody can edit is an example of such a server. A "Massive Multiauthor Collaboration" (or "MMC") contained in the site means any set of copyrightable works thus published on the MMC site. "CC-­‐BY-­‐SA" means the Creative Commons Attribution-­‐Share Alike 3.0 license published by Creative Commons Corporation, a not-­‐for-­‐profit corporation with a principal place of business in San Francisco, California, as well as future copyleft versions of that license published by that same organization. "Incorporate" means to publish or republish a Document, in whole or in part, as part of another Document. An MMC is "eligible for relicensing" if it is licensed under this License, and if all works that were first published under this License somewhere other than this MMC, and subsequently incorporated in whole or in part into the MMC, (1) had no cover texts or invariant sections, and (2) were thus incorporated prior to November 1, 2008. The operator of an MMC Site may republish an MMC contained in the site under CC-­‐BY-­‐SA on the same site at any time before August 1, 2009, provided the MMC is eligible for relicensing. To tireless visionaries and unsung heroes around the
world who work to document, understand, and preserve
the biodiversity of the planet.
Brief Table of Contents
PART 1
Introducing Biota
Chapter 1 Quick Start
Chapter 2 Biodiversity Data and Relational Databases
Chapter 3 Key Concepts
Chapter 4 Biota Menus and Menu Items: An Annotated Guide
Chapter 5 Overview of Biota’s Tools and Features
Chapter 6 A Brief Tutorial With the Demo Database
PART 2
Entering Data
Chapter 7 Overview of Record Input Screens
Chapter 8 Record Codes
Chapter 9 Special Data Types
Chapter 10 Working With Records In Record Listing and Input Screens
Chapter 11 Input—Table by Table
PART 3
Finding and Revising Data
Chapter 12 Finding and Updating Records
Chapter 13 Creating, Finding, and Updating Specimen Series
PART 4
Printing Reports and Labels
Chapter 14 Printing Reports
Chapter 15 Printing Labels
PART 5
Customizing Biota
Chapter 16 User-Defined Auxiliary Fields and the Project System
Chapter 17 Default Entries and Entry Choice Lists (Pick Lists)
Chapter 18 Re-naming Fields
PART 6
Special Tools and Features
Chapter 19 Images
Chapter 20 References
Chapter 21 The Specimen Loan System
Chapter 22 Determination Histories
Chapter 23 Synonymy System
Chapter 24 Host-Guest Relations
Chapter 25 Temporary Taxa for Approximate Determinations
Chapter 26 Security: Passwords and Access Privileges
PART 7
Exporting and Importing Data
Chapter 27 Exporting Data
Chapter 28 Importing Data
Continues....
—Click any entry to go to the corresponding page—
PART 8
Biota and the Internet
Chapter 29 Internet Strategies
Chapter 30 Biota's Onboard Web Server
Chapter 31 Web Browser Mode and the Web Assistant
Chapter 32 Database Client Mode
Chapter 33 Exporting Static Web Pages
PART 9
Appendixes
Appendix A Biota Tables, Fields, and Relational Links
Appendix B Setting Preferences
Appendix C Keyboard Shortcuts
Appendix D The 4D Label Wizard
Appendix E The 4D Quick Report Editor
Appendix F Updating Biota 1.x Data Files to Biota 2 Format
Appendix G Merging Two Biota Data Files
Appendix H Using Biota4D with 4D Server or 4th Dimension
Appendix I Data File Backup, Recovery, Compacting, Indexing, and Segmenting
Appendix J Biota Data File Conversion: Mac OS and Windows
Appendix K Barcodes
Appendix L Troubleshooting and Support
—Click any entry to go to the corresponding page—
Detailed Table of Contents
PART 1
INTRODUCING BIOTA
CHAPTER 1 QUICK START
Quick-Start Strategies
Special Strategies for Special Uses of Biota
Upgrading from Biota 1.x
Updating Biota 1.x Data Files
New Tools and Features in Biota 2
CHAPTER 2 BIODIVERSITY DATA AND RELATIONAL DATABASES
Biodiversity Data
Why Use a Relational Database?
Flatfiles
The Relational Model
Linking Fields
Efficiency of Data Input and Updating
Efficiency of Relational Searches
CHAPTER 3 KEY CONCEPTS
Tables
Core Tables
Peripheral Tables
Fields and Records
Key Fields
Duplicate Key Errors
Linking Fields: Parent and Child Records
Data Files
Opening a Biota Data File When Launching Biota
Creating an Empty Biota Data File While Launching Biota
Opening a Biota Data File or Creating a New Biota File from Within Biota
Saving Changes in a Biota Data File
To Find Out Which Data File Is Currently Open
Selections and Processes
Record Sets
The Record Set Options Screen
How Biota Uses Record Sets
To Display a Record Set
To Empty All Record Sets
Record Set Pointer Files
Saving a Record Set Pointer File: First Method
Saving a Record Set Pointer File: Second Method
Loading a Record Set Pointer File
Loaded Record Set Pointer Files and the Current Record Set
CHAPTER 4 BIOTA MENUS AND MENU ITEMS: AN ANNOTATED GUIDE
Biota Menus: Quick Reference
Access Privileges for Menu Items
The Menu Bar
The File Menu
—Click on any entry to go to the corresponding page—
Page 1
Detailed Table of Contents
The Edit Menu
The Input Menu
The Series Menu
The Find Menu
The Display Menu
The Labels Menu
The Import/Export (Im/Export) Menu
The Loans Menu
The Special Menu
The Help Menu
The Shortcut Screen
CHAPTER 5 OVERVIEW OF BIOTA’S TOOLS AND FEATURES
Architectural Features
Multitasking
Single-user vs. Client/Server Versions
Biodiversity Information Types
Specimen-Based Data
Living Organisms
“Lot”-Based Data
Site-Based Species Lists With No Specimens
Plot-Based Data
Special Data Types
Images
Literature Reference System
Recursive Specimen Relations (“Host-Guest” Links)
Tools for Customizing Biota
Field Aliases
Auxiliary Fields and Projects
Date Formats
Spatial Reference (Georeference) Formats
Spanish Dialog Screens
Table Colors for Input and Record Listing Screens
Information Input
Record Sets
Automatic Prompting for Parent Record Entry
Wildcard Entry for Linking Fields
Lookup Tool for Entering Record Codes in Linking Fields
Default Entries and Entry Choice Lists (Pick Lists)
Field Value Defaults
Using an Existing Record as a Template for a New One
Automated Entry of Specimen Record Series
Automatic Record Code Assignment
Barcode Entry of Record Codes
Record Retrieval and Manipulation: General Tools
Multifunction Record Listing Screens
Simultaneous Display of Records from Any Number of Tables
Displaying Record Sets
Ad Hoc Queries for All Tables
Special Tools for Finding Records in One Table Based on a Set of Records in
Another Table
—Click on any entry to go to the corresponding page—
Page 2
Detailed Table of Contents
Page 3
Finding Records for Lower Taxa Based on Higher Taxa
Finding Records for Higher Taxa Based on Lower Taxa
Finding Place Records (Collection or Locality) for Specimens or Species
Finding Specimen or Species Records for Places (Collections or Localities)
Sequential, Cross-Hierarchy Searches
Finding Records by Record Code
Single Records
Unordered Specimen Series
Ordered Specimen Series
Special Tools for Updating Records
Updating Specimen Determinations and Other Specimen Information: Ordered
Specimen Series
Updating Records (Any Table) by Importing Information from Text Files
The Find and Replace Tool
Keeping Track of Synonymies
Tools for Maintaining Database Security and Integrity
User Password System
User Access (Privilege) Levels
Data File Password Link
Automatic Updating of Linking Fields in Child Records
Finding Orphan and Childless Records
Record Deletion Control
Record Creation Control
Automatic Recording of Specimen Determination Histories
Duplicate Species Checking
Automatic Record Dating
Maintenance and Repair Tools
Reports and Labels
Printed Reports
Labels for Fluid-Preserved, Pinned, Slide-Mounted, or Herbarium Specimens
Custom Label Printing
Species Labels
Specimen Loan System
Lending Specimens
Recording Returns
Loan Forms
Text Flatfile Export of Specimens Loaned
Importing Data
The Import Editor
Importing Images
Exporting Data
The Export Editor
Exporting Images
Exporting Specimen Flatfiles
Exporting Taxonomic Flatfiles
Exporting Notes
Exporting Auxiliary Field Values
Exporting Character Matrices in the NEXUS Format
Exporting Place- by-Taxon Incidence or Abundance Tables
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Exporting “Specimens Examined” Lists
Custom Export
Internet Publishing Tools
On-board Web Server: Dynamic Access
Exporting Static Web Pages
Accessibility Features
Keyboard Shortcuts
CHAPTER 6 A BRIEF TUTORIAL WITH THE DEMO DATABASE
Installing Biota and Opening the Demo Data File
What’s in the Demo Data File?
Lesson 1. Displaying and Editing Existing Records
Step by Step
Lesson 1 Review
Lesson 2. Creating New Records One Table at a Time
Step by Step
Lesson 2 Review
Lesson 3. Creating New Records “On the Fly”
Step by Step
Lesson 3 Review
Lesson 4. Finding Records (Queries)
Step by Step
Lesson 4 Review
On Your Own—What to Try Next
(Contents continued on the next page)
—Click on any entry to go to the corresponding page—
Page 4
Detailed Table of Contents
Page 5
PART 2
ENTERING DATA
CHAPTER 7 OVERVIEW OF RECORD INPUT SCREENS
Screen Colors
To Change the Screen Color Scheme
Entry Areas and Default Entry Order
Input Screen Tabs and Buttons
Input Screen Tabs
Keyboard Shortcuts for Input Screen Tabs
Keyboard Shortcuts for Input Screen Buttons
Entering Data in Linking Fields
“On-the-Fly” Creation of Linked Records
Table-by-Table Creation of Linked Records
A Powerful Shortcut: Wildcard Data Entry for Linking Fields
Overriding Wildcard Input for Linking Fields
CHAPTER 8 RECORD CODES
Record Code Concepts
Why Does Biota Require and Display Record Codes?
Why Does Biota Require Species Codes?
Guidelines and Suggestions for Designing Record Code Systems
Specimen Codes
Sequential Specimen Codes
Unified Record Code Systems: Specimen, Collection, and Locality Codes
Locality Codes
Species Codes
Sorting Records by Record Codes
Using Entry Choice Lists to Enter Record Code Prefixes
Assigning New Record Codes Automatically During Data Entry
The Format of Automatically Generated Record Codes
Setting Record Code Prefixes and Lengths
Assigning New Record Codes Using an “Assign” Button: Step by Step
Setting Default Prefixes for Recognizing Specimen and Species Record Codes
Using Alphanumeric Specimen Codes with the Series Tools
Setting Up for Automatic Record Code Prefix Recognition
Substituting Different Prefixes for Barcode Prefixes in the Data File
CHAPTER 9 SPECIAL DATA TYPES
Intermediate Taxonomic Levels (Subtaxa and Supertaxa)
The Dilemma of Intermediate Levels
How Biota Handles Intermediate Taxonomic Levels
Default Names for Intermediate Taxon Fields
Renaming an Intermediate Taxon Field
Defining Additional Intermediate Levels
Updating Intermediate Taxa
Dates
Automatically Recorded Dates
Date Formats in Biota: U.S. and International Formats
Entering Dates
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Page 6
Entering Today’s Date
Entering a Default Date
Date Displays on Record Listing Screens
Partial Dates
How Biota Handles Partial Dates
Importing and Exporting Partial Dates
Collection Date Ranges
Collection Date Ranges on Labels and in Exported Text Files
Spatial Coordinates
Options for Recording Spatial Coordinates in Biota
Spatial Coordinate Fields in The Collection Table
Latitude and Longitude (Locality Table)
Conversion Formulas for Latitude and Longitude Unit Systems
Setting the Display Format and Internal Resolution for Latitude and Longitude
Setting Latitude and Longitude Display Resolution for Individual Locality
Records
Alternate Coordinates (Locality Table)
Setting the Display Format for Alternate Coordinates in the Locality Record
Listing Screen
Suggestions for Use of the Alt Coordinate Fields
Converting Non-Latitude/Longitude Coordinates to Latitude and Longitude
Latitude/Longitude and Alternate Coordinates on Labels or Reports and in Exported
Text Files
CHAPTER 10 WORKING WITH RECORDS IN RECORD LISTING AND INPUT SCREENS
Displaying Records in a Standard Record Listing Screen
Changing the Fields Displayed in a Record Listing Screen
Fields Available for Display in Record Listing Screens
Viewing, Editing, Printing, or Deleting Individual Records from an Input Screen
To View an Entry That Is Longer Than the Entry Area
To Return to the Record Listing Screen
Editing and Saving Changes to the Record
Duplicating a Record Displayed in the Input Screen Using the “Carry” Button
Printing a Single Record Displayed in an Input Screen
Deleting a Record Displayed in the Input Screen
Moving Up the Table Hierarchies from an Input Screen: Parent Record Buttons
Displaying Records with the Parent Record Button
Editing Records Displayed with the Parent Record Button
Moving Down the Table Hierarchies From an Input Screen: Child Records Buttons
Displaying Records with a Child Records Button
Using the Add Record Button
Using an Existing Record as a Template for a New Record
Creating a Sub-Selection of Records
Deleting a Group of Records from the Record Listing Screen
Sorting Records in Record Listing Screens
Using Fields from Related Tables for Sorting Records
Guidelines for Using Fields from Related Tables as Sort Criteria
Using Formulas to Sort Dates by Day, Month, or Year
Using a Formula to Sort Numbers in an Alphanumeric Field
Printing Reports or Creating Text Files Based on Records in a Record Listing
Screen
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Page 7
Printing a Report Based on Records in a record Listing Screen
Exporting a Text Flatfile Based on Records in a Record Listing screen
Keyboard Shortcuts for Record Listing Screens
Keyboard Shortcuts Always Available
Optional Keyboard Shortcuts
Using the Optional Keyboard Shortcuts for Record Selection and Revision
CHAPTER 11 INPUT—TABLE BY TABLE
Specimen Input
Entering Specimen Data: The “General” Tab
Entering Specimen Data: The “Determination” Tab
Entering Specimen Data: The “Preparation” Tab
Entering Specimen Data: The “Images,” “Aux Fields,” “Notes,” and “Refs” Tabs
Collection Input
Entering Collection Data: The “General” Tab
Entering Collection Data: The “Host Record,” “Georeference,” “Images,” “Aux
Fields,” “Notes,” and “Refs” Tabs
Specimen and Collection Combined Input
Specimen and Collection Combined Input: How It Works
Specimen and Collection Combined Input: Tabs of the Input Screen
Specimen and Collection Combined Input: The General Tab
Specimen and Collection Combined Input: The Collection Tab
Specimen and Collection Combined Input: The “Determination,” “Preparation,”
“Images,” “Aux Fields,” “Notes,” and “Refs” Tabs
Locality Input
Entering Locality Data: The “General” Tab
Entering Locality Data: Entering Latitude and Longitude in the “Georeference”
Tab
Entering Locality Data: Entering Alternate Coordinates in the “Georeference” Tab
Entering Locality Data: The “Images,” “Aux Fields,” “Notes,” and “Refs” Tabs
Species Input
Entering Species Data: The “Classification” Tab
Entering Species Data: The “Subsp/Names” Tab
Entering Species Data: The “Dist/Types” Tab
Entering Species Data: Display, Printing, and Export of Infraspecific Taxon,
Distribution, and Type Information
Entering Species Data: The “Synonymy,” “Images,” “Aux Fields,” “Notes,” and
“Refs” Tabs
Genus, Family, Order, Class, Phylum, and Kingdom Input
Differences among the Higher Taxon Input screens
A Special Problem for Genera: Legitimate Duplicate Generic Names
Entering Data in a Higher Taxon Input Screen: Step by Step
Personnel Input
Entering Personnel Data: The “General” Tab
Entering Personnel Data: The “Group” Tab
Entering Personnel Data: The “Notes” Tab
Displaying, Changing, or Reordering Group Membership for an Existing Group
Personnel Record
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Page 8
Notes Input
Entering a New Note in the Note Tab (Species, Specimen, Collection, Locality,
and Loans)
Viewing, Editing, or Deleting a Note
Carrying Notes
(Contents continued on the next page)
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Page 9
PART 3
FINDING AND REVISING DATA
CHAPTER 12 FINDING AND UPDATING RECORDS
Finding and Displaying All Records for a Table
Finding Records Using the Taxonomic Hierarchy
Special Tools for Finding Records in One Table Based on a Set of Records in
Another Table
Finding Records for Lower Taxa Based on Higher Taxa
Finding Records for Higher Taxa Based on Lower Taxa
Finding Place Records (Collection or Locality) for Specimens or Species
Finding Specimen or Species Records for Places (Collections or Localities)
Sequential, Cross-Hierarchy Searches
The Query Editor, a General-Purpose Tool for Finding Records Based on Content
Using the Query Editor: Step by Step
Using Fields from Parent Tables in the Query Editor
Using Fields from Child Tables in the Query Editor
Using the Query Editor to Find Records Based on Notes
Using the Query Editor with Auxiliary Field Values
Using the Query Editor with Auxiliary Field Values in Combination with Other
Criteria
Finding Records by Record Codes
Finding Host and Guest Specimens and Collections
Finding Childless and Orphan Records
Finding Childless Records
Finding Orphan Records
Automatically Updating Child Records by Changing a Parent Record
Updating All Child Records by Changing a Parent Record
“Splitting” a Taxon: Linking a Subset of the Child Records to a New Parent
Record
Updating Records Using the Find and Replace Tool
Using the Find and Replace Tool: Step by Step
Using the Find and Replace Tool for Auxiliary Fields and Notes Tables
Updating Records Using the Import Editor
CHAPTER 13 CREATING, FINDING, AND UPDATING SPECIMEN SERIES
Using the “Input Specimen Series” and “Input and Identify Specimen Series” Tools
Specimen Series Input: Step by Step
Using the “Find Specimen Series” and “Find and Identify Specimen Series” Tools
Finding (or Finding and Identifying) Specimen Series: First Steps
If You Choose “In Any Order”
If You Choose “In Consecutive Order”
If You Choose “Use the Specimen Record Set”
Finding (or Finding and Identifying) Specimen Series: Final Steps
PART 4
PRINTING REPORTS AND LABELS
CHAPTER 14 PRINTING REPORTS
Printing and Previewing Procedures for Reports and Labels
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Page 10
Printing an Individual Record
Printing a Report Based on a Selection of Records
Printing a Report Based on the Active Record Set for a Table
Printing a Report Based on a Record Set Pointer File
Printing a Standard or Custom Report Based on the Records in a Record Listing
Screen
Printing a Specimen Count by Taxon Report
Designing and Printing Reports with the Quick Report Editor
Launching the 4D Quick Report Editor
Left Margins in Quick Reports
Special Biota Date, Georeference, and Agent Formats in Quick Reports
CHAPTER 15 PRINTING LABELS
Printing and Previewing Procedures for Labels
Label Option Windows
Sort Options
Data Options
Output Options
Collection Labels
Information Included on Collection Labels
Printing or Exporting Collection Labels: Step by Step
Pin and Vial Specimen Locality Labels
Information Included on Pin and Vial Locality Label Text
Printing or Exporting Pin or Vial Specimen Locality Labels: Step by Step
Pin and Vial Specimen Determination Labels
Information Included in Pin and Vial Determination Label Text
Printing Pin or Vial Specimen Determination Labels: Step by Step
Slide Specimen Labels
Information Included in Slide Specimen Label Text
Printing or Exporting Slide Specimen Labels: Step by Step
Herbarium Specimen Labels
Information Included in Herbarium Specimen Label Text
Printing or Exporting Herbarium Specimen Labels: Step by Step
Species Labels
Information Included on Species Labels
Printing Species Labels: Step by Step
Designing and Printing Custom Labels
Launching the 4D Label Wizard
PART 5
CUSTOMIZING BIOTA
CHAPTER 16 USER-DEFINED AUXILIARY FIELDS AND THE PROJECT SYSTEM
Core Fields and Auxiliary Fields
How Auxiliary Fields Work
Auxiliary Field Value Tables
Auxiliary Field Name Tables
The “Auxiliary Fields” Field in Parent Tables
Sorting Parent Records Based on Auxiliary Fields
Creating, Editing, and Ordering Auxiliary Field Names
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Page 11
Opening the Field Name Editor
Using the Field Name Editor
Entering and Displaying Data in Auxiliary Fields
Entering New Data or Editing Data in Auxiliary Fields
Carrying Auxiliary Fields
Displaying Auxiliary Fields and Their Values for a Selection of Records
Displaying Auxiliary Fields in the Standard Format: Records as Rows, Auxiliary
Fields as Columns
Displaying Auxiliary Fields in the Transposed Format: Auxiliary Fields as Rows,
Records as Columns
Printing Auxiliary Fields
Printing Auxiliary Fields in Matrix (Row-by-Column) Format
Printing Auxiliary Fields in Standard Triplet Format (Record Code, Auxiliary Field
Name, Auxiliary Field Value)
Printing Auxiliary Fields in Transposed Triplet Format (Auxiliary Field Name,
Record Code, Auxiliary Field Value)
Exporting Auxiliary Field Values
Exporting Auxiliary Fields in the NEXUS Format
The Project System and Auxiliary Fields
Project Input
Entering Project Data: The “General” Tab
Entering Project Data: The “Auxiliary Field Set” Tab
Using the Active Project Floating Window
To Declare a Different Project to be the Active Project
To Dismiss or Hide the Active Project Floating Window
To Display the Active Project Floating Window
Maintaining and Repairing the Auxiliary Fields and Project Systems
CHAPTER 17 DEFAULT ENTRIES AND ENTRY CHOICE LISTS (PICK LISTS)
Setting Default Entries: Field Value Defaults
To Set Field Value Defaults
Using Entry Choice Lists
Activating or Deactivating Choice Lists
Adding, Deleting, Editing, or Re-ordering Items in a Choice List
Using an Entry Choice List to Enter Data in a Record
Deleting All the Items in an Entry Choice List or Lists
Importing Choice List Data From a Text File
Transferring Choice Lists to a Different Biota Data File
CHAPTER 18 RE-NAMING FIELDS
Renaming Core Fields: Setting Aliases
Checking Field Aliases
Clearing All Aliases and Resetting to Defaults
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Page 12
PART 6
SPECIAL TOOLS AND FEATURES
CHAPTER 19 IMAGES
How Biota Works With Images
Special Components: QuickTime and QPix
How and Where Images Are Archived
Image Sources
Image Size and Shape
Image Color Depth
Image File Formats
Image Compression
Creating a New Image Record in Biota
Displaying an Image Input Screen
Importing an Image From an External File
Pasting an Image From the Clipboard
Acquiring an Image From a TWAIN-compliant Digital Device
Saving and Naming a New Image
Adding an Image Note
Exporting and Importing Images
Exporting Individual Images
Exporting Groups of Images
Importing Individual Images
Importing Groups of Images
Displaying, Zooming, Reordering, or Deleting Images in the Image Input screen
Displaying an Image in the Input Screen
Zooming Images in the Input Screen
Changing the Order of Linked Image Records in the Input Screen
Deleting an Image Record From the Input Screen
Editing or Compressing Images Displayed in the Image Input screen
Editing an Image
Compressing an Image
Displaying Thumbnail Images in Record Listing Screens
Using the Scroll Images Record Listing Screen
Using the Page Images Record Listing Screen
Deleting Images for a Species, Specimen, Collection, or Locality Record Set
Maintaining and Repairing Image Links
(Contents continued on the next page)
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Page 13
CHAPTER 20 REFERENCES
Reference Input
Entering Reference Data: The “Reference” Tab
Examining or Deleting Reference Links: The “Links” Tab
Linking or Unlinking a Reference to a Species, Specimen, Collection or Locality
Record
Linking a Reference to a Species, Specimen, Collection or Locality Record
Unlinking a Reference from a Species, Specimen, Collection or Locality Record
Editing a Reference Record “On the Fly” From a Species, Specimen, Collection or
Locality Record
Importing and Exporting References
Importing References
Exporting References
Maintaining and Repairing Reference Links
CHAPTER 21 THE SPECIMEN LOAN SYSTEM
How Biota Keeps Track of Specimen Loans
Recording a New Loan
Previewing, Printing, and Exporting Loan Records
Displaying and Editing an Existing Loan
Adding More Specimens to an Existing Loan
Recording Specimen Returns
Using the Specimen Record Set to Record Returns
Two Ways to Use the Loan Records Screens to Record Returns
CHAPTER 22 DETERMINATION HISTORIES
Determination History Records
Enabling or Disabling the Determination History System
Displaying the Determination History for a Specimen Record
How and When Changes in Determination Are Recorded
Changing a Determination in an Individual Specimen Record
Changing a Determination in a Specimen Record Series
Changing a Determination in a Species Record
Changing a Determination in a Genus Record
Changing a Determination Using the Synonymy Tool
Displaying, Editing, or Deleting Determination History Records
Importing and Exporting Determination History Records
CHAPTER 23 SYNONYMY SYSTEM
How Biota Keeps Track of Species Synonymies
Displaying the Synonymy Status of a Species Record
The Synonymy Status display
To Enable or Disable Full Synonymy Display
If Full Synonymy Display Is Not Enabled
If Full Synonymy Display Is Enabled
The Synonymy Display after Using the Synonymy Screen
Declaring a Species a Junior Synonym and Transferring Its Specimens
Clearing All Synonymies
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Page 14
Displaying Specimen Records for Junior Synonyms
Finding Valid Species, Species With Synonyms, or Junior Synonym Records
Finding Orphan Junior Synonym Records
CHAPTER 24 HOST-GUEST RELATIONS
How Biota Handles Links Between Specimens
Host–Guest Relations: An Example
Recording Information in the Guest Collection Record
Host Information in Guest Specimen Labels and Printed Reports
Creating a Host Specimen Link
Creating Guest Collection Records Automatically
Creating Guest Collection Records Automatically: Step by Step
Creating Guest Collection Records Automatically: Error Messages
Finding Host and Guest Records
Finding Host Specimens and Host Collections
Finding Guest Specimens and Guest Collections
Finding Host Specimens for Guest Specimens
Finding Guest Specimens for Host Specimens
CHAPTER 25 TEMPORARY TAXA FOR APPROXIMATE DETERMINATIONS
Biota’s Convention for Temporary Taxon Records
Automatic Creation of Temporary Taxon Records
Enabling or Disabling Automatic Creation of Temporary Taxon Records
How Biota Creates Temporary Taxon Records
Automatic Creation of Temporary Taxon Records for Imported Records
Eliminating Unused Temporary Taxon Records
Temporary Taxa on Determination Labels
CHAPTER 26 SECURITY: PASSWORDS AND ACCESS PRIVILEGES
Activating and Deactivating the User Password system
Activating the User Password system
Deactivating the User Password system
Launching a Password-Protected Copy of Biota
Changing Your User Password
Using the Password Editor
Users, User Names, Passwords, Access Levels, and Privileges
Opening and Closing the Password Editor
Editing a User's Password and Profile
Adding a New User Record
Assigning Users to and Removing Users from Access Groups
Pitfalls to Beware and Features to Ignore in the Password Editor
Moving User Names, User Passwords and Access Group Assignments to a New
Copy of Biota
Using the Data File Password Link
Activating the Data File Password Link
Changing the Data File Password
Deactivating the Data File Password Link
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Page 15
Opening a Password-Protected Data File with a New Copy or New Version of
Biota
Using the Data File Password Link with Backup Files
If You Need High Security
(Contents continued on the next page)
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Page 16
PART 7
EXPORTING AND IMPORTING DATA
CHAPTER 27 EXPORTING DATA
Exporting Data by Tables and Fields
Key Fields
Field Types and Field Lengths
Exporting by Tables and Fields: Step by Step
Exporting Notes
Exporting Notes with the Export Editor
Exporting Notes Records Linked to Records in the Current Parent-Table Record
Set
Exporting All Notes Records for a Notes Table
Exporting Notes Records Based on Their Own Content
Exporting Notes Records Based on the Content of Parent Records
Exporting Notes Records Using the Export Notes Tool
Exporting Taxonomic Flatfiles
Using the Export Taxonomic Flatfile Tool: Step by Step
Exporting Specimen Flatfiles
Using the Export Specimen Flatfile Tool: Step by Step
Exporting Custom Flatfiles
When to Use the Custom Flatfile Tool
Using the Export Custom Flatfile Tool: Step by Step
Examples of Custom Flatfiles Exported by Biota
Exporting “Specimens Examined” Lists for Publications
What the Specimens Examined Tool Exports
Exporting a Specimens Examined List: Step by Step
Examples of Specimens Examined Lists Exported by Biota
Exporting Place- by-Taxon Incidence or Abundance Tables
Exporting Place-by-Taxon Tables: Step by Step
An Example of a Collections-by-Species Table Exported by Biota
CHAPTER 28 IMPORTING DATA
Import Step 1: Match Fields
Import Step 2: Prepare the Text Files
The Column Heading Row Option
Automatic Stripping of Initial and Terminal Space Characters
Key Fields and the Importing Process
Field Types and Field Lengths
Import Step 3: Set Up and Launch the Import, Update, or Merge
Displays and Error Messages During Record Importing or Updating
The Import Progress Indicator
Importing New Records: Undoing an Aborted Import
Updating Existing Records: Redoing an Aborted Import
Too Many Fields Error
Missing Key Error: Importing New Records
Missing Key Error: Updating Existing Records
Duplicate Key Error: Importing New Records
Update Key Match Error: Updating Existing Records
Blank Key Error
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Page 17
Field Length Error
Mixed Characters Error
Invalid Date Error
Boolean Field Error
Importing Data to Notes Tables or to the Determination History Table
No Unique Key Update Error
Unknown Key Error
Importing New Records and Updating Existing Records in Auxiliary Fields Tables
Importing or Updating Records in Field Name Tables
Importing or Updating Records in Field Value Tables
Auxiliary Field Setup Error
Auxiliary Field Blank Value Error
Duplicate Auxiliary Field Value Key Error: Importing New Records
Auxiliary Field Value Key Match Error: Updating Existing Records
Missing Auxiliary Field Name Error: Importing New Field Value Records
Checking and Repairing Auxiliary Fields After Importing
Importing Records for the Lists and List Items Tables
Importing Records Into the Lists Table
Importing Records Into the List Items Table
A Strategy for Importing Text Files Into Hierarchically Linked Tables
Strategy: Importing Hierarchically Linked Records from an Existing Text Flatfile
Step by Step: Importing Hierarchically Linked Records from an Existing
Taxonomic Flatfile
Step by Step: Importing Hierarchically Linked Records from an Existing
Specimen Flatfile
Merging Two Biota Data Files or Moving All Records To a New Data File
PART 8
BIOTA AND THE INTERNET
CHAPTER 29 INTERNET STRATEGIES
Relative Costs of Internet Strategies
CHAPTER 30 BIOTA'S ONBOARD WEB SERVER
Web Server: Quick Start
Web Server Settings and Controls
The Start/Stop Tab
The Home Page Tab
The Server Settings Tab
The Database Client Tab
The Web Browser Tab
The License Tab
Installing a 4D Web Extension License for Biota4D and BiotaApp
Security and Passwords with the Web Server
Using Biota’s Password System to Control Web Access
CHAPTER 31 WEB BROWSER MODE AND THE WEB ASSISTANT
Web Assistant Settings Files
How and Where Web Assistant Settings Are Saved
Changing the Name of the Biota Application or Installing a New Version
Enabling and Launching the Web Assistant and Web Browser Mode
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Enabling the Web Assistant and Web Browser Mode
Launching Web Browser Mode from a Gateway Home Page
Customizing the Gateway Home Page for Web Browser Mode
Customizing Dynamic Pages for Web Browser Mode
Setting the List of Tables Available for Search
Web Assistant Settings
Setting Tables and Fields Preferences
Using the Web Assistant HTML Editor
Using the Web Assistant Appearance Editor
CHAPTER 32 DATABASE CLIENT MODE
Enabling and Launching Database Client Mode
Enabling Database Client Mode and Changing Settings
Launching Database Client Mode from a Static Web Page
Customizing the Static Web Page That Launches Database Client Mode
Customizing Graphic Elements and Page Background
Customizing Command Links
Using Command Links
Differences from the Corresponding Desktop Commands
CHAPTER 33 EXPORTING STATIC WEB PAGES
Choosing a Strategy for Exporting Web Pages
Exporting Web Pages: Step by Step
(Contents continued on the next page)
—Click on any entry to go to the corresponding page—
Page 18
Detailed Table of Contents
Page 19
PART 9
APPENDIXES
APPENDIX A BIOTA TABLES, FIELDS, AND RELATIONAL LINKS
Overview of Tables
Core tables
Peripheral Tables
Biota Fields and Relations: Table by Table
Links to the Figures on the Following Pages
Figure 1: Specimen, Determination History, Loans, and Linked Peripheral Tables
Figure 2: Specimen, Species, and Linked Peripheral Tables
Figure 3: Species and Higher Taxon Tables
Figure 4: Collection, Locality and Linked Peripheral Tables
Figure 5: Personnel, Group, Project, and Aux Index Tables
Figure 6: Project and Auxiliary Fields System Tables
Figure 7: Reference System Tables, Image Archive Table, and List Items Table
Figure 8: The Lists Table
APPENDIX B SETTING PREFERENCES
The “Sorting” Tab
The “Coordinates” Tab
The “Colors” Tab
The “Language” Tab
The “Shortcuts” Tab
The “Other Settings” Tab
The “Admin Settings” Tab
The “Reset All Defaults” Button
APPENDIX C KEYBOARD SHORTCUTS
Keyboard Shortcuts for Input Screens
Keyboard Shortcuts for Input Screen Tabs
Keyboard Shortcuts for Input Screen Buttons
Keyboard Shortcuts for Record Listing Screens
Keyboard Shortcuts Always Available
Optional Keyboard Shortcuts
Using the Optional Keyboard Shortcuts for Record Selection and Revision
APPENDIX D THE 4D LABEL WIZARD
The Label Wizard
Opening the Label Wizard
Label Page
Layout Page
The Label Wizard Toolbar
Creating a Label Design
How the Label Wizard Handles Blank Fields
Clearing Fields
Working with Label Wizard Objects
Creating Graphic Objects
Aligning Objects
Distributing Objects
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Layering Objects
Duplicating Objects
Moving Objects
Resizing Objects
Adding a Border to an Object
Adding Foreground or Background Colors
Setting Fill Patterns
Setting Border Patterns
Setting Line Width
Restoring the Default Look
Adding a Graphic to the Label
Deleting Objects
Specifying the Label Layout
Saving and Loading Label Designs
Saving Label Designs
Loading Lablel Designs
Printing Labels
APPENDIX E THE 4D QUICK REPORT EDITOR
Quick Report Basics
Creating a New Quick Report
Loading and Saving a Quick Report Design
The Quick Report Editor
Resizing Areas in the Editor
The Quick Report Contextual Menus
Working with the Quick Report Editor
Selecting Rows, Columns, and Cells
Adding and Modifying Text
Specifying Font Attributes
Adding Columns to the Report
Inserting Columns
Deleting Columns
Replacing Columns
Sizing Columns
Adding Formulas to a Quick Report
Sorting Records and Creating Breaks
Specifying a Sort Order
Deleting a Field or Formula from the Sort List
Setting Break Levels
Using the Values of Break Fields in Labels
Adding Summary Calculations
Displaying Repeated Values for Break Columns
Setting Display Formats
Numeric Formats
Alpha Formats
Entering the Display Format
Hiding and Showing Rows and Columns
Showing a Hidden Row or Column
Adding Page Headers and Footers
Specifying Font, Attributes
Printing a Quick Report
Printer
Disk File
Print to Graph
—Click on any entry to go to the corresponding page—
Page 20
Detailed Table of Contents
Page 21
APPENDIX F UPDATING BIOTA 1.X DATA FILES TO BIOTA 2 FORMAT
Tools for Data File Conversion
Data File Conversion: Step by Step
A. Decide on a Conversion Strategy
B. Export All Images from the Biota 1 Data File
C. Compact the Biota 1.x Data File
D. If Necessary, Repair the Biota 1.x Data File
E. Convert the Data File to Biota 2 Format
F. Import Linked Thumbnails or Full Images Into the Biota 2 Data File
APPENDIX G MERGING TWO BIOTA DATA FILES
In the Donor Data File
In the Recipient Data File
APPENDIX H USING BIOTA4D WITH 4D SERVER OR 4TH DIMENSION
Overview of Biota and 4D Architecture
How to Get Started With 4D Server
Licensing for 4D Server/Client, Biota 4D, QPix, and the Web Server
4D Server: Caveats and Recommendations
Running Biota4D under 4th Dimension (Single User)
APPENDIX I DATA FILE BACKUP, RECOVERY, COMPACTING, INDEXING, AND SEGMENTING
Backup Strategies for Data Files
Using 4D Tools to Check, Recover, Compact or Index a Biota Data File
Opening a Biota Data File With 4D Tools
Checking and Repairing a Data File
Compacting or Re-indexing a Data File
Moving All Records To a New Data File
Segmenting Data Files
Segmenting a New Data File
Adding a New Segment to an Existing Data File
Deleting Existing Segments or Splitting an Existing Data File into Segments
APPENDIX J BIOTA DATA FILE CONVERSION: MAC OS AND WINDOWS
Data File Conversion: Step by Step
APPENDIX K BARCODES
APPENDIX L TROUBLESHOOTING AND SUPPORT
Troubleshooting
Problems with Data Files
Problems with Passwords
Problems with Biota Windows and Records
English and Spanish Screens and Dialogues
Error Messages
—Click on any entry to go to the corresponding page—
Detailed Table of Contents
Biota Support
“How To” Questions
Visit the Biota Web Site for Help and Information
Support by Electronic Mail
Bug Reports
Suggestions for Improving Biota
—Click on any entry to go to the corresponding page—
Page 22
Preface
How Biota Began
I originally developed the prototype of Biota to manage biodiversity information for the
Arthropods of La Selva (ALAS) project at La Selva Biological Station in Costa Rica
(http://viceroy.eeb.uconn.edu/ALAS/ALAS.html), which I have co-directed with Jack
Longino (The Evergreen State College) for the past decade.
A quantitative, ecologically-structured inventory of rainforest insects and arachnids,
Project ALAS is an institutional collaboration between the Organization for Tropical
Studies (OTS) and the Costa Rican Instituto Nacional de Biodiversidad (INBio), with
nearly a hundred systematist collaborators in Latin America, North America, and Europe.
ALAS began using Biota in early 1992. By mid-1996, the application had been used
intensively by ALAS personnel for more than four years, with continual addition of
functionality, refinement of structure, and improvement of the user interface in response
to the daily needs of the project. During that period, records for nearly 80,000
specimens, with associated collection and taxonomic information, were entered into the
database, with no data-entry backlog. Trained local parataxonomists were primarily
responsible for data entry.
Biota 1
Based on comments and enthusiasm of visitors to the ALAS laboratory in Costa Rica
and from the response of colleagues elsewhere (including NSF program directors), it
became apparent that, if Biota could be made sufficiently flexible, it might meet the
needs of a wide variety of individual ecologists, systematists, and conservation biologists
for an inexpensive but powerful toolkit for managing all kinds of biodiversity information
for their own research.
Moreover, many field stations, reserves, museums, and herbaria were (and some still
are) relying on either antiquated or “home-made” database systems of limited usability
and scalability, but could afford the cost of developing custom software or of licensing
existing high-end specimen management systems.
Biota 1 was published by Sinauer Associates at the end of 1996 to help fill these needs.
Initially, Biota operated only in the Macintosh operating system, but within a year the first
Windows version (Version 1.2) was released, and Biota has been a completely crossplatform application ever since. Compared with the ALAS prototype, Biota 1 was quite
general in its design, with many ways to customize entry, archival, and analysis of
biodiversity data and images.
Over the following six years, Biota 1 was continually broadened to accommodate the
needs of a wide variety of projects in ecology, biogeography, systematics, and
collections management. Six major (and several minor) upgrades of Biota 1 were
released, all free to registered owners of Biota 1. By the end of 2002, Biota 1 had a
thousand or so users, with registrants in more than 40 countries and in 47 U.S. States.
Biota 2
While retaining Biota’s popular and familiar features and basic structure, Biota 2
incorporates a thorough re-design of the input interface, based on tabbed input screens.
Preface – Page 2
Image-handling capability is greatly enhanced and extended to the Specimen,
Collection, and Locality tables. Images may now reside in external files in virtually any
format, with transparent links to thumbnails inside Biota. Major new features in Biota 2
include a literature Reference system and a Project system to control views of Auxiliary
Fields. The most innovative feature is an on-board Web server, which allows any Biota
owner to publish a Biota Data File on the internet with no additional software. (Biota 1.x
users can review all the changes in “New Tools and Features in Biota 2” in Chapter 1.)
Development of Biota 2 began in 2000, with the first beta version in testing in March,
2001. By the time of this writing, in September, 2003, Biota 2 has been through 24 beta
versions, tested by some 50 beta testers in a wide variety of contexts.
My objective with Biota 2 is unchanged: to provide a low-cost, but highly capable,
flexible, and scalable application for managing specimen-based, biodiversity data in
virtually all its forms. Biota is my contribution to helping projects around the world
(especially low-budget ones) to inventory, catalogue, curate, observe, and carry out
experiments on Earth’s biota, with the conviction that we cannot conserve what we do
not understand.
Acknowledgments
Although I personally designed every form and wrote every line of code in Biota and
every word of this Manual (with the exception of two appendices), my debt of gratitude to
many others runs deep.
The launching of Project ALAS and the development of the prototype of Biota 1 would
not have been possible without grants from the U.S. National Science Foundation (BSR
90-25024). Through my professorial salary, the University of Connecticut supported me
throughout the development of Biota. Although Project ALAS continues to be supported
by the U.S. National Science Foundation and the Organization for Tropical Studies,
Biota has been completely self-supporting since its publication in 1994. My royalties are
ploughed back into software licensing and other development costs.
Several of the Biota’s most innovative and useful features are the direct result of the
suggestions and taxonomic experience of Jack Longino. The ALAS parataxonomists—
Danilo Brenes, Flor Cascante, Nelci Oconotrillo, Maylin Paniagua, and Ronald Vargas,
and other members of the ALAS team have put Biota to the acid test of daily use for a
decade, and continually contribute ideas for improvement.
Many Biota beta testers in many countries have contributed suggestions, bug reports,
enthusiasm, and occasional despair to the development of Biota 2, just as they did with
Biota 1. I have never met many of you, in person, but I take this opportunity to offer my
heartfelt thanks. I could not have done this without you!
This manual would not be in your hands were it not for Andy Sinauer's steadfast
confidence in the Biota project and his infinite patience with many delays. The Sinauer
team has made it possible to produce a truly usable and elegant manual for Biota that
stands ready to help you efficiently when you need it. I am particularly grateful to Dean
Scudder, Jason Dirks, Sydney Carroll, Mara Silver, and Parker Morse. The cover art is
the generous contribution of my dear friend Shahid Naeem.
To all I am thankful, but to no one more than my wife, Robin Chazdon, for her gifts of
unwavering support and understanding.
Robert K. Colwell
University of Connecticut, USA
PART
1
Introducing Biota
Chapter 1
Quick Start
NOTE TO BIOTA 1 USERS: If you are updating from Biota 1.x, and already know how to
use Biota 1, proceed directly to “Upgrading from Biota 1.x,” later in this chapter.
Quick-Start Strategies
Different people approach the task of learning how to use software in different ways.
This section attempts to guide you based on common learning strategies.
Regardless of your strategy, you should read or scan Chapter 2, “Biodiversity
Data and Relational Databases,” and Chapter 3, “Key Concepts,” before using
Biota. It will save you time, even if you are a trial-and-error learner.
If you prefer to by learn by trial and error, with reference to a manual only when
necessary:
◊
Your next step should be a session with the Biota2Demo Data File. Feel free
to add records, delete records…whatever. You can always load another copy of
the Biota2Demo Data File if you want a clean copy later. (Starting out with an
empty Data File does not make as much sense, since there is nothing to look at
until you create it yourself.)
◊
Take a look at Appendix A, “Biota Tables, Fields, and Relational Links,” to get
an idea of Biota’s design.
◊
Scan Chapter 4, “Biota Menus and Menu Items: An Annotated Guide,” to get an
idea about Biota’s tools and where to find them. Each menu command
description in that section has a hyperlink to the appropriate section of this
Manual for further details, if you need them.
◊
If you are not already burned out on manual reading, continue by scanning
Chapter 5, “Overview of Biota’s Tools and Features.”
If you prefer to spend some time with the Manual first, before trying Biota:
◊
Read Chapter 2, “Biodiversity Data and Relational Databases,” and Chapter 3,
“Key Concepts.”
◊
Scan Chapter 4, “Biota Menus and Menu Items: An Annotated Guide,” to get an
idea about Biota’s tools and where to find them. Each menu command
description in that section has a hyperlink to the appropriate section of this
Manual for further details, if you need them.
Chapter 1 – Page 2
◊
Read Chapter 5, “Overview of Biota’s Tools and Features”.
◊
Do the Tutorial in Chapter 6, “A Brief Tutorial With the Demo Database.”
◊
Read or scan Part 2, “Entering Data” (5 chapters) and Part 3, “Finding and
Revising Data” (2 chapters, especially Chapter 12, “Finding and Updating
Records”).
Special Strategies for Special Uses of Biota
This section attempts to guide you to special tools you may find useful, based on
common specialized uses of Biota. It is assumed that you have already mastered the
basics, covered in Part 1 (“Introducing Biota”), Part 2 (“Entering Data”), and Chapter 12
(“Finding and Updating Records”).
If you need to move data from a Biota 1 Data File, do nothing until you read
“Upgrading from Biota 1.x,” later in this chapter. If you don’t want to read even that, at
least read Appendix F, “Updating Biota 1.x Data Files to Biota 2 Format.”
If you need to populate a Biota Data File by importing data from another source,
see Chapter 28, “Importing Data,” especially the section “A Strategy for Importing Text
Files into Hierarchically Linked Tables.”
If you are using Biota in a biodiversity survey or inventory (a particular strength
of Biota’s because of its history), you may find the tools described in the following
chapters particularly useful:
◊
Chapter 8, “Record Codes”
◊
Chapter 13, “Creating, Finding, and Updating Specimen Series”
◊
Chapter 15, “Printing Labels”
◊
Chapter 17, “Default Entries and Entry Choice Lists (Pick Lists)”
◊
Chapter 19, “Images”
◊
Chapter 21, “Specimen Loan System”
◊
Chapter 22, “Determination Histories”
◊
Chapter 25, “Temporary Taxa for Approximate Determinations”
◊
Appendix K, “Barcodes”
If you are using Biota in museum or herbarium for historical specimens, you
may find the tools described in the following sections and chapters particularly
useful:
◊
“Specimen and Collection Combined Input” in Chapter 11 (specifically designed
for historical specimens)
◊
Chapter 8, “Record Codes”
◊
Chapter 14, “Printing Reports”
◊
Chapter 15, “Printing Labels”
◊
Chapter 17, “Default Entries and Entry Choice Lists (Pick Lists)”
◊
Chapter 18, “Renaming Fields”
◊
Chapter 19, “Images”
◊
Chapter 21, “Specimen Loan System”
◊
Chapter 20, “References”
Chapter 1 – Page 3
◊
Chapter 22, “Determination Histories”
◊
Chapter 23, “Synonymy System”
◊
Chapter 26, “Security: Passwords and Access Privileges”
◊
Part 8, “Biota and the Internet”
◊
Appendix H, “Using Biota4D with 4D Server or 4th Dimension”
◊
Appendix K, “Barcodes”
If you are a systematist using Biota for specimens involved in systematic revision,
you may find the tools described in the following sections and chapters particularly
useful:
◊
“Specimen and Collection Combined Input” in Chapter 11 (specifically designed
for historical specimens)
◊
Chapter 8, “Record Codes”
◊
Chapter 16, “User-Defined Auxiliary Fields and the Project System,” for
character data, especially the section “Exporting Auxiliary Fields in the NEXUS
Format”
◊
Chapter 17, “Default Entries and Entry Choice Lists (Pick Lists)”
◊
Chapter 19, “Images”
◊
Chapter 21, “Specimen Loan System” (to keep track of borrowed material)
◊
Chapter 20, “References”
◊
Chapter 22, “Determination Histories”
◊
Chapter 23, “Synonymy System”
◊
“Exporting ‘Specimens Examined’ Lists for Publications” in Chapter 27
If you are an ecologist or conservation biologist using Biota for data on living
organisms or plot-based specimen data, you may find the tools described in the
following sections and chapters particularly useful:
◊
Chapter 8, “Record Codes”
◊
Chapter 13, “Creating, Finding, and Updating Specimen Series”
◊
Chapter 16, “User-Defined Auxiliary Fields and the Project System,” to add
environmental or morphological data fields
◊
Chapter 17, “Default Entries and Entry Choice Lists (Pick Lists)”
◊
Chapter 19, “Images”
◊
Chapter 22, “Determination Histories”
◊
“Exporting Place- by-Taxon Incidence or Abundance Tables” in Chapter 27, for
exporting data from Biota to statistical or spreadsheet applications
Chapter 1 – Page 4
If you manage data for a field station or natural area and use Biota for data on
living organisms, you may find the tools described in the following sections and
chapters particularly useful:
◊
“Specimen and Collection Combined Input” in Chapter 11 (specifically designed
for historical specimens)
◊
Chapter 13, “Creating, Finding, and Updating Specimen Series”
◊
Chapter 14, “Printing Reports”
◊
Chapter 15, “Printing Labels”
◊
Chapter 16, “User-Defined Auxiliary Fields and the Project System,” to add
environmental or morphological data fields
◊
Chapter 17, “Default Entries and Entry Choice Lists (Pick Lists)”
◊
Chapter 18, “Renaming Fields”
◊
Chapter 19, “Images”
◊
Chapter 20, “References”
◊
Chapter 23, “Synonymy System”
◊
Chapter 26, “Security: Passwords and Access Privileges”
◊
Part 8, “Biota and the Internet”
Upgrading from Biota 1.x
Updating Biota 1.x Data Files
Biota 1 Data Files are fully compatible with Biota 2. You can update a Data File created
under any version of Biota 1, from the first version,1.0, to the final version, 1.6.1.
Although you could simply open the Biota 1.x Data File with Biota 2, and allow Biota 2 to
convert it, this approach is not recommended. Instead, please follow the instructions in
Appendix F, “Updating Biota 1.x Data Files to Biota 2 Format.”
New Tools and Features in Biota 2
There a hundreds of changes in Biota 2, but here are the principal ones. If you are a
Biota 1.x user, you should at least scan this list for items of interest to you. Below are
links to the paragraphs of this section:
Tabbed Input screens
Greatly enhanced Image-handling capability
Literature Reference system
Project System
New Entry Choice List (Pick List) System
Specimen and Collection combined Input screen for historical specimens
On-board Web server
Opening and creating Biota Data Files from within Biota
Table and field lists in the Search and Sort editors
Expanded scope of export place-by-taxon tools
Chapter 1 – Page 5
Enhanced Label tools
Expanded keyboard shortcuts
Tabbed Input screens. While retaining Biota’s popular and familiar features and
basic structure, Biota 2 incorporates a thorough re-design of the input interface,
based on tabbed Input screens. Instead of clicking an onscreen button to open a
subsidiary screen (e.g. for Determination Histories, Subspecies, Notes, or Auxiliary
Fields), as in Biota 1.x, ancillary input screens for each Core table input screen are
placed on tabs in Biota 2 (see Chapter 11, “Input—Table by Table” for illustrations).
The enormous advantage of the tab design is that the Input Screen navigation
buttons (as well as Save, Carry, Delete, Print, and Cancel buttons) are accessible
from all tabs. So if you want to scan through a series of records to see the Notes,
Images, References, or Auxiliary Fields attached to them, just go to the appropriate
tab and use the navigation buttons.
Where appropriate, control automatically shifts to the next tab when you complete
the last item in a previous tab (e.g. the Preparation tab screen opens automatically
when you complete the General tab in the Specimen Input screen). You can switch
tabs quickly using keyboard shortcuts (see “Keyboard Shortcuts for Input Screen
Tabs” in Chapter 7).
Greatly enhanced Image-handling capability. Support for images, available only
for the Species table in Biota 1, are extended to the Specimen, Collection, and
Locality tables in Biota 2. Equally important, images may now reside in external files
in virtually any format, with transparent links to corresponding thumbnails inside
Biota. New image-comparison screens have been added, and a comprehensive set
of image-editing tools is available in the new QPix Image Console, as well as direct
TWAIN device capture ability (scanners, digital cameras, etc.). Biota 2 supports
batch import (linked thumbnails or full images) as well as batch export of external
images files. See Chapter 19, “Images.”
Appendix F, “Updating Biota 1.x Data Files to Biota 2 Format,” explains the tools
available for quickly transferring your Biota 1.x Images to the Biota 2 format.
Literature Reference system. In Biota 2, a capable and flexible Reference system
has been added. A separate Reference table, designed around a subset of
EndNote reference styles and fields, holds Reference records that can be quickly
linked (many-to-many) to any record in the Species, Specimen, Collection, or
Locality table. References exported from EndNote can be directly imported to the
Reference table. Records from other reference management applications can be
imported with appropriate preparation of the input file. See Chapter 20,
“References.”
Project System. In Biota 2, you can create any number of Projects (in a new
Project table). Each Project record can be one-to-one with a Personnel record to
allow you to keep track of overlapping sets of participants and contacts for different
Projects (because a Personnel Project record can simultaneously be a Personnel
Group record).
Projects also allow different views of Auxiliary Fields. In Biota 1.x, all Auxiliary Fields
for a parent table (e.g. for the Species table) were visible in each parent record (e.g.
all Species records), whether appropriate or not. Thus, if you had a database with
moths and host plants, with Species Auxiliary Fields for moth morphometric
characters as well as host plant phenology, all were shown at all times. In Biota 2,
you could create a Moth Project and a Host Plant Project and choose which
Species Auxiliary Fields were associated with each.
Chapter 1 – Page 6
When you convert a Biota 1.x Data File to Biota 2 format, all your Auxiliary Fields
are initially placed in a “Global Project,” and the Biota 1.x Personnel Project record
(if you have one) is converted to a Project table record. See Chapter 16, “UserDefined Auxiliary Fields and the Project System.”
New Entry Choice List (Pick List) System. A new “List Items” table has been
incorporated in Biota 2, replacing the off-the-shelf 4D pick list system in Biota 1. You
can easily import and export List Items for any of the fields in Biota that support
Entry Choice Lists. A new, drag-and-drop List Editor make it easy to manage List
Items for each field. The new Choice List pick screen has a “type-ahead” feature, so
you can type in the first letter and letters of the entry you want and Biota
automatically scrolls to the corresponding point in the pick list.
When you convert a Biota 1.x Data File to Biota 2 format, your Entry Choice Lists
are automatically transferred to the List Items table, and they will continue to
function in the same way you set them up. See “Using Entry Choice Lists” in
Chapter 17.
Specimen and Collection combined Input screen for historical specimens.
Many Biota 1.x users, especially those cataloging specimen collections in museums
and herbaria, complained about the need to create a separate Collection record for
each Specimen record when entering data for historic material, for which each
specimen generally has distinct collection data. Adding fields to the Specimen table
is not a good approach, since Biota must continue to support “inventory-style” data,
with many Specimen records linked to each Collection record—a powerful design
for inventories and ecological studies.
The solution Biota 2 provides is a single (multi-tab) Input screen (Input menu Input
Specimen and Collection) that offers all the functionality of the Biota 2 Specimen
Input screen, with provision to enter key fields from the Collection table on a tab
panel. A new Collection record, linked to each new Specimen record is
automatically created and linked, to accommodate the collecting-event data while
conforming to Biota's data structure. See “Specimen and Collection Combined
Input” in Chapter 11.
On-board Web server. Biota 2 offers a fully-imbedded, on-board Web server that
allows any Biota owner to publish a Biota Data File on the internet with no additional
software (although for anything but trial use, you must purchase a Web Extension
license from Sinauer). You can use any computer to run the Web server. See Chapter
29, “Internet Strategies,” and especially Chapter 30, “Biota's Onboard Web Server.”
You can choose to publish your Biota Data File on the Web in either or both of two
modes: (1) Web Browser Mode allows you to control exactly which tables and fields
are accessible to website visitors, in classic browser mode. (2) Database Client
Mode emulates Biota’s desktop interface, allowing full access to Biota’s powerful
search tools. See Chapter 31, “Web Browser Mode and the Web Assistant,” and
Chapter 32, “Database Client Mode.”
Opening and creating Biota Data Files from within Biota. In Biota 2, two new
commands have been added to the File menu: “Open Data File” and “Create New
Data File,” solving a long-standing annoyance for Biota 1.x users (thanks to new
commands now available in 4D). You may continue to use the traditional Biota 1
methods for opening a different Data File or creating a new one if you prefer. See
“Opening a Biota Data File or Creating a New Biota File from Within Biota” in
Chapter 3.
Table and field lists in the Search and Sort editors. In Biota 2, table and field
lists appear in alphabetical order in the in Search and Sort Editors (and in other
Chapter 1 – Page 7
places, such as in the Quick Report Editor). Even better, field lists in these tools
now include any Core Field Aliases you have set up, instead of the corresponding
internal field names. The awkward (and ugly) floating “Field Alias” windows of Biota
1.x have been eliminated, thanks to new programming capabilities in 4D. See
Chapter 18, “Renaming Fields” for information on Aliases.
Expanded scope of export place-by-taxon tools. In Biota 2, you can export
incidence (presence-absence) or abundance-based place-by-taxon tables, based
on either the Locality or Collection table and a taxon table at any level, Species or
above. For example, you can export a Localities-by-Families table, based on a
variety of different Record Set options. See “Exporting Place- by-Taxon Incidence or
Abundance Tables” in Chapter 27.
Enhanced Label tools. In Biota 2, you can export labels of any kind directly to a
tab-delimited text file, adding greater flexibility for external processing or importing
to other applications.
Expanded keyboard shortcuts. Biota 2 offers many new keyboard shortcuts for
buttons and tabs in Input screens and for records in Record Listing screens, while
maintaining those available in Biota 1. This comprehensive set of keyboard
shortcuts represents an important new feature for people with disabilities, including
mouse-related repetitive motion disorders, and to any user who dislikes using the
mouse. Windows users can also tab between buttons and use the menu shortcuts
that Windows automatically provides. See “Keyboard Shortcuts for Input Screen
Tabs” and “Keyboard Shortcuts for Input Screen Buttons” in Chapter 7, and
“Keyboard Shortcuts for Record Listing Screens” in Chapter 10. These sections are
summarized in Appendix C, “Keyboard Shortcuts.”
Chapter 2
Biodiversity Data
and Relational Databases
Biodiversity Data
Consider an ecologist who needs to record data for a quadrat-based plant survey of a
large area being considered for protection as a reserve. Imagine a systematist or a
biogeographer who must keep track of the classification and geographical origin of a
large number of research specimens. Or, imagine a museum or herbarium with
specimens from thousands of taxa, collectors, and localities.
In each of these examples (and many others in ecology, conservation biology,
systematics, biogeography, and evolutionary biology), we need to record not only
taxonomic information (Species, Genus, Family, and so on) for each specimen or group
of specimens, but also collection and location data (collector or observer, collection or
observation date, method, site characteristics, map coordinates, and names for localities
and political units). This manual will refer to information with these characteristics as
specimen-based biodiversity data.
Why Use a Relational Database?
Each individual organism in a biodiversity data set has two allegiances. It belongs to a
particular species, and it belongs to a particular place and date (a particular observation
or collecting event). The organism shares with all other members of its species—
wherever they are—precisely the same taxonomic data, all the way up the Linnean
hierarchy. At the same time, it shares with all organisms from the same collecting
event—whatever their species—the same date and locality data.
Flatfiles
To record all these data for each specimen in a single column-by-row table requires
repeating all the taxonomic data for each member of the same species and all the
collection data for each specimen from a given collecting event. This kind of table is
called a flatfile (or a spreadsheet). As anyone who has made a large one knows, flatfiles
for floristic, faunistic, and collections data are not only clumsy and error-prone, but highly
repetitive and therefore wasteful of skilled human effort—the most precious scientific
resource of all.
The Relational Model
A powerful alternative to a flatfile is a relational database, a design for storing and
retrieving data in linked tables that reduces repetitive input and redundant storage of
data to an absolute minimum. Each row of a table represents a record (sometimes called
an instance or a case). Each column represents a field (or attribute).
Chapter 2 – Page 2
For hierarchical data, the familiar format of an indented text table is a good model for a
relational database, because both have non-repetitive entries. In the indented taxonomic
table below, each taxon name appears only once, regardless of taxonomic rank.
Family
Campanulaceae
Genus
Centropogon
Lobelia
Siphocampylus
Ericaceae
Anthopterus
Cavendishia
Ceratostema
Macleania
Specific Name
caoutchouc
erianthus
laxiflora
salicifolia
ecuadoriensis
sanguineus
scandens
verticillatus
forreroi
gilgiana
leucantha
lindauiana
nodosum
peruvianum
reginaldi
bullata
cf. ericae
coccoloboides
glabra
In fact, translating an indented table, like the one above, to the relational equivalent is
straightforward. Each column of the indented table forms the basis for a separate
relational table. In this example, three separate tables (for Family, Genus, and Specific
Name) are required.
Linking Fields
In the indented format, the physical layout of the table indicates the generic membership
of each species and the familial membership of each genus. In the separate tables of the
relational equivalent, illustrated below, the generic membership of each species is
recorded by adding a linking field—the Genus column, to the Specific Name table.
Likewise, the familial membership of each genus is indicated in a linking field—the
Family column in the Genus table. (Relational database jargon for “linking field” is
“foreign key.”)
Chapter 2 – Page 3
Specific Name Table
Genus Table
Specific
Name
caoutchouc
erianthus
laxiflora
salicifolia
ecuadoriensis
sanguineus
scandens
verticillatus
forreroi
gilgiana
leucantha
lindauiana
nodosum
peruvianum
reginaldi
bullata
cf. ericae
coccoloboides
glabra
Genus
Genus
Family
Centropogon
Centropogon
Lobelia
Lobelia
Siphocampylus
Siphocampylus
Siphocampylus
Anthopterus
Cavendishia
Cavendishia
Cavendishia
Cavendishia
Ceratostema
Ceratostema
Ceratostema
Macleania
Macleania
Macleania
Macleania
Centropogon
Lobelia
Siphocampylus
Anthopterus
Cavendishia
Ceratostema
Macleania
Campanulaceae
Campanulaceae
Campanulaceae
Ericaceae
Ericaceae
Ericaceae
Ericaceae
Family Table
Family
Campanulaceae
Ericaceae
Although the taxonomic example above used a familiar hierarchy to illustrate the
relational representation of data, the relational model can accommodate any logical
structure, not just hierarchies.
Biota’s structure, discussed in detail in the Chapter 3, “Key Concepts,” and shown in
Appendix A, “Biota Tables, Fields, and Relational Links,” takes advantage of the
relational model to represent and manage data for a variety of non-hierarchical logical
relationships, as well as for the taxonomic and geographic hierarchies.
Efficiency of Data Input and Updating
Biota organizes biodiversity information according to the relational data model. For each
class of information, such as the names and other attributes of species, genera,
localities, or personnel connected with a data set, Biota records information in a
separate relational table, with just one record for each genus, locality, or person.
Because of the repeated values in linking fields, it might appear that the relational design
is not much of an improvement over a flatfile, in terms of avoiding data entry error and
the burden of updating records. In fact, an efficient interface for a relational design
allows one-time entry for each distinct value and automatic updating for linking fields, if
necessary.
In a new Species record in Biota, for example, the specific name and author of a species
need be entered exactly once. If a correction or update is required later, the correction is
made in just one record.
Using Biota’s Lookup and wildcard entry tools, you can quickly enter the linking field
values for new records (for example, new Species records), when the related parent
record (a Genus record, in this example) is already in your database (Chapter 11,
Chapter 2 – Page 4
“Input—Table by Table”). In short, none of the repetitive data that are characteristic of
flatfiles ever need be entered more than once.
Efficiency of Relational Searches
Relational databases are much more quickly searched and sorted than equivalent large
flatfiles, especially for complex queries. Suppose you want a list of the Collection records
for all 14,000 individual ant specimens in a Biota Data File of 150,000 records. Using
Biota’s “Lower Taxa for Higher Taxa” tool (see “Finding Records for Lower Taxa Based
on Higher Taxa” in Chapter 12), the ant Specimen records can be found and displayed
in about 2 seconds, simply by constructing the query: “Find all Specimens of the Family
Formicidae.” A second query, “Find all Collections for the Specimen Record Set” using
the “Places for Specimens or Species” tool (see “Finding Specimen or Species Records
for Places (Collections or Localities)” in Chapter 12) then displays the desired Collection
records in another 2 seconds.
The speed of the search is entirely a result of the relational structure of the data and the
use of powerful relational commands in the programming language (4th Dimension, in
the case of Biota). In contrast, a flatfile search tool would have to look at the Family
column of each of the 150,000 specimen records to find those listed as Formicidae
(ants). Once the ant records were found, you would need to eliminate—manually—all
redundant collection data for specimens derived from the same collecting events, or
work out a spreadsheet macro to do the job.
Chapter 3
Key Concepts
Tables
As explained in Chapter 2 (“Biodiversity Data and Relational Databases”), a relational
database embodies the structure of data by means of linked tables. This section
introduces Biota’s data tables. For details, see Appendix A, “Biota Tables, Fields, and
Relational Links.” Biota’s tables are internal components of the database and thus do not
appear as ordinary files on your hard disk.
Core Tables
Biota is structured around 14 Core Tables of data. You need to understand what each
Core Table is used for, since all Biota records are entered and displayed through the
Core Tables. The diagram below (in database jargon, an “entity-relationship” diagram),
shows most of the links between Core Tables in Biota.
The taxonomic hierarchy includes the Specimen table and a table for each of the
seven obligatory levels of the Linnean classification system: Species, Genus,
Family, Order, Class, Phylum, and Kingdom (see Chapter 11, “Input—Table by
Table”).
The place hierarchy has two levels. The Collection table records data for collecting
events (including collector and collection date), whereas each record in the Locality
table keeps track of the geographical site of one or more collecting events (see
“Collection Input” and “Locality Input” in Chapter 11).
Chapter 3 – Page 2
Literature references are recorded in the References table. Reference records can
be linked to records in the Species, Specimen, Collection, and Locality tables (see
Chapter 20, “References”).
Names and contact data for collectors, preparators, borrowers, Project
participants, and authors of Notes are recorded in the Personnel table (see
“Personnel Input” in Chapter 11).
To allow several projects to share the same Data File, the Project table keeps
track of project names and descriptions, and provides project-specific views of
Auxiliary Fields (see Chapter 16, “User-Defined Auxiliary Fields and the Project
System”).
To keep track of specimen loans, the Loans table records which specimens have
been loaned, borrowed, and returned (see Chapter 21, “Specimen Loan System”).
Peripheral Tables
In addition to the14 Core Tables, Biota’s relational structure encompasses an additional
20 Peripheral Tables (see Appendix A, “Biota Tables, Fields, and Relational Links.”).
Peripheral Tables keep track of supporting or ancillary data related to Core Table
records.
For data entry, you will generally not need to think about what data the Peripheral Tables
record, or how they are linked to each other or to the Core Tables. But you will need to
understand them fully if you wish to import data into Peripheral Tables or export data
directly from them.
Images are saved in the Image Archive table, which is linked with the Species,
Specimen, Collection, and Locality tables (see Chapter 19, “Images”).
Notes are saved in the Specimen Notes, Species Notes, Collection Notes, Locality
Notes and Loan Notes tables (see “Notes Input” in Chapter 11).
User-Defined Auxiliary Field Names and Auxiliary Field Values for the Species,
Specimen, Collection, and Locality tables are recorded in four Field Name and four
Field Value tables (see Chapter 16, “User-Defined Auxiliary Fields and the Project
System”).
Entry choice lists (pick lists) are enabled by settings in the Lists table. The list
values themselves are saved in the List Items table (see Chapter 17, “Default
Entries and Entry Choice Lists (Pick Lists)”).
Field name aliases for re-namable fields are also saved in the Lists table (see
Chapter 18, “Renaming Fields”).
Specimen determination histories are kept in the Det History table (see Chapter
22, “Determination Histories”).
Personnel groups are defined by records in the Group table (see “Entering
Personnel Data: the 'Group' Tab” in Chapter 11).
References are linked to Species, Specimen, Collection, or Locality records
through entries in the Reference Links table (see Chapter 20, “References”).
Projects are linked to Auxiliary Field names by means of records in the Aux
Index table (see Chapter 16, “User-Defined Auxiliary Fields and the Project
System”).
Chapter 3 – Page 3
Fields and Records
Each Biota table consists of a unique set of fields that represent data elements
(attributes) appropriate to that table. These fields are listed for each table in Appendix A,
“Biota Tables, Fields, and Relational Links.”
Most of Biota’s input (detail) screens, record listing screens, and printed reports and
labels combine fields from several tables at once. The Specimens Report, for example,
lists specimens organized by the taxonomic hierarchy, with collection and locality data
for each specimen—it thus includes fields from 10 different tables.
The information in each table is organized by records. Each record in a table may
include entries for each field in that table. For example, in the Specimen table, each
record represents an individual specimen (or a group of specimens that share the same
data), with entries for that specimen’s unique Specimen Code, the Collection Code for
the sample or collection site from which the specimen came, the Species Code for the
species to which the specimen has been assigned or determined, the name of the
person who made that assignment (Determined By), and so on through the fields listed
for the Specimen table in Appendix A, “Biota Tables, Fields, and Relational Links.”
You can think of an individual database table as a spreadsheet, with fields as columns
and records as rows—indeed, records and fields appear in this format in most Biota
record listing screens.
Key Fields
In most relational database tables (including all of Biota’s Core Tables) each record must
be uniquely identifiable and retrievable. For this reason, one field (in some tables a pair
of fields) in each such table is designated as the Key field—or simply the Key. Every
record in such a table must have a unique alphanumeric value for the Key field (or a
unique combination of values for a two-valued or composite key). In Biota, the Key field
for the Locality, Collection, Specimen, Species, and Loans tables is a unique
alphanumeric Record Code for each record. (You can define Record Codes yourself, or
ask Biota to supply them automatically). Chapter 8, “Record Codes,” discusses these
codes in depth.
For taxon tables above the species level, the taxon name itself is the Key field, relying
on the uniqueness criterion of the Rules of Nomenclature. Names of genera, however,
may sometimes be ambiguous. If you need to record generic junior synonyms, or in the
rare cases in which genera in two or more Kingdoms share the same genus name and
are listed in the same database, you will need to add a distinguishing suffix to generic
names.)This approach and Biota’s ability to exclude special characters appended to
generic names on labels are discussed in the section “A Special Problem for Genera:
Legitimate Duplicate Generic Names” in Chapter 11.
The Key field for the Personnel table is a user-defined, unique “Short Name” (initials and
last name for a person, for example, or an acronym for an institution). The uses of Short
Names are discussed in the section “Entering Personnel Data: The 'General' Tab” in
Chapter 11.
Duplicate Key Errors
If you enter a value in a Key field that duplicates the Key field entry for any existing
record in the same table in your database, Biota will post an error message like the one
shown on the next page. You will have to choose a different value for the Key, or change
Chapter 3 – Page 4
the Key in the existing record, which you can display for comparison using the “Display
the Matching Record” button.
Linking Fields: Parent and Child Records
Relational links (or relationships) join tables through linking fields (see Chapter 2,
“Biodiversity Data and Relational Databases”).These links give a relational database its
power and efficiency. Appendix A, “Biota Tables, Fields, and Relational Links,” shows
the relational links between Biota’s data tables.
The Specimen table lies at the base of two hierarchies of many-to-one relationships.
In the place hierarchy, the Specimen table is linked to the Collection table through
the Collection Code linking field. (There may be many specimens in one collection.)
In turn, the Collection table is linked to the Locality table through the Locality Code
linking field. (There may be many collections from one locality.)
In the taxonomic hierarchy, the Specimen table is linked to the Species table
through the Species Code linking field. (There may be many specimens of one
species). The Species table, in turn, is linked to the Genus table (there may be
many species in one genus), and so on up the Linnean hierarchy.
In menus, screens, and dialogs and in most contexts in this manual, Biota does not use
the formal “many-to-one” or “one-to-many” terminology. Instead, a “parent-child”
metaphor is used. For example, a particular Family record is the parent record for all the
Genus records for all genera in that family—the child records. Of course, in many cases
a particular record is both parent and child; a Genus may be the child record of a Family
record, and at the same time parent record to one or more Species (child) records. (The
parent-child metaphor works well here, since each of us may be both child and parent,
as our own parents undeniably were.)
The metaphor is carried further in the concepts of orphan records (those that are not
linked to any record in the parent table) and childless records (those not linked to any
record in the child table, for a particular database relation). For example, a Genus record
not linked to any Family record is an orphan record. A Genus record not linked to any
Species record is a childless record. Orphan records, especially, and childless records,
to a lesser extent, tend to be “invisible” in relational searches. (In relational database
terminology, orphan records compromise the referential integrity of the database.) Biota
offers optimized search tools for finding and displaying orphan and childless records
(see “Finding Childless and Orphan Records” in Chapter 12).
Chapter 3 – Page 5
Data Files
To use Biota effectively, it is essential to understand the distinction between four
representations of Biota data records, discussed and contrasted in this section and the
three that follow. The figure below shows graphically some of the important distinctions
among the four ways Biota handles groups of records.
The actual records for a table are recorded in a Biota Data File, in an special format that
can be opened only by Biota. The figure above illustrates a Biota Data File in the dashed
rectangle, with the Genus table as an example. Biota Data Files are separate from the
application file itself (BiotaApp or Biota4D).
Opening a Biota Data File When Launching Biota
To choose among existing Biota Data Files when you launch Biota, follow these steps.
1.
Launch Biota.
If you have not enabled the user password system (see Chapter 26,
“Security: Passwords and Access Privileges”), immediately press and hold the
OPTION key (Mac OS) or ALT key (Windows).
If you have enabled the password system, the Password request screen
appears. Enter your password, then press and hold the OPTION key (Mac OS) or
ALT key (Windows) while clicking the “Connect” button. (In the illustrations below,
the Mac OS screen is illustrated on the left, the Windows screen on the right).
Chapter 3 – Page 6
The Open Data File (Mac OS) or Open (Windows) screen for your operating system
appears.
2.
Find the Data File you want to open, select it, then click the “Open” button.
Creating an Empty Biota Data File While Launching Biota
NOTE TO WINDOWS USERS: Due to a 4D bug, BiotaAppWin does not perform consistently
using this method for creating a new Data File. (Biota may freeze.) Until the problem is
resolved, please use the method in the next section instead ("Opening a Biota Data File
for Creating a New Biota Data File from Within Biota"). This limitation does not apply to
Biota4DWin.
To create a new, empty Biota Data File while launching Biota, follow these steps.
1.
Launch Biota.
If you have not enabled the user password system (see Chapter 26,
“Security: Passwords and Access Privileges”), immediately press and hold the
OPTION key (Mac OS) or ALT key (Windows).
If you have enabled the password system, the Password request screen
appears. Enter your password, then press and hold the OPTION key (Mac OS) or
ALT key (Windows) while clicking the “Connect” button. (In the illustrations below,
the Mac OS screen is illustrated on the left, the Windows screen on the right).
Chapter 3 – Page 7
The Open Data File (Mac OS) or Open (Windows) screen for your operating system
appears.
2.
Click the “New” button (not the “Open” button), shown above. A Save File window
for your operating system appears, with the instruction “Create a data file.”
3.
Name and place the file then click the “Save” button. Biota will take a few
moments to create the Data File, so be patient.
Opening a Biota Data File or Creating a New Biota File from Within Biota
While you are working with Biota, you can switch to a different, existing Biota Data File
or create a new, blank Biota Data File without quitting Biota. Because you cannot have
two Data Files open at once under the same copy of Biota, the Data File you currently
have open will first be closed, after automatically saving any recent changes.
To switch to a different Biota Data File, choose “Open Data File” from the File
menu and follow the onscreen instructions.
To create a new, blank Biota Data File, choose “Create New Data File” from the
File menu and follow the onscreen instructions, which allow you to create a new
folder for the blank Data File if you wish.
Chapter 3 – Page 8
NOTES:
(a) If you have enabled the User Password System (see Chapter 26, “Security:
Passwords and Access Privileges”), only the Administrator can use these menu
items to open or create Biota Data Files. This precaution is intended to prevent
accidental change to a different Biota Data File by data entry personnel.
(b) These menu items cannot be used from 4D Server or 4D Client. Under 4D
Server, you must change to a different Data File or create a new one using the
methods in the previous sections, “Opening a Biota Data File When Launching
Biota” and “Creating an Empty Biota Data File While Launching Biota.”
Saving Changes in a Biota Data File
Biota uses temporary buffers in RAM to keep track of any changes you make in the
active Data File. Every three minutes, Biota automatically saves these changes to disk
and clears the buffers.
There is one exception: Each group of new records you create or modify using
commands from the Series menu is saved immediately.
If you want to force Biota to save changes immediately, press the keys
COMMAND+W (Mac OS) or CTRL+W (Windows) at any time.
When you quit Biota, any changes made since the last automatic save are recorded in
the Data File.
The small window shown here appears in the corner of the screen
during a save operation. Other ongoing operations may be
momentarily slowed, but are not halted.
NOTE TO MAC OS USERS: The key combination COMMAND+W, normally used for closing
windows in Macintosh applications, is reserved by 4th Dimension for saving data to disk
from the buffers. To close a Biota window from the keyboard, press OPTION+W instead.
The same shortcut also works in the Windows versions of Biota.
To Find Out Which Data File Is
Currently Open
Biota can open only one Data File at a time. If you
have enough memory available, however, you can
launch two or more copies of Biota simultaneously
on the same computer, each with a different Data
File. (It is acceptable under the License
Agreement to make copies for this purpose, as
long all copies are in use by a single user.)
You can find out which Data File is open by
selecting “About the Current Data File” from the
File menu. The information window that appears
also tells you how many records there are in each
Biota table in the current Data File.
Chapter 3 – Page 9
Selections and Processes
Because a database may become very large, displaying all the records in a table every
time you want to look up a record, correct mistakes, or view a set of recent entries after
entering them would soon become extremely cumbersome and time-consuming. To
solve this problem, Biota displays in a window (or prints) only those records in a
Selection for a particular table. Selections of records are the second way Biota handles
records (illustrated below in the dashed rectangle).
A Selection can include all of the records for a table or any subset of them. If you use
Biota’s search tools to find all records in the Species table for the Family Ericaceae, for
example, all the Species records for ericads will become the current Selection for the
Species table, and Biota will display them in the record listing screen for the Species
table. If a Selection is empty, which will happen, for example, if a search fails to find a
match for your query, no records are displayed.
In short, a Selection is simply a “list” of selected records from a particular table in the
database. The records in the Selection may be sorted, displayed on the screen, opened
one at a time to view or edit, or printed.
NOTE: Placing records in a Selection or removing records from a Selection has
absolutely no effect on their presence in the Data File itself.
During data entry, as each record is accepted, it is added to the Data File itself. Once
entered, each record remains in the Data File until and unless it is specifically deleted,
regardless of how often it is included in or removed from a Selection.
Biota is based on a multi-process or multi-tasking architecture. Each time you choose an
item from one of Biota’s menus, an independent process is launched, rather like a miniapplication within Biota. You can launch as many independent processes as memory
permits. (New processes are also launched by certain buttons on Biota screens.)
Each process maintains its own Selection for every Biota table, although most
Selections will be empty at any given moment. Thus, you can retrieve and display
several Selections for the same table simultaneously in different windows. Because
simultaneous Selections are entirely independent of one another, they can include
distinct, overlapping, or even identical sets of records.
Chapter 3 – Page 10
NOTE: To maintain record integrity, however, you may edit an individual record in only
one input (detail) screen at a time. You can read about record locking in Appendix L,
“Troubleshooting and Support.”
Record Sets
The third way you can represent and work with records is by using Record Sets. You
can tell Biota to “remember” a Selection of records from a particular table and process
by establishing it as a Record Set for the table (illustrated below in the dashed
rectangle).
Each of Biota’s 14 Core Tables (see Core Tables, earlier in this chapter), plus the
Determination History table (see Chapter 22, “Determination Histories”), has its own
current Record Set, at all times.
Unlike Selections for a particular table, of which many can exist simultaneously in
different processes (see “Selections and Processes,” earlier in this chapter), there is
always only one current Record Set per table. (You can save and retrieve as many
Record Sets per table as you wish, however. See “Record Set Pointer Files,” later in this
chapter.) When you launch Biota, all Record Sets are empty and remain empty until you
retrieve or create Selections of records to place in them.
The Record Set Options Screen
Understanding the Record Set options screen is the key to working effectively with
Record Sets in Biota. The options screen (illustrated below) appears whenever you click
the “Done” button in a record listing screen.
Chapter 3 – Page 11
The Record Set options screen offers the following primary alternatives:
Make it the [table name] Record Set. If you choose this option, the current
Selection of records is declared the current Record Set for the table.
Add it to the existing [table name] Record Set. This option allows you to combine
the current Selection with the current Record Set for the table. If the current Record
Set is empty, this option and the “More Choices” button are disabled (dimmed) and
a message appears reading: “The [table name] Record Set is empty,” as illustrated
below.
Save it to disk as a Record Set Pointer File. This option saves a disk file that
allows you to reload the Selection quickly at a later time. See “Saving a Record Set
Pointer File: First Method,” later in this chapter.
Dismiss it. Choosing this option dismisses the Selection of records without
affecting the current Record Set for the table.
NOTE: You can achieve the same result as the “Dismiss it” option by bypassing the
Record Set options screen entirely. To do so, simultaneously press the COMMAND
key plus the HYPHEN key (Mac OS) or the CTRL key plus the HYPHEN key (Windows),
to dismiss any record listing screen, instead of clicking the “OK” button. (You can
also use this keyboard shortcut to dismiss most input screens, instead of clicking
the “Cancel” button.) The HYPHEN key is the key next to the ZERO key; do not
confuse it with the MINUS key on the numeric keypad, if you have one.
The “More Choices” button. If the current Record Set for the
table is not empty, the “More Choices” button in the Record
Set options screen is enabled. (If the current Record Set is
empty, the button is dimmed.) If you click the “More Choices”
button when it is enabled, the Record Set options screen
expands to include not only the four original options (illustrated above) but three
additional options that allow other operations (“set mathematics”) on Record Sets in
relation to the current Selection. (See the next page.)
Chapter 3 – Page 12
You will probably use the additional options infrequently, but when you need them,
they offer powerful and unique solutions to handling Selections and Record Sets.
The Venn diagrams show each set operation graphically, on the left side of the
screen.
Make it the [table name] Record Set. The Selection itself
becomes the new current Record Set for the table (the assignment
set operation). This option is the same as the first of the options
offered in the principal Record Set options screen.
Add it to the existing [table name] Record Set. The union of the
Selection and the Record Set becomes the new current Record Set
for the table. This option is the same as the second of the options
offered in the principal Record Set options screen.
Subtract it from the existing [table name] Record Set. The set
of all records in the current Record Set that are not in the Selection
(the difference between the Record Set and Selection) becomes
the new current Record Set for the table.
NOTE: To subtract the current Record set from the Selection, instead, save the
current Record Set as a Record Set Pointer File (see “Saving a Record Set Pointer
File: Second Method,” later in this chapter), make the Selection the new current
Record Set, then load the saved Record Set Pointer File (see “Loading a Record
Set Pointer File,” later in this chapter) and use the subtract operation.
Make shared records the new Record Set. The intersection of
the Selection and the Record Set becomes the new current Record
Set for the table.
Make unshared records the new Record Set. The set of all
records in either the Selection or the current Record Set, but not
both, becomes the new current Record Set for the table.
Chapter 3 – Page 13
Save it to disk as a Record Set Pointer File. This option saves a disk file that
allows you to reload the Selection quickly at a later time. See “Saving a Record Set
Pointer File: First Method,” later in this chapter. This option is the same as the third
of the options offered in the principal Record Set options screen.
Dismiss it. Choosing this option dismisses the Selection of records without
affecting the current Record Set for the table. This option is the same as the fourth
of the options offered in the principal Record Set options screen.
How Biota Uses Record Sets
Biota uses Record Sets to define groups of records for several kinds of special tasks.
For example, the Query Editor can, as an option, search within a Record Set instead of
searching through all records in a table (see “The Query Editor, a General-Purpose
Tool for Finding Records Based on Content,” in Chapter 12).
Four search tools find records in one table based on the current Record Set for another
table: Lower Taxa for Higher Taxa, Higher Taxa for Lower Taxa, Places for Specimens
Or Species, and Specimens or Species for Places (see “Special Tools for Finding
Records in One Table Based on a Set of Records in Another Table” in Chapter 12).
All of Biota’s Export tools can (some of them must) use the appropriate Record Set as
the basis for export (see Chapter 27, “Exporting Data,” and “Exporting and Importing
Images” in Chapter 19). All Labels tools print labels for a Record Set (see Chapter 15,
“Printing Labels”).
A new Specimen Loan can be made for the current Specimen Record Set, or the current
Specimen Record Set can be recorded as a returned loan (see Chapter 21, “Specimen
Loan System”).
The Find and Replace tool can be used on Record Sets, as an option (see “Updating
Records Using the Find and Replace Tool” in Chapter 12).
To Display a Record Set
As their only function, commands in the Display menu display the current Record Set for
each of the Core Tables. These records are presented in the standard record listing
screen for each table, with all the usual tools for output and input screens available (see
Chapter 10, “Working with Records in Record Listing and Input Screens”). If the current
Record Set is empty, Biota informs you that the Record Set you asked to display is
currently empty, and nothing is displayed.
NOTE: The command for displaying the current Record Set for the Det History
(Specimen Determination History) table is in the Special menu (see Chapter 22,
“Determination Histories”). If you have activated the user password system, only a user
with Administration access privileges can use this command (see Chapter 26, “Security:
Passwords and Access Privileges”).
To Empty All Record Sets
You can empty all current Record Sets by selecting “Empty Record Sets” from the
Special menu. Record Sets always start out empty each time you launch Biota.
Chapter 3 – Page 14
Record Set Pointer Files
Record Set Pointer Files, the fourth way to represent Biota records, allow you to save
the results of searches, input sessions, or import operations for later use, even between
Biota sessions. A Record Set Pointer File is illustrated below in the dashed rectangle.
Internally, Record Sets themselves are simply lists of “pointers” to records, not the
records themselves. (Record pointers are a very compact and efficient way to keep track
of Selections of records.) A Record Set Pointer File is simply a disk file (which you name
as you wish) containing a set of record pointers, which can later be loaded from disk to
recover a Selection of records for a particular table.
You can create as many Record Set Pointer Files as you wish for each Core Table.
They take up virtually no disk space, and they are saved or loaded instantaneously.
Record Set Pointer Files are not readable or useable with other applications. If you want
to create a text file from a set of records, use one of the export tools described in
Chapter 27, “Exporting Data.”
Saving a Record Set Pointer File: First Method
You use this method to create a Record Set Pointer File for a Selection of records when
you close a record listing screen with the “Done” button. If a Record Set representing a
different group of records already exists for the table, creating a Record Set Pointer File
with this method leaves the existing Record Set unchanged.
1.
Choose “Save it to disk as a Record Set Pointer File” in the Record Set option
window that appears when you close a record listing screen (see “The Record Set
Options Screen,” earlier in this chapter).
Chapter 3 – Page 15
2. Click the “OK” button in the option
window. A message appears
reminding you to name the disk file
appropriately.
3.
Click the “OK” button in the
reminder message. The Save File
window for your operating system
appears.
4.
Name and place the Record Set
Pointer File.
5.
Click the “Save” button (Mac OS) or the “OK” button (Windows) in the Save
File window.
Saving a Record Set Pointer File: Second Method
You can use this method at any time to create a Record Set Pointer File for the current
Record Set of a particular table. No records need be displayed.
1.
Choose Save Record Set Pointer File from the File menu. A table selection
window appears.
2.
Choose the table name from the popup list in the table selection window.
The Save File window for your operating system appears.
Chapter 3 – Page 16
3.
Name and place the Record Set Pointer File. Be sure to name the Record Set
Pointer File appropriately.
4.
Click the “Save” button (Mac OS) or the “OK” button (Windows) in the Save
File window.
Loading a Record Set Pointer File
To load a Selection of records using a saved Record Set Pointer File, follow these steps.
1.
From the File menu, choose Load Record Set Pointer File.
A table selection window appears.
2.
From the popup list in the table selection window (above), select the Biota
table for which you intend to retrieve records.
3.
Click the “Load” button when ready (above). The file navigation window appears.
4.
Find the Record Set Pointer File in your folder or directory structure and open it.
Chapter 3 – Page 17
WARNING: Be certain that the file you choose applies to the Biota table you have
selected in Step 2. If not, you will have unpredictable results—or no results. If you
have added or deleted records in the table since saving the Record Set Pointer File,
the Selection may not be accurate when you load the Record Set Pointer File.
The records representing the saved Record Set Pointer File you loaded are
displayed as a Selection in the record listing screen for the appropriate table.
The Selection displayed is not automatically made the current Record Set for the
table. See “Loaded Record Set Pointer Files and the Current Record Set,” below.
5.
If you wish to make the displayed Selection the current Record Set, click the
“Done” button in the listing screen and use the Record Set Options screen to
designate the Selection as the current Record Set for the table.
Loaded Record Set Pointer Files and the Current Record Set
The Selection of records retrieved and displayed using a saved Record Set Pointer File
is not automatically designated the current Record Set for the appropriate table. If you
want to make this Selection the current Record Set or add it to the current Record Set
for the table, you must do so in the usual way, using the Record Set Option screen that
is displayed when you click the “Done” button in the record listing screen (see “The
Record Set Options Screen,” earlier in this chapter).
Why does Biota not declare a retrieved Selection to be the current Record Set
automatically? Were that the case, you would be unable to use the “set mathematics”
tools in the Record Set Options screen to work with selections saved as separate
Record Set Pointer Files, nor could you use these operations on a Selection from a new
search and a saved Record Set.
Chapter 4
Biota Menus and Menu Items:
An Annotated Guide
Biota Menus: Quick Reference
This section briefly describes the function of each item in the Biota menus and directs
you to the appropriate pages of this Manual for full details. The menus and their items
(commands) are listed in the order they appear on the screen.
NOTE: The notation used for each item is “Menu Name → Menu Item.”
Access Privileges for Menu Items
If the User Password system has been activated, each user is assigned an access
privilege level. Depending on the privileges you have been assigned, certain menu
commands may be unavailable to you. If so, Biota posts an explanatory message when
you select the item. A complete tabulation of commands and the privilege level required
to use them appears in the section “Users, User Names, Passwords, Access Levels, and
Privileges” in Chapter 26.
The Menu Bar
Because Biota supports simultaneous procedures (multitasking), the menu bar does not
change. All menus are present and active at all times.
The File Menu
File → Open Data File. Presents a file navigation
screen to allow you to close the present Biota Data
File and open a different one. See “Opening a Biota
Data File or Creating a New Biota File from Within
Biota” in Chapter 3.
File → Create Data File. Presents a file navigation
screen to allow you to close the present Biota Data
File and create a new, empty one. See “Opening a
Biota Data File or Creating a New Biota File from
Within Biota” in Chapter 3.
Chapter 4 – Page 2
File → Save Record Set Pointer File. Creates a disk file with pointers to the
records in the current Record Set for any Core Table or for the Determination
History table. See “Saving a Record Set Pointer File: Second Method” in Chapter 3.
File → Load Record Set Pointer File. Loads the Selection of records indicated by
the record pointers in a saved Record Set Pointer File. See “Loading a Record Set
Pointer File” in Chapter 3.
File → Print. Prints (see “Printing a Report Based on a Selection of Records” in
Chapter 14) or exports to disk file (see “Printing Reports or Creating Text Files
Based on Records in a Record Listing Screen” in Chapter 10) a report for the current
Selection of records displayed in an Record Listing screen. (This command is
disabled if no records are displayed.)
File → About Biota. Displays the copyright notice, version, and release date for
your copy of Biota, as well as the website and support e-mail address for Biota.
File → About the Current Data File. Displays the name and location (path) of the
Data File that is currently open, plus a scrolling list of the number of records in each
Biota table in the Data File. See “To Find Out Which Data File Is Currently Open” in
Chapter 3.
File → Quit Biota. Choose this command to shut down Biota. See “Saving
Changes in a Biota Data File” in Chapter 3.
The Edit Menu
The Edit Menu contains the standard text editing commands for your operating system.
See your operating system manual.
The Input Menu
Input → Specimen. Presents the Specimen Input screen.
See “Specimen Input” in Chapter 11.
Input → Specimen & Collection. Presents the Specimen
Input screen. See “Specimen and Collection Combined
Input” in Chapter 11.
Input → Collection. Presents the Collection Input screen.
See “Collection Input” in Chapter 11.
Input → Locality. Presents the Locality Input screen. See
“Locality Input” in Chapter 11.
Input → Species. Presents the Species Input screen. See
“Species Input” in Chapter 11.
Input → Genus, Family, Order, Class, Phylum or
Division, or Kingdom. Presents the Input screen for the
corresponding table. See “Genus, Family, Order, Class, Phylum, and Kingdom
Input” in Chapter 11.
Input → Personnel. Presents the Personnel Input screen. See “Personnel Input” in
Chapter 11.
Input → Project. Presents the Project Input screen. See “Project Input” in Chapter
16.
Input → Reference. Presents the Reference Input screen. See “Reference Input” in
Chapter 20.
Chapter 4 – Page 3
The Series Menu
Series → Input Specimen Series. Presents an Input
screen for the efficient creation of sets of Specimen
records that share Collection data. See “Using the ‘Input
Specimen Series’ and ‘Input and Identify Specimen Series’
Tools” in Chapter 13.
Series → Input & Identify Spcm Series. Presents an Input screen for the efficient
creation of sets of Specimen records that share Collection and determination
(identification) data. See “Using the ‘Input Specimen Series’ and ‘Input and Identify
Specimen Series’ Tools” in Chapter 13.
Series → Find Specimen Series. Presents a query tool for finding Specimen
records efficiently by Specimen Code. The Specimen Codes may be either
sequential or non-sequential. (The same command appears in the Find menu.) See
“Using the ‘Find Specimen Series’ and ‘Find and Identify Specimen Series’ Tools” in
Chapter 13.
Series → Find & Identify Specimen Series. Presents a query and record update
tool for finding Specimen records efficiently by Specimen Code, and for adding
determination (identification) data and/or certain other fields in the Specimen table.
The Specimen Codes may be either sequential or non-sequential. See “Using the
‘Find Specimen Series’ and ‘Find and Identify Specimen Series’ Tools” in Chapter
13.
The Find Menu
Find → Using the Query Editor. Presents the Query
Editor, a general purpose query tool for finding records in a
particular table based on the content of fields in those
records or the content of fields in linked records of other
tables. See “The Query Editor, a General-Purpose Tool for
Finding Records Based on Content” in Chapter 12.
Find → Lower Taxa for Higher Taxa. Presents a query
tool for finding all records in the Specimen table or a taxon
table that are linked to a single record or a Record Set in a
higher taxon table (e.g., all Specimens of a Species or a
Genus, all Genera for a set of Orders). (The same
command appears in the Tree menu.) See “Finding
Records for Lower Taxa Based on Higher Taxa” in Chapter
12.
Find → Higher Taxa for Lower Taxa. Presents a query
tool for finding all records in the Species table or a higher
taxon table that are linked to a Record Set for the
Specimen table or any lower taxon table (e.g., all Species
for the Specimen Record Set; all Orders for the Genus
Record Set). (The same command appears in the Tree
menu.) See “Finding Records for Higher Taxa Based on
Lower Taxa” in Chapter 12.
Find → Places for Spcms or Species. Presents a query
tool for finding all records in the Collection table or Locality
table that are linked to a Record Set for the Specimen table
Chapter 4 – Page 4
or the Species table (e.g., all Localities for the Specimen Record Set; all Collections
for the Species Record Set). See “Finding Place Records (Collection or Locality) for
Specimens or Species” in Chapter 12.
Find → Spcms or Species for Places. Presents a query tool for finding all records
in the Specimen table or Species table that are linked to a Record Set for the
Collection table or the Locality table (e.g., all Species for the Locality Record Set; all
Specimens for the Collection Record Set). See “Finding Specimen or Species
Records for Places (Collections or Localities)” in Chapter 12.
Find → By Specimen Code. Finds and displays a Specimen record based on
single Specimen Code. See “Finding Records by Record Codes” in Chapter 12.
Find → By Specimen Code Series. Presents a query tool for finding groups of
Specimen records efficiently by Specimen Code. The Specimen Codes may be
either sequential or nonsequential. (The same command appears in the Series
menu.) See “Using the ‘Find Specimen Series’ and ‘Find and Identify Specimen
Series’ Tools” in Chapter 13.
Find → By Collection Code. Finds and displays a Collection record based on
single Collection Code. See “Finding Records by Record Codes” in Chapter 12.
Find → By Locality Code. Finds and displays a Specimen record based on single
Locality Code. See “Finding Records by Record Codes” in Chapter 12.
Find → By Species Code. Finds and displays a Species record based on single
Species Code. See “Finding Records by Record Codes” in Chapter 12.
Find → All Specimens, All Collections, All Localities, All Species, All Genera,
All Families, All Orders, All Classes, All Phyla or Divisions, All Kingdoms, or
All Personnel. Finds and displays all records for the specified table. See “Finding
and Displaying All Records for a Table” in Chapter 12.
Find → All Valid Species. Finds and displays all Species records that are not
junior synonyms (i.e., all Species records for which the Species Code equals the
Valid Species Code). See “Finding Valid Species, Species With Synonyms, or
Junior Synonym Records” in Chapter 23.
Find → Species With Junior Synonyms. Finds and displays all Species records
for which the Species Code is identical to Valid Sp Code that have at least one
Junior Synonym. See “Finding Valid Species, Species With Synonyms, or Junior
Synonym Records” in Chapter 23.
Find → Junior Synonyms. Finds and displays all Species records for which the
Species Code differs from the Valid Sp Code, whether or not the Valid Sp Code
matches the Species Code of a valid Species (senior synonym). See “Finding Valid
Species, Species With Synonyms, or Junior Synonym Records” in Chapter 23.
Find → Host Specimens and Collections. Finds and displays host Specimen
records and linked host Collection records based on a search of all Specimen
records or a search of the Specimen Record Set. See “Finding Host Specimens and
Host Collections” in Chapter 24.
Find → Guest Specimens and Collections. Finds and displays guest Specimen
records and linked guest Collection records based on a search of all Specimen
records or a search of the Specimen Record Set. See “Finding Guest Specimens
and Guest Collections ” in Chapter 24.
Find → Guest Spcms for Host Spcms. Finds and displays all guest Specimen
records that are linked to host Specimen records in the Specimen Record Set. See
“Finding Host Specimens for Guest Specimens” in Chapter 24.
Chapter 4 – Page 5
Find → Host Spcms for Guest Spcms. Finds and displays all host Specimen
records that are linked to guest Specimen records in the Specimen Record Set. See
“Finding Guest Specimens for Host Specimens” in Chapter 24.
Find → Childless Records. For a specified parent table, finds all records that are
not linked to any child record in a Core table. (For example, you could find all
Species records that are not linked to any Specimen records.) See “Finding
Childless Records” in Chapter 12.
Find → Orphan Records. For a specified child table, finds all
records that are not linked to any parent record in a Core table.
(For example, you could find all Specimen records that are not
linked to any Species record.) See “Finding Orphan Records” in
Chapter 12.
The Display Menu
Display → [Table Name] Set. Displays the current Record Set
for the specified table. See “To Display a Record Set” in Chapter
3.
The Labels Menu
Labels → Collection Labels. For each record in the current
Collection Record Set, prints or exports (to a text file) a label that
includes most fields from the Collection record and its linked
Locality record. See “Collection Labels” in Chapter 15.
Labels → Pin Labels: Locality. For each record in the current
Specimen Record Set, prints a standard entomological locality
label for a pinned specimen, including appropriate fields from
linked Collection and Locality records and (optionally) the
Specimen Code. See “Pin and Vial Specimen Locality Labels” in
Chapter 15.
Labels → Pin Labels: Determination. For each record in the
current Specimen Record Set, prints a standard entomological
determination label for a pinned specimen, including appropriate
fields from the Specimen record and from linked Species and
Genus records. See “Pin and Vial Specimen Determination Labels” in Chapter 15.
Labels → Slide Labels: Locality. For each record in the current Specimen Record
Set, prints a standard locality label for a slide mounted specimen, including
appropriate fields from linked Collection and Locality records and (optionally) the
Specimen Code. See “Slide Specimen Labels” in Chapter 15.
Labels → Slide Labels: Determination. For each record in the current Specimen
Record Set, prints a standard determination label for a slide mounted specimen,
including appropriate fields from the Specimen record and from linked Species,
Genus, and Family records. See “Slide Specimen Labels” in Chapter 15.
Labels → Vial Labels: Locality. For each record in the current Specimen Record
Set, prints a standard locality label for a fluid preserved specimen, including
appropriate fields from linked Collection and Locality records and (optionally) the
Specimen Code. See “Pin and Vial Specimen Locality Labels” in Chapter 15.
Labels → Vial Labels: Determination. For each record in the current Specimen
Record Set, prints a standard determination label for a fluid-preserved specimen,
Chapter 4 – Page 6
including appropriate fields from the Specimen record and from linked Species,
Genus, and Family records. See “Pin and Vial Specimen Determination Labels” in
Chapter 15.
Labels → Herbarium Labels. For each record in the current Specimen Record Set,
prints one or more standard herbarium labels, including appropriate fields from the
Specimen record and from linked Collection, Locality, Species, Genus, and Family
records. See “Herbarium Specimen Labels” in Chapter 15.
Labels → Species Labels. For each record in the current Species Record Set
and/or for Species records found using the Species Labels screen search tools,
prints a label including appropriate fields from the Species record and from the
linked Genus record, plus (optionally) the determiner’s name. See “Species Labels”
in Chapter 15.
Labels → Design & Print Custom Labels. For each record in the current Record
Set for any Core table, prints a label that you design using the 4D Label Wizard,
using fields from the selected table and linked records in parent tables. See
“Designing and Printing Custom Labels” in Chapter 15.
The Import/Export (Im/Export) Menu
Im/Export → Import by Tables and Fields.
Presents the Import Editor, which imports
delimited, column-by-row text files into the fields
you specify for any table in Biota’s structure. See
Chapter 28, “Importing Data.”
Im/Export → Export by Tables and Fields.
Presents the Export Editor, which exports
delimited, column-by-row text files based on the
fields you specify for any table in Biota’s structure.
See “Exporting Data by Tables and Fields” in
Chapter 27.
Im/Export → Import Image Files. Based on an
Image File List, imports and links thumbnails from
groups of external image files, or imports the full
image. See “Importing Groups of Images” in
Chapter 19.
Im/Export → Export Image Files. For each record in the current Species,
Specimen, Collection, or Locality Record Set, exports either the first linked image or
all linked images, creating a separate disk file for each image exported and an
Image File List that can be used to import the images to another Biota Data File,
using the “Import Image Files” command. See “Exporting Groups of Images” in
Chapter 19.
Im/Export → Export Notes. For the current Species, Specimen, Collection,
Locality, or Loans Record Set, exports (to a text file in report format, or to a recordsby-fields text file) the full record for each attached Note, certain fields from each
parent record in the Record Set, and appropriate fields from other linked Core
tables. See “Exporting Notes Records Using the Export Notes Tool” in Chapter 27.
Im/Export → Export Auxiliary Fields. For the current Species, Specimen,
Collection, or Locality Record Set, exports (to a tab-delimited text file) Auxiliary Field
values in matrix format (standard or transposed) or NEXUS format. See “Exporting
Auxiliary Field Values” in Chapter 16.
Chapter 4 – Page 7
Im/Export → Export References. Exports all records for the current Reference
Record Set, in American Naturalist format, to a text file. See “Exporting References”
in Chapter 20.
Im/Export → Export Taxonomic Flatfile. Exports a tab-delimited text file table with
the Record Set for a lower taxonomic level as rows and information on the higher
classification of those taxa as columns, based on the range of taxonomic levels you
specify. See “Exporting Taxonomic Flatfiles” in Chapter 27.
Im/Export → Export Specimen Flatfile. Exports a tab-delimited text file table with
the current Specimen Record Set as rows and fields from any linked Core table as
columns. See “Exporting Specimen Flatfiles” in Chapter 27.
Im/Export → Export Custom Flatfile. For any Core table, exports a text file based
on the current Record Set with selected fields from the focal table and related
tables, using a custom format that you design using the Quick Report Editor. See
“Exporting Custom Flatfiles” in Chapter 27.
Im/Export → Export Specimens Examined List. For the current Species Record
Set, exports (to a text file) draft text for a Specimens Examined section of a
taxonomic monograph, based on linked Specimen records. See “Exporting
‘Specimens Examined’ Lists for Publications” in Chapter 27.
Im/Export → Colls x Taxon Table. Based on the Collection, Specimen, or Taxon
(Species or higher rank) Record Set, exports a tab-delimited text file table, with
Collections as rows and Taxa as columns, specifying the incidence
(presence/absence) or abundance of Specimens of each Taxon in each Collection.
See “Exporting Place- by-Taxon Incidence or Abundance Tables” in Chapter 27.
Im/Export → Locs x Taxon Table. Based on the Locality, Collection, Specimen, or
Taxon (Species or higher rank) Record Set, exports a tab-delimited text file table,
with Localities as rows and Taxa as columns, specifying the incidence
(presence/absence) or abundance of Specimens of each Taxon in each Locality.
See “Exporting Place- by-Taxon Incidence or Abundance Tables” in Chapter 27.
Im/Export → Create Web Pages. Exports hierarchically linked Web pages, ready
for posting on a Web server, for any range of taxonomic levels, based on Record
Sets that you define. You can include any fields from the Specimen, Collection, or
Locality tables, as well as images and host information. See Chapter 33, “Exporting
Static Web Pages.”
The Loans Menu
Loans → New Loan. Creates a new Loan record, marks
Specimen records and produces documents and text
files for a new Specimen loan, based on the current
Specimen Record Set and/or on ad hoc entry of
Specimen Codes. See “Recording a New Loan” in
Chapter 21.
Loans → Record Returns. Updates an existing Loan
record and marks Specimen records to record the return of loaned specimens,
based on the current Specimen Record Set, the Specimens in the Loan, and/or on
ad hoc entry of Specimen Codes. See “Recording Specimen Returns” in Chapter
21.
Loans → Display All Loans. Finds and displays all records for the Loans table.
See “Displaying and Editing an Existing Loan” in Chapter 21.
Chapter 4 – Page 8
Loans → Display Loan Record Set. Displays the current Record Set for the Loans
table. See “Displaying and Editing an Existing Loan” in Chapter 21.
Loans → Print List of All Loans. Prints a list of all records for the Loans table, with
pertinent information from other tables. See “Displaying and Editing an Existing
Loan” in Chapter 21.
The Special Menu
Special → Preferences. Presents the Preferences
screen. See Appendix B, “Setting Preferences,” for a
guide to page references for each option in the
Preferences screen.
Special → Web Server. Presents the Web Server
control and options screen. See Chapter 30, “Biota's
Onboard Web Server.”
Special → Empty Record Sets. Empties the Record
Set for each Core table and for the Determination
History table. See “To Empty All Record Sets” in
Chapter 3.
Special → Find and Replace. Presents the Find and
Replace tool, which allows you to replace a specified
text string with a new string in a specified field in a
specified Biota table, for all records or for selected
records. See “Updating Records Using the Find and
Replace Tool” in Chapter 12.
Special → Change User Password. Changes a
validated current User Password to a new password
that you choose. See “Changing Your User Password”
in Chapter 26. The Administrator can enable or disable
the User Password system using this command. See
“Activating the User Password system” and
“Deactivating the User Password system” in Chapter
26.
Special → Edit User Password System. Presents the Password Editor, which the
Administrator can use to assign or change user names, User Passwords, access
privilege levels, and default language settings for users. See “Using the Password
Editor” in Chapter 26.
Special → Edit Data File Password Link. Enables or disables the Data File
Password Link or changes a validated current Data File Password Link to a new
one. See “Using the Data File Password Link” in Chapter 26.
Special → Field Value Defaults. Allows you to set default values for data entry in
many fields. See “Setting Default Entries: Field Value Defaults” in Chapter 17.
Special → Entry Choice Lists. Allows you to enable or disable an Entry Choice
List for rapid entry of repetitive data in many fields. See “Using Entry Choice Lists”
in Chapter 17.
Special → Core Field Aliases. Allows you to rename many Core fields. An Alias
appears on all input and Record Listing screens and in certain reports instead of the
corresponding Internal Field Name. See Chapter 18, “Re-naming Fields.”
Chapter 4 – Page 9
Special → Record Code Settings. Allows you to specify default prefixes for
Specimen, Species, Collection, or Locality Record Codes and to set parameters for
using barcodes. See “Assigning New Record Codes Automatically During Data
Entry” and “Setting Default Prefixes for Recognizing Specimen and Species Record
Codes” in Chapter 8.
Special → Maintenance Utilities. Presents an options screen with tools for
maintaining and repairing several table linking systems in Biota. See “Maintaining
and Repairing the Auxiliary Fields and Project Systems “ in Chapter 16,
“Maintaining and Repairing Image Links” in Chapter 19, or “Maintaining and
Repairing Reference Links” in Chapter 20.
Special → Make Guest Collection Records. Automatically creates a new
Collection record for the “guests” of each Specimen in the current Specimen (host)
Record Set. See “Creating Guest Collection Records Automatically” in Chapter 24.
Special → Specimen Count by Taxon. Prints a report, organized by the taxonomic
hierarchy, showing the number of Specimens for each Species and for each higher
taxon in the Specimen Record Set. See “Printing a Specimen Count by Taxon
Report” in Chapter 14.
Special → Clear All Synonymies. Sets the Valid Species Code equal to the
Species Code for all Species records. See “Clearing All Synonymies” in Chapter 23.
Special → Delete Images by Record Set. Deletes all the Image Archive records
linked to particular group of parent records in the Species, Specimen, Collection, or
Locality table. See “Deleting Images for a Species, Specimen, Collection, or Locality
Record Set” in Chapter 19.
Special → All Determination Histories. Finds and displays all records for the
Determination History table. See “Displaying, Editing, or Deleting Determination
History Records” in Chapter 22.
Special → Display Determination Histories. Displays the current Record Set for
the Determination History table. See “Displaying, Editing, or Deleting Determination
History Records” in Chapter 22.
Special → Det Hists for the Spcm Rec Set. Displays all Determination History
records for the current Specimen Record Set. See “Displaying, Editing, or Deleting
Determination History Records” in Chapter 22.
Special → Spcms for the Det Hist Rec Set. Displays all Determination History
records for the current Specimen Record Set. See “Displaying, Editing, or Deleting
Determination History Records” in Chapter 22.
Special → Display Active Project Window. Displays the Active Project floating
window, which allows you to switch between Projects quickly. See “To Display the
Active Project Floating Window” in Chapter 16.
Special → Show Shortcut Screen. Displays the Shortcut screen, which offers
buttons for several common Biota menu commands. See “The Shortcut Screen”
later in this chapter.
Special → Add Data Segment. Presents the 4D “Segments” screen. See
“Segmenting Data Files” in Appendix I.
Special → Biota License Code. Displays the installed Biota License Code, if any.
If no Biota License Code has been installed, the License installation dialog appears.
Chapter 4 – Page 10
The Help Menu
The Help menu in Biota is not functional. Unfortunately, there is no way to eliminate it
from the program. This Manual and the (onscreen “Help” buttons that appear in some
Biota windows) are your source of information.
The Shortcut Screen
The Shortcut Screen is simply a set a of buttons that execute a small subset of the most
frequently used commands from Biota’s menus. It is intended for users just getting
started with Biota, but some experienced users may find it useful as well.
New, empty Biota Data Files, and the Biota2Demo Data File, initially display the
Biota Shortcuts screen.
The Shortcuts screen reappears each time
Biota is launched, unless you turn it off by unchecking the “Show this screen at startup”
checkbox on the Shortcut screen.
To re-display the Shortcuts screen, choose
“Show Shortcut Screen” from the Special menu,
and check the “Show this screen at startup”
checkbox.
Chapter 5
Overview of Biota’s Tools
and Features
This chapter briefly scans the tools and features that Biota offers. Often, there are
several different ways to accomplish the same task with Biota. General-purpose tools
(like the Query Editor, see “The Query Editor, a General-Purpose Tool for Finding
Records Based on Content” in Chapter 12) are included to cover all possible cases, but
for many purposes Biota offers special tools that have been optimized to do a specific
task.
Reading through this chapter now (or at least scanning the titles) will save you time later
when you need to accomplish tasks for which special tools exist. Active links lead you to
a more detailed presentation elsewhere in the Manual, if you need help.
Architectural Features
Multitasking
Each Biota tool or screen that you use runs in an independent process that automatically
shares microprocessor time with all concurrent Biota processes, independent of the
operating system. This means you can open as many windows and carry out as many
tasks simultaneously as your hardware will allow. For example, in a large database you
could launch a time-consuming search (e.g., for all records for specimens of
Verbenaceae collected between 1989 and 1991 in Heredia Province, Costa Rica, by a
particular collector) and, while it is running, print herbarium labels for a different set of
specimens, while entering data for a third set.
Single-user vs. Client/Server Versions
BiotaApp is the stand-alone, single-user version of Biota. The vast majority of Biota
users rely solely BiotaApp. Biota4D is intended primarily for multi-user, client/server use,
running under 4D Server, but can also run in single-user mode under 4th Dimension.
See Appendix H, “Using Biota4D with 4D Server or 4th Dimension” for information on
Biota4D. Data Files and all tools and features (except for multi-user capability) are
identical with BiotaApp and Biota4D, including the ability to run Biota’s onboard Web
server to publish your database (see Chapter 30, “Biota's Onboard Web Server”).
Biodiversity Information Types
Specimen-Based Data
Because Biota was originally designed for a quantitative, specimen-based,
geographically referenced biotic inventory (see the Preface), its data-input and analysis
tools have been crafted for maximum efficiency in dealing with individual specimens
from new collections. But many of the same tools have proven themselves worthy in
Chapter 5 – Page 2
facilitating specimen-based work in systematics and collections management for
historical collections, and many special tools for museum and herbarium needs are
included.
Living Organisms
Although Biota was designed to handle specimen-based data from inventories or
collections, it is easy to use for surveys of living individual organisms (for example, forest
stands or bird sightings).
“Lot”-Based Data
In “lot”-based collections, groups of specimens share site (collection) data, but
specimens are simply enumerated by species within each lot, without giving each
specimen a separate identifier. (In some disciplines, a lot is a set of specimens from a
single species from a single collecting event.) Lot systems are easily handled by Biota’s
“voucher” system, by creating just one voucher Specimen record for each species in
each lot, with the number of specimens in the lot entered in the [Specimens]Abundance
field (see “Specimen Input” in Chapter 11). If you later need to create individual
specimen records for certain specimens (e.g., a mounted series, or types), Biota lets you
use the original voucher Specimen record as a template for the new records, using the
Carry button (see “Using an Existing Record as a Template for a New Record” in
Chapter 10).
Site-Based Species Lists With No Specimens
By creating one “pseudospecimen” record for each species/site combination, Biota can
accommodate species-based data (faunal or floral lists) for which no specific specimens
are entered in the database. In this case, the pseudospecimens link taxonomic
information with site information. (In technical terms, the pseudospecimens serve as a
“relating record” for the many-to-many relation between Species and Collections or
Localities; see Chapter 3, “Key Concepts”). This technique also allows records for actual
specimens of parasites, commensals, herbivores, etc., to be linked with host species
records for which no specific specimen exists (see Chapter 24, “Host-Guest Relations”).
Plot-Based Data
Biota has been quite successfully used for plot-based vegetation data, using the “place
hierarchy” (Locality and Collection records) to reference stands and plots within stands.
For further levels, systems of hierarchical Record Codes have been successfully used.
See “Unified Record Code Systems: Specimen, Collection, and Locality Codes” in
Chapter 8. Biota’s Export Place-by-Taxon matrix tools (see “Exporting Place- by-Taxon
Incidence or Abundance Tables” in Chapter 27) make preparing data for statistical
analysis of plot-based data a breeze.
Special Data Types
Images
For each Species, Specimen, Collection, and Locality table record, you can link any
number of digitized images, in virtually any image format. Images may reside in external
files in virtually any format, with transparent links to corresponding thumbnails inside
Chapter 5 – Page 3
Biota, or the image itself can be stored in the Biota Data File. Image-comparison screens
help you compare images within and among parent records, and a comprehensive set of
image-editing tools is available within Biota, as well as direct TWAIN device capture
ability (scanners, digital cameras, etc.). Biota supports batch import (linked thumbnails or
full images) as well as batch export of external images files. See Chapter 19, “Images.”
Literature Reference System
Biota offers a capable and flexible literature Reference system. A separate Reference
table, designed around a subset of EndNote reference styles and fields, holds Reference
records that can be quickly linked (many-to-many) to any record in the Species,
Specimen, Collection, or Locality table. References exported from EndNote can be
directly imported to the Reference table. Records from other reference management
applications can be imported with appropriate preparation of the input file. See Chapter
20, “References.”
Recursive Specimen Relations (“Host-Guest” Links)
Biota handles recursive relations between specimens—“host-guest” relationships—by
including the “host” specimen as one of the attributes of the Collection record of the
“guest” specimen. For example, a DNA sample taken from the tissue of a wasp reared
from a caterpillar, found feeding on the leaves of an epiphyte that was growing on a tree,
would produce a five-level host-guest recursive chain. Host data are included as an
option on locality labels. See Chapter 24, “Host-Guest Relations.”
Tools for Customizing Biota
Field Aliases
For many Core fields distributed among Biota’s 14 Core tables, you can assign a Field
Alias (using the Core Field Alias tool from the Special menu; see Chapter 18, “Renaming Fields”). Assigning an Alias changes the field name that is displayed in the
Query Editor, the Sort Editor, and the Quick Report Editor, as well as the entry area for
the field on input screens, for column headers on output (record listing) screens, in
exported files (see Chapter 27, “Exporting Data”) and printed reports (see Chapter 14,
“Printing Reports”). For example, a marine biologist might re-name the Elevation field in
the Collection table Depth. A botanist might re-name the [Specimen]Stage/Sex field “Life
Form.” In some groups of arthropods, the rank of Cohort is interposed between Suborder
and Superfamily. The Biota field Family Custom 1 could be given the Field Alias Cohort
to accommodate this requirement.
Auxiliary Fields and Projects
For the Species, Specimen, Collection, and Locality tables, you can define any number
of Auxiliary Fields, named as you wish, and assign values to them for each record in the
related Core Table. Auxiliary Fields and their values are part of your Data File, not the
Biota application itself, so you must redefine them for each new database you create.
The number of Auxiliary Fields you define is unlimited.
You can define any number of Projects for a single Biota Data File. For each Project,
you can specify which Auxiliary Fields should be displayed in Input and Record Listing
screens. You can quickly switch between Projects using the Active Project floating
window.
Chapter 5 – Page 4
If you intend to use Auxiliary Fields, be sure to read about how they are created and be
aware of their limitations. Using Core fields is always preferable, if feasible for your
needs. See Chapter 16, “User-Defined Auxiliary Fields and the Project System.”
Date Formats
Biota automatically complies with the Date Format setting in your operating system:
International (dd/mm/yyyy) or U. S. (mm/dd/yyyy). For importing and exporting data, you
are automatically offered a choice of International, U.S., or ANSI (yyyy/mm/dd) format,
regardless of the current setting in your operating system.
For collection dates, Biota supports full dates, month-year dates, and year-only dates, as
well as date ranges based on any mixture of these formats. See “Dates” in Chapter 9.
Spatial Reference (Georeference) Formats
Biota offers a comprehensive set of options for recording spatial reference data,
including decimal degrees (Biota’s internal representation for latitude/longitude),
degrees-minutes-seconds, integer degrees-decimal minutes, and fields for alternate
coordinate systems (UTM, Lambert, etc.) See “Spatial Coordinates” in Chapter 9.
Spanish Dialog Screens
Biota is partially bilingual. Spanish language versions are available for all “dialog
screens” (instructions, options, warnings, error messages, result reports, and the
Preferences screen itself) that are accessible to users with “Read Write Export,” “Read
Export,” or “Read Only” access privileges.
Biota tools and screens accessible only to users with “Administration” access privileges
are available in English only. The justification for this design is that the Administrator
needs to be able to read this manual, to use Biota’s most powerful tools safely. All menu
bars and menus are in English for all users.
You can enable or disable the Spanish version of the dialog screens in the “Language”
tab of the “Preferences screen (Special menu) or by means of the Startup Procedure
assigned to a particular User in the User Password system. See “The ‘Language’ Tab” in
Appendix B, “Setting Preferences.”
Table Colors for Input and Record Listing Screens
Biota uses a set of default colors, one for each Core table, to help you tell which table
you are using. If you want a different color scheme, or you prefer the “Microsoft-gray”
look, you can change the scheme using the Colors tab of the Preferences screen
(Special menu). See “To Change the Screen Color Scheme” in Chapter 7.
Chapter 5 – Page 5
Information Input
Record Sets
A Record Set is a temporary selection of records from among those permanently stored
in the database. For each Biota Core table (Specimen, Collection, Species, etc.), you
can define any number of Record Sets and save them to disk as Record Set Pointer
Files for later rapid recall. Only one Record Set per table can be active (current) at a
given time, however. During data entry, you can elect to add new records to the current
Record Set or start a new Record Set. Record Sets are also used in printing reports,
labels, making or returning loans, and for export options. You can display the current
Record Set for a table at any time using commands from the Display menu. See “Record
Sets” in Chapter 3.
Automatic Prompting for Parent Record Entry
Although you can enter data table by table (enter all Genera, then all Species, then all
Specimens, etc.), you may also work directly from records lower in a hierarchy—for
example, directly from Species entry. With the latter approach, Biota queries you
automatically when new entries are required in a related (parent) table (e.g., the Genus
table, if you enter a new Genus name in a Species record), then returns you
automatically to the lower-level (e.g., Species) entry screen. See “Entering Data in
Linking Fields” in Chapter 7.
Wildcard Entry for Linking Fields
During data entry, when the appropriate record already exists in a related table (e.g., the
Genus record already exists for a Species record currently being entered), the linking
field is automatically looked up and entered, based on the first letter or first few letters
you enter. (Press TAB to launch the search.) If more than one related record matches the
entry, Biota presents you with an alphabetic list to choose from, including an additional,
“helper” field from the related table. For example, if you are entering Genus as a relating
field in a new Species record, and you enter the letter P, every Genus that starts with P
will appear in a scrollable list along with its Family. You can sort the list by either Family
or Genus by clicking the correct record to enter it in the new Species record. This
wildcard entry feature minimizes not only input effort, but spelling errors. See “A
Powerful Shortcut: Wildcard Data Entry for Linking Fields” in Chapter 7.
Lookup Tool for Entering Record Codes in Linking Fields
Each record in the Specimen, Species, Collection, and Locality tables must have a
unique Record Code (see Chapter 8, “Record Codes”). Although you can use any name
or mnemonic you like for these codes, they can be hard to remember when you need to
enter them in relating fields during data entry. Although wildcard entry is the fastest way
to enter data for these relating fields, Biota also provides “Look Up” buttons that open
windows with scrollable lists of existing records in the related table, based on criteria you
specify, and sorted at your option by one of several criteria. See “Entering Specimen
Data: The ‘General’ Tab” in Chapter 11 for an example.
Chapter 5 – Page 6
Default Entries and Entry Choice Lists (Pick Lists)
Some fields in your database will probably have a limited number of repetitive entries—a
field for sex or life stage, for example. For many non-inking fields in Biota, you can
activate an Entry Choice List that presents entry options in a floating window whenever
the entry area for the field is accessed during input, and you have activated the Choice
List for that field. When the window appears, you simply click an item on the list to enter
it, then type in the first letter or first few letters of the entry to find it in the list. You
construct each list by entering items with the List Editor or importing to the List Items
table. Biota saves the lists you have created as part of your Data File, whether activated
or not, until you change or erase them. Since Choice lists eliminate misspellings, they
are especially useful when someone else enters data for you. See Chapter 17, “Default
Entries and Entry Choice Lists (Pick Lists).”
Field Value Defaults
If you repeatedly enter a single value for a field, or one value is used in a large
proportion of your records, you may want to assign a Field Value Default for that field
(Special menu). The default will be automatically entered in the field as soon as a new
record is initiated on an input screen. Biota supports Field Value Defaults for 16 Core
Fields in the Specimen, Collection, and Locality tables. See Chapter 17, “Default Entries
and Entry Choice Lists (Pick Lists).”
Using an Existing Record as a Template for a New One
Every input screen includes a Carry button, which allows you to make a new record
using the current record as a template. (If it is a new or edited record, the template
record is saved first, automatically, when you click Carry.) Since, in many cases, only
one or two fields needs changing between a template record and a new one, this
capability saves a great deal of effort. A saved, existing record can also be used as a
template. Display it in the input screen, click Carry, and a new record will appear,
repeating all but the Key field of the template record. (Auxiliary Fields and Notes can be
carried or not, according to a setting in the Preferences screen, from the Special menu.)
See “Using an Existing Record as a Template for a New Record” in Chapter 10.
Automated Entry of Specimen Record Series
Extending the Carry concept, two powerful input options (from the Series menu) speed
the entry of sets of Specimen records that share either the same Collection data (Input
Specimen Series) or both Collection and taxonomic data (Input and Identify Specimen
Series). These options require entry of only the first and last Specimen Code numbers
(with or without prefixes) and one-time data entry for the other fields for each set of
specimens. All records in the specified range are then generated automatically, with
sequential Specimen Codes. See Chapter 13, “Creating, Finding, and Updating
Specimen Series.”
Automatic Record Code Assignment
Record Codes for Specimen, Species, Collection, and Locality records may be any
arbitrary, unique (within tables) alphanumeric code you choose. Alternatively, sequential
codes can be automatically assigned with either a default alphanumeric prefix (which
you define with the Record Code Prefixes utility in the Special menu) for each table, an
ad hoc prefix you assign during record input, or no prefix. See “Assigning New Record
Codes Automatically During Data Entry” in Chapter 8.
Chapter 5 – Page 7
Barcode Entry of Record Codes
All Record Code entry areas (including Specimen Code fields for specimen Loans and
returns) automatically accommodate barcode entry. All record entry and record retrieval
areas for Specimen and Species Codes also provide for barcode prefix recognition and
optional substitution of an abbreviated or different code prefix in the database. Barcode
entry can be freely mixed with manual entry in the same Data File. See “Setting Default
Prefixes for Recognizing Specimen and Species Record Codes” in Chapter 8, and
Appendix K, “Barcodes.”
Record Retrieval and Manipulation: General Tools
Multifunction Record Listing Screens
A uniform interface for displaying records allows you to carry out ad hoc sorts, select
consecutive or nonconsecutive records to redefine a current selection of records (using
the Subselection button), delete records, modify existing records (double-click and
modify the record in the input screen, add new records, or use an existing record as a
template for a new one that shares information with the template. In each case, Biota
immediately displays the result using the same uniform interface, ready for the next
action. See Chapter 10, “Working With Records in Record Listing and Input Screens.”
Simultaneous Display of Records from Any Number of Tables
The number of open windows Biota can display simultaneously is limited only by the
memory allocated to Biota. In fact, you can display different groups of records (or saved
Record Sets) in different windows for the same Core table, simultaneously.
Displaying Record Sets
The active Record Set (if any) for each Core table can be displayed and manipulated
using commands from the Display menu.
Ad Hoc Queries for All Tables
A general-purpose query construction tool (the Query Editor) allows you to use the
content of records, including values in related fields of other tables, to find records. You
can choose to search among all records in a table or only among those in a Record Set.
If your query can be accommodated by using one or more of the special tools described
in “Special Tools for Finding Records in One Table Based on a Set of Records in
Another Table” (in Chapter 12), the search will invariably be much faster than building
the query in the Query Editor. See “The Query Editor, a General-Purpose Tool for
Finding Records Based on Content” in Chapter 12.
Special Tools for Finding Records in One Table Based
on a Set of Records in Another Table
Biota offers four special tools, with a common interface, for the frequent task of finding
related records up, down, and across the taxonomic and place hierarchies. As an option,
Biota will keep the linking records for all intermediate tables as Record Sets for those
tables. These tools support rapid and intuitive query construction and optimized,
Chapter 5 – Page 8
extremely fast search and display. They can also be used sequentially for complex
searches. For many users, they are among the most frequently used features of Biota.
Finding Records for Lower Taxa Based on Higher Taxa
The Lower Taxa for Higher Taxa (“top-down”) search tool finds all records for a lower
taxonomic level that belong to a higher taxon or a selection of higher taxa. It does not
matter whether the two levels are adjacent in the taxonomic hierarchy or not. For
example, you could find all Specimens of a Family, or all Genera of three Orders
(nonadjacent levels), or all Specimens for a selection of Species or all Classes for a
Phylum (adjacent levels). For nonadjacent levels, you can tell Biota to keep all related
taxa at intermediate levels as Records Sets. See “Finding Records for Lower Taxa
Based on Higher Taxa” in Chapter 12.
Finding Records for Higher Taxa Based on Lower Taxa
The Higher Taxa for Lower Taxa (“bottom-up”) search tool finds all records for a higher
taxonomic level that belong to the active Record Set for a lower taxonomic level. For
example, you could find all Orders for the Specimen Record Set (nonadjacent levels) or
all Families for the Genus Record Set (adjacent levels). For nonadjacent levels, you can
tell Biota to keep all related taxa at intermediate levels as Records Sets. See “Finding
Records for Higher Taxa Based on Lower Taxa” in Chapter 12.
Finding Place Records (Collection or Locality) for Specimens or Species
The Places for Specimens or Species search tool finds all Locality or Collection records
for the active Specimen or Species Record Set, according to your query. For example,
your could find all Locality records for a set of Species (a cross-hierarchy query). You
can tell Biota to keep the related Specimen and Collection records (intermediate tables
in the search) as Record Sets. See “Finding Place Records (Collection or Locality) for
Specimens or Species” in Chapter 12.
Finding Specimen or Species Records for Places (Collections or Localities)
The Spcms or Species for Places search tool finds all Specimen or Species records for
the active Collection or Locality Record Set, as you request. For example, you could find
all Species records for a Locality (a cross-hierarchy query). You can tell Biota to keep
the related Collection and Specimen records (intermediate tables in the search) as
Record Sets. See “Finding Specimen or Species Records for Places (Collections or
Localities)” in Chapter 12.
Sequential, Cross-Hierarchy Searches
If you want to find Collections or Localities for taxa above the level of Species, or higher
taxa represented in Collections or Localities, you can use the appropriate pair of the
above tools sequentially. For example, to find all the Localities for an Order, first find all
Species for the Order (using the first tool), declare the result to be the Species Record
Set, then find all Localities for the Species Record Set (using the third tool). See
“Sequential, Cross-Hierarchy Searches” in Chapter 12.
Chapter 5 – Page 9
Finding Records by Record Code
Single Records
You can quickly find an individual Species, Specimen, Collection, or Locality record by
entering its Record Code manually or with a barcode reader. See “Finding Records by
Record Codes” in Chapter 12.
Unordered Specimen Series
The Find Specimen Series tool (Series menu) accepts two kinds of entries. In the
“Unordered Series” mode (click “In any order”), you simply enter any Specimen Code,
press TAB, then toggle on the “Auto Accept” button. For all subsequent records, just
enter the next code, press TAB, and repeat, as Biota retrieves and collects the records.
With a barcode reader set to enter carriage returns automatically, this is a completely
hands-off operation (neither keyboard nor mouse is needed). When you are done, the
records are displayed for examination, modification, or saving as a Specimen Record
Set for other operations. See “Using the ‘Find Specimen Series’ and ‘Find and Identify
Specimen Series’ Tools” in Chapter 13.
Ordered Specimen Series
In “Ordered Series” mode (click “In consecutive order”), the Find Specimen Series tool
lets you find, in a single action, any series of records that have numerically sequential
Specimen Codes. When the search is complete, the records are displayed for
examination, modification, or saving as a Specimen Record Set for other operations.
See “Using the ‘Find Specimen Series’ and ‘Find and Identify Specimen Series’ Tools” in
Chapter 13.
Special Tools for Updating Records
Updating Specimen Determinations and Other Specimen Information:
Unordered Specimen Series
Two tools for rapid updating of data in existing Specimen records share the Identify or
Store Specimen Series screen (Series menu). In “Unordered Series” (Auto Carry) mode
(click “In any order”), you enter a Specimen Code (manually or with a barcode reader),
then enter the Species Code for a new determination or other new information
(Determined By, Date Determined, Stage/Sex, Storage, Type Status). Then click the
Auto Carry button. Press TAB, enter the next code, press TAB, and so on, as Biota
retrieves and updates the records with the same new information. With a barcode reader
set to enter carriage returns automatically, updating is a completely hands-off operation
(neither keyboard nor mouse is needed). When updating is complete, the records are
displayed for examination, further modification, or designation as a Specimen Record
Set for other operations. See “Using the ‘Input Specimen Series’ and ‘Input and Identify
Specimen Series’ Tools” in Chapter 13.
Chapter 5 – Page 10
Updating Specimen Determinations and Other Specimen Information:
Ordered Specimen Series
In Ordered Series mode (click “In consecutive order”), the Identify or Store Specimen
Series screen (Series menu) lets you update, in a single action, any series of records
that have numerically sequential Specimen Codes. When the updating is complete, the
records are displayed for examination, modification, or designation as a Specimen
Record Set for other operations. See “Using the ‘Input Specimen Series’ and ‘Input and
Identify Specimen Series’ Tools” in Chapter 13.
Updating Records (Any Table) by Importing Information from Text Files
The Import by Tables and Fields tool (Im/Export menu) includes an Update Records
option for updating existing records in any table. Biota matches up the imported data
with the existing record based on the Key Field for each record. See Chapter 28,
“Importing Data.”
The Find and Replace Tool
The Find and Replace tool (Special menu) is a powerful (and therefore dangerous!)
utility for correcting errors or updating records in any table in the Biota structure. Not only
Core tables but Peripheral tables can be accessed. Changes can be made either in
records of a current Record Set (for tables that have them) or for all records in a table.
Be sure you know what you are doing before using this tool, and always be sure you
have a backup copy of your Data File first! Changes made cannot be undone. If the User
Password system has been enabled, only a user with Administration access privileges
can use this tool. See “Updating Records Using the Find and Replace Tool” in Chapter
12.
Keeping Track of Synonymies
A species Synonymy system (based on the Valid Species Code field of the Species
table) allows you to keep track of historical or new synonymies among Species records.
(In inventory work, this system can be used to document the “synonymies” that often
arise in pooling several temporarily determined sets of Specimens.) The Synonymy
button in the Species input screen finds and displays either the senior synonym for a
Species, or a scrollable list of its junior synonyms, if any. A species “Look up” button
speeds the recording of new synonymies, and special query tools are available for
finding various kinds of synonyms. See Chapter 23, “Synonymy System.”
Tools for Maintaining Database Security and Integrity
User Password System
Biota provides a comprehensive User Password system that you can enable and
configure to your needs. To activate the system, you give the Administrator a nonblank
password. The Database Administrator can use the Password Editor to set up a system
of passwords for other users. A selection of generic user names (e.g., Collaborator,
Browser, etc.) with different access levels (see next paragraph) have been preset, but
may be changed as you wish. Any user can change his or her password using the
Change Password item in the Special menu.
Chapter 5 – Page 11
User Access (Privilege) Levels
The Password Editor allows the Administrator to assign each user to one of four access
levels: (1) Super User (set User Passwords, assign access levels, set the Data File
password link (see below), plus all privileges of the Administration access level; (2)
Administration (create, delete, display, modify, print, export, or import records; change
master settings); (3) ReadWriteExport (create, delete, display, modify, print, or export
records); (4) ReadExport (display, print, or export records); or (5) ReadOnly (display
records only). See Chapter 26, “Security: Passwords and Access Privileges.”
Data File Password Link
The User Password system protects your copy of the Biota application from
unauthorized use but does not in itself protect Biota Data Files from unintended or
unauthorized access. You can create a secure link between a particular copy of Biota
and a particular Data File (or Files) using a Data File password link. You need not
activate the User Password system in order to activate the Data File password link,
although it usually makes sense to activate the User Password system if the Data File
link is used. (The two systems are technically independent.) See “Using the Data File
Password Link” in Chapter 26.
Automatic Updating of Linking Fields in Child Records
If you need to change the name of a higher taxon (Genus, Family, Order, etc.), or the
Record Code for a Species, Specimen, Collection, or Locality in the parent (one-table)
record, Biota will ask if you want to update the linking field in all linked child (many-table)
records automatically. For example, suppose you misspelled the genus
Excelsotarsonemus in the parent (Genus table) record and used the same misspelling in
the Genus linking field of the Species records for all species of the genus. You can
correct the name in the Genus record and in all linked Species records with one entry (or
change only the Genus record, if you choose). See “Automatically Updating Child
Records by Changing a Parent Record” in Chapter 12.
Finding Orphan and Childless Records
An orphan record is one that is not linked to any record in the next higher table in a
hierarchy—for example, a Specimen record that either has no Species Code recorded,
or has a Species Code that does not correspond to any Species record. A childless
record is one that has linked records in the next lower table in a hierarchy—for example,
a Genus record that has no linked Species records. Using commands from the Find
menu (Find Orphan Records and Find Childless Records) you can find, display, and, if
you wish, modify such records easily. See “Finding Orphan Records” and “Finding
Childless Records” in Chapter 12.
Record Deletion Control
Biota will not allow you to orphan records inadvertently. In other words, if you attempt to
delete a record that is linked to records at the next lower table in a hierarchy, Biota
warns you that you are about to orphan certain records. You then have the option of
doing so, in spite of the warning, or simply canceling the action. See “Automatically
Updating Child Records by Changing a Parent Record” in Chapter 12.
Chapter 5 – Page 12
Record Creation Control
Whenever you enter a value in the parent linking field of a child record (e.g., when you
enter a family name in the [Genus] Family field while creating a new Genus record),
Biota checks automatically to see if the record already exists in the parent table (the
Family table, in this example). If no parent record exists, Biota prompts you to create one
“on the fly,” then returns you to the child record in progress. (If you wish, you can go
ahead and create an orphan record, as an option. This option is especially useful for the
[Collection] CollectedBy field, linked to the Personnel table, for historical specimens
when the collector’s personal data are either unknown or of no interest. See “‘On-the-Fly’
Creation of Linked Records” in Chapter 7.
Automatic Recording of Specimen Determination Histories
If you enable the Determination History system, whenever the identification
(determination) of a Specimen is changed, all pertinent information for the old
determination (Genus, Species, Author, Determined By, Date Determined) is recorded in
a new record in the Determination History table, along with a record of where the
determination was changed (in the Specimen record, the Specimen Series tool, the
linked Species record, the Synonymy system, or the linked Genus record), when it was
changed (current date), and by whom (based on password sign-on). You can view the
determination history for a Specimen record on the Determination tab of the Specimen
Input screen. See Chapter 22, “Determination Histories.”
Duplicate Species Checking
Although the Key field of the Species table is Species Code, not Species Name (specific
epithet), Biota checks for uniqueness each time you enter a new Species Name value, if
you enable this feature. (You cannot enter two records with the same Species Code). Of
course, more than one record for sativum may legitimately exist, in different genera, but
you would not want to create two species records for Pisum sativum L. Thus, Biota
warns you if one or more Species records exist with the same specific epithet (Species
Name), and offers to display any such records. You must then decide how to proceed.
(Exceptions include “sp.,” “sp. nov.,” and related abbreviations.) See Step 3 in “Entering
Species Data: The ‘Classification’ Tab,” in Chapter 11.
Automatic Record Dating
For Specimen, Species, Collection, Locality, Personnel, Loans, References, and Project
records, Biota automatically registers the date each record was created and the most
recent date it was changed. (The identity of the user making the most recent change is
also recorded, if this option is enabled in the “Admin Settings” tab of the Preferences
screen. See Appendix B, “Setting Preferences”).
If the Determination History option has been activated, the current date is recorded any
time the determination of a specimen is updated, directly or indirectly (see Chapter 22,
“Determination Histories”).
Maintenance and Repair Tools
Under normal operations, Biota correctly maintains links between parent records in the
Specimen, Species, Collection, and Locality tables and records in the tables that contain
information on Auxiliary Fields (the FieldValue and FieldName tables), References, and
Images. Power failures, system crashes, and incorrectly imported data, however, can
Chapter 5 – Page 13
produce anomalies (orphan or duplicate links). You can correct all these problems,
without in any way affecting legitimate records, by running Biota’s Maintenance Utilities
(Special menu). See “Maintaining and Repairing the Auxiliary Fields and Project
Systems” in Chapter 16, “Maintaining and Repairing Image Links” in Chapter 19, or
“Maintaining and Repairing Reference Links” in Chapter 20.
More serious problems with Biota Data Files can often be repaired with 4D Tools, a
general-purpose checking a and repair application. See “Checking and Repairing a Data
File” in Appendix I.
Reports and Labels
Printed Reports
Biota offers a variety of printed reports designed for biodiversity information, as well as
user-designed, ad hoc reports (using the built-in Quick Report Editor). See Chapter 14,
“Printing Reports.”
Labels for Fluid-Preserved, Pinned, Slide-Mounted, or Herbarium
Specimens
Biota prints locality and determination specimen labels for fluid-preserved, pinned
entomological, or slide-mounted specimens. Herbarium labels are printed in customary
format, including (optionally) both locality and determination data, as well as an option to
include a descriptive field note. Numerous other options allow control over the
information included on labels. Data for all label types can optionally be exported to a
delmited text file, for further processing in other applications. See Chapter 15, “Printing
Labels.”
Custom Label Printing
Using the Label Wizard (a built-in 4D tool), you can design your own labels in any size or
format for the current Record Set of any Biota Core table and save the template to disk,
if you wish. See “Designing and Printing Custom Labels” in Chapter 15.
Species Labels
Species labels (for entomological unit trays or herbarium folders, for example) can be
printed from the Species Record Set or from any arbitrary set of Species Codes entered
in a special input screen. See “Species Labels” in Chapter 15.
Specimen Loan System
Lending Specimens
Biota provides a simple bookkeeping system for specimen Loans. Groups of specimens
to be loaned can be selected using any of Biota’s usual selection tools, or one-by-one by
entering each Specimen Code (with barcodes supported). The Deposited field of the
Specimen table is used for recording the Specimen Loan Code in each Specimen
record. See Chapter 21, “The Specimen Loan System.”
Chapter 5 – Page 14
Recording Returns
Specimen returns can be recorded by selecting records on-screen from the list of those
in the original loan, by recording the current Specimen Record Set as returned, or by
entering Specimen Codes one-by-one. The Unordered option of the Find Specimen
Series tool (Series menu) is particularly useful for gathering records from several loans
that have been returned together. See “Recording Specimen Returns” in Chapter 21.
Loan Forms
For each new loan, Biota generates a standard loan agreement form, with the name of
your project, museum, or herbarium if you wish, with complete lender and borrower
information. As an option, the Loan system produces a full, taxonomically organized,
printed listing of all specimens loaned. See “Previewing, Printing, and Exporting Loan
Records” in Chapter 21.
Text Flatfile Export of Specimens Loaned
As an additional option, Biota will export a text file listing the specimens in any loan,
including, for each specimen, all fields from the database that you designate, with blank
or partially completed species identification fields. The text file can be opened and
modified using any spreadsheet program. Identification fields can then be filled in by the
borrower as the specimens are determined and the determinations returned to the
lender in the updated flatfile, which can be used to update records in the Biota Data File.
See “Previewing, Printing, and Exporting Loan Records” in Chapter 21.
Importing Data
The Import Editor
New records can be directly imported into Biota tables, one table at a time, from plaintext flatfiles using Biota’s Import Editor (Import by Tables and Fields, Im/Export menu).
You can specify the order of fields to match your flatfile, skip fields in the flatfile, specify
field and record delimiters, and account for a column header in the flatfile.
The Import Editor supports three modes: Import new records, Update existing records,
and Merge imported records. The Update option matches Record Code in the input file
to Record Codes in the Data File, and updates any other fields specified. The Merge
option ignores duplicated Record Codes, and imports only records with unique Record
Codes.
Biota does extensive error checking (validation for correct field types, field lengths,
duplicated Key fields, nonexistent dates, etc.) with informative error dialogs. If an error is
found, the guilty record is displayed, and you are offered the option of keeping any
records already imported successfully, or deleting them and starting “clean” after fixing
the problem in the text file. See Chapter 28, “Importing Data.”
Importing Images
Based on an Image File List, Biota can import and link thumbnail images from groups of
external image files. Alternatively, you can specify to import the full image. See
“Importing Groups of Images” in Chapter 19.
Chapter 5 – Page 15
Exporting Data
The Export Editor
Any field of any Biota record or set of records can be exported, one table at a time, to a
plain-text flatfile (readable by spreadsheet, word processing, or other database
applications) using Biota’s Export Editor (Export by Tables and Fields, Im/Export menu).
For a given table, you can specify any order for the exported fields, specify field and
record delimiters, and export a column header in the flatfile. Plain-text flatfiles are the
lingua franca of data exchange among databases, spreadsheets, and statistical
applications. When something you like better than Biota comes along, or you need to
send data somewhere in electronic form, you can always get your data out of Biota Data
Files. See “Exporting Data by Tables and Fields” in Chapter 27.
Exporting Images
For each record in the current Species, Specimen, Collection, or Locality Record Set,
Biota can export either the first linked image or all linked images, creating a separate
disk file for each image exported and an Image File List that can used to import the
images to another Biota Data File, using the “Import Image Files” command. See
“Exporting Groups of Images” in Chapter 19.
Exporting Specimen Flatfiles
For any Specimen Record Set, you can export a flatfile, with specimens as rows, that
includes columns for any set of fields from Biota Core tables. You choose the export
fields simply by clicking checkboxes on a selection screen. See “Exporting Specimen
Flatfiles” in Chapter 27.
Exporting Taxonomic Flatfiles
A taxonomic flatfile is a list of taxa at a particular level (the base level), displaying, for
each taxon, its membership in one or more higher taxa (for example, a list of species
that includes the genus and family of each, or a list of genera that includes the family,
suborder, and order for each genus). Biota can export such files based on any
taxonomic base level, with additional higher levels (columns) that you specify by clicking
checkboxes. See “Exporting Taxonomic Flatfiles” in Chapter 27.
Exporting Notes
You can export plain-text reports or delimited text files of Notes for Record Sets from the
Species, Specimen, Collection, Locality, and Loans tables. See “Exporting Notes
Records Using the Export Notes Tool” in Chapter 27.
Exporting Auxiliary Field Values
If you have defined Auxiliary Fields and entered values for them, you can export matrix
with records as rows and Auxiliary Fields as columns directly to a plain-text file, for a
Record Set in the Specimen, Species, Collection, or Locality tables. Exported Auxiliary
Field data can then be printed, or joined with Core Field data for the same set of records
using a spreadsheet application. See “Exporting Auxiliary Field Values” in Chapter 16.
Chapter 5 – Page 16
Exporting Character Matrices in the NEXUS Format
If you have defined Auxiliary Species Fields and have entered single-digit or single-letter
values in them, you can export a complete, PAUP- or MacClade-ready NEXUS file,
using an option in the Export Auxiliary Fields dialog. Biota also supports this option for
Auxiliary Fields of the Specimen, Collection, and Locality tables. See “Exporting Auxiliary
Field Values” in Chapter 16.
Exporting Place- by-Taxon Incidence or Abundance Tables
Based on the Locality, Collection, Specimen, or Taxon (Species or higher rank) Record
Set, Biota can export a tab-delimited text file table, with Localities or Collections as rows
and Taxa as columns, specifying the incidence (presence/absence) or abundance of
Specimens of each Taxon in each Locality or Collection. These data are the raw material
for graphical and statistical estimation of species richness from samples, and for
ordination, sample classification, and other statistical techniques. See “Exporting Placeby-Taxon Incidence or Abundance Tables” in Chapter 27.
Exporting “Specimens Examined” Lists
For any Species Record Set, Biota can export a draft text file of Specimens Examined
(Exsiccatae) for a taxonomic monograph, organized within species by Locality and
Collection, then by Stage/Sex and host (if any), based on linked Specimen records. See
“Exporting ‘Specimens Examined’ Lists for Publications” in Chapter 27.
Custom Export
The Quick Report Editor (a 4D utility) is a powerful and flexible tool for exporting text files
to disk, as well as for printing reports. Quick Report formats are easily created and can,
themselves, be stored on disk for repeated use. For any Core table, the Quick Report
Editor in Biota exports a text file based on the current Record Set, with selected fields
from the focal table and related tables, using a custom format that you design using the
Quick Report Editor. See “Exporting Custom Flatfiles” in Chapter 27.
Internet Publishing Tools
On-board Web Server: Dynamic Access
Biota 2 offers a fully-imbedded, on-board Web server that allows any Biota owner to
publish a Biota Data File on the internet with no additional software (although for
anything but trial use, you must purchase a Web Extension License). You can
use any computer to run the Web server. See Chapter 29, “Internet Strategies,”
especially Chapter 30, “Biota's Onboard Web Server.”
You can choose to publish your Biota Data File on the Web in either or both of two
modes: (1) Web Browser Mode allows you to control exactly which tables and fields are
accessible to website visitors, in classic browser mode. (2) Database Client Mode
emulates Biota’s desktop interface, allowing full access to Biota’s powerful search tools.
See Chapter 31, “Web Browser Mode and the Web Assistant,” and Chapter 32,
“Database Client Mode.”
Chapter 5 – Page 17
Exporting Static Web Pages
If you prefer, or are restricted by your Internet Service Provider or institution to
publishing static Web pages, Biota will guide you through the setup for completely
automated export of hyperlinked Web pages, ready to post on any Web server. (These
are “static” pages, not “dynamic,” on-line access to your Data File from the Internet.) You
can export hierarchically linked pages for any range of taxonomic levels (including
intermediate levels such as Subfamily), for Record Sets that you define with either a topdown or bottom-up search.
If you include Specimen records, you can select any set of fields in the Specimen,
Collection, or Locality tables for inclusion as Specimen data. You can include images for
Species records. Other options include custom page footnotes, hyperlinking of host and
“guest” Specimen records, and non-ASCII character translation to HTML character
codes. See Chapter 33, “Exporting Static Web Pages.”
Accessibility Features
Keyboard Shortcuts
Biota offers many keyboard shortcuts for buttons and tabs in Input screens, and for
records in Record Listing screens. This comprehensive set of keyboard shortcuts
represents an important feature for people with disabilities, including mouse-related
repetitive motion disorders, and to any user who dislikes using the mouse. Windows
users can also tab between buttons and use the menu shortcuts that Windows
automatically provides. See “Keyboard Shortcuts for Input Screen Tabs” and “Keyboard
Shortcuts for Input Screen Buttons” in Chapter 7, and “Keyboard Shortcuts for Record
Listing Screens” in Chapter 10.
Chapter 6
A Brief Tutorial
With the Demo Database
It is difficult to see Biota in action with a new, empty Data File. This chapter takes you on
a quick tour of Biota’s basic capabilities using the “Biota2Demo” Data File that you
received on the distribution CD or downloaded from the Biota website at
http://viceroy.eeb.uconn.edu/biota. More advanced and less frequently used features are
covered in the chapters that follow.
Don’t be intimidated by the number of pages in this chapter. They go by very quickly,
and the chapter is broken up into separate lessons so that you need not do the entire
tutorial at one sitting. Although each lesson stands alone, later lessons assume you
have done the earlier ones first.
Before starting the tutorial tour, please read Chapter 2, “Biodiversity Data and Relational
Databases,” and Chapter 3, “Key Concepts.”
Installing Biota and Opening the Demo Data File
If you have not yet installed Biota, please install it, following the instructions in the
“Installing Biota” file on the Biota CD or in the materials you downloaded from the Biota
website.
1.
Launch Biota in “Data File finding mode,” by immediately pressing and holding
ALT key (Windows) or the OPTION key (Mac OS) after launching Biota to force the file
navigation window to open.
BiotaApp in Windows. Select the icon for BiotaApp.exe then choose “Open”
from the Windows File menu while depressing the OPTION key. Or launch
BiotaApp from the Windows “Programs” menu, then immediately press the
OPTION key. (You can also launch Biota by double-clicking its icon, then
immediately depressing the OPTION key, but if you get the timing wrong, you get
the Properties window instead.)
BiotaApp in Mac OS. Select the icon for BiotaApp, then choose “Open” from the
File menu in the Mac OS Finder, while depressing the OPTION key. Or, doubleclick the BiotaApp icon while depressing the OPTION key.
Biota4D in Windows or Mac OS. See Appendix H, “Using Biota4D with 4D
Server or 4th Dimension.”
Chapter 6 – Page 2
Note: If the password system has been enabled (see Chapter 26, “Security:
Passwords and Access Privileges”), the Password request screen appears at this
point.
Enter your password, then press and hold the OPTION key (Mac OS) or ALT key
(Windows) while clicking the “Connect” button. (In the illustrations above, the Mac
OS screen is illustrated on the left, the Windows screen on the right).
2.
When the file navigation window appears, find and open the Biota2Demo Data
File.
Macintosh: The file is named “Biota2Demo.data.” Find it and open it when the
“Open a data file” window appears.
Windows: The Demo Data File is named “Biota2Demo.4DD.” (The extension
may not be visible.) Find it in the “Open which data file” window and open it.
(The folder containing the Biota2Demo filed will be different than the one illustrated
above.)
Once you have opened a particular Biota Data File using this method, the same
Data File will be opened automatically next time you launch Biota—without having
to use the OPTION/ALT key technique.
Chapter 6 – Page 3
The Biota startup screen appears briefly while the program sets up.
Then you will see the “Shortcut Screen” and menu bar for Biota. (The Macintosh
menu bar is shown, but the Windows one is functionally identical.)
The Shortcut screen displays buttons for a few of the most frequently use
commands from Biota’s menus. You can dismiss it at any time if you prefer to use
the menu commands. (To re-display the Shortcut screen, choose “Show Shortcut
Screen” from the Special menu.)
Chapter 6 – Page 4
3.
From the File menu, choose “About the Current
Data File” to confirm that the Demo Data File has
been loaded.
A screen identifying the Data File appears,
specifying its location on your hard disk, and listing
the number of records it currently contains for each
Biota table. (You will have to scroll the list to see all
tables.)
What’s in the Demo Data File?
The Demo Data File began life as an actual research dataset from a project on the
hummingbird flower mites associated with tropical plants of the families Ericaceae and
Campanulaceae. The mites were collected from host flowers preserved in fluid, collected
by James Luteyn of the New York Botanical Garden. (You will see Luteyn’s name in
many places in the file.)
The file thus includes records for both plant and mite taxa and specimens, and
demonstrates the “host–guest” capability of Biota (see Chapter 24, “Host-Guest
Relations”).
For this tutorial, in the hope of creating some simple examples using species familiar to
all biologists, a small set of fictitious Specimen records for Darwin’s finches was added,
along with appropriate higher taxon, Collection, and Locality records.
In addition to mites, their host plants, and fictitious finch specimens, a few records of
insects from the Project ALAS database at La Selva Biological Station in Costa Rica (for
which Biota was originally developed, see the “Preface”) have been added to
demonstrate Biota’s image capability.
Chapter 6 – Page 5
Lesson 1. Displaying and Editing Existing Records
Biota displays groups of records in Record Listing screens. In a Record Listing screen,
you can sort the records displayed, print a list of them, select some of them to delete
from the Data File, or select some of them to retain as a Sub-selection and dismiss the
rest from the display. When you leave a Record Listing screen, you can declare the
Selection of records last displayed in the Record Listing screen to be a Record Set.
An individual record can be displayed and edited in an Input screen. In an Input screen,
you can change the content of the record, attach Notes, References, Images, or
Auxiliary Field Values, use the record as a template for a new record, or delete the
record. The Input screen, as the name suggests, is also used when you create new
records from scratch, as you will do in a later lesson of the tutorial.
Step by Step
1.
Click the “Find All Species” button in the Shortcut
Screen, or select “All Species” from the Find menu.
All Species records in the Demo Data File appear in the
Species Record Listing screen.
(The Record Listing screen expands vertically to fit your monitor, although you can
adjust the size of the window manually. The Tutorial illustrations use a window that
has been adjusted in size vertically to save space on the page.)
Notice that the Species records are sorted, by default, by Genus and Specific Name
(you can change the default in the Preferences screen). See “Sorting Records by
Record Codes” in Chapter 8.
2.
To sort the records on a different field
in the Record Listing screen, click the
“Sort” button at the bottom of the
display.
Chapter 6 – Page 6
The Sort Editor appears, with the title “Order by.”
3.
Select “Species Code” in the “Available Fields” panel on the left, then click the
“add to list” button
the right.
to enter “Species Code in the sort criteria panel on
Chapter 6 – Page 7
Species Code is the Key field for the Species table, with a unique value for each
record. Species Code is added to the sort criteria.
You can add additional criteria—including fields from related tables—or change the
direction of the sort; see “Sorting Records in Record Listing Screens” in Chapter 10.
4.
In the “Order by” window, click the “Order by” button.
The Record Listing screen reappears, with the records sorted by
Species Code (the left-most column).
5.
To display an individual Species record, double-click its record in the Record
Listing screen. Try it with the record for the tropical ant Azteca xanthocroa, as
shown above. The full record appears in the Species Input screen (next page).
Chapter 6 – Page 8
The Species Input screen is organized by tabs:
Notice that the tabs for Images, Notes, and Refs include numbers in parentheses,
indicating that this record has 5 linked Images, 3 Notes, and 3 literature References.
In the Input screen, any data entry area can be edited. You save any changes by
clicking the “Save” button.
(Information in some areas, such as the green “Classification” area on the right of
the Species Input screen, showing data from the linked Family and Order records, is
for display only, and cannot be edited in this screen.)
The Synonymy panel shows
that Azteca xanthochroa is a
valid name. See Chapter 23,
“Synonymy System.”
Chapter 6 – Page 9
6.
To view the Images for this ant Species, click the Image tab (or use the keyboard
shortcut; see “Keyboard Shortcuts for Input Screen Tabs” in Chapter 7). The Image
tab screen appears, displaying the first Image for this species, with a list of other
Images for this Species on the left.
To display a different Image from the list for this Species, just click the Image
name in the list on the left.
To see the Image at its original resolution, click the “Zoom”
button.
Chapter 6 – Page 10
To see the first 4 Images for this Species at higher
resolution, click the “Zoom 4 Images ” button.
The Image tab screen has many other functions: You can Edit, Compress or
Delete an existing Image record, create additional thumbnail links with images in
external image files, and acquire images from the Clipboard or from imaging
devices from within Biota. You can copy images to the Clipboard or export
images to disk files in many different formats. For full details, see Chapter 19,
“Images.”
7.
To view the Notes for this record, click the “Notes” tab in the Species Input
screen.
The Species Notes tab screen appears. Click a Note in the upper panel to display it
in full in the lower panel. (See next page.)
Chapter 6 – Page 11
The first of three notes on this ant species has been displayed in the illustration
above.
In this same window, you can create new Notes for this Species (using the “New
Note” button) or delete the Note displayed (using the “Delete Note” button in the
Notes window). See “Notes Input” in Chapter 11 for details.
8.
To view the literature References for this Species record, click the “Refs” tab
in the Species Input screen.
The Species References tab screen appears. Click a Reference in the upper panel
to display it in full in the lower panel. (See next page.)
Chapter 6 – Page 12
The second of three References linked to this Species record has been displayed in
the illustration above. (The same Reference record can be linked to any number of
other Species, Specimen, Collection or Locality references.)
Using the buttons in the Reference tab screen, you can create new Links to existing
Reference records (the “Link a Ref” button); remove existing Links (the “Unlink a
Ref” button); create a new, linked record in the References table (the “New Ref”
button); or edit the Reference record for any linked Reference (the “Edit Ref”
button).
You can also enter new Reference records using the “Reference” command from
the Input menu, or import them from reference management software. See Chapter
20, “References.”
9.
For a look at the
References table,
select the third
Reference in the
References tab screen:
Then click the “Edit Ref” button.
The selected Reference appears, in a new window, in the References Input screen.
Chapter 6 – Page 13
Notice that this particular Reference record is of the type “Online Source,” and that
the “Go to URL” button is enabled. If you click the “Go to URL” button, your default
Web browser application (e.g., Netscape or Internet Explorer) is launched and the
referenced Web page for this species, from Longino’s “Ants of Costa Rica,” appears
in your browser.
The Reference table also supports three other Reference types: Journal Article,
Book, and Book Chapter. Use the Reference Type popup to explore the differences,
if you want. (All types include a URL field.)
For full details on Biota’s Reference system, see Chapter 20, “References.”
10. Click the “Cancel” button in the References Input screen (don’t save any changes
you made), to return to the Species Input screen.
Chapter 6 – Page 14
11. To move through the Species records that were listed
in the Species Record Listing screen, you can use the
record navigation buttons, from any tab in the Species
input screen. (Left to right, the buttons take you to the
First, Previous, Next, and Last record in the current Selection of records.)
Go back to the Images tab and experiment with the navigation buttons. There are
keyboard shortcuts for these buttons and for most others. See
“Keyboard Shortcuts for Input Screen Buttons” in Chapter 7.
12. Dismiss the Species Input screen by clicking its “Cancel” button.
The Species Record Listing screen reappears, with the records
sorted in the same sorted order they were when you left it.
13. In the Species Record Listing screen, click the “Scroll” button in the “Display
Images” panel.
Images for the first few records appear in the Image Record Listing screen.
Each row of Images belongs to one Species record. (The name of the species, its
Species Code, and its Family appear above its Image row.) A row of blank frames
appears if no Images are linked to a Species record; if fewer than four Images are
Chapter 6 – Page 15
linked, the remaining frames are blank. If the Species records are still sorted by
Species Code, the first three records will be ants with Images, of which two are
shown above.
14. Click the “Done” button in the Image Record Listing screen to dismiss it. The
Species Record Listing screen reappears.
15. In the Species Record Listing screen, click the “Page” button in the “Display
Images” panel.
An option screen appears.
Click the “Four” image option,
then the “OK” button.
Images for the first four
Species records appear in the
“Page” Image Record Listing
screen.
The Page Image display and comparison screen has many special tools. You can
get a brief introduction to them, as you explore this screen on your own, by clicking
the “Help” button at the bottom left of the Page Image screen, illustrated above.
16. Dismiss the Page Image screen by clicking the “Done” button.
Biota returns you the Species Record Listing screen.
Chapter 6 – Page 16
17. Sort the Species records by Genus and Species Name. (See Steps 2-4, earlier
in this section, if necessary.)
18. Select a set of records in the Species Record Listing screen. Select any
records you wish, but be sure to include the Galápagos finch Camarhynchus
parvulus (Species Code “camaparv”), which is needed for a later step.
To select consecutive records, click the first record in the group then hold
down the SHIFT key while you click the last record in the group.
To select nonconsecutive records, hold down the the CTRL key (Windows) or
the COMMAND ( ) key (Mac OS) or while clicking the individual records.
19. Click the “Sub-Selection” button to dismiss all unselected
records.
The Species Record Listing screen is now shows only the
Species records you selected.
NOTE: Dismissing records from a Selection (or including them in one) does not
affect the records in the Data File in any way. You can prove it to yourself by
choosing All Species from the File menu again, leaving the current window open.
The same records can simultaneously be part of any number of different Selections
or Record Sets (see Chapter 3, “Key Concepts”).
20. In the Species Record Listing screen, select the record for Camarhynchus
parvulus (Species Code “camaparv”).
Chapter 6 – Page 17
21. Click the “Delete Selection” button in the Species Record Listing screen
(illustrated above). A warning message appears.
22. Click the “OK” button in the warning window shown above. (The deletion will
be canceled in the next warning screen).
A second warning screen appears.
If a record you propose to delete has any linked child records in a Core table (see
Chapter 3, “Key Concepts” for definition), a second warning message appears, like
the one above.
In this example, there are records for two Specimens of Camarhynchus parvulus in
the database, which will no longer be linked to any Species record (and thus no
longer linked to a Genus record, Family record, or higher ranks) if you confirm the
deletion.
23. Click the Cancel button in the warning screen above to avert the pending
deletion. The Species Record Listing screen reappears, with the Camarhynchus
parvulus record intact. As the warning screen above describes, there is an easy
way to take a look at linked Specimen records for Camarhynchus parvulus. You will
do this next.
NOTE: If you clicked the “OK to Delete” button in error, the Demo Data File can
always be reloaded from the distribution diskette if you later want a full copy—a
good example of why you should always make backup copies of your own Data
Files.
Chapter 6 – Page 18
24. Double-click Camarhynchus parvulus in
the Species Record Listing screen. The
record appears in the Species Input screen.
Notice that the “Show Specimens” button
indicates that there are 2 linked Specimen
records for this Species. (If there are none, the
button reads “Show Specimens (None)” and it
is disabled—dimmed.)
25. Click the “Show Specimens” button in the
Species Input screen.
NOTE: The Input screen for each Core table
has an analogous button to display linked
child records. The name of the button is
always the name of the child table (in plural
form); generically, these are called Child
Records buttons (see “Linking Fields: Parent
and Child Records” in Chapter 3).
The two Specimen records for Camarhynchus
parvulus appear in the Specimen Record
Listing screen in a new window. The Species
Input screen remains open in its own window,
although it may be hidden.
Female
Rank 12 NHM0051
26. Double-click one of the records in the Specimen Record Listing screen. The
record appears in the Specimen Input screen. (See next page.)
Chapter 6 – Page 19
Like the Species Input screen, the Specimen Input screen is organized by tabs.
The tabs for Images, AuxFields (Auxiliary Fields), Notes, and References are
identical to those for the Species Input screen—and the same for the Collection and
Locality Input screens, as well.
The “General” tab of the Specimen Input screen shows not only fields from the
Specimen table, but essential information from the linked Species record (in the
blue inset) and the linked Collection record (in the yellow inset). You will see more
of this screen later in the tutorial.
(This is the record for a fictitious specimen that exists only in the Demo Data File,
although the collector and collection dates are plausible, based on The Voyage of
the Beagle.)
27. Click the “Cancel” button in the Specimen Input screen to
dismiss it. The Specimen Record Listing screen reappears.
28. Click the “Done” button in the Specimen Record Listing
screen.
The Record Set option screen appears.
Chapter 6 – Page 20
29. Click the “Dismiss it” option, then the “OK” button in the Record Set option
screen (above). See “Record Sets” in Chapter 3 for a discussion of the other
options offered. You will create a Record Set in the next lesson.
30. Return to the record for Camarhynchus parvulus displayed in the Species Input
screen.
31. Click the “Show Genus Record” button in the
Species Input screen. This is the Parent Record
button for the Species Input screen.
The full Genus record for Camarhynchus appears
in the Genus Input screen.
If you want to see the full record for Fringillidae, the linked Family record, you can
click the “Show Family” (Parent record) button in the Genus Input screen, above,
then Cancel the Family Input screen.
The Input screen for each Core table (except for Kingdom and Locality) offers a
Parent Record button. These buttons make it easy to display information on parent
records—all the way to the top of the taxonomic and place hierarchies (see “Linking
Fields: Parent and Child Records” in Chapter 3).
32. Click the “Cancel” button in the Genus Input screen. The Species Input screen
reappears.
33. Click the “Cancel” button in the Species Input screen. The Species Record
Listing screen reappears.
34. Click the “Done” button in the Species Input screen. The Record Code option
window appears.
Chapter 6 – Page 21
Notice the small note in the lower-left corner: “To bypass this option window, press
COMMAND and HYPHEN while the Record Listing screen is open.” (This is the
Macintosh screen. The Windows version substitutes CONTROL for COMMAND.)
You may not always want to declare the current Selection of records to be a Record
Set, add it to the existing Record Set, or save it to disk as a Record Set Pointer File.
In the next two steps, you will learn the keyboard bypass explained in the small
note, which has the same effect as the “Dismiss it” option in the screen above.
35. Click the “Cancel” button in the Record Set Option window (above). The
Species Record Listing screen reappears.
36. This time, dismiss the Species Record Listing screen from the keyboard,
bypassing the Record Set option window:
Windows: Hold down the CTRL key and press the HYPHEN key (above the P
key on the keyboard, not the MINUS key in the numeric keypad).
Macintosh: Hold down the COMMAND key ( ) and press the HYPHEN key
(above the P key on the keyboard, not the MINUS key in the numeric keypad).
NOTE: You can use this keyboard shortcut to dismiss virtually any Record Listing
screen, Input screen, or setup screen in Biota. In the case of an Input screen, it is
the equivalent of clicking the Cancel button in the screen. There are many useful
keyboard equivalents for onscreen buttons and tabs, as well; See “Keyboard
Shortcuts for Input Screen Tabs” and “Keyboard Shortcuts for Input Screen Buttons”
in Chapter 7, and “Keyboard Shortcuts for Record Listing Screens” in Chapter 10.
Lesson 1 Review
In this lesson, you entered the Biota structure through the Species table by choosing “All
Species” from the Find menu. Once “inside,” you learned how to:
Sort records in the Record Listing screen.
Delete records from the Record Listing screen.
Make a Sub-selection of records in the Record Listing screen.
Display an individual record in the Input screen.
Move down a hierarchy using Child Records buttons (e.g., the “Show Specimens”
button in the Species Input screen).
Move up a hierarchy using Parent Record buttons in Input screens (e.g., the
“Show Genus Record” in the Species Input screen).
Each of the above techniques applies to Record Listing and Input screens throughout
Biota’s structure—regardless of how and where you enter the structure (which will
depend on the task at hand).
You also learned how to:
Display Images from Input and Record Listing screens.
Chapter 6 – Page 22
Display Notes from Input screens.
Display References from Input screens.
The Images, Notes, and Reference techniques apply identically to the Species,
Specimen, Collection, and Locality tables (Loans records also have Notes).
Lesson 2. Creating New Records One Table at a Time
This lesson shows you how to create new records for one table at a time. In Lesson 3,
you will learn how to create records in related tables “on the fly,” as they are needed.
The Input screen for each table is the tool you use to create and enter data in new
records for that table. As much as possible, all of Biota’s Input screens share the same
features. These common elements are discussed in Chapter 7, “Overview of Record
Input Screens,” and Chapter 10, “Working With Records in Record Listing and Input
Screens.”
Step by Step
1.
From the Input menu, choose “Specimen.” The Specimen Input screen appears,
with the insertion point (blinking cursor) in the Specimen code entry area. You are
going to add new records to the Demo Data File for additional fictitious specimens
from Darwin’s visit to the Galápagos Islands.
Chapter 6 – Page 23
2.
Enter HMSB018 in the Specimen
Code entry area and press the TAB
key.
The insertion point moves to the
Species Code entry area. Let’s say
this is a specimen of the Small Tree
Finch, Camarhynchus parvulus, collected on Santiago Island (James Island, in
Darwin’s time) on October 9, 1832, when the Beagle was anchored there.
NOTE: If you get an error message indicating that this record already exists, and you
are certain you entered HMSB018, it means that someone has already done the
tutorial using this copy of the Demo Data File. Either quit Biota and install a fresh
copy of the Demo Data File from the distribution CD, or delete the existing
HMSB018 Specimen record. (Select “All Specimens” from the Find menu, find it and
delete it).
The next step is to link this Specimen record with the Species record for
Camarhynchus parvulus, which is done by entering the Species Code for
Camarhynchus parvulus. Suppose you recall that the Species Code starts with
“cam,” but you are not sure of the rest of it.
3.
Enter cam in the Species Code entry area
and press TAB.
Biota presents a list of all Species records for
which the Species Code begins with “cam.”
(This way of finding the correct entry for a
linking field is called the wildcard method.)
Chapter 6 – Page 24
4.
Click the line in the Species Records list (above) for Camarhynchus parvulus.
The Species Code is automatically entered in the Specimen record, with additional
information about the Species record you have just linked, displayed in the blue
Species information panel.
The insertion point moves on to the Collection Code entry area. The next step is to
link this Specimen record with the Collection record for Darwin’s specimens from
Santiago Island on October 9, 1832.
You do not know whether such a Collection record even exists yet, nor its Collection
Code if it does. This time, to seek the Collection record, you will use the “Look Up”
button instead of the wildcard method you used to find the Species record. (Notice,
above, that there is also a “Look Up” button for Species Codes, which you will use
later.)
5.
Click the “Look Up” button in the Collection Code panel in the Specimen Input
screen.
The Look Up Collection option window appears.
Chapter 6 – Page 25
This option window helps you narrow the search for existing Collection records—
although the first option in the screen (the default) displays them all if you prefer. (If
there are hundreds or thousands of Collection records in database, finding a record
among those displayed can take a long time.)
Each of the other five option buttons in the Look Up Collection screen limits the
search by a different attribute (field) of the Collection records (Locality, Collector,
Site, Source, or Method). If you choose the last option in the list, Biota opens the
Query Editor (see “The Query Editor, a General-Purpose Tool for Finding Records
Based on Content” in Chapter 12) to allow searches not covered by the other
options.
6.
Click the button labeled “For the Collector” in the Look up Collection window,
since you know the record you are looking for will have Darwin listed as Collector.
When you click the button, Biota creates a list of all collectors represented in the
database. The first entry from the list (“ALAS” in this case) is displayed in the popup
area to the right of the “For the Collector” button to let you know the list has been
completed. The rest of the list is hidden in the popup list.
NOTE: If there are many values, Biota displays the list of values in a scrollable list,
instead of a popup menu. See “Entering Specimen Data: The ‘General’ Tab” in
Chapter 11.
7.
Click and hold the popup list to the right of the “For the Collector” button to
display the list of collectors’ names.
Chapter 6 – Page 26
8.
Select “C. Darwin” from the popup list (illustrated above).
Biota shows the selected value in the popup area (below).
You can try out the other button and popup lists if you want. No selection is final
until you click the “OK” button in the Look Up Collection option window. If you do
this, be sure the “For the Collector” button is selected and “C. Darwin” has been
selected in the popup before you take the next step.
9.
Click the “OK” button in the Look Up Collection option window. The Look Up
Collection display screen appears, listing all Collection records for “C. Darwin.”
The fourth record is the one you want: Santiago Island on October 9, 1832—but
don’t select it just yet.
Chapter 6 – Page 27
If there were many records in the display screen, you might want to use the Sort
buttons at the top of each column to sort the records by the values in that column.
Try the “Date” button now.
10. Click the record for Santiago Island, October 9, 1832. The Look Up Collection
window is dismissed. The Collection Code for the record you selected is entered in
the Specimen record, with additional information about the Collection record you
have just linked, displayed in the yellow Collection information panel.
NOTE: If you want to check the full Collection record, click the “Show Collection
Record” button in the Collection Code panel, above, then return to the Specimen
Input screen.
The insertion point moves on to the “Stage/Sex” entry area, and an Entry Choice
List window appears with the title “Stage/Sex.”
NOTE: As distributed, the Demo Data File has the List for the [Specimen]StageSex
field enabled. If the List does not appear, however, a previous user of the Demo
Data File may have disabled it. When you are done with this lesson, choose Entry
Choice Lists from the Special menu and enable the List if you like.
Chapter 6 – Page 28
Entry Choice Lists are under your control. You can enable or disable a list for most
fields (the settings are in “Entry Choice Lists” in the Special menu; see “Activating or
Deactivating Choice Lists” in Chapter 17 for details).
Using the List Editor, you can change the items in the List or the order in which the
items displayed.
11. To take a look at the List Editor, click the “Modify” button in the Stage/Sex
entry choice windows now. A series of editing buttons appears on the right, with
brief instructions at the top.
To learn how to use the List Editor, see “Adding, Deleting, Editing, or Re-ordering
Items in a Choice List” in Chapter 17.
NOTE: You may have noticed that the first item in the Stage/Sex list is blank. Placing
a blank item in the first position in the List makes it easy to enter a blank as the
default (if that is something you often need to do), or to enter a blank and then
change it to an ad hoc entry for which there is no List item. On the other hand, if you
don’t want blanks or ad hoc entries in your records, don’t offer a blank item.
12. Click the “Done” button in the List Editor window. The Editor buttons disappear,
but the Stage/Sex Entry Choice List remains. Suppose the Small Tree Finch that
Darwin collected was a juvenile of undetermined sex.
13. Type the letter j in the “Type to match” entry area at the top of the Stage/Sex
Entry Choice List. The entry “Juvenile” is automatically selected in the List, since it
is the first (only) entry beginning with the letter j.
Chapter 6 – Page 29
14. Click the “OK” button or press the ENTER key (Windows) or the RETURN key (Mac
OS).
The insertion point moves on to the “Medium” field (intended to record the method
of preparation of a physical specimen).
NOTE: To override a Choice List and make a manual entry, click the Cancel button
in the Entry Choice List window when it appears, or use the blank entry method
outlined in the Note to Step 13.
15. Press the TAB key repeatedly, or make any entry followed by TAB if you wish, to
move through the fields Storage, Deposited, Specimen Custom 1, Specimen
Custom 2, and Type Status.
NOTE: Each of the fields you just moved through can be re-named as you require,
using the “Core Field Aliases” tool in the Special menu. See Chapter 18, “ReNaming Fields.” (The “Deposited” field has a special use in the Loans system,
however. See “How Biota Keeps Track of Specimen Loans” in Chapter 21.
16. Press the TAB key again (or make an entry followed by TAB) to move to the
“Abundance” field.
Notice that the Abundance field already has a “1” entered, indicating the default
assumption that this record represents a single physical specimen. If, instead, this is
a “voucher” record for several specimens (called a “lot” in some disciplines) that
share the same Species and Collection data, enter the number of physical
specimens that the record represents. If this is a “pseudospecimen” record (see
“Site-Based Species Lists With No Specimens” in Chapter 5), you might want to
enter a zero.
Chapter 6 – Page 30
17. Press the TAB key again (or make an entry followed by TAB) to leave the
“Abundance” field.
The “Determination” tab screen appears, with the insertion point in the “Last
Determined By” entry area (highlighted in the illustration below).
(The upper panel in the Determination tab screen will record any future changes in
the determinations for this Specimen, if the Determination History system is
enabled. See Chapter 22, “Determination Histories.”)
The next step is to record the name of the person who identified this Small Tree
Finch specimen. We will pretend that it was last determined by Peter Grant on July
8, 1988.
The “Last Determined By” field of the Specimen table is linked to the Personnel
table (notice the double-bordered entry area, which always indicates a link to a
parent table).
You could type in the letter p to see if “P. R. Grant” appears in pick list, as you did
when you entered cam in the Species Code entry area to find “camaparv” in Step 3
of this lesson. This time you will use a different method, just to demonstrate it.
18. In the “Last Determined By” entry area, enter @ (the “at”
character), then press the TAB key.
All records from the Personnel table are displayed in a choice
window. (See next page.)
Chapter 6 – Page 31
This trick works for any linking field (double-bordered entry area). The @ character
is Biota’s wildcard character.
19. Click the “Last Name” button to sort the list by the “Last
Name” (surname) field of the Personnel table.
The list is sorted.
20. Click the entry for “Grant.” The record is entered in
the “Last Determined By” entry area of the Specimen
record.
The next step is to enter the Date Last Determined.
21. Enter 07 in the “Mo” entry area, 15 in the “Dy”
area, and 1988 in the “Yr” area.
NOTES:
a.
Do not use the TAB key following each entry. The insertion point moves
automatically, as long as you enter 2 digits for month and for day, and 4 for
year.
b.
The order of the fields in date entry areas in
Biota is determined by the current Control Panel
setting in your operating system for Date format.
If you have it set to International format, the entry
area looks like this instead.
c.
The “Today” button enters the date from your computer’s internal clock.
d.
See “Dates” in Chapter 9 for complete details on dates in Biota.
Chapter 6 – Page 32
The “Preparation” tab screen appears, with the insertion point in the “Prepared By”
entry area.
(The “Medium” field appears here, as well as on the “General” tab. You can make
an entry in either place.)
The next step is to record the name of the person who prepared this Small Tree
Finch specimen. We will assume it was done by Darwin himself on some unknown
date in 1832.
22. Enter “C. Darwin” in the “Prepared By” entry area, and
just the year 1832 in the “Yr” entry area. Leave the
month and day entry areas blank.
Biota supports partial dates (month and year only, or just
the year) in the Prepared By or Determined By fields of
Specimen records, or in the Collected By field of Collection
records.
The record is now complete (for purposes of the Tutorial).
23. Click the “Carry” button in the Specimen Input
screen.
Two things happen when you click the “Carry” button.
The record you have been working on (HMSB018) is
accepted, and Biota displays a new Specimen record with
all information except for the Specimen Code “carried
over” (copied in) from the record you just completed.
24. Enter HMSB019 in the Specimen Code entry
area of the new record and press the TAB key.
Using the “Carry” button saves time when you
are entering a series of records that share information. (You can also click the
“Carry” button to use a saved record as a template for a new one; see “Using an
Existing Record as a Template for a New Record” in Chapter 10.)
For the new record HMS019, assume that Darwin also collected a female
Camarhynchus parvulus on the same day and in the same tree as the juvenile
whose record you just completed. Thus only the Stage/Sex field needs to be
changed.
Chapter 6 – Page 33
25. With the mouse, click in the “Stage/Sex” entry area. The Entry Choice List
appears, as in Step 10 above.
26. Type the letter f in the “Type to match” entry area at the top of the Stage/Sex Entry
Choice List, then press the ENTER key (Windows) or the RETURN key (Mac OS).
“Female” is entered in the record.
27. Click the “Save” button in the Specimen Input screen.
The record is accepted into the Demo Data File and a new,
blank Specimen record appears.
28. Click the “Cancel” button in the Specimen Input screen
to dismiss the blank record.
The two records you created appear in the Specimen
Record Listing screen.
29. Click the “Done” button in the
Specimen Record Listing screen, or
press the ENTER key (Windows) or
the RETURN key (Mac OS). The Record Code Option window appears.
30. Click the “OK” button in the Record Code Option screen, or press the ENTER
key (Windows) or the RETURN key (Mac OS), to accept the default option, “Make it
the Specimen Record Set.”
The Specimen Record Listing screen is dismissed and the two records you created
are declared the current Specimen Record Set.
NOTE: For all double-bordered (“default”) buttons, like the “Done” button in Record
Listing screens and the “OK” button in the Record Set option window, you can
always use the ENTER key (Windows) or the RETURN key (Macintosh) to execute the
button action, instead of clicking the button with the mouse.
31. From the Display menu, select “Specimen Set.” The Specimen Record Listing
screen appears with the two records you created. Once the records are displayed,
you can use all the operations for working with records that you have learned.
Chapter 6 – Page 34
NOTE: Choosing a command for a Biota table from the Display menu always
displays the records in the current Record Set for that table. If the current Record
Set is empty, Biota posts a message.
32. Click the “Done” button in the Specimen Record Listing screen. The screen is
dismissed without displaying the Record Set Option window, since these records
have already been declared the current Specimen Record Set.
If you had changed the Selection of records after displaying the Record Set (by
using the “Sub-Selection” button, the “Add Specimen” button, or by deleting one or
more of the displayed records from the database), the Record Set Option window
would have appeared.
Lesson 2 Review
In this lesson, you learned how to:
Create a Specimen record and link it to a Species Record, to a Collection
Record, and to a Personnel record. The very same techniques apply to creating
records for each of Biota’s other tables and to linking them to existing parent
records.
Use the wildcard entry method for entering data in linking fields. You used this
method to enter the Species Code based on its first few characters, and, later, to
display all records from the Personnel table using the @ character.
Use a “Look Up” button to find the right link to a parent table. You used the “Look
Up” collection button to find an existing Collection record.
In the Collection Input screen, a “Look Up” Locality button for linking Collection
records to Locality records works just like the “Look Up” Collection button you
learned about in this lesson.
There is also a “Look Up” Species button in the Specimen Input screen for finding
an existing Species record. When you click it, Biota asks for the Genus of the
Species you are looking for, then displays all Species records for that Genus in the
selection window. You will use this tool in the next lesson.
Use an Entry Choice List to enter data in a field. You can set Entry Choice Lists
for many fields in Biota, or have Biota enter a particular value in a field automatically
(not demonstrated in the lesson; see “Setting Default Entries: Field Value Defaults”
in Chapter 17).
Use the “Carry” button to accept a record, then use that record as a template for
the next new record.
Use the “Save” button to accept a new, single record.
Create and display a Record Set.
For a comprehensive treatment of special features of particular Input screens consult
Chapter 8, “Record Codes,” Chapter 9, “Special Data Types,” and Chapter 11, “Input—
Table by Table.”
Chapter 6 – Page 35
Lesson 3. Creating New Records “On the Fly”
In Lesson 2, you learned to link new records to related records in a parent table. The
Species, Collection, and Personnel records to which you linked the new Specimen
records were, conveniently, already in the Data File. Often, of course, this will not be the
case.
When entering a new record or editing an existing one, it is often necessary to create a
new record in a parent table. This lesson teaches you how to use Biota’s ability to do this
“on the fly” as you create or edit the primary record.
Step by Step
1.
From the Input menu, choose “Specimen.” The Specimen Input screen appears.
You are going to add a new record to the Demo Data File for yet another fictitious
specimen from Darwin’s visit to the Galápagos Islands.
2.
Enter HMSB020 in the Specimen Code entry area and press the TAB key. The
insertion point moves to the Species Code entry area.
NOTE: If you get an error message indicating that this record already exists, see the
Note at Step 2 in Lesson 1.
Let’s say this is a specimen of the Charles Mockingbird, Nesomimus trifasciatus,
collected by Darwin on Floreana Island (Charles Island, in Darwin’s time) on
September 24, 1832.
3.
To find out if there is already a record for this Species in the database, click
the “Look Up” button in the Species Code panel of the Specimen Input screen.
The Look Up Species selection window appears.
You use this tool by entering a Genus name—or the first part of a Genus name
using the wildcard method—in the entry area at the top of the window, then press
TAB. Biota then looks in the Genus table for matching entries.
Chapter 6 – Page 36
If Biota finds only one match among Genus records, all Species records linked
to that Genus record are displayed in the lower panel. You click the one you are
looking for to enter it in the Specimen record.
If Biota finds more than one match among Genus records, the list of
candidates is displayed, as you will see in the next step.
4.
Enter the letter “n” in the Genus entry area of the “Look Up Species” window and
press TAB.
A list of 5 genera that begin with the letter “n” is displayed, including Nesomimus.
5.
Click the entry for Nesomimus in the list of genera (see above). The “Look Up
Species” window now shows three Species records for Nesomimus species.
If the species you were looking for were here, you would click its name to enter it in
the Specimen record. But, clearly, trifasciatus is not yet in the database.
6.
Click the “Cancel” button in the Look Up
Species window since the record you seek
is not listed. You will need to create a new
Species record for N. trifasciatus.
Chapter 6 – Page 37
7.
Type “nesotri” in the Species Code entry area of the Specimen Input screen
and press TAB.
nesotri
The new record option window appears.
"nesotri"
"nesotri"
"nesotri"
8.
With the first (default) option selected, click the “OK” button in the new records
option window (illustrated above).
The Species Input screen appears, with the new Species Code already entered,
and the insertion point blinking in the Genus entry area.
nesotri
9.
In the Genus entry area, type “nes”
and press TAB. The wildcard entry
system completes the entry for
Nesomimus, since no other Genus name
in the database starts with nes.
nesotri
Chapter 6 – Page 38
NOTE: If the genus record had not existed, you could create a new one “on the fly,”
just as you are in the process of doing for a new Species record. In fact, you could
create new records all the way to Kingdom this way, Saving each as you work your
way back down.
10. In the Specific Name entry area, type
“trifasciatus” and press TAB.
11. Click the “Save” button in the Species Input
screen. The Species Input screen is dismissed and
you return to the Specimen record in progress.
NOTE: If you click the “Cancel” button in the Specimen Input screen now, instead of
clicking the “Save” button, the Species record you just created will nonetheless
remain in the database.
12. Click the “Look Up” button in the Collection Code panel of the Specimen Input
screen to find and enter the Collection Code for the record of Darwin’s collections
on Floreana Island for September 24, 1832. If you need help, refer to Steps 5–10 in
Lesson 2.
13. In the “Stage/Sex” input area, record the specimen as “Female.”
14. Save the Specimen record.
15. Click the “Done” button in the Specimen Record Listing screen and dismiss
the Record Set option screen.
Lesson 3 Review
This lesson covered the creation of new records and how to link them to parent records
that you create “on the fly.” In this lesson, you learned how to:
Find out if a parent record already exists. You did this for a Species record from
the Specimen Input screen, using the Look Up Species tool.
For higher taxa (e.g., to see whether a Family record exists when you need to link a
new Genus record), just enter the first few letters of the name you seek (or @ for all
records) and press TAB. Biota will complete the entry if there is just one match, list
all candidates if there are several matches, or post a message if nothing matches.
Create a new parent record when you need one. Just enter the new name. Biota
gives you the option of displaying the parent record Input screen.
Chapter 6 – Page 39
For a comprehensive treatment of special features of particular Input screens consult
Chapter 8, “Record Codes,” Chapter 9, “Special Data Types,” and Chapter 11, “Input—
Table by Table.”
Lesson 4. Finding Records (Queries)
In Lesson 1, you learned how to display all the records for a Biota table by using the
“All…” commands from the File menu. In a large database, however, displaying all
records is not a very efficient way to find a record.
In this lesson, you will learn two very efficient ways to find records using tools from the
Find menu. You will: (1) find records in a table in the taxonomic hierarchy based on a
record or records in a higher table, and (2) find records in the place hierarchy (Collection
and Locality tables), based on a Species Record Set. Chapter 12, “Finding and Updating
Records,” provides a comprehensive reference for Biota’s search and update
capabilities, only some of which can be covered in this tutorial.
Step by Step
1.
From the Find menu, choose “Lower Taxa for Higher Taxa.” The query setup
screen appears.
You will use this tool to find all Species records for the Family Fringillidae (finches)
present in the database.
2.
In the list of tables in the left panel (the panel labeled “1. Select a Lower Taxon”),
click the “Species” button. This is called the target table—the table containing the
records you seek.
Chapter 6 – Page 40
The “Query” panel displays the beginning of the query at the bottom of the screen.
3.
In the list of tables in the right panel (the panel labeled “2. Select a Higher
Taxon”), click the “Family” button—the button for the table to be used in the
selection criterion (the criterion table).
The word “Family” is added to the Query.
4.
In the entry area beneath the button labeled
“…Family named,” type “fri” and press the TAB
key. (The entry area is in the upper-right corner
of the screen.)
Notice that, instead of entering a Family name,
you could have clicked the lower button in the
panel to use a Family record set as a search
criterion.
Biota completes the entry so that it reads “Fringillidae,” and completes the query to
read “Find all Species for the Family Fringillidae.”
Chapter 6 – Page 41
5.
Click the “Find” button to launch the search (above). The 14 Species records for
the Family Fringillidae (including species of six different genera) are displayed in the
Species Record Listing screen.
6.
Click the “Done” button in the Species Record Listing screen, then click the
“OK” button in the Record Set option screen to make these records the current
Species Record Set.
In the next group of steps, you will use this Species Record Set to find all Localities
linked to these Species records.
Notice that the target and criterion tables in the search just completed are not
adjacent in the hierarchy (the Genus table lies between the Species and Family
tables). The Record Set you just declared could not be made easily or directly by
finding the Family record for Fringillidae, then clicking the “Genera” (Child) record
button. Child record buttons are limited to finding groups of records that share a
single parent record.
Chapter 6 – Page 42
7.
From the Find menu, choose “Places for Specimens or Species.” The query
setup screen appears.
You will use this tool to find all Specimen records linked to the finch Species Record
Set, all the Collection records linked to those Specimen records, and all the Locality
records linked to those Collection records—all at once.
8.
In the list of tables in the left panel (the panel
labeled “1. Select a Target Table”), click the
“Localities” button.
The Query panel displays the beginning of the query.
9.
In the list of tables in the right panel (the panel
labeled “2. Select a Record Set”), click the
“Species” button.
Chapter 6 – Page 43
The Query panel completes the query, “Find all Localities for the Species Record
Set.”
10. In the panel labeled “Create
Intervening Record Sets?” click the
checkbox, to set it.
When you set this option, Biota creates
Record Sets automatically for the target
table records and for the linking records
in any intervening tables—in this case,
for the Specimen and Collection tables (see Appendix A, “Biota Tables, Fields, and
Relational Links”).
As you learned earlier in this lesson with the “Lower Taxa for Higher Taxa” tool
(which has an identical checkbox), it is not necessary to check this option in order to
find the target table records you are searching for, nor in order to create a Record
Set for them.
11. Click the “Find” button to launch the search.
Four Locality records (for four Galápagos Islands) are
displayed in the Locality Record Listing screen. Because
you checked the checkbox, they have already been declared the Locality Record
Set. These are the Localities for Collections of Specimens representing Species in
the Species Record set.
12. Without closing the Locality Record Listing screen, select “Specimen Set”
from the Display menu. The Specimen Record Listing screen shows the Record
Set you just created for all finch Specimen records (including the ones you created
in earlier lessons, if you did not delete them).
13. Without closing the Locality or Specimen Record Listing screens, select
“Collection Set” from the Display menu. The Collection Record Listing screen
shows the Record Set you just created for all Collections for the Specimens in the
Specimen screen.
(Notice that Biota can open as many simultaneous windows as your computer’s
memory can support.)
14. Open a few Locality and Collection records to see what the Input screens and
their tabs look like, then close them with the “Cancel” button.
Chapter 6 – Page 44
15. Click the “Done” buttons in all three Record Listing screens to close them (or
use the keyboard shortcut,
Lesson 4 Review
In this lesson, you learned how to:
Find records in a table in the taxonomic hierarchy based on a record or
records in a higher table.
You may have noticed in the Find menu that there is an “opposite” tool, “Higher
Taxa for Lower Taxa.” It works the same way in reverse (but requires a lower taxon
Record Set to be established first). You could use it, for example, to find all Order
records that are linked through intermediate tables to a set of Specimen records.
Find records in the place hierarchy (Collection and Locality tables), based on
a Species Record Set. You can use the same tool to find records based on other
combinations spanning this series of linked tables.
Again, the Find menu offers an “opposite” tool, “Specimens or Species for Places.”
It works for the same table combinations, but in reverse order. You could use it, for
example, to find all Species records linked through intermediate tables to a set of
Locality records.
If you do this based on the Locality set you just created, for example, it will yield not
only the finch Species records you started with, but also the Species record for the
mockingbird Nesomimus trifasciatus that you created in Lesson 3—a nice
demonstration of why both tools are needed.
Create Record Sets automatically for the target table and all intervening
tables. This capability enables you to create linked subsets of your data for several
tables at once (for export, for example).
On Your Own—What to Try Next
The lessons in this tutorial have covered many important features of Biota, but there are
just as many others you will eventually want to learn about. Here are a few suggestions
for next steps on your own.
Learn to use the Query Editor. From the Find menu, choose “Using the Query
Editor.” Then see “The Query Editor, a General-Purpose Tool for Finding Records
Based on Content” in Chapter 12, for instructions.
Learn to use Record Set Pointer Files. Read or review “Record Set Pointer Files”
in Chapter 3.
Learn how to print or export labels. Choose a section of Chapter 14, “Printing
Labels,” that is relevant to your work.
Learn how to create and use Auxiliary Fields and Projects, in Chapter 16,
“User-Defined Auxiliary Fields and the Project System.” This feature enables you to
create an unlimited number of special fields that you can name as you like, for the
Species, Specimen, Collection, or Locality tables.
Learn how to customize Biota by setting preferences, changing the displayed
names of fields, adding Choice Lists and default entries, or setting up Record Code
Prefixes. See Chapter 17, “Default Entries and Entry Choice Lists (Pick Lists),”
Chapter 18, “Re-naming Fields,” and Appendix B, “Setting Preferences.”
Chapter 6 – Page 45
Scan Chapter 4, “Biota Menus and Menu Items: An Annotated Guide” and/or
Chapter 5, “Overview of Biota’s Tools and Features” for additional items that
interest you or solve a problem, and use the links there to find the relevant section
of the manual.
PART
2
Entering Data
Chapter 7
Overview of Record Input Screens
Each Core Table (See “Core Tables” in Chapter 3) in Biota has a screen for listing
records (the record Listing screen) and a screen for entering and displaying data for a
single record (the record Input screen). This chapter outlines conventions and shortcuts
common to Input screens throughout Biota. Details of particular Input screens appear in
Chapter 11, “Input—Table by Table.”
Screen Colors
Each of the 14 Core Tables has been assigned its own characteristic screen color, to
help you navigate the database. All record Input and Listing screens associated with a
particular table share the same background color.
If an Input screen for one table contains information from a linked table, the information
from the linked table appears in a panel displaying the table color for the linked table.
For example, in the Specimen Input screen below (gray, the default color for the
Specimen table), classification information appears in a pale blue panel (the Species
table color), whereas collection data are shown in a pale yellow panel (the Collection
table color).
Chapter 7 – Page 2
To Change the Screen Color Scheme
1.
To change the screen color scheme, choose Preferences from the Special menu,
then click the Colors tab.
To set all table colors to Microsoft gray, click the “Set All Table Colors to
Gray” button and skip the rest of the steps below.
To reset all table colors to Biota defaults, click the “Reset Table Colors to
Biota Defaults” button and skip the rest of the steps below.
2.
Using the radio buttons on the left, select the Core Table color you want to
change.
3.
In the color palette on the right, click the color you want to assign to the selected
table.
4.
Repeat Steps 2 and 3 for any other changes you want to make.
5.
Click the “Save” button.
NOTE: You can also control the table colors that the onboard Biota Web server uses in
Database Client Mode. See “The Database Client Tab” in Chapter 30.
Chapter 7 – Page 3
Entry Areas and Default Entry Order
In all Biota Input screens, you enter data in a series of white, empty boxes (entry areas).
For each Input screen, there is a default entry order. Once you have made an entry, you
can press the TAB key to move on to the next entry area in the default order. Arrows
show the default entry order for the Specimen Input screen, below.
At any time, you can override the default entry order and move directly to any entry area
on an Input screen, using the mouse. When you click in another area, the entry in the
field you just left is registered, whether or not you first pressed the TAB key.
All entries can be edited using standard screen-editing techniques. For example, an
entry can be changed by selecting characters with the mouse and cursor or selecting an
entire entry area with a double click, then typing in the new information. If you change an
entry, but have not yet pressed the TAB key or clicked in another field, you may select
Undo from the Edit menu to restore the previous entry.
Input Screen Tabs and Buttons
Input Screen Tabs
Information on Input screens for many Biota Core Tables are arranged on tabs. From left
to right across the top of an Input Screen, tabs particular to that table appear first, with
tabs common to several tables following.
Chapter 7 – Page 4
In the example below, from the Species Input Screen, the first four tabs (Classification,
Subsp/Names, Synonymy, and Dist/Types) appear only for the Species table, whereas
the Images, Aux Fields, Notes, and Refs tabs are found in the Input screens for the
Specimen, Collection, and Locality tables as well. Notice that, for each of these last four
tabs, the number of linked records appear in parentheses after the tab name.
Keyboard Shortcuts for Input Screen Tabs
To avoid using the mouse, you can use keyboard shortcuts to move between tabs in the
Input screens for Biota Core tables. The first table below shows the shortcuts that apply
to several Core Tables, and the second table below displays shortcuts that apply only to
a particular Core Table or Input screen. (See also the next section in this chapter,
“Keyboard Shortcuts for Input Screen Buttons.” and “Keyboard Shortcuts for Record
Listing Screens” in Chapter 10, summarized in Appendix C, “Keyboard Shortcuts.”)
FUNCTION
MAC OS
General tab
COMMAND–G (
Images tab
COMMAND–I (
Aux Fields tab
COMMAND–M (
–M)
CTRL–M
Notes tab
COMMAND–N (
–N)
CTRL–N
Refs tab
COMMAND–R (
–R)
CTRL– R
FUNCTION
WINDOWS
–G)
–I)
MAC OS
CTRL–G
CTRL–I
WINDOWS
Specimen Input screen
Determination tab
COMMAND–D (
–D)
CTRL–D
Preparation tab
COMMAND–B (
–B)
CTRL–B
Specimen & Collection (combined) Input screen
Specimen tab
COMMAND–G (
–G)
CTRL–G
Collection tab
COMMAND–H (
–H)
CTRL–H
Determination tab
COMMAND–D (
–D)
CTRL–D
Preparation tab
COMMAND–B (
–B)
CTRL–B
Primary Fields tab
COMMAND–G (
–G)
CTRL–G
Other Fields tab
COMMAND–H (
–H)
CTRL–H
Classification tab
COMMAND–G (
–G)
CTRL–G
SubSp/Names tab
COMMAND–H (
–H)
CTRL–H
Specimen Series Input screens
Species Input screen
Chapter 7 – Page 5
Synonymy tab
COMMAND–B (
–B)
CTRL–B
Dist/Types tab
COMMAND–D (
–D)
CTRL–D
Host record tab
COMMAND–H (
–H)
CTRL–H
Georeference tab
COMMAND–B (
–B)
CTRL–B
COMMAND–B (
–B)
CTRL–B
Create/Edit Group tab
COMMAND–R (
–R)
CTRL–R
Create/Edit Note tab
COMMAND–N (
–N)
CTRL–N
COMMAND–M (
–R)
CTRL–M
Reference tab
COMMAND–R (
–R)
CTRL–R
Links tab
COMMAND–L (
–L)
CTRL–L
Collection Input screen
Locality Input screen
Georeference tab
Personnel Input screen
Project Input screen
Auxiliary Fields Set tab
Reference Input screen
Loan Input and Loan Return screens
Loan tab
COMMAND–L (
–L)
CTRL–L
Returns tab
COMMAND–R (
–R)
CTRL–R
Keyboard Shortcuts for Input Screen Buttons
Keyboard shortcuts are available for most Input screen buttons. (The exceptions are the
“Delete” button and a few others that have far-reaching consequences. These require
use of the mouse, for safety’s sake.) The table below lists button shortcuts that apply to
record Input screens for several tables. (See also the previous section in this chapter,
“Keyboard Shortcuts for Input Screen Tabs”, and “Keyboard Shortcuts for Record Listing
Screens” in Chapter 10, summarized in Appendix C, “Keyboard Shortcuts.”)
FUNCTION
MAC OS
WINDOWS
Any default button (double
border), regardless of function
RETURN
( –RETURN)
ENTER
“Cancel” button
COMMAND–RETURN
( –RETURN)
CTRL–ENTER
“Save” button
COMMAND–S (
COMMAND–J (
CTRL–S
or CTRL–J
“Carry” button
COMMAND–K
( –K)
CTRL–K
“Print” button
COMMAND–P
( –P)
CTRL–P
Next record button
COMMAND–RIGHT ARROW
( –RIGHT ARROW)
–S) or
–J)
CTRL–RIGHT ARROW
Chapter 7 – Page 6
Previous record button
COMMAND–RIGHT ARROW
( –RIGHT ARROW)
CTRL–RIGHT ARROW
Show parent record button
(e.g., “Show Genus” Record on
the Species Input screen)
COMMAND–UP ARROW
( –UP ARROW)
CTRL–UP ARROW
Show child record(s) button
(e.g., “Show Specimens” on the
Species Input screen)
COMMAND–DOWN ARROW
( –DOWN ARROW)
CTRL–DOWN ARROW
First “Assign” button on a screen
COMMAND–EQUALS
CTRL–EQUALS (=)
Second “Assign” button on same
screen
OPTION–EQUALS
(OPTION– =)
ALT–EQUALS (=)
Third “Assign” button on same
screen
COMMAND–OPTION–EQUALS
( –OPTION– =)
CTRL–ALT–EQUALS
First “Look Up” button on a
screen
COMMAND–L
CTRL–L
Second “Look Up” button on
same screen
OPTION–L
First “Today” button on a screen
COMMAND–T
Second “Today” button on same
screen
OPTION–T
ALT–T
Dismiss screen (without saving;
same as “Cancel” button, for
Input screens)
COMMAND–HYPHEN
( –HYPHEN)
CTRL– HYPHEN
( – =)
( –L)
(=)
ALT–L
( –L)
CTRL–T
The following table lists shortcuts that apply to only a particular Input screen or tab.
FUNCTION
MAC OS
WINDOWS
Image tab (Specimen, Species, Collection, and Locality Input screens)
“Zoom” (first image) button
COMMAND–E (
–E)
CTRL–E
“Zoom 4” (first 4 images) button
COMMAND–F (
–F)
CTRL–F
“Save” image button
COMMAND–Y (
–Y)
CTRL–Y
Notes tab (Specimen, Species, Collection, Locality and Loans Input screens
“New Note” button
COMMAND–T (
–T)
CTRL–T
“Save Note” button
COMMAND–Y (
–Y)
CTRL–Y
Reference tab (Specimen, Species, Collection, and Locality Input screens
“New Reference” button
COMMAND–T (
–T)
CTRL–T
“Link Reference” button
COMMAND–L (
–L)
CTRL–L
Specimen Input screen
“Show Species Record” button
(first parent record button)
COMMAND–UP ARROW
( –UP ARROW)
CTRL–UP ARROW
Chapter 7 – Page 7
“Show Collection Record” button
(second parent record button)
OPTION–UP ARROW
ALT–UP ARROW
Input & Identify Specimen Series screen
“Show Species Record” button
(first parent record button)
COMMAND–UP ARROW
“Show Collection Record” button
(second parent record button)
OPTION–UP ARROW
CTRL–UP ARROW
( –UP ARROW)
ALT–UP ARROW
Loan Input and Loan Return screens
“Add More Specimens” button
COMMAND–J (
–J)
CTRL–J
“Reprint Loan Form” button
COMMAND–P (
–P)
CTRL–P
“List Specimens” button
COMMAND–DOWN ARROW
( –DOWN ARROW)
CTRL– DOWN ARROW
Entering Data in Linking Fields
For most Biota tables, the record Input screen includes entry areas that link the table
with a related table. These special linking fields (see “Linking Fields: Parent and Child
Records” in Chapter 3) consistently appear with a double-bordered data entry area in all
Biota Input screens (for example, the fields for Species Code and Collection Code in the
Specimen Input screen, a portion of which is shown below).
“On-the-Fly” Creation of Linked Records
Double-bordered data entry areas for linking fields work in a special way. Once you
enter a value in the field and press TAB, Biota checks to see whether a record already
exists for that value in the related (parent) table. If the parent record exists, you can
move on to the next field. If it does not exist, Biota offers you the option to create the
parent record “on the fly” and then return to the table where you started.
1. Enter a value for a linking field. Suppose, for example, you enter the genus
Drosophila in the Genus entry area of the Species Input screen.
Chapter 7 – Page 8
2.
If your entry already exists in the related table, your entry will be accepted and
the cursor will move on to the next field. In the example, if Drosophila were already
in the Genus table, Biota would accept the entry and you move on to the Specific
Name field.
3.
If your entry does not match any entry in the related table, Biota presents the
screen below. (The screen illustrates the Drosophila example.)
If you choose the first option, “Create a Genus record for Drosophila” (the
default), the Input screen for the related table appears (the Genus Input screen,
in this example), with the entry you made in the linking field already entered in
the correct field of the new Input screen. This method of creating a new parent
record “on the fly” is available for all linking fields.
If you choose the second option, “Accept ‘Drosophila’ in the Genus field of the
Species record, but do not create a Genus record for it,” no link to the parent
table will exist for this record. In other words, it will be an orphan record (see
“Linking Fields—Parent and Child Records” in Chapter 3). You can add a record
Chapter 7 – Page 9
in the related table later (a Genus record for Drosophila, in this example), but it is
generally more efficient to add new, related records when this query appears—or
use the table-by-table method outlined in the next section, “Table-by-Table
Creation of Linked Records”.
NOTE: One common exception arises for the “Collected By” field of the Collection
table. With historical collections of specimens, you may not want to create a
Personnel record for every collector—some of whom may be long deceased and
their particulars unknown.
4.
Repeat at additional levels, if necessary. If you choose the first option (create a
new record “on the fly” in the linked table), you may now need to make an entry in a
linking (double-bordered) data entry area in the second Input screen. If you do so,
the process repeats itself. In the Drosophila example, if you make an entry in the
Family field on the Genus Input screen that is not in the Family table, Biota will ask
if you wish to create a new Family record.
You can continue to create new records in related tables as prompted by Biota.
Eventually you will reach a screen for which your entry is already present in the
related table, or you will reach a screen that has no linking fields (e.g., the Kingdom
Input screen at the top of the taxonomic hierarchy or the Locality Input screen at the
top of the place hierarchy).
5.
Accept and return to previous levels. When you have created the record or
records you wish to in related tables, click the “Save” button at the bottom of the
current Input screen. The Input screen for the next-lower level will appear.
6.
Enter data in any remaining fields that you wish to record, then click the “Save”
button, at each level.
7.
Continue with this process, working back down the hierarchy, until you get back
to the original screen (the Species Input screen, in the Drosophila example).
Table-by-Table Creation of Linked Records
In addition to, or instead of on-the-fly creation of records in related tables, as described
in the previous section, new records can simply be entered directly for any table by
selecting the corresponding Input command from the Input menu.
For example, you could begin the entry of a hundred specimens by first entering the
names of all genera, using the Genus Input screen (choose Input Genus from the Input
Chapter 7 – Page 10
menu). Then, when species names are entered, the genera would already be available
for wildcard entry (see the next section).
Your choice of approach will depend upon the circumstances. If minimizing the handling
of delicate specimens is a consideration, allowing Biota to request new records for linked
fields, when needed, permits each specimen to be handled only once when data are
entered directly from specimen labels.
A Powerful Shortcut: Wildcard Data Entry for Linking Fields
For any double-bordered linking field (but not for any other fields), you can save much
time and effort by using the wildcard entry option.
1.
Enter the first letter, or the first few letters of a linking-field value (taxonomic
name, Personnel Short Name, or Record Code (Specimen Code, Species Code,
Collection Code, or Locality Code) that you know or suspect is already recorded in
the related table.
NOTE: To get a full list of all records in the related table, enter @ (the wildcard
character in Biota), in place of any letters in the linking field entry area.
2.
Press the TAB key.
3.
If only one record in the related table matches your entry, the match will be
entered in the linking field automatically.
4.
If more than one entry in the related table begins with the sequence of
characters you entered, all matching values will appear in an alphabetized,
scrolling list. For example, if you entered the two letters dr in the entry area for
Genus in the Species input screen and there were existing records for several
genera beginning with Dr in your Data File, Biota would present a pick list of the
options, as shown below.
Chapter 7 – Page 11
5.
If you see the entry you want, just click it in the list and it will be entered in the
linking field. (Drosophila is being clicked in the illustration.)
6.
A second (or second and third), "helper" field is also listed. In the example
above, Family is listed for each Genus.
7.
The values in the list can be sorted by either column by clicking once on the
column header button. (For example, to sort the Genera in the window above by
Family, you would click the “Family” button in the window.)
8.
If Biota enters a value automatically that you did not intend, it means your
intended value is not present in the related table. Select the incorrect entry with the
mouse and enter the correct value manually. For example, suppose you wanted
Drosophila, so you entered “Dr” in the Genus entry area. If Drymys were in fact the
only genus in the Genus table starting with Dr, Biota would complete your entry as
Drymys. You would then have to change the entry manually to Drosophila (spelled
out fully), then proceed as in Step 3, above.
Overriding Wildcard Input for Linking Fields
In one rather uncommon circumstance, you may need to override Biota’s wildcard entry
for linking fields. This circumstance is best explained with an example.
Suppose you are entering a new Species record for the species Musanga recta, and you
have an existing record in the Genus table for the genus Musanga. As explained in the
previous section, you can type “musa” in the Genus field of the Species input screen and
Biota will automatically fill in Musanga (or display it in a choice window along with any
other existing Genus names that begin with the letters “musa”).
Instead, however, suppose you need to create a Species record for Musa nana. If you
enter “musa” in the Genus field of the Species input screen, Biota will incorrectly
complete the entry as Musanga. In this case, you need to force Biota to allow creation of
a new Genus record for Musa.
In general terms, when you need to create a parent record on the fly for a Linking field
value that precisely matches the initial letters of a longer value in the Key field of the
parent table, you need to override the wildcard lookup. (See why the example was
better?)
You can override the wildcard lookup of parent records in any double-bordered linking
field very simply.
1.
Type in the value for which you want to create a new parent record (Musa in the
example).
2.
Depress the OPTION key (Macintosh) or the ALT key (Windows) while pressing
the TAB key to enter the new value. Biota will offer to create the new parent record.
3.
Create the new parent record in the normal way (see “‘On-the-Fly’ Creation of
Linked Records” earlier in this chapter).
Chapter 8
Record Codes
Record Code Concepts
As introduced in Chapter 3 (“Key Concepts”), the Key fields for the Specimen, Species,
Collection, and Locality tables rely on Record Codes, rather than actual names of taxa or
places, although Record Codes can be names if you wish. In Biota, Record Code is a
general term for Specimen Codes, Species Codes, Collection Codes, and Locality
Codes.
For any Record Code, you may use any combination of up to 30 ASCII characters that
you wish. The only restrictions on Record Codes are that each record within a table must
have a unique Record Code, and a Record Code may not start or end with a space
character (Biota enforces both restrictions, in case you forget). On the other hand,
careful planning of a Record Code system for your particular database can enhance the
usefulness of the database you create. Some examples appear later in this chapter.
If you want, you can use the same code for records in different tables. Although this
might seem a useful approach for related records, it makes little sense when many
records in one table (e.g., many Specimen records) are linked to a single record in a
related table (e.g., a Species record), since each of the “many” records will require a
different Record Code. In general, it is likely to be less confusing to use Record Codes
that are globally unique throughout a Data File.
An exception to this rule of thumb concerns the Input Specimen and Collection tool
(Input menu), which is used primarily to enter data for historical specimens that have a
one-to-one relationship between Specimen and Collection records (see “Specimen and
Collection Combined Input” in Chapter 11). This tool automatically creates a Collection
record linked to each Specimen record you enter, with identical Specimen and Collection
Record Codes. (If you prefer, you can use the Record Code Settings tool to
automatically assign a sequential Collection Record Code. (See “Assigning New Record
Codes Automatically During Data Entry” later in this chapter.)
Why Does Biota Require and Display Record Codes?
In database applications designed for business (such as airline reservation systems) or
for scholarly applications (such as literature reference management programs)—unique
identifiers for records are normally created automatically and are often never seen by the
user. Each record can be found by other criteria, though often less efficiently. When the
airline reservation agent gives you a “record locator” (the automatically generated unique
Record Code for your reservation) the airline hopes you will use it when you call to
reconfirm or change your plans, because it saves the company time and money over
having the agent find your record by date, flight, and name. Likewise, in Biota, the
Record Code is the fast lane to the record.
User control over Record Codes has a number of advantages:
You can design a system of codes that is meaningful in your research or
institution.
Chapter 8 – Page 2
You can avoid conflicts (identical codes) when combining data from two or more
Biota Data Files.
Museums and herbaria can use an established system of accession numbers or
collection codes.
You can use unique records codes you have already created for data imported
from existing flatfiles or field notebooks. This advantage is especially applicable to
Collection Codes and Specimen Codes, for which a collector’s own scheme of
unique codes may be appropriate.
Accessible Record Codes permit you to use machine-readable barcodes or
image codes to identify records uniquely (see Appendix K, “Barcodes”). Biota offers
special support for Specimen and Species Record Code recognition, especially for
barcodes (see “Setting Default Prefixes for Recognizing Specimen and Species
Record Codes” later in this chapter), although barcodes may be used for Collection
and Locality Codes, as well.
Why Does Biota Require Species Codes?
You may wonder why Biota uses Record Codes for the Species table, while relying on
scientific names in the Key Fields for higher taxon tables (Genus, Family, Order, etc.).
Species Codes are necessary for several reasons.
Specific epithets are not unique. Specific epithets (specific names) are obviously
unsuitable as unique identifiers of Species records because of the redundancy of
published specific epithets among genera.
Temporary groupings of specimens are often needed. In revisionary
systematics and especially in biotic inventory projects, Species records are often
needed to unite groups of Specimen records, long before a specific epithet can be
applied to those specimens.
Unidentified or undescribed species. In a relational database, a Species record
is required to connect Specimen records to a Genus record, when the genus is
known but the species is uncertain or undescribed.
Guidelines and Suggestions for Designing Record Code
Systems
Although you may use any system you wish, this section provides some suggestions for
designing Record Code systems, based on the experience of Biota users. The four
tables that require you to create Record Codes for new records differ in how Biota users
generally assign Record Codes.
Specimen Codes
For some groups of organisms (vertebrates, for example), traditions of unique specimen
codes or accession numbers for individual specimens have long existed, in museums
and herbaria. Whenever possible, it makes sense to use such an existing system for
assigning Specimen Codes to records in a Biota Data File.
The use of barcodes for individual specimens or specimen lots (see “Setting Up for
Automatic Record Code Prefix Recognition” later in this chapter) suggests another
obvious recommendation: simply use the specimen barcode (or possibly an abbreviated
version of it; see “Setting Default Prefixes for Recognizing Specimen and Species
Chapter 8 – Page 3
Record Codes” later in this chapter) as the Specimen Code for Biota records (see
Appendix K, “Barcodes”).
Sequential Specimen Codes
A special consideration in designing a code system applies to Specimen Codes. The
Series menu (Chapter 13, “Creating, Finding, and Updating Specimen Series”) provides
a set of powerful input, search, and specimen-identification utilities. These utilities can
be used to their greatest advantage only if Specimen Codes for related groups of
Specimen records can be assigned Specimens Codes that end with a consecutive
integer counter (including leading zeros as necessary; see the Warning below), with or
without an alphanumeric prefix.
WARNING: Because Record Code fields are alphanumeric, sorts on record fields treat
numerals “alphabetically.” Thus, Record Codes A1, A20, and A100 will sort in the order:
A1, A100, A20. Likewise, codes 3, 5, 31, and 40 will sort in the order: 3, 31, 40, 5. To
avoid this problem, use imbedded or leading zeroes: A001, A020, A100; 03, 05, 31, 40.
These series will sort in the order listed.
A “group” of specimens, in this sense, may share any characteristic that you consider
important or convenient, such as being from the same mass collection or lot, from the
same locality, from the same collector, or from the same species.
For detailed instructions on how to set Biota up to use commercial barcodes as
sequential counters with the Series tools, see “Setting Up for Automatic Record Code
Prefix Recognition” later in this chapter.
Unified Record Code Systems: Specimen, Collection, and Locality Codes
In some cases, it may make sense to create a joint system of Collection Codes and
Specimen Codes. A group of specimens from the same collecting event share the same
Collection Code, which may form a prefix for their Specimen Codes. For example, if the
Collection Code is Peru89-01234, the Specimen Codes for three specimens from that
collection might be Peru89-01234:001, Peru89-01234:002, and Peru89-01234:003.
A vegetation study that used Biota to keep track of trees, shrubs, and seedlings in a
complex layout of sites, transects, and quadrats designed a three-level nested system of
Record Codes for the Locality, Collection, and Specimen tables. Each site/transect
combination had a Locality record, with the Locality Code made up of a site abbreviation
and transect number, for example, LOC2. The quadrats within the LOC2 transect each
had a Collection record, with Collection Codes of the form LOC2-T034, LOC2-T035, etc.
for the tree (T) quadrats of the transect. Smaller quadrats on the same transect used for
shrubs (S) had Collection Codes such as LOC2-S011, LOC2-S012, and so on, with a
third series for the even-smaller seedling quadrats. Finally, each plant species that
occurred within each quadrat was recorded in a separate Specimen record, with the
Abundance field registering the number of individuals of that species in that quadrat. The
Specimen Codes for trees were of the form LOC2-T034-003, LOC2-T034-004, or, for
shrubs, LOC2-S012-026, LOC2-S012-027, and so on.
Biota could easily find all the Specimen records for a particular locality, transect, or
quadrat in this study, using fields and relations, regardless of what values had been
assigned for Record Codes. In practice, however, the use of meaningful Record Codes
helped the researchers and data input personnel keep track of progress and make
Chapter 8 – Page 4
sense out of patterns more easily—especially once records were exported to text files
for statistical or spatial analysis.
NOTE: You can ask Biota to enter alphanumeric Record Code prefixes automatically. For
manual input of the rest of the code (integer or alphanumeric), after the prefix, you can
use Entry Choice Lists to enter the prefix (see “Using Entry Choice Lists to Enter Record
Code Prefixes” later in this chapter). For automatic generation of unique integer counters
appended to a prefix you specify (but with the integers not under your control), see
“Assigning New Record Codes Automatically During Data Entry” later in this chapter.
WARNING: If you use a hierarchical system for Locality, Collection, and Specimen Codes,
be sure to avoid ending up with Collection or Specimen Codes too long for the Record
Code field (30 characters maximum), as records accumulate.
Locality Codes
For biogeographical databases of all kinds, Locality Codes present special problems.
First of all, of course, one must decide at what level in the hierarchy of places a “locality”
will be defined, but this is an issue that will depend on the nature of your data.
There exist place-name authority lists (gazetteers), complete with established locality
codes, for some place names within countries and smaller political entities. Obviously, if
these are appropriate and available, one would do well to use the established codes as
Biota Locality Codes. If you wish, you can import place name lists for use in Biota’s Entry
Choice List system (see Chapter 17, “Default Entries and Entry Choice Lists (Pick
Lists)”).
Otherwise, if you are on your own to invent Locality Codes, the most meaningful
approach is probably to base the Locality Code closely on whatever you enter for the
Locality Name field of the Locality record. The Locality Name field is a text field, and may
thus contain up to 32,000 characters (not that you would normally use that many). With
this approach, if the Locality Name entry is longer than 30 characters, you will have to
abbreviate it to a unique but recognizable form, 30 characters or fewer, to create a
Locality Code. When you need to find an existing Locality record to link a Collection
record, you can, of course, use the Lookup Locality tool (see “Entering Collection Data:
The 'General' Tab” in Chapter 11). However, for Locality Codes that abbreviate Locality
Names, it is faster to use the wildcard data entry system (see “ A Powerful Shortcut:
Wildcard Data Entry for Linking Fields” in Chapter 7).
Species Codes
One obvious way to create Species Codes is to concatenate the generic name (or its
initial characters) with the specific epithet (or its initial characters), e.g., glycinemax for
Glycine max, or drosophmelano for Drosophila melanogaster. For combinations longer
than 30 characters (a rather common circumstance), you will need to abbreviate either
the genus or the epithet or both. Some Biota users settle on a standard system, such as
the first N characters of the genus (if there are that many) followed by the first M
characters of the specific name (if there are that many), with a numerical suffix in case of
ambiguity. N plus M should not exceed 29, to allow for a numerical suffix if necessary.
You can leave a space or use a separator character between the genus and species
names or abbreviations if you like (e.g., glycine max or drosoph_melano). For some taxa
or institutions, there may be established codes for species that should be used instead.
Chapter 8 – Page 5
Especially for systematics databases, this approach has the slight disadvantage that a
species may subsequently be reassigned to a different genus, or its epithet changed for
various reasons. If this happens, and you wish to use Species Codes based on species
names, you can always change the Species Code when you change other parts of the
Species record. Biota will automatically offer to change the Species Code in linked
Specimen records (see “Automatically Updating Child Records by Changing a Parent
Record” in Chapter 12).
In survey work and systematic revisions, Species Codes are usually needed long before
there are secure names to apply to the corresponding Species records. Fortunately,
temporary Species Codes are easily accommodated by Biota—there is a special utility to
create them automatically, if you wish (see Chapter 25, “Temporary Taxa for
Approximate Determinations”).
Or, you can create your own temporary Species Codes, which you need to link
Specimen records (and thus Collection and Locality data as well) to known affinities at
higher taxonomic ranks. A “species” that starts out with the Species Code
hystrix_hairy#1 can later be changed to Hystrix _hirsuta when it has been described or
determined authoritatively, by making a single change in the Species record (see
“Automatically Updating Child Records by Changing a Parent Record” in Chapter 12).
Sorting Records by Record Codes
As the default, Biota displays records for all tables except Species sorted by the Key
field for each table in Record Listing screens. This means that Specimen, Collection, and
Locality records will be sorted by Record Code, and taxon tables—Genus and above—
by taxon name. As the default, however, Species records are sorted by Genus, then by
Species Name (specific epithet), rather than by Species Code.
In the Sorting tab of the Preferences screen (Special menu), you can switch to either of
two other options, or return to the default.
Records not sorted automatically on Record Listing screens (faster). Records
will appear in the order they were created. This option produces faster displays and
is therefore useful for large data files when you intend to sort records on some other
criterion anyway, once they are displayed.
Auto-sort records on Record Listing screens by Key field (slower). With this
option selected, records for all tables are sorted by Key field, including Species
records (which are sorted by Species Code).
Auto-sort Species records by Genus and Species, other tables by Key field
(slower). This is the default setting when you create a new Data File or click the
“Reset All Defaults” button on the Preferences screen.
Chapter 8 – Page 6
NOTE: You can sort records any way you wish by using the “Sort” button on each Record
Listing screen, once they are displayed (see “Sorting Records in Record Listing
Screens” in Chapter 10).
WARNING: Because Record Code fields are alphanumeric, sorts on record fields treat
numerals “alphabetically.” Thus, Record Codes A1, A20, and A100 will sort in the order:
A1, A100, A20. Likewise, codes 3, 5, 31, and 40 will sort in the order: 3, 31, 40, 5. To
avoid this problem, use imbedded or leading zeroes: A001, A020, A100; 03, 05, 31, 40.
With their leading or embedded zeros, these series will sort in the order listed.
Using Entry Choice Lists to Enter Record Code Prefixes
Once you decide on a system of Record Codes for your database, Biota offers some
help with the input process. If you plan to enter the same prefix for the Record Codes in
a series of records, but you need to control the remainder of each Record Code yourself,
using an Entry Choice List can save you time and mistakes. (If you want to set the prefix,
but let Biota create a unique integer counter to complete each Record Code, see the
next section, “Assigning New Record Codes Automatically During Data Entry.”)
You can activate and set up an Entry Choice List for any Record Code field ([Species]
Species Code, [Specimen] Specimen Code, [Collection] Collection Code, or [Locality]
Locality Code), using the procedures described in detail in Chapter 17, “Default Entries
and Entry Choice Lists (Pick Lists).” If you prepare the list of entry options with the
Record Code prefix you are currently using as the first (or only) option, you can enter it
simply by pressing the RETURN or ENTER key.
NOTE: An alternative way to enter a Record Code prefix automatically, with no integer
counter, is to set it up for automatic entry using the Assignment tab of the Record Code
Settings screen (Special menu), with the “Number of Digits” setting at zero. See
“Assigning New Record Codes Automatically During Data Entry” later in this chapter.
Chapter 8 – Page 7
Assigning New Record Codes Automatically
During Data Entry
You can create and apply your own complete system of Record Codes (a general term
for Specimen Codes, Species Codes, Collection Codes, and Locality Codes), one at a
time, or you can rely on Biota to generate Record Codes automatically, based on
settings you specify in the Prefix settings screen.
All settings for automatically generated Record Codes are found in the Assignment tab
of the Record Code Settings screen (Special menu).
In this screen, you can control the following settings, independently for Specimen Codes,
Species Codes, Collection Codes, and Locality Codes:
Set the alphanumeric prefix (any alphanumeric string up to 26 characters in
length) for Records Codes.
Set a starting value for the sequential integer counter part of the Record Code.
Set the number of digits in the integer counter (up to 9 digits), to control
formatting.
Specify whether Biota should use the user-defined integer sequence or the
internal record sequence number as the integer counter part of automatically
generated Record Codes.
Specify whether automatically generated Record Codes are also to be entered
automatically by Biota, without your confirmation, or, instead, through use of the
“Assign” buttons on input screens.
Chapter 8 – Page 8
The Format of Automatically Generated Record Codes
A Record Code of the form A1B2CD01234 is said to be made up of the alphanumeric
prefix A1B2CD and the integer counter 01234. In other words, a Record Code prefix
generally ends with the rightmost nonnumeric character in the Record Code (although
you can end a prefix with a numeral if you wish), and the integer counter comprises any
remaining characters (which must all be digits).
When Biota generates Record Codes automatically, you can tell Biota to base the
integer counter either on a starting integer you specify in the Record Code Settings
screen, or on the sequence number for the corresponding table—the number of records
entered in the table since the Data File was created. The sequence number increases by
one every time a record is created, no matter how many records are later deleted.
In either case, leading zeros are automatically added to the integer counter, if
necessary, to make all instances of the counter carry the number of digits you specify in
the Record Code Settings screen, so that alphabetic sorting will work correctly (see the
Warning at the end of the section “Sorting Records by Record Codes” earlier in this
chapter).
The length of a Record Code (a Specimen Code, Species Code, Collection Code, or
Locality Code) may not exceed 30 characters, whether created manually or
automatically. For automatically created Record Codes specified in the Record Code
Settings screen, the maximum length of an alphanumeric prefix is 26 characters and the
maximum length of the integer counter is 9 characters—potentially totaling 35
characters—but Biota enforces a total of no more than 30 characters when you set the
specifications. For example, if you enter a 22-character prefix in the Record Code
Settings screen, the integer counter may not be set any longer than 8 characters. Dialog
screens guide you through the process, as illustrated in the next section.
Setting Record Code Prefixes and Lengths
When you first create a new Biota Data File (an “empty” database; see “Creating an
Empty Biota Data File While Launching Biota” in Chapter 3), Biota assigns the following
default Record Code settings:
LOC for the Locality Code alphanumeric prefix.
COL for the Collection Code alphanumeric prefix.
SPM for the Specimen Code alphanumeric prefix.
SPP for the Species Code alphanumeric prefix.
Six digits for the integer counter for each table (Locality, Collection, Specimen,
and Species)
The User Defined Counter option off (unchecked), for each table. (Sequence
numbers will be used to create the counters, with this setting.)
The Assign Without Asking option off (unchecked), for each table. (The
“Assign” buttons on input screens must be used to generate the automatic
Record Codes, with this setting.)
With these default settings 999,999 unique Record Codes can be generated for each of
the four tables. If you need more than that, you must modify the prefix or the number of
digits in the integer counter.
Chapter 8 – Page 9
To change the default prefix, to adjust the number of digits in the integer counter, or to
change the settings for automatic generation of integer counters and Record Codes,
take the following steps:
1.
Select Record Code Settings from the Special menu. The Record Code Settings
screen appears.
2.
Enter or edit the Record Code prefix settings in the Assignment tab of the
screen. You can enter any prefix you want for each of the four Record Codes
(Locality Code, Collection Code, Specimen Code, and Species Code), up to 26
characters for each prefix.
NOTES:
a.
Leading space characters are not permitted in a Record Code prefix, but you
may include internal space characters if you wish.
b.
If you want to use the integer counter alone to generate Record Codes,
leave (or make) the alphanumeric prefix setting blank.
c.
If the number of characters you
specify as a prefix plus the
number of digits set for the integer
counter exceeds 30, Biota posts a
message such as the one shown
here.
Chapter 8 – Page 10
3.
Set the “User-Defined Counter” checkbox option.
To use your own integer counter sequence, as specified in the next step of
these instructions, the checkbox for the appropriate table must be checked.
To use the sequence number (the number of records entered in the table since
the Data File was created) as the integer counter for a table, the checkbox must
be unchecked.
4.
If the “User-Defined Counter” checkbox is checked, you may edit the userdefined counters shown in the entry areas labeled “Next Value of Integer Counter.”
NOTE: If the “User-Defined Counter” checkbox is unchecked, the value shown in the
“Next Value of Integer Counter” entry area is the sequence number for the table,
which cannot be edited or deleted.
5.
Specify the number of digits for the integer counter in “Number of Digits” entry
areas. You may enter any value between 3 and 9. Thus, the maximum number of
unique records with a particular prefix can vary from 999 (for 3 digits) to
999,999,999 (for 9 digits). If the number you specify plus the number of characters
in the alphanumeric prefix exceeds 30, Biota posts a message such as the one
shown in Step 2, above.
WARNING: If you set the number of digits for the counters too low and you reach the
limit, Record Codes will begin to repeat, and Biota will post a Duplicate Key Error
message (see “Duplicate Key Errors” in Chapter 3). At that point, you must change
to a different prefix.
6.
Set the “Assign Code Without Asking” checkbox option.
If the checkbox for a table is checked, Biota will automatically create and enter
a Record Code, according to your specifications in Steps 2-5, above, for the table
indicated.
If the checkbox for a table is unchecked, you must use the appropriate
“Assign” button in input screens to enter a Record Code created according to
your specifications in steps 2-5 above, for the table indicated. (Using “Assign”
buttons to enter automatically generated Record Codes is discussed in the next
section, “Assigning New Record Codes Using an ‘Assign’ Button: Step by Step”.)
7.
Click the “Save” button. Until you change them again, the settings you have
established will be used for all subsequent new Record Codes automatically
created by Biota.
NOTE: The settings you establish using the Record Code Settings screen are
recorded in your Biota Data File. They remain just as you set them until you change
them, regardless of how many times you start up or shut down Biota. If you start a
new Data File, you will have to set them again.
Chapter 8 – Page 11
Assigning New Record Codes Using an “Assign” Button: Step by Step
“Assign” buttons are used to enter automatically-generated Record Codes while creating
or modifying records. These buttons appear in the Input screens for the Specimen,
Species, Collection, and Locality tables. Each of these Input screens has an “Assign”
button for its own Record Code, plus an “Assign” button for “on-the-fly” creation of new
Record Codes for parent tables (Species and Collection tables for Specimen records
and the Locality table for Collection records). The Specimen Input screen appears below
as an example, with its three “Assign” buttons.
Here are the steps you follow to assign automatically generated Record Codes using an
“Assign” button, while creating or modifying records.
1.
Click the “Assign” button. During data entry, you may elect to click the “Assign”
button next to a Record Code entry area, instead of typing in a Record Code or
having Biota enter an automatically generated Record Code without asking (see the
previous section, “Setting Record Code Prefixes and Lengths”). A dialog window
appears, offering two options.
Chapter 8 – Page 12
2.
Choose an option for assigning the Record Code.
Default Prefix. If you click the “Default Prefix” button (or press the RETURN or
ENTER key), Biota creates and assigns a Record Code that begins with the
Default Prefix shown in the window, followed by an integer counter.
Enter Prefix, Accept Prefix. Alternatively, you may type up to 26 characters in
the “Enter Prefix “ entry area as an ad hoc prefix for the record you are currently
creating or editing. Then click the “Accept Prefix” button in the dialog window.
Biota creates and assigns a Record Code that begins with the ad hoc prefix you
entered, followed by an integer counter.
NOTE: For either option, the integer counter is created according to specifications
set in the Record Code Settings screen (see the previous section, “Setting Record
Code Prefixes and Lengths”).
Setting Default Prefixes for Recognizing
Specimen and Species Record Codes
Biota has the capacity to recognize, automatically, particular Specimen Code and
Species Code prefixes that you specify, whether the codes were created by you,
generated by a commercial producer of barcodes, or assigned automatically by Biota.
The codes you specify are recognized automatically wherever these Record Codes are
required in the Biota interface—including Input screens, search query screens, and
Loans screens.
Here’s how it works. When you enter any value in a Specimen Code or Species Code
entry area, either manually or using a barcode reader, Biota checks to see if the value
you entered begins with an alphanumeric prefix you specified in the Recognition tab of
the Record Code Settings screen (Special menu). If the entry does not start with a
specified alphanumeric prefix you have specified, it is treated as an ordinary entry.
Thus, Specimen Codes and Species Codes whose attributes you have specified in the
Recognition tab of the Record Code Settings screen can be freely mixed with Record
Codes with other prefixes, barcodes of any origin, Biota-generated codes, ad hoc codes
you make up for each specimen, and any existing Specimen codes (e.g., museum or
herbarium accession numbers) or Species codes (from authority files), all in the same
database.
There are two reasons you might want to exploit Biota’s ability to recognize particular
prefixes.
To use the Specimen Series tools. To use the tools of the Series menu (Chapter
13, “Creating, Finding, and Updating Specimen Series”) efficiently, either from the
keyboard or using barcodes and a barcode reader, you need to use automatic
Specimen Code recognition. (See the next section of this chapter, “Using
Alphanumeric Specimen Codes with the Series Tools.”)
To abbreviate or change Specimen Code or Species Code prefixes entered as
barcodes. To substitute an abbreviated barcode prefix for a long barcode prefix or to
replace a barcode prefix with a different prefix in Specimen Codes or Species Code,
you can instruct Biota to recognize specified barcode prefixes and make the
substitutions automatically in records. (See “Substituting Different Prefixes for
Barcode Prefixes in the Data File” later in this chapter.)
Chapter 8 – Page 13
Using Alphanumeric Specimen Codes with the Series Tools
Much time and effort can often be saved by using commands from the Series menu to
enter, update, or find consecutive series of Specimen Codes—although the Series tools
can also be used for nonconsecutive Specimen Codes (Chapter 13, “Creating, Finding,
and Updating Specimen Series”).
If you are using Specimen Codes that have an alphanumeric prefix followed by an
integer counter (see “The Format of Automatically Generated Record Codes” earlier in
this chapter), you can tell Biota to look for that particular prefix, and when it finds it, to
use the integer part of the Specimen Code as a starting or stopping point to create a
series of new Specimen records, to find an existing series, or to find and update an
existing series.
There are two ways to tell Biota to look for a particular Specimen Code prefix.
Manual input of the prefix. You can enter the alphanumeric prefix manually. Click
the “Prefix” button in any Series screen, then use the Enter Prefix/Accept Prefix
option (see “Assigning New Record Codes Using an “Assign” button: Step by Step”
earlier in this chapter). Unless you need to do this for only one or two series of
Specimen Codes, this method is likely to be far less efficient than the automatic
Specimen Code prefix recognition (below).
Automatic Specimen Code prefix recognition. With this approach, you use the
settings of the Recognition tab of the Record Code Settings screen to inform Biota
about the alphanumeric prefix for the Specimen Codes you are using. (See the next
section of this chapter.)
Setting Up for Automatic Record Code Prefix Recognition
Follow these steps to set Biota up to recognize Specimen Code prefixes and/or Species
Code prefixes automatically.
1.
Select Record Code Prefixes from the Special menu. The Prefix setting screen
appears.
2.
Click the Recognition tab.
Chapter 8 – Page 14
Notice that you may specify two different Specimen Code recognition profiles and
one Species Code recognition profile. The primary reason for offering two different
Specimen Code recognition systems is to permit a mixture of two different systems
of Specimen barcodes to be used simultaneously (for example, Specimen barcodes
for your own institution’s collection and barcodes for specimens on loan from
another institution, bearing a different prefix).
3.
Enter the Original Record Code prefixes. In the entry areas labeled “Original
Alphanumeric Prefix,” enter the alphanumeric prefix that appears in the full
Specimen Codes and/or Species Codes you will use. These prefixes may be up to
20 characters in length.
4.
Enter the Substitute (or repeat the Original) Record Code prefixes.
If you want to use Original Specimen Code prefixes with the Series tools: In
the entry areas labeled “Substitute Alphanumeric Prefix,” repeat precisely the
same alphanumeric prefix that you entered in the corresponding entry area
labeled “Original Alphanumeric Prefix.” Prefixes may be up to 20 characters in
length.
If you want to substitute different prefixes for barcode prefixes: In the entry
areas labeled “Substitute Alphanumeric Prefix,” enter the alphanumeric prefix
that you want Biota to substitute for the full Specimen Codes and/or Species
Codes on barcode labels you will use. Prefixes may be up to 20 characters in
length. (See the next section of this chapter, “Substituting Different Prefixes for
Barcode Prefixes in the Data File,” for details and warnings about substituting
prefixes for barcode prefixes.)
5.
Enter the number of digits for the integer counter. Finally, in the fields labeled
“Number of Digits in Integer Counter,” enter the number of digits that follow the
Chapter 8 – Page 15
alphanumeric prefix in your Specimen Codes or Species Codes, so Biota can
correctly format the regenerated Record Codes. Integer counters may be up to 10
digits in lengths.
Substituting Different Prefixes for Barcode Prefixes in the Data File
A barcode reader is simply an alternative to the keyboard for entering data. If you read a
barcode into a text document or a Biota field, you will simply see whatever is coded on
the barcode label. (See Appendix K, “Barcodes,” for general information on barcode
readers and barcodes.)
Specimen barcodes usually have a long alphanumeric prefix, identifying country,
institution, and series, followed by a long, unique integer counter. (For example,
barcodes for specimens collected by or for the Instituto Nacional de Biodiversidad in
Costa Rica—INBio—all start with INBIOCRI00, followed by a unique, seven-digit
integer.) Some projects also use barcode labels for Species Codes, in which case the
barcode for a species can be attached to the species label in specimen storage units.
Although the complete barcode is essential on the specimen itself, it may not be
necessary in your database—but see the warning at the end of this section. Biota allows
you to use either the original barcode (with any mixture of barcode prefixes from different
institutions or collections), or to strip off all or whatever part of the prefix you specify and
replace it with a substitute (perhaps abbreviated) prefix, or with none.
If you want, you can specify a substitute for a particular alphanumeric barcode prefix
using the Recognition tab of the Prefix Setting screen (see the previous section, “Setting
Up for Automatic Record Code Prefix Recognition”). You can do this separately and
independently for Specimen Codes (two different prefixes can be recognized and two
different prefixes substituted) and Species Codes. Each time a Specimen Code or
Species Code is entered, Biota checks to see if it begins with the specified prefix. If so,
the prefix is replaced by the substitute prefix you have specified, followed by the original
value of the integer counter.
For example, if the original barcode reads IntlMusNatHist001234, and you have
specified that IntlMusNatHist is be replaced by IMNH, Biota will assign the Specimen
Code IMNH001234 to a new Specimen record when you scan in the barcode in the
Specimen input screen.
Later, suppose you search for the record using the “By Specimen Code” tool from
the Find menu, or the “Find Specimen Series” tool from the Series menu. You can
find the record by entering either the shortened code, which is actually on the record
in the Data File, or the full, original barcode (IntlMusNatHist001234), which Biota will
recognize and translate to the abbreviated equivalent to make the search.
If you want to use barcodes for Species Codes, you can shorten or replace Species
barcode prefixes in the same way.
WARNING: Abbreviating or substituting prefixes in institutional specimen barcodes is
generally not advisable. Prefixes that have been designed to be universally unique are
best recorded in full, to avoid ambiguity when data are pooled in aggregated databases.
Even if you do not substitute, however, you need to register the Original Prefix, with an
identical “Substitute Prefix,” in the Prefix setting screen to be able to use the Series
commands. See “Setting Up for Automatic Record Code Prefix Recognition” earlier in
this chapter.
Chapter 8 – Page 16
NOTE: Long barcodes, and long Record Codes in general, will not be visible in full in
some Biota Record Listing screens. To view the complete Record Code, you may have
to open the record in the Input screen by double-clicking it in the Record Listing screen.
Chapter 9
Special Data Types
Certain special data types are notoriously troublesome in biodiversity databases. This
chapter describes how Biota handles intermediate taxonomic levels (ranks), dates, and
geographical coordinates (latitude and longitude).
Intermediate Taxonomic Levels (Subtaxa and Supertaxa)
Biota’s taxonomic tables (Species, Genus, Family, Order, Class, Phylum, and Kingdom)
represent only the obligatory levels (ranks) of the Linnean hierarchy, in the sense that
every organism must be assigned to a taxon at each of the seven levels. In fact, of
course, systematists use many intermediate levels in classifying organisms: Subclasses,
Suborders, Superfamilies, Cohorts, Tribes, and so on.
The Dilemma of Intermediate Levels
The problem is that each group of organisms (or each group of taxonomists) uses
different intermediate levels, so that even sister taxa are frequently classified to different
numbers of levels. For this reason, it is not feasible to create a separate table for each
possible intermediate level (e.g., a Subfamily table), since some child records (e.g.,
Genus records) would have a Subfamily parent but others only a Family parent.
The ideal (and cladistically correct) solution is to implement a recursive taxonomic
design. A recursive taxonomic rank system allows an indefinite and potentially unlimited
number of taxonomic levels within any clade.
There are some practical drawbacks to the recursive design, however. In addition to
providing the programmer with a permanent source of migraines, recursive relations can
produce a significant computational overhead, slowing operation of many features of a
database. For example, in a recursive design, finding all Specimens for an Order
requires following each branch and subbranch of a clade from its ordinal root to each
specific or subspecific tip, then finding all specimens for each tip, tip by tip. In contrast, a
strictly hierarchical model requires a single command (a single line of program code) to
do the same search.
The key consideration in electing to use a traditional design for Biota, however, was to
simplify for the user, both in concept and in fact, the processes of importing and
exporting text files. It is much easier to conceptualize these processes when the table
and field structure of the database is only one step away from the form in which most
biologists are used to listing taxa on paper or the computer screen.
How Biota Handles Intermediate Taxonomic Levels
Biota uses fields within the obligatory taxon tables (Species, Genus, Family, Order, etc.)
for intermediate taxonomic levels (see Appendix A, “Biota Tables, Fields, and Relational
Links”). For example, the Family Formicidae (the ants) is divided into several subfamilies
(Myrmicinae, Formicinae, etc.), and each subfamily is further classified into tribes (e.g.,
within the Subfamily Myrmicinae: Tribes Cephalotini, Attini, Dacetini, etc.).
Chapter 9 – Page 2
Biota treats membership in a particular Tribe and subfamily as attributes of each Genus
record. Thus, the Genus table in Biota contains two fields for taxonomic levels between
the generic and the familial level: [Genus] Tribe and [Genus] Subfamily (see Appendix A,
“Biota Tables, Fields, and Relational Links”). Each ant genus gets its own Genus record,
with the appropriate values in the [Genus] Tribe and [Genus] Subfamily fields. In other
words, there is no single record for a Tribe or Subfamily, as there must be for each taxon
in the database at the obligatory levels. Nonetheless, you can search, sort, select, and
display, and therefore print or export records based on intermediate taxonomic levels.
For groups not requiring certain intermediate taxonomic levels (or if you choose to ignore
them), simply leave the fields for intermediate levels blank.
Default Names for Intermediate Taxon Fields
Biota provides predefined fields for the following intermediate taxonomic ranks (see
Appendix A, “Biota Tables, Fields, and Relational Links”).
[Species] Subgenus
[Species] Section
[Genus]
Tribe
[Genus]
Subfamily
[Family]
Superfamily
[Family]
Suborder
[Order]
Superorder
[Order]
Subclass
[Class]
Subphylum
[Phylum]
Subkingdom
[Kingdom] Superkingdom
Renaming an Intermediate Taxon Field
If the organisms you work with require a name for an intermediate taxonomic level that
does not correspond to the default names listed above, you can rename any of these
fields to suit your needs (see Chapter 18, “Renaming fields”).
Defining Additional Intermediate Levels
If you need more intermediate levels than Biota has provided with default names (see
“Default Names for Intermediate Taxon Fields” earlier in this chapter), use one of the
many Custom fields (e.g., [Genus] Genus Custom1, see Appendix A, “Biota Tables,
Fields, and Relational Links”) and rename it appropriately(see Chapter 18, “Renaming
fields”).
Remember, an intermediate level is always an attribute (field) of the next lower
obligatory level.
Updating Intermediate Taxa
To add intermediate taxonomic names to existing records, rename an existing
intermediate taxon, or specify certain records to be recorded as a new intermediate
taxon, take these steps.
Chapter 9 – Page 3
1.
Define a Record Set (see “Record Sets” in Chapter 3) for the records you want
update.
2.
Use the Find and Replace tool (see “Updating Records Using the Find and
Replace Tool” in Chapter 12) from the Special menu to add or change the
intermediate taxon name for all records in the Record Set.
Dates
Date information appears in many places in Biota tables and records. You can record
the date of a collecting event (or the beginning and ending dates for a collecting period),
the date each specimen was prepared, the date each was last determined, the date a
Note record was added to a parent record, and the date a Specimen Loan was made or
returned.
Automatically Recorded Dates
For Specimen, Species, Collection, Locality, Personnel, Loans, References, and Project
records, Biota automatically registers the date each record was created and the most
recent date it was changed. (The identity of the user making the most recent change is
also recorded, if this option is enabled in the “Admin Settings” tab of the Preferences
screen. See Appendix B, “Setting Preferences”).
If the Determination History option has been activated, the current date is recorded any
time the determination of a specimen is updated, directly or indirectly (see Chapter 22,
“Determination Histories”).
Date Formats in Biota: U.S. and International Formats
Along with preserving other endangered historical curiosities such as inches and acres,
the USA stands alone in placing the day of the month first, followed by month and year,
while the rest of the world does it the sensible way, day-month-year, from smallest to
largest unit of time.
Fortunately for the user, Biota does not care which way you set the date format
(International vs. US) in your computer’s operating system (Windows or MacOS). Biota
figures out which OS date setting is in use and observes the following conventions:
On Input screens, Record Listing screens, and in printed reports, dates always
match the system setting.
In the Sort and Query Editors, all dates match the system setting. When using
the Search Editor for a date field, be sure to enter the date using the same format
as the system setting.
On labels, all dates are in International format, regardless of the system setting. On
labels, you can choose to express the month as either the English three-letter
abbreviation (12 Apr 1994) or with Roman numerals (12 IV 1994).
In the Import and Export Editors, if you select a date field to import or export,
Biota offers a choice of International, US, or ANSI (YYYYMMDD) date format,
regardless of the system setting.
In all other Export tools, dates match the system setting.
All Biota Data Files are completely date-cross-compatible, regardless of the
current system setting, the system setting under which they were created, the Biota
Chapter 9 – Page 4
version under which they were created (all the way back to Version 1 in 1995), or
the platform (Windows or Mac OS) on which they were created.
If you change the Date Format setting in your operating system after launching
Biota, you will be reminded by an appropriate message.
Entering Dates
To enter a date in a record, you enter numerals in three separate, labeled fields, as
shown here. (The entries Dy:, Mo:, and Yr: are simply guides to the fields, which are
always present. You enter only the numbers.)
If your computer operating system is set to International date format:
If your computer operating system is set to US date format:
Chapter 9 – Page 5
Entering Today’s Date
To enter today’s date (more precisely, the date set in your computer’s operating system),
click the “Today” button next to a date entry area or use the keyboard equivalent.
FUNCTION
MAC OS
First “Today” button on a screen
COMMAND–T (
Second “Today” button on same
screen
OPTION–T
WINDOWS
–L)
CTRL–T
ALT–T
Entering a Default Date
You can use the Field Value Defaults tool (Special menu) to enter any date automatically
as the default, for any user-enterable date field. See Chapter 17, “Default Entries and
Entry Choice Lists (Pick Lists).”
Date Displays on Record Listing Screens
In Record Listing screens, Biota displays dates in International or US date format,
according to your operating system setting. The three-letter English abbreviation is used
for the month, to avoid any ambiguity in work settings that use both systems.
Partial dates (see the next section in this chapter, “Partial Dates”) are displayed as
Month (abbreviated) Year, or Year.
Collection Date ranges (see “Collection Date Ranges” later in this chapter) are displayed
in condensed format, but may nonetheless be too long to be seen in full in a Record
Listing screen. To view a Collection Date range in full, you may need to open the record
in the Input screen by double-clicking it in the Record Listing screen.
Partial Dates
Partial dates are allowed in several of Biota’s date fields. Especially for historic
specimens, the exact dates of collection, preparation, and determination are often not
Chapter 9 – Page 6
known. Instead, collection dates on specimen labels often show only month and year, or
just the year. For collection, preparation, and determination dates, Biota allows you to
enter dates in any of three formats:
International date format:
◊
Complete date: DD/MM/YYYY (e.g., enter 17/05/1975 for 17 May 1975)
◊
Month-year date: MM/YYYY (e.g., enter 00/05/1975 for May 1975)
◊
Year-only date: YYYY (e.g., enter 00/00/1975 for 1975)
US date format:
◊
Complete date: MM/DD/YYYY (e.g., enter 05/17/1975 for May 17, 1975)
◊
Month-year date: MM/YYYY (e.g., enter 05/00/1975 for May, 1975)
◊
Year-only date: YYYY (e.g., enter 00/00/1975 for 1975)
How Biota Handles Partial Dates
For most purposes, there is no reason to pay any attention to how Biota handles partial
dates internally. But if you need to import or export partial dates, you will need to read
this section and the next one. In addition, you may want to read this section to
understand how records are sorted when some records have complete dates and some
have partial dates.
Biota keeps track of complete and partial dates by means of a second, internal Date
Flag field paired with each of the date fields that allow partial dates (see Appendix A,
“Biota Tables, Fields, and Relational Links”). Thus, Date Determined is paired with a
field called Date Det Flag, an integer field of length 1 that has the value 0 if you enter a
complete date for Date Determined, the value 1 if you enter a month-year date, and the
value 2 if you enter a year-only date.
Partial dates are actually recorded as complete dates (4th Dimension accepts only
complete dates in a date field). For screen display, labels, or printed reports, however,
Biota displays or prints only month and year from records with month-year dates and
only the year for year-only dates (as flagged by the corresponding Date Flag field).
Specifically, Biota uses the following internal conventions to record complete and partial
dates:
Complete date (e.g., 17 May 1975): Biota records the complete date plus a 0 in the
corresponding Date Flag field.
Month-year date (e.g., May 1975): Biota records the first day of the month (1 May
1975), plus a 1 in the corresponding Date Flag field.
Year-only date (e.g., 1975): Biota records the last day of the year (31 December
1975), plus a 2 in the corresponding Date Flag field.
Importing and Exporting Partial Dates
The only time you will ever see or need to be concerned with Date Flag fields is if you
need to export partial dates using the “Export by Tables and Fields” tool (see Chapter
27, “Exporting Data”) or import partial dates using the “Import by Table and Fields” tool
(see Chapter 28, “Importing Data”).
For importing partial dates, you can use any convention you wish (e.g., middle day of the
month for month-year dates, middle day of the year for year-only dates), as long as you
import the correct Date Flags.
Chapter 9 – Page 7
Collection Date Ranges
Sometimes specimens are collected automatically in traps or nets over a period of time
(even seeds in seed traps), so that the exact date of capture for a specimen is not
known. Or, specimens are known to have been collected on a certain expedition or
cruise for which the start date and end date are known, even though no specific
collection date was recorded for individual specimens.
In such cases, you may enter the first date for the collection period in the “Date
Collected” field and the last date for the collection period in the “Date Collection
Completed” field (internally called “DateCollEnd”), both in the Collection table. Both fields
allow any mixture of complete and partial dates.
Collection Date Ranges on Labels and in Exported Text Files
Collection Dates and Collection Date ranges are always printed or exported in
International format for labels, condensed “intelligently” (see “Collection Labels” in
Chapter 15) and in some kinds of exported text files (see Chapter 27, “Exporting Data”).
If both the Date Collected field and the Date Collection Completed (internally, “Date Coll
End”) fields have been entered in a Collection record, a Collection or Locality label made
using that record will include the date range, condensed if possible. Here are the rules
with examples:
COSTA RICA: Cartago
Cerro de la Muerte, La Georgina
Cordillera de Talamanca
Elev 3100m, 9°41’0”N83°52’0”W
coll. R. Colwell, 9-12 Jan 1976
COSTA RICA: Cartago
Cerro de la Muerte, La Georgina
Cordillera de Talamanca
Elev 3100m, 9°41’0”N83°52’0”W
coll. R. Colwell, 29 Jan-2 Feb 1976
COSTA RICA: Cartago
Cerro de la Muerte, La Georgina
Cordillera de Talamanca
Elev 3100m, 9°41’0”N83°52’0”W
coll. R. Colwell, Jan-Mar 1976
COSTA RICA: Cartago
Cerro de la Muerte, La Georgina
Cordillera de Talamanca
Elev 3100m, 9°41’0”N83°52’0”W
coll. R. Colwell, Jan 1975-Mar 1976
Complete dates in the same month: The label for a collection made between 9
January 1976 and 12 January 1976 would read 9-12 Jan 1976.
Complete dates in the same year, but not the same month: The label for a
collection made between 29 January 1976 and 2 February 1976 would read 29 Jan2 Feb 1976.
Month-Year dates in the same year: A collection made during the period January
through March in 1976 would be labeled Jan-Mar 1976.
Month-Year dates in the different years: A collection made during the period
December 1975 through March 1976 would be labeled Jan 1975-Mar 1976.
One date complete, one partial: You can even use a complete date for Date
Collected and a partial date for Date Collection Completed, or vice versa, but no
Chapter 9 – Page 8
attempt is made to condense the label format. A collection made between an
unknown day in December 1975 and 20 January 1976 would be written Dec 197520 Jan 1976 on a label, to avoid ambiguity.
Spatial Coordinates
Information on collection of specimens has always included geographical data, with
steadily increasing precision as the centuries have passed. At present, two trends in
georeferencing are evident.
First, museums and herbaria are struggling to add geographical coordinates to historical
specimen data based on place names. This is a difficult and tedious task that can be
automated to only a certain degree by using geographical place name databases and
Geographic Information Systems (GIS). How to interpret a collector’s notation “25 km
NW Guadalajara, Jalisco, Mexico” requires human judgment: Did the collector mean 25
km along a road or in a direct line? Was the distance measured from the center of the
city or from the edge (and if the edge, where was the edge at the time of collection)?
How precisely was the distance measured? And, of, course, many older collections use
political units as their only locality data: “Bolivia,” or “Park County, Colorado” or historical
political units like “Veragua.” What do you enter in a database for the latitude and
longitude of Bolivia?
Second, more recent collections usually carry specific latitude and longitude information
(or the equivalent in UTM, Lambert, or other coordinate systems). Collectors now use
Geographic Positioning System (GPS) devices that provide latitude and longitude
information accurate to within a few meters, and GPS units of even greater accuracy will
soon be in the backpack, or pocket, or on the wrist of every collector of new specimens.
Again, however, the problem of precision arises for coordinate data. If a collector used a
large-scale map to guess at the coordinates of a collecting site, the precision will be less
than if a high-resolution topographic map was used, and far less than if a GPS device
was used. For these reasons, specimen databases need to provide a way to record not
only geographical coordinates, but also a way to record and display their estimated level
of accuracy.
Meanwhile, ecological studies often require a way to record the spatial coordinates of
quadrats or sampling sites within a grid or geographical locality.
Options for Recording Spatial Coordinates in Biota
Biota’s data structure (see Appendix A, “Biota Tables, Fields, and Relational Links”)
provides three ways to record geographical coordinate data and to indicate its accuracy.
The X Coordinate, Y Coordinate, and XY Accuracy fields of the Collection table.
(See the next section in this chapter, “Spatial coordinate fields in the Collection
table.”)
The Latitude, Longitude, and Lat-Long Accuracy fields of the Locality table. (See
“Latitude and Longitude (Locality Table),” later in this chapter.)
The three Alternate Coordinates fields of the Locality table. (See “Alternate
Coordinates (Locality Table),” later in this chapter.)
Spatial Coordinate Fields in the Collection Table
The Collection table offers three fields for recording spatial coordinates: X Coordinate, Y
Coordinate, and XY Accuracy. These fields have several possible uses.
Chapter 9 – Page 9
Because Collection records have a many-to-one relation with Locality records (Appendix
A, “Biota Tables, Fields, and Relational Links”), you might use a single Locality record to
register approximate or historical coordinates for a named place (for example, a
watershed, region, or county) as the parent record for many Collection records. The
linked Collection records might be a mixture of modern and historical records for latitude
and longitude. The modern records might include GPS readings (in decimal degrees),
while the historical records leave these fields blank.
Alternatively, for a quadrat-based sampling study, you could use the X Coordinate and Y
Coordinate fields of the Collection table for quadrat coordinates and a parent Locality
record to identify and record Latitude and Longitude for the plot grid.
Input for these fields is located on the Georeference tab of the Collection Input screen.
NOTE: The X Coordinate and Y Coordinate fields of the Collection table are real number
fields, whereas the XY Accuracy field is alphanumeric. Values for the X Coordinate may
take any numeric value, negative or positive.
Latitude and Longitude (Locality Table)
Biota stores Latitude and Longitude data in units of decimal degrees—the standard
system used in Geographic Information Systems (GIS) work. Nonetheless, Biota offers
three unit systems for the entry and display of latitude and longitude values in the
Locality table. You can enter data using any of the three systems and freely use different
systems for different records in the same data file. As you make an entry in any of the
systems, Biota instantly translates the value into the other two and displays all three
versions in the Coordinates panel of the Locality input screen. See “Entering Locality
Data: The 'General' Tab” in Chapter 11 for details and instructions.
System 1: Degrees/Minutes/Seconds (DMS). This is the traditional system found
in most gazetteers and atlases—but see the important warning, below.
System 2: Integer Degrees, Decimal Minutes. This is the system used by most
Geographical Positioning System (GPS) instruments.
System 3: Decimal Degrees. This is the system used in Geographical Information
Systems (GIS).
WARNING: Some gazetteers list Latitude and Longitude values in DMS, but use a format
that looks like Integer Degrees with Decimal Minutes. For example, 24° 48.39 actually
means 24° 48’ 39” in these gazetteers. The easiest way to detect this deceptive format is
to see if you can find any values in the gazetteer to the right of the ”decimal point” that
exceed 59. If not, those values are Seconds, not the decimal part of true Decimal
Minutes.
Conversion Formulas for Latitude and Longitude Unit Systems
Here are the formulas Biota uses to convert to and from Decimal Degrees (the internal
storage format in Biota), where Int means the integer part of a real number, Abs means
absolute value, and Round means round to the nearest integer:
Chapter 9 – Page 10
Degrees = Int [Abs (Decimal Degrees)]
Decimal Minutes = [Abs (Decimal Degrees) — Degrees] * 60
Minutes = Int (Decimal Minutes)
Decimal Seconds = (Decimal Minutes — Minutes) * 60
Seconds = Round (Decimal Seconds)
Decimal Degrees = Degrees + (Minutes/60) + (Seconds/3600)
Setting the Display Format and Internal Resolution for
Latitude and Longitude
Using settings in the Coordinates tab of the Preferences screen (Special menu), you can
control the onscreen display for the geographical reference fields of the Locality table
and the resolution for decimal degrees of latitude and longitude.
In the upper panel of the Coordinates tab, “Coordinate display on listing
screens,” you can select one of three options for coordinates in Record Listing
screens.
◊
Show Latitude and Longitude in decimal degrees. Because Latitude and
Longitude are stored internally by Biota in decimal degrees, display in this format
is faster than for the second option.
◊
Show Latitude and Longitude in D/M/S (Degrees/Minutes/Seconds). This
option is slower than the preceding option, because Biota must compute the
degree/minute/seconds (DMS) equivalents for each record as it is displayed.
◊
Show Alternate Coordinates. This option is explained in the section “Alternate
Coordinates” later in this chapter.
In the lower panel of the Coordinates tab, “Resolution of decimal degrees for
Latitude and Longitude,” use the popup list to set the number of decimal places that
Biota records internally for decimal degrees of Latitude and Longitude. You can
select any setting from zero through 6 decimal places. The default value is 5
decimal places. (Spatial resolution at 6 decimal places is about 1 cm.)
This setting also controls the number of decimal places shown for decimal degrees
in the Georeference tab of Locality Input screen, as well as the display in Record
Chapter 9 – Page 11
Listing screens when the “Coordinate display on listing screens” option is set to
“Show Latitude and Longitude in decimal degrees.”
Setting Latitude and Longitude Display Resolution for
Individual Locality Records
In individual Locality records, you can use special key words in the “Lat-Long Accuracy”
field (the “Accuracy” input area in the Georeference tab of the Locality Input screen) to
control the display, printing, and export of Latitude and Longitude data.
Degrees and Minutes only option. In particular Locality records, Latitude and
Longitude data may be accurate to Degrees and Minutes, but not to Seconds,
especially for most historic data and for coordinates taken from maps. You can tell
Biota to display, print, and export only Degrees, Minutes, and Hemisphere by
entering the value “Minutes” (or “Minutos,” for the Spanish interface) in the Lat Long
Accuracy field. (Do not enter the quotation marks.)
Degrees only option. Likewise, if the Latitude and Longitude values in a Locality
record are accurate only to Degrees, you can enter “Degrees” (or “Grados”) in the
Lat Long Accuracy field to instruct Biota to display, print, and export only Degrees
and Hemisphere.
If you enter any other value besides “Minutes,” “Minutos,” “Degrees,” or “Grados” (in
either lowercase, uppercase, or mixed case) in the “Lat Long Accuracy” field or if you
leave the field blank, Biota displays, prints, and exports full data for Degrees, Minutes,
and Seconds for each record in which either Latitude or Longitude or both are not blank
(zero).
This format option affects the Locality Input and Record Listing screens and the
Collection Input screen (if the DMS display option is set); exported or printed locality
labels of all kinds (see Chapter 15, “Printing Labels”); exported Specimen Flatfiles and
Specimens Examined Lists (see Chapter 27, “Exporting Data”); and exported Web
pages (see Chapter 33, “Exporting Static Web Pages”).
Alternate Coordinates (Locality Table)
In cartography and in Geographic Information System (GIS) software, the spherical
coordinate system used for latitude and longitude (also called GRS for Geographic
Reference System or Global Reference System) forms the underlying basis for all map
projections, for transformations among map projections and map coordinate systems
(latitude/longitude is not considered a map projection), and for adjustment of coordinates
for different models of the Earth’s shape (“datums”). Biota offers full support for
latitude/longitude entry and display (see “Latitude and Longitude (Locality Table),” earlier
in this chapter).
Other coordinate systems, however, are used for geographical reference data in many
parts of the world and are often found in label or catalog data for historic specimens.
Biota accommodates alternate (non-latitude/longitude) geographical coordinate systems,
such as UTM or Lambert coordinates, or the Township-Range-Section system of U.S.
Public Land Surveys, by means of three “Alternate Coordinate” Core fields in the Locality
table.
The default names of the Alternate Coordinate fields are “Alternate Coordinate 1,”
“Alternate Coordinate 2,” and “Alternate Coordinate 3.” (The internal names are “Alt
Coordinate 1,” “Alt Coordinate 2,” and “Alt Coordinate 3.”) Each is an 80-character
alphanumeric field.
Chapter 9 – Page 12
The fields may be renamed (see Chapter 18, “Renaming Fields”). Some examples
are presented in the section “Suggestions for Use of the Alt Coordinate Fields,” later
in this chapter.
The fields support Entry Choice Lists (Pick Lists), if you wish to activate and
create them (see Chapter 17, “Default Entries and Entry Choice Lists (Pick Lists)”).
NOTE: Although intended primarily for coordinate data, the Alternate Coordinate fields
can be used for any alphanumeric locality data you wish. (If you use the fields for noncoordinate data, be sure to uncheck the “Show Alternate Coordinates” display option in
the Coordinates tab of the Preferences screen; see “Setting the Display Format and
Internal Resolution for Latitude and Longitude,” earlier in this chapter.)
Setting the Display Format for Alternate Coordinates in the Locality
Record Listing Screen
In the Coordinates tab of the Preferences screen (Special menu), you can set Biota to
display data from the Alternate Coordinates fields instead of Latitude and Longitude in
Record Listing screens.
In the upper panel of the Coordinates tab, “Coordinate display on listing screens,” select
“Show Alternate Coordinates.” (The other options on the Coordinates tab are explained
in the section “Setting the Display Format and Internal Resolution for Latitude and
Longitude,” earlier in this chapter.)
Suggestions for Use of the Alt Coordinate Fields
Dozens of map projections and map coordinate systems are used in cartography (for
example, ARC/INFO GIS software supports 38 map projections1). Here are suggestions
for using Biota's Alternate Coordinate fields for three systems commonly used by
biologists for recording collection or observation sites for specimens. (Other coordinate
systems can be similarly accommodated, as necessary.)
UTM (Universal Transverse Mercator) Rectangular Coordinates. In the UTM
system, Earth is divided into 60 zones, each spanning six degrees of longitude
between 84°N and 80°S latitude. UTM coordinates are always positive, seven-digit
integers that represent the number of meters east (the easting or “X” coordinate on
1
Snyder, J. P. 1992. Map Projections and Coordinate Management: Concepts and
Procedures (ARC/INFO User’s Guide). Redland, CA: Environmental Systems Research
Institute, Inc.
Chapter 9 – Page 13
a map) and north (the northing or “Y” coordinate on a map) of the southwest corner
of the UTM zone. (There are actually two sets of coordinates for each zone, one for
the Southern and one for the Northern Hemisphere.) Thus, coordinate values alone
are not sufficient to identify a point on Earth; the UTM Zone and hemisphere must
also be specified. (In addition, the datum—the ellipsoid used to model Earth—
affects UTM coordinates and all other map coordinate values.)
In the United States, USGS (U.S. Geological Service) and BLM (Bureau of Land
Management) topographic maps (except for older ones) have a UTM grid, or at
least UTM tick marks in the margins, with the UTM coordinate value for each grid
line in the map margins. (UTM grids on many U.S. topographic maps are actually
“alien grids,” since many of the maps themselves are not Universal Transverse
Mercator projections but Lambert or Polyconic projections. UTM coordinates can
nonetheless be read accurately off such maps.2) The UTM Zone for any map that
includes UTM coordinates can usually be found in the map legend (on U.S.
topographic maps, in lower-left corner).
For UTM coordinates, if all three Alternate Coordinate fields are available, it would
be logical to use the Alternate Coordinate 1 field for the easting value (which, by
convention, is the first of the pair), Alternate Coordinate 2 for the northing value, and
Alternate Coordinate 3 to record the UTM Zone (including the hemisphere, if you
are likely to have data from both the Northern and Southern hemispheres in your
Data File). You can rename the fields appropriately (see Chapter 18, “Renaming
Fields”). You might consider preceding the easting value by “UTM” so that labels
(see below) clearly indicate what the coordinates are. The Alternate Coordinates
panel of the Coordinates tab of the Locality Input screen would then appear as
below (for San Vito de Java, Costa Rica).
NOTE: Be sure to include leading zeroes for coordinate values so that all have
exactly seven digits—otherwise, alphanumeric sorts will not make sense.
Lambert Rectangular Coordinates. In some countries (Costa Rica, for example),
Lambert rectangular coordinates appear on high resolution maps prepared in the
Lambert Conformal Conic projection (with no UTM grid or tick marks
superimposed). As with UTM (see above), the Lambert coordinates are northings
and eastings from the southwest corner of a particular, named Lambert zone,
defined by a standard point of origin. The recommendations for UTM, above, are
easily applied to Lambert coordinates.
2
Thompson, M. M. 1987. Maps for America: Cartographic Products of the U.S.
Geological Survey and Others, Third Edition. Washington, D. C.: U.S. Department of the
Interior, Geological Survey, U.S. Government Printing Office.
Chapter 9 – Page 14
Township, Range, and Section (TRS). The TRS system has been used in the
United States since 1785 for Public Lands Surveys. TRS is neither a map projection
nor a unified coordinate system, but rather, a series of more than 30 independent,
historically fixed land surveys, each ranging in the four cardinal directions from a
different, largely arbitrary point of origin, covering twenty-nine States3. In effect, TRS
data combine large scale coordinates (Township for the north-south coordinate,
Range for the east-west coordinate) with Section data, which identify land areas
within Townships.
Despite the idiosyncratic nature of TRS data, museums and herbaria in Public
Lands States sometimes need to database specimens that are referenced to TRS
data. To avoid ambiguity, the named principal meridian that uniquely identifies each
Public Lands Survey should be specified for the TRS data for each locality record in
a database—although the combination of State plus County or Parish can also
suffice (e.g., Biota's State/Province and District fields).
If all three Alt Coordinate fields are available, one option for recording TRS data
(which follows legal land title usage), is to use Alternate Coordinate 1 for Township
(north-south), Alternate Coordinate 2 for Range (east-west) and principal meridian,
and Alternate Coordinate 3 for Section (and subsection) data (e.g., with semicolons
separating fields, “T18S; R1E of 6th Principal Meridian; NW1/4 of NW1/4 of Sec.
29”). Alternatively, with three fields, Alternate Coordinate 1 could be Township,
Alternate Coordinate 2 could be Range and Section, and Alternate Coordinate 3 the
principal meridian name, as shown in this example, with data for a site in Colorado.
If two of the Alternate Coordinate fields are used for TRS data, one field could
accommodate Township, Range, and Section data (e.g., “T18SR1E, NW1/4 NW1/4
of Sec. 29”) and the other the principal meridian (“6th Principle Meridian”).
If only one field is to used for TRS data, the principal meridian could be omitted, or
incorporated as a code, as in the example on the next page for “More than one nonlatitude/longitude system.”
NOTE: If you intend to use the utility program TRS2LL (see the Note in the section
“Converting Non-Latitude/Longitude Coordinates to Latitude and Longitude,” later in
this chapter) to convert TRS data to latitude and longitude, or the reverse, be sure
to study the TRS format required for TRS2LL input and follow it in your Biota Data
File, either in a single Alt Coordinate field or split among Alt Coordinate fields in a
format easily combined in a text editor.
3
Thompson, M. M. 1987. Maps for America: Cartographic Products of the U.S.
Geological Survey and Others, Third Edition. Washington, D. C.: U.S. Department of the
Interior, Geological Survey, U.S. Government Printing Office. Pp. 80-87.
Chapter 9 – Page 15
More than one non-latitude/longitude system. If you need to record coordinates
for records using more than one non-latitude/longitude coordinate system, you
should consider using a single field for each system. (The 80 characters allowed for
each field should be sufficient.) Here is an example for Latitude and Longitude,
UTM, TRS, and the State Plane System (a third system used for US States), with
data for a site in Colorado. (The TRS data are in the format required for the
transformation program TRS2LL; see the Note in the section “Converting NonLatitude/Longitude Coordinates to Latitude and Longitude,” later in this chapter)).
Alternatively, you could use Locality Auxiliary Fields (see Chapter 16, “User-Defined
Auxiliary Fields and the Project System”), defined as you wish, but they will not
appear on standard Biota labels and reports (see “Latitude/Longitude and Alternate
Coordinates on Labels or Reports and in Exported Text Files” later in this chapter).
Converting Non-Latitude/Longitude Coordinates to Latitude and Longitude
Biota itself does not convert non-latitude/longitude coordinates (or TRS data) to latitude
and longitude, or the reverse. Utility programs exist to do so, however, and Biota’s data
import-export tools make it painless to get data in and out of your Biota Data File for
such conversions.
Take the following steps to convert non-latitude/longitude coordinates to latitude and
longitude. (The reverse process is analogous.)
1. Enter the non-latitude/longitude coordinates in the Alternate Coordinate fields.
2. Use the Export Editor to export the coordinate data to a text file (see Chapter
27, “Exporting Data”). Export only Locality Code and the appropriate Alternate
Chapter 9 – Page 16
Coordinate fields for each Locality record affected—plus Country, State/Province,
and or District (County) if needed by the conversion utility.
NOTE: If the non-latitude/longitude coordinate data are in Locality Auxiliary Fields,
use the Export Auxiliary Fields tool instead of the Export Editor (see “Exporting
Auxiliary Field Values” in Chapter 16.)
3. Using a utility program with the text file as input, transform the map
coordinates to Latitude and Longitude. The Latitude and Longitude values must
be in decimal degrees. It they are not, you will need to transform them to decimal
degrees using the formulas in the section “Conversion formulas for latitude and
longitude unit systems” earlier in this chapter.
4. Use the “Import Update” capability of Biota's Import Editor (see Chapter 28,
“Importing Data”) to add the Latitude and Longitude data to the existing Locality
records, leaving the Alternate Coordinate data intact.
NOTES:
a. To transform UTM to Latitude and Longitude or the reverse (as well as to and
from State Plane coordinates, for specific ellipsoids), an easy-to-use, interactive
shareware program by John Banta, called “Coordinate Transform,” is available
from SeisSoft Co. at www.connect.net/jbanta/Welcome.html. A commercial, filebased version is also available. The U.S. Geological Survey also offers a variety of
software for cartographic transformations (available through www.usgs.gov).
b. To translate TRS data into latitude and longitude or the reverse, for most U.S.
Public Lands states, a freeware program called TRS2LL is available from Martin
Wefald (http://www.geocities.com/jeremiahobrien/trs2ll.html). The
Latitude/Longitude output (for estimated Section centers) is already in decimal
degrees, but you must add the minus sign to all longitude values to indicate
location in the Western Hemisphere (TRS is endemic to the U.S.), before importing
into Biota.
Chapter 9 – Page 17
Latitude/Longitude and Alternate Coordinates on Labels
or Reports and in Exported Text Files
For geographic reference data on Locality labels that Biota prints or exports, and in the
standard printed report for the Locality table, you can choose between either Latitude
and Longitude (expressed in the Degrees/Minutes/Seconds system, see “Latitude and
Longitude (Locality Table)” earlier in this chapter) or Alternate Coordinate field values.
To print or export label data that includes Alternate Coordinates on pin, slide,
or vial Locality labels or herbarium labels (see Chapter 15, “Printing Labels”) take
the following steps:
1. Set the display format in the Coordinates tab of the Preferences screen
(Special menu) to the Alternate Coordinates option, as shown in the section
“Setting the Display Format for Alternate Coordinates in the Locality Record
Listing Screen” earlier in this chapter.
2. Create a Specimen Record Set that includes the Specimen records for which
you want to print or export data for Locality labels.
3. Choose a Locality label style for Specimens from the Labels menu. (The
Specimen Locality label tools are “Pin Labels: Locality,” “Slide Labels: Locality,”
“Vial Labels: Locality,” and “Herbarium Labels.”) An option screen appears.
4. Click the Alternate Coordinates option to enable the Alt Coordinate field
checkboxes.
If you have defined Aliases for the Alternate Coordinate fields, the Aliases appear
in the option screen by the checkboxes, instead of the default Alternate
Coordinate field names. (See Chapter 18, “Renaming Fields.”)
5. Check the checkbox for each of the three fields you want to include on the
labels or report, as shown above.
WARNING: It is up to you to ensure that the data you intend to show on labels or a
Locality report can be accommodated in the space available.
Chapter 9 – Page 18
To print or export label data that includes Latitude and Longitude for pin, slide,
or vial locality labels or on herbarium labels (see Chapter 15, “Printing Labels”), you
can use either of two methods:
Either: Set the display format in the Coordinates tab of the Preferences screen
(Special menu) to either of the Latitude/Longitude options, as shown in the
section “Setting the Display Format and Internal Resolution for Latitude and
Longitude” earlier in this chapter.
Or: Follow the steps, above, for printing Alternate Coordinates but choose the
Latitude/Longitude (default) option in Step 4, above.
To include Alternate Coordinate data in exported Collection label data, see the
instructions in Chapter 15, “Printing Labels.”
To include Alternate Coordinate data in exported Specimen flatfiles or Loan
records, check the appropriate boxes in the “Export Specimen Flatfile” setup
screen (see “Exporting Specimen Flatfiles” in Chapter 27).
To include Alternate Coordinate data in exported Specimen Web pages, check
the appropriate boxes in the “Specimen Fields” options screen (see Chapter 33,
“Exporting Static Web Pages”).
To display Alt Coordinate fields in the Locality Record Listing screen, in
addition to Latitude and Longitude, see the section “Changing the Fields
Displayed in a Record Listing Screen” in Chapter 10.
To include Alternate Coordinates on the standard printed Locality Report, set
the display format in the Coordinates tab of the Preferences screen (Special menu)
to the Alternate Coordinates option, as shown in the section “Setting the Display
Format for Alternate Coordinates in the Locality Record Listing Screen” earlier in
this chapter.
Chapter 10
Working With Records
In Record Listing and Input Screens
Every Core table in Biota (see “Core Tables” in Chapter 3) uses the same standard
format for listing records. These Record Listing screens all share many functions that are
explained in detail in this chapter. Once you know how to use the standard Record
Listing screen for one Biota Core table, you know how to use them all.
Biota also uses two other kinds of screens to list records, which differ in some important
ways from the standard Record Listing screens for Core tables. These are explained in
other chapters.
Record Listing screens for Auxiliary Fields. See Chapter 16, “User-Defined
Auxiliary Fields and the Project System,” if you need help with viewing or
manipulating information in Auxiliary Fields.
Record Listing screens for Images. See Chapter 19, “Images,” if you need help
working with Image Listing screens.
In the rest of this chapter, the term Record Listing screen refers the standard Record
Listing screen.
Displaying Records in a Standard Record Listing Screen
Biota offers many tools for finding records (see Chapter 12, “Finding and Updating
Records” and Chapter 13, “Creating, Finding, and Updating Specimen Series”). For
every tool in the Find menu (and the record-finding tools in the Series menu), records
are displayed in the standard Record Listing screen for the appropriate table.
Chapter 10 – Page 2
Here are the Genus records for a group of records for Galápagos Finches, shown in the
Genus Record Listing screen.
Changing the Fields Displayed in a
Record Listing Screen
You can change the fields displayed in certain columns of the Specimen, Species,
Collection, and Locality Record Listing screens. The columns are labeled Variable Field
1 and Variable Field 2 (as well as 3 and 4, in the Locality Record Listing screen). You
control the display using the button labeled “Change Var Fields” found at the base of the
Record Listing screen.
For example, to change the fields displayed in the Specimen Record Listing screen,
follow these steps. (The procedure is identical for the Species, Collection, and Locality
Record Listing screens.)
1.
Display any selection of records in the Specimen Record Listing screen, using
tools from the Input, Series, Find, or Display menus.
Notice the labels Var Field 1 and Var Field 2 above
the columns that currently display the [Specimen]
Method and [Specimen] Stage/Sex fields (the default
fields displayed in these columns).
2.
To change the fields displayed, click the “Change Var Fields” button, found on
the lower left of the Record Listing screen.
Chapter 10 – Page 3
The Variable Fields selection window appears, showing the current field for each of
the two Var Field columns in the Record Listing screen.
3.
From the popup lists in the field
selection window, choose the fields
you want to display.
The selection of records is re-displayed, showing the fields you selected for display
([Collection] Date Collected and [Collection] Locality Code, in the example below).
NOTE: Each time you launch Biota, all Variable Fields in Record Listing screens are set
to the default fields (see the next section, “Fields Available for Display in Record Listing
Screens”). If you change the fields displayed using the method above, the changes
remain in effect for the duration of the current Biota session unless you change them
again. (With Biota4D running under 4D Server, each Client has independent control over
Variable Fields.)
Fields Available for Display in Record Listing Screens
The previous section, “Changing the Fields Displayed in a Record Listing Screen,”
explains how to use the Variable Fields feature of the Specimen, Collection, Locality,
Chapter 10 – Page 4
and Species Record Listing screens. Here are the fields you can display for each of
these screens.
NOTE: In the lists that follow:
(a) An asterisk indicates a field that can be re-named using the Core Field Alias
(see Chapter 18, “Renaming Fields”). If you have defined an Alias for such a field,
the Alias, not the Internal Field Name listed below, appears in the popup lists for
field selection as well as in the Record Listing screen header.
(b) A number symbol (#) indicates a
“Record Changed By” field. These
fields are available only if the checkbox
“Show Record Changed By field in Input
screens” is checked in the “Admin
Settings” tab of the Preferences screen (Special menu).
In the Specimen Record Listing screen, you can display any of the following 20
fields in either of two Variable Field columns:
◊
Fields of the Specimen table: Species Code, Determined By, Date Determined,
Prepared By, Date Prepared, Stage/Sex*, Medium*, Specimen Custom 1*,
Specimen Custom 2*, Type Status*, Abundance, Specimen Record Date,
Specimen Record Changed Date, and Specimen Record Changed By#.
◊
Fields of the Collection table: Locality Code, Date Collected, Collection
Method*, Site*, Source*, and Host Specimen Code.
◊
Default fields: [Collection] Method* and [Specimen] Stage/Sex*.
In the Collection Record Listing screen, you can display any of the following 17
fields in either of two Variable Field columns:
◊
Fields of the Collection table: Locality Code, Collection Method*, Site*,
Source*, Host Specimen Code, Collection Record Date, Collection Record
Changed Date, and Collection Record Changed By#.
◊
Fields of the Locality table: District*, State/Province*, Country*, Elevation*,
Latitude (in decimal degrees), Longitude (in decimal degrees), Alt Coordinate 1*,
Alt Coordinate 3*, and Alt Coordinate 3*.
◊
Default fields: [Collection] Method* and [Collection] Site*.
In the Locality Record Listing screen, you can display any of the following 12
fields in any of four Variable Field columns:
◊
Fields of the Locality table: District*, State/Province*, Country*, Elevation*,
Latitude (in decimal degrees), Longitude (in decimal degrees), Alt Coordinate 1*,
Alt Coordinate 2*, Alt Coordinate 3*, Locality Record Date, Locality Record
Changed Date, and Locality Record Changed By#.
◊
Default fields: [Locality] District*, [Locality] State/Province*, [Locality] Country*,
and [Locality] Elevation*.
In the Species Record Listing screen, you can display any of the following 21
fields in either of two Variable Field columns:
◊
Fields of the Species table: Species Author, Subgenus*, Section*, Subspecies,
Subspecies Author, Variety, Variety Author, Common Name*, Distribution*, Type
Locality*, Type Depository*, Valid Sp Code, Species Record Date, Species
Record Changed Date, and Species Record Changed By#.
Chapter 10 – Page 5
◊
Fields of the Genus table: Family, Tribe*, Subfamily*, Genus Custom 1*, Genus
Custom 2*, and Genus Custom 3*.
◊
Default fields: [Genus] Family and [Species] Subgenus*.
Viewing, Editing, Printing, or Deleting Individual
Records from an Input Screen
To open an individual record from the Record Listing screen for any Core table, simply
double-click the record (or use keyboard shortcuts to select and open the record; see
“Keyboard Shortcuts for Record Listing Screens” later in this chapter).
The record for the genus Geospiza is being double-clicked in the example in the
illustration in the previous section. The record appears in the Input (single-record) screen
for the table.
With the record open in the Input screen, you can view the record, edit any field in the
record and save the changes, duplicate (Carry) the record, print it, delete it, or access
linked records in the parent table (the Family table, in the example) or the child table
(Species, in the example).
Some Input screens, like the Genus screen above, consist of a single page. Others,
such as the Species input screen below, consist of several pages, accessed by a series
of tabs. (You can use keyboard shortcuts to move between tabs in these screens. See
“Keyboard Shortcuts for Input Screen Tabs” in Chapter 7.)
Chapter 10 – Page 6
To View an Entry That Is Longer Than the Entry Area
In Biota Input screens, the entry area for some
fields are too short to display a very long entry
in full. To view the entire entry, click the
“zoom” icon placed just to the right of the entry
area. Biota shows the full entry in a special
window.
Chapter 10 – Page 7
To Return to the Record Listing Screen
To dismiss a record displayed in an Input screen and return
to the Record Listing screen, without making any changes in
the record, click the “Cancel” button. Biota returns you to the
Record Listing screen, with the record selected.
KEYBOARD SHORTCUT: Instead of clicking the “Cancel” button,
simultaneously press the CTRL and ENTER keys (Windows) or
the COMMAND ( ) and RETURN keys (Mac OS).
Editing and Saving Changes to the Record
To edit a field, click in the field and use standard editing techniques. Any changes you
make can be saved by either of two methods:
Either: Click the “Save” button. In this case, Biota saves all changes and
returns you to the Record Listing screen, with the same record selected.
Or: Click any of the Navigation buttons. To accept any changes and move to
another record in the current selection, click any button in the “Navigate Records”
panel (the arrow buttons). This action automatically saves any changes.
KEYBOARD SHORTCUTS: Instead of clicking the “Save” button, simultaneously press the
CTRL and S keys (Windows) or the COMMAND ( ) and S keys (Mac OS). To move to the
next record, press the CTRL and RIGHT ARROW keys (Windows) or the COMMAND ( ) and
RIGHT ARROW keys (Mac OS). To move to the previous record, press the CTRL and LEFT
ARROW keys (Windows) or the COMMAND ( ) and LEFT ARROW keys (Mac OS).
NOTE: If the “Save,” “Carry,” and “Delete” buttons are
dimmed on the Input screen, it means you do not have
Write privileges. The record is in Read-only mode. You
must either click “Cancel” or a navigation button to dismiss
the record (or use the keyboard equivalent).
Chapter 10 – Page 8
Duplicating a Record Displayed in the Input Screen
Using the “Carry” Button
Every Input screen includes a “Carry” button that allows you
to make a new record using the current record as a
template. Because, in many cases, only one or two fields
need changing between a template record and a new one,
this capability saves a great deal of effort.
1. Click the “Carry” button in the Input screen. A new
record appears with the Key field (see “Key Fields” in
Chapter 3) blank but all or most other fields (depending on
the table) already filled in with the same information as the
existing record. (The record below uses the Geospiza
record as a template.)
2.
Enter a new value for the Key field. You can also change any other fields you
wish in the new record.
Either: Click the “Save” button to accept the new record and return to the
Record Listing screen.
Or: Click the “Carry” button again to accept the new record and use it as a
template for an additional new record.
In either case, if you have made any changes in the current record or it is a new
record, the template record is saved first, automatically, when you click the “Carry”
button.
Notes:
a. A saved, existing record can also be used as a template. See “Using an Existing
Record as a Template for a New Record” later in this chapter.
b. Auxiliary Fields and Notes can be carried or not, according to a setting in the “Other
Settings” tab of the Preferences screen (Special menu). See “Carrying Auxiliary
Fields” in Chapter 16 and “Carrying Notes” in Chapter 11.
KEYBOARD SHORTCUT: Instead of clicking the “Carry” button, simultaneously press the
CTRL and K keys (Windows) or the COMMAND ( ) and K keys (Mac OS).
Printing a Single Record Displayed in an Input Screen
Click the “Print” button in the Input screen to print the information for the record shown in
the Input screen, using the standard report format for the table. (See Chapter 14,
“Printing Reports” for other printing options.)
KEYBOARD SHORTCUT: Instead of clicking the “Print” button, simultaneously
CTRL and P keys (Windows) or the COMMAND ( ) and P keys (Mac OS).
press the
Chapter 10 – Page 9
Deleting a Record Displayed in the Input Screen
1.
Click the “Delete” button.
2.
Confirm or Cancel the deletion. Unless the record is a new one that has not yet
been saved, Biota presents you with one of two kinds of warnings.
For tables that have no linked Images, Auxiliary Fields, Notes, and/or
References, such as the Genus table, Biota presents a simple warning.
For tables that have associated Notes, Auxiliary Fields, or Image records
(the Species, Specimen, Collection, Locality, and Loans tables), deleting a record
automatically deletes any linked child records in Peripheral tables (Images,
Auxiliary Fields, Notes, and/or Reference links, plus Determination History
records linked to Specimen records). In such cases, Biota presents the warning
below.
Chapter 10 – Page 10
3.
Confirm or Cancel the orphaning of Core table child records. If the record is
linked to one or more child records in other Core tables (but not otherwise), Biota
also posts the warning below, with the appropriate table names (Genus and
Species, in this example). (For information on displaying linked records, as
suggested in the warning, see “Displaying Records With a Child Records Button”
later in this chapter.)
4.
Deleting a Personnel Record. In the case of Personnel records, which may be
linked to child records in several Core and Peripheral tables, the warning screen is
more complex.
KEYBOARD SHORTCUT: For safety’s sake, there is no keyboard shortcut for the “Delete”
button.
Chapter 10 – Page 11
Moving Up the Table Hierarchies from an Input Screen:
Parent Record Buttons
With an individual record open in the Input screen, you can display and edit the related
parent record by clicking the “Show…” button with the name of the parent table. These
buttons are referred to collectively as Parent Records buttons, although each button has
its own name (e.g., “Show Family” in the Genus Input screen, “Show Locality” in the
Collection Input screen). (See “Linking Fields: Parent and Child Records” in Chapter 3
for the definition of a parent table.)
Parent Record buttons are available on the Input screen for each level (rank) of the
taxonomic hierarchy, with the exception of Kingdom, which has no parent table. The
Specimen Input screen has Parent Record buttons for both Species and Collection, and
the Collection Input screen has a Parent Record button for Locality. Locality has no
parent table, so it has no Parent Record button.
Displaying Records with the Parent Record
Button
For example, with the genus record for Geospiza
open in the Genus Input screen (right), the principal
fields from the linked Family record (Fringillidae) are
shown in the “Classification” panel of the Genus
Input screen. To see the full record for Family
Fringillidae, click the “Family” button. (The Genus
record remains open in its own window.)
The full record for the Family Fringillidae then
appears in the Family Input screen (below).
Information from the related Order record (for Order
Passeriformes) appears in the “Classification” panel
of the Family Input screen. Click the “Show Order”
button to see the full record for the Order
Passeriformes.
If you want, you can continue on up the taxonomic
hierarchy by clicking Parent Record buttons. To return
to the original record, click the “Cancel” button—or the
“Save” button, if you have made changes.
Chapter 10 – Page 12
KEYBOARD SHORTCUT: Instead of clicking a Parent Record button, simultaneously press
the CTRL and UP ARROW keys (Windows) or the COMMAND ( ) and UP ARROW keys (Mac
OS). For the Specimen Input screen, those shortcuts apply to the “Show Species”
button; for the “Show Collection” button simultaneously press the ALT and UP ARROW
keys (Windows) or the OPTION ( ) and UP ARROW keys (Mac OS)
Editing Records Displayed with the Parent Record Button
You can open a parent record using the Parent Record button, edit it, and save any
changes by clicking the “Save” button in the Input screen for the record you edited.
Moving Down the Table Hierarchies From an Input
Screen: Child Records Buttons
With an individual record open in the Input screen,
you can display all related records in the next lower
table in the hierarchy (child records) by clicking the
“Show…” button with the name of the child table. In
the example at the right, the “Show Species” button is
being clicked. (See “Linking Fields: Parent and Child
Records” in Chapter 3 for the definition of a child
table.)
These buttons are referred to collectively as Child
Records buttons, although each button has its own
name. For example, the Child Records button in the
Family Input screen is labeled Genera, whereas the
Child Records button in the Locality Input screen is
labeled Collections. (See Appendix A, “Biota Tables,
Fields, and Relational Links,” for table hierarchies.)
Child Records buttons are available on the Input
screen for each level (rank) of the taxonomic
hierarchy, as well as for the Locality and Collection
Input screens. The Specimen table has no child tables
(among the Core tables), so the Specimen Input
screen has no Child Records button.
Biota displays a number next to each Child Records
button, showing the number of child records for the parent record currently displayed. In
the example above, the “Show Species” button indicates that 6 Species records are
linked to the Genus record for Geospiza.
If there are no child records, the number displays zero and the Child Records button is
disabled.
Chapter 10 – Page 13
When you display child records using a Child Records button, they appear in an the
standard Record Listing screen in a new window. Meanwhile, the parent record remains
open in its own window. You can close the parent window if you want, and the Child
Records window will remain open.
Displaying Records with a Child Records Button
For example, with the genus record for Geospiza open in the Genus Input screen, the
“Show Species” button is enabled, and the number in the parentheses in the button text
shows that there are six Species records linked to Geospiza.
If you click the “Show Species” button, the six species of Geospiza finches are displayed
in the Species Record Listing screen.
If you wish, you can now open and edit any of the child records listed to view or edit, or
repeat the process by displaying the child records (Specimen records, in this example)
for one of the Species displayed.
To return to the parent record (Geospiza, in the example), click the “Done" button on the
child table Record Listing screen (above).
KEYBOARD SHORTCUT: Instead of clicking a Child Record button, simultaneously press
the CTRL and DOWN ARROW keys (Windows) or the COMMAND ( ) and DOWN ARROW keys
(Mac OS).
Chapter 10 – Page 14
Using the Add Record Button
The Add Record button at the base of the Record Listing screen for each Core table
opens a new, blank record in the Input screen for the table. Although these buttons are
referred to collectively as Add Record buttons, each button has its own name. For
example, the Add Record button in the Genus Record Listing screen is labeled “Add
Genus,” the Add Record button in the Collection Record Listing screen is labeled “Add
Collection,” and so on for each Core table.
Once the Input screen is displayed by clicking an Add Record button, you can complete
the new record. Click the “Save” button to accept the new record and return to the
Record Listing screen, the “Carry” button to accept the new record and use it as a
template for an additional new record, or Cancel to dismiss the Input screen without
saving the new record.
In fact, adding a new record in this way is exactly like adding a new record using a
command from the Input menu (see Chapter 11, “Input—Table by Table”), with one
exception. With the Add Record approach, when you are done entering data in the
record and click the “Save” button you are returned to the Record Listing screen, with
the new record highlighted. To add another record, click the Add Record button again.
(From the Input menu, the “Save” button accepts the record and presents a new, blank
record.)
KEYBOARD SHORTCUT: Instead of clicking an Add Record button (for example, the “Add
Genus” button illustrated above) in a Record Listing screen, simultaneously press the
CTRL and J keys (Windows) or the COMMAND ( ) and J keys (Mac OS).
Using an Existing Record as a Template for a
New Record
Sometimes you need to create a new record that duplicates much of the information in
an existing record listed in the Record Listing screen. You can use the existing record as
a template for the new one.
1.
Double-click the existing record in the Record Listing screen. The existing
record opens in the Input screen. Make no changes in the existing record.
2.
Click the “Carry” button in the Input screen. A new record appears, with the Key
field blank, but with all, or most, other fields (depending on the table) already filled in
with the same information as the existing record. (The record below uses the
Geospiza record as a template.)
Chapter 10 – Page 15
3.
Enter a new value for the Key field. You can also change any other fields you
wish in the new record.
Either: Click the “Save” button to accept the new record and return to the
Record Listing screen.
Or: Click the “Carry” button again to accept the new record and use it as a
template for an additional new record.
NOTE: As another variation, you can open an existing record, make changes in the
existing record, then click Carry to accept the edited record and use it as a template for a
new record.
Creating a Sub-Selection of Records
Often, you will want to select one or more of the records displayed in a record Listing
screen and dismiss the rest of the records. To do this, you use the “Sub-Selection”
button at the bottom of the Record Listing screen.
1.
Select the records that will form the new Sub-Selection.
To select a single record, click it once to highlight it.
To select consecutive records, click the first record of the group once to
highlight it, then press and hold the SHIFT key and click the last record in the
group.
To select nonconsecutive records, click the first record once to highlight it.
Then press and hold the CTRL key (Windows) or the COMMAND ( ) key
(Macintosh) while single-clicking each additional record you want to select.
KEYBOARD SHORTCUTS: For information on keyboard shortcuts for selecting records
from Record Listing screens, see “Keyboard Shortcuts for Record Listing Screens”
later in this chapter.
2.
Click the “Sub-Selection” button when all the records you want to include in the
Sub-Selection are highlighted.
The Record Listing subsequently displays only the records in the Sub-Selection.
KEYBOARD SHORTCUT: Instead of clicking the “Sub-Selection” button,
simultaneously press the CTRL and N keys (Windows) or the COMMAND ( ) and N
keys (Mac OS).
Chapter 10 – Page 16
3.
To designate the Sub-Selection as the current Record Set for the table, click the
“Done” button, then the “OK” button in the standard Record Set option screen (see
“The Record Set Options Screen” in Chapter 3).
Deleting a Group of Records from the
Record Listing Screen
In the Record Listing screen, you can select records and delete them using the “Delete
Selection” button.
NOTE: The database Administrator can set a limit on the number of records that can be
deleted at each use of the “Delete Selection” button, to prevent accidental deletion of
large numbers of records. See “The ‘Admin Settings’ Tab” in Appendix B.
1.
Select the records that will form the new Sub-Selection.
To select a single record, click it once to highlight it.
To select consecutive records, click the first record of the group once to
highlight it, then press and hold the SHIFT key and click the last record in the
group.
To select nonconsecutive records, click the first record once to highlight it.
Then press and hold the CTRL key (Windows) or the COMMAND ( ) key
(Macintosh) while single-clicking each additional record you want to select.
KEYBOARD SHORTCUTS: For information on keyboard shortcuts for selecting records
from Record Listing screens, see “Keyboard Shortcuts for Record Listing Screens”
later in this chapter.
2.
Click the “Delete Selection” button when all the records you want to delete are
highlighted.
KEYBOARD SHORTCUT: For safety’s sake, there is no keyboard shortcut for the
“Delete Selection” button.
Chapter 10 – Page 17
3. Confirm or Cancel the deletion. Biota
displays two kinds of warnings.
For tables that have no linked Images,
Auxiliary Fields, Notes, and/or
References, such as the Genus table,
Biota presents a simple warning.
For tables that have associated Notes,
Auxiliary Fields, or Image records (the
Species, Specimen, Collection, Locality, and Loans tables), deleting a selection
of records automatically deletes any linked child records in Peripheral tables
(Images, Auxiliary Fields, Notes, and/or Reference links, plus Determination
History records linked to Specimen records). In such cases, Biota presents a
warning like this.
4.
Decide whether to orphan Core table child records. If the records to be deleted
are linked to one or more child records in other Core tables (but not otherwise),
Biota also posts the following warning, with the appropriate table names (Genus
and Species, in this example).
If you see this warning, you can Cancel the deletion; choose to delete only those
selected records that are not linked to any Core table child records; or delete all the
selected records anyway, leaving some records orphaned.
Chapter 10 – Page 18
NOTE: If you choose the second option (delete all selected records, even though
some child records will be orphaned), you can find the orphaned records later using
the “Find Orphan records” tool from the Find menu.
5.
Deleting Personnel records. In the case of Personnel records, which may be
linked to child records in several Core and Peripheral tables, the warning screen is
more complex. Before deleting a group of Personnel records, you should consider
whether you really intend to lose all the links listed in the warning screen.
Sorting Records in Record Listing Screens
To sort the records displayed in a record Listing screen, you use the Sort Editor
displayed by clicking the “Sort” button at the bottom of the Record Listing screen. The
Species Record Listing screen will be used as an example in this section, but the
procedures are the same for all Record Listing screens.
1.
Click the “Sort” button at the bottom of the Record Listing screen.
KEYBOARD SHORTCUT: Instead of clicking the “Sort” button in a Record Listing
screen, simultaneously press the CTRL and R keys (Windows) or the COMMAND ( )
and R keys (Mac OS).
Chapter 10 – Page 19
The Sort Editor (“Order by”) window appears.
In the “Available Fields” panel on the left, you will see the names of all fields for the
current table (the Species table, in the example). Field names in boldfaced type are
indexed fields, which sort faster than non-indexed fields, but you can sort on any
field. (Indexes take up space in data files and require processor time to maintain, so
not all fields in Biota are indexed.)
NOTE: If you have defined any Core Field Aliases (see Chapter 18, “Renaming
Fields”) the field aliases appear in the list instead of the default field names.
2.
To sort on a field for the current table (Species, in the example), double-click a
field name in the “Available Fields” panel, or select the field name and click the
“insert” button (the blue, right-pointing triangle). The “Species Author” field is being
selected in the example below.
Chapter 10 – Page 20
The field name appears in the “Ordered by Fields/Formula” panel on the right, with
an upward-pointing triangle to the right of the field name. This is the sort direction
indicator. (Notice also that the “remove” button (the red, left-pointing triangle) and
the “remove all” button (the red, left-pointing double triangle) are activated.
An upward sort direction indicator (above) means a normal alphanumeric sort
(0 to 9, then A to Z).
A downward sort direction indicator (below) means a reverse alphanumeric
sort (Z to A, then 9 to 0).
3.
Changing the direction of a sort. Click the
sort direction indicator to toggle between
normal and reverse sorts.
4.
Removing a sort level. If you make a
mistake and want to remove a sort level from
the list of sort criteria, select the sort level
you want to remove (click once on it to
highlight it), then click the “remove” button
(the red, left-pointing triangle). To remove all
fields at once, click the “remove all” button
(the red, left-pointing double triangle).
5.
Adding additional sort levels. To add an
additional level to the sort criteria, click
another field name in the field name panel,
as in Step 2. The sort proceeds
hierarchically from the top of the list of sort
criteria to the bottom. In the example
below, Species records will be sorted
alphabetically by Genus within those
described by each Species Author.
6.
Launching the Sort. When all sort criteria are ready, click the “Order by” button at
the bottom of the Sort Editor (“Order by”) window to launch the sort.
Chapter 10 – Page 21
Using Fields from Related Tables for Sorting Records
You can use fields from related (linked) tables as sort criteria, as long as a child-parent
relation exists between the current table (the table whose records you are sorting) and
the table you use to add a sort criterion. For example, in sorting Species (child table)
records, you can use fields from the Genus table (parent table).
NOTE: This section assumes you are familiar with the previous section of this chapter,
“Sorting Records in Record Listing Screens.”
1.
Display the fields for the related (parent) table by clicking on the list expansion
icon (blue triangle) next to the name of the linking field in the current table. In the
example below, the Sort Editor (“Order by”) screen has been displayed for the
Species table, and the list expansion icon is being clicked for the Genus field in the
“Available Fields” list.
The list of fields for the related table (the Genus table, in the example below) is
displayed.
Chapter 10 – Page 22
2.
Select a sort field from the related table. Once the fields for the related table
appear in the field list, you can add fields as sort criteria, using the same techniques
described in the section “Sorting Records in Record Listing Screens” earlier in this
chapter.
3.
Mixing sort criteria from different tables. You can mix sort criteria from related
tables. In the example below, Species records will be sorted alphabetically by
Species Author (a field from the Species table), then within authors by Family (a
field from the Genus table), then within Families by Genus (using the Genus field
from the Species table).
NOTE: When you have a choice between using a linking field in a child table and
Key field in a parent table as a sort criterion, the sort will be faster if you use the
linking field in the child table. In the example above, the [Species] Genus field was
added to the list instead of the [Genus] Genus field. It does not really matter which
way you do it, however, and the difference in sort speed will not be noticeable
unless there are many records.
Guidelines for Using Fields from Related Tables as Sort Criteria
It is up to you to ensure that a sort on a field in a related table makes sense. Here are a
few guidelines:
You cannot sort the records in a parent table based on a field in a child table.
For example, you cannot sort Species records based on a field in the Specimens
table. It makes no sense to sort Species records according to any field in the
Specimens table, since there may be different values in Specimen fields for different
specimens of the same Species.
You cannot sort the records of a table in one hierarchy (e.g., the taxonomic
hierarchy) based on a field in the other hierarchy (the place hierarchy). It makes
no sense to sort Species records, for example, by the Locality Name field of the
Locality table, since a species may have specimens from many localities.
Consult Appendix A, “Biota Tables, Fields, and Relational Links,” if you are unsure how
Biota tables are linked.
Using Formulas to Sort Dates by Day, Month, or Year
If you sort on a date field (e.g., [Collection] Date Collected) in the usual way (see
“Sorting Records in Record Listing Screens” earlier in this chapter), Biota sorts records
chronologically according to complete dates. Sometimes you may want to use partial
dates to perform a sort. To study seasonal patterns, for example, you might want to sort
by month, disregarding year and day of the month.
NOTE: This section assumes you are familiar with the previous section of this chapter,
“Sorting Records in Record Listing Screens.”
Chapter 10 – Page 23
1.
Display the records to be sorted in the Record Listing screen. Suppose you
want to sort Collection records by month of collection, ignoring years and days.
2.
Click the “Sort” button at the bottom of the Record Listing screen. The Sort
Editor (“Order by”) screen appears.
3.
Click the “Add Formula” button near the bottom of the Sort Editor (“Order by”)
screen.
The 4D Formula Editor appears.
Chapter 10 – Page 24
You can re-size the Sort Editor (“Order by”) screen or the Formula Editor
screen by dragging on the right and/or lower border.
The upper panel of the Formula Editor is the formula entry area, where you
construct the Sort (“Order by”) formula. You can type all entries in this area
manually if you wish. In this example, we will construct the sort criterion: “Month
of ([Collection] Date Collected).”
To enter mathematical operators, you can use the row of buttons just above
the formula entry panel.
The lower left panel, labeled “Related Tables,” lists the fields available for
use in the constructed formula. The default list is identical to the “Available
Fields” list in the main Sort Editor (“Order by”) screen, and it works the same way
as that list for related tables. (See “Using Fields from Related Tables for Sorting
Records” earlier in this chapter.)
The lower right panel, labeled “Commands by Themes,” offers a series of
command groups with boldfaced titles. If you click and hold down the mouse
button on one of these boldfaced titles, a popup list of commands appears.
Chapter 10 – Page 25
4.
Find the boldfaced item “Date and Time” in the “Commands by Themes”
panel. Click on the item and hold the mouse button down. A popup list of date and
time functions appears.
5.
Click “Month of,” “Day of,” or “Year of,” as required for the formula. The
function will be entered in the formula entry area. In the example above, the “Date
and Time” category is being clicked, and the “Month of” command is being selected
with the mouse. The command appears in the formula entry area.
6.
Enter a left parenthesis using an operator button, or type it on the keyboard.
7.
In the “Related Tables” panel, showing fields available, click a date field. In the
example, the [Collection] DateCollected field is being clicked.
8.
Enter a right parenthesis using an operator button, or type it on the keyboard. In
the example, the formula now reads: “Month of ([Collection] Date Collected).”
9.
Click the “OK” button in the Formula Editor. The Formula Editor is dismissed
and the Sort Editor (“Order by”) screen reappears with the formula entered in the
“Ordered by Fields/Formulas” panel. (You cannot type it in directly in this area.)
Chapter 10 – Page 26
10. If you need to edit a formula, select it in the
“Ordered by Fields/Formulas” panel and click
the “Modify” button below the panel.
11. When the formula is entered correctly, click
the “Order by” button on the Sort Editor
(“Order by”) screen.
12. Saving and loading formulas. Notice that the Formula Editor includes “Save” and
“Load” buttons. If you use a complicated formula often, you might want to save it to
a disk file and reload it when you need it.
CRITICAL WARNING: There are hundreds of other 4D
commands and nearly 2000 Biota methods listed in
the “Commands by Themes” list that appears in the
Formula Editor. There are a few other functions that
users familiar with 4D might use, but under no
circumstances attempt to use any of the italicized
Biota methods in a formula. You may do irreparable
damage to your data file if you do so.
Using a Formula to Sort
Numbers in an Alphanumeric Field
Sometime, you may choose to use an alphanumeric field for numerical data. (See
Appendix A, “Biota Tables, Fields, and Relational Links,” for information on Biota field
types.) For example, a plant ecologist might re-name the [Specimen] Medium field DBH
and use it to record the diameter at breast height (dbh) of living trees in a quadrat-based
study.
Using an alphanumeric field for numerical data causes no problems for data entry or
display, but if you sort on an alphanumeric field, Biota sorts by ASCII code, left to right.
This means that the numbers 1, 2, 3, 9, 10, 20, and 30 will sort in the order 1, 10, 2, 10,
3, 30, 9.
To sort then numerically, you must use the Num function in a sort formula. (The Num
function ignores any non-numeric characters.)
NOTE: This section assumes you are familiar with the previous sections of this chapter,
“Sorting Records in Record Listing Screens” and “Using Formulas to Sort Dates by Day,
Month, or Year.”
Chapter 10 – Page 27
1.
Display the records to be sorted in the Record Listing screen for the table.
Suppose you want to sort Specimen records by numerical values in the [Specimen]
Medium field, for example.
2.
Click the “Sort” button at the bottom of the Record Listing screen. The Sort
Editor (“Order by”) screen appears.
3.
Click the “Add Formula” button at the bottom of the Sort Editor (“Order by”)
window. The Formula Editor appears.
4.
Review the introduction to the Formula Editor in the previous section (“Using
Formulas to Sort Dates by Day, Month, or Year”), if necessary.
5.
Enter the formula Num ([Field Name]). The easiest way to do this is to type Num
in the formula entry area, add an opening parenthesis, click the appropriate field
name in the “Related Tables” panel, then add the closing parenthesis to complete
the formula.
In the illustration below, the sort criterion Num([Specimen]Medium) was entered in
this way.
NOTE: Although any Biota Core field aliases you have set up (see Chapter 18,
“Renaming Fields”) appear in place of internal field names in the “Related Tables” panel
of the Formula Editor, when you double-click an alias to add a field to a formula, the
equivalent internal field name is entered instead of the alias. For example, even though
the field [Specimen] Medium had been re-named DBH, the formula uses the internal
field name, as shown in the illustration, above.
Printing Reports or Creating Text Files Based on
Records in a Record Listing Screen
For each Core table and for the Determination History table, Biota offers a preformatted
report that you can print, listing all records in the current Selection, including fields from
related tables where appropriate (see “Printing a Report Based on a Selection of
Records” in Chapter 14). Or, you can print the records using a custom report layout that
you design yourself using the Quick Report Editor (see “Designing and Printing Reports
with the Quick Report Editor” in Chapter 14). As a third option, you can use the Quick
Report Editor to export information from the records and related tables to a text flatfile
(see “Exporting Custom Flatfiles” in Chapter 27).
Printing a Report Based on Records in a record Listing Screen
1.
Display the records to be printed.
Chapter 10 – Page 28
2.
Click the “Print” button at the bottom of the Record Listing screen.
Alternatively, you can select Print from the File menu while the records are
displayed in the Record Listing screen.
KEYBOARD SHORTCUT: Instead of clicking the “Print” button in a Record Listing
screen, simultaneously press the CTRL and P keys (Windows) or the COMMAND ( )
and P keys (Mac OS).
3.
Choose a print option. A print option window appears offering two or three
choices, depending on the table for which you are printing records. (The
Determination History table has no options.) Three different option windows are
illustrated below.
Sort by [Record] Code before printing. Use this option to print a report with the
records sorted by Record Code (Species Code, Specimen Code, Collection
Code, or Locality Code). The Loans report can be sorted by Loan Code.
Print using the existing order. If you have used the Sort tool to create a special
order for the records that you want maintained in the report, choose this option.
Design and print a special report. If you choose this option, Biota presents the
4th Dimension Quick Report Editor, which you can use to design, save, and/or
load custom report formats that you create yourself (see “Designing and Printing
Reports with the Quick Report Editor” in Chapter 14). The report will be based on
the selection of records in the Record Listing screen when you clicked the “Print”
button or selected Print from the File menu.
Chapter 10 – Page 29
Sort taxonomically before printing. For records from taxonomic tables
(Species, Genus, Family, etc., and Specimen as well), this option prints the
records for the table in alphabetical order within taxonomic levels (ranks) in a
hierarchical report organized by rank (as in the table in the section “The
Relational Model” in Chapter 2).
Include Host data in the report. For the Specimen table, an additional option is
offered. If the “Include Host data” checkbox is checked, the report will include, for
each Specimen record, the Specimen Code of the Host for that specimen (see
Chapter 24, “Host-Guest Relations”).
NOTE: This option is automatically checked if any Specimen records in the
current selection have host data. Otherwise, it appears unchecked. In either
case, you can override the setting manually. The host data checkbox is disabled
when the “Design and print a special report” option is clicked.
4.
Click the “OK” button in the print option screen.
If you choose the standard Biota report, see “Printing and Previewing Procedures
for Reports and Labels” in Chapter 14.
If you choose Design and Print a Special Report, see “Designing and Printing
Reports with the Quick Report Editor” in Chapter 14
Exporting a Text Flatfile Based on Records in a Record Listing screen
1.
Display the records to be exported to a text file.
2.
Click the “Print” button at the bottom of the Record Listing screen.
Alternatively, you can select Print from the File menu.
3.
When the print option screen appears, choose “Design and print a special
report.” The option windows are illustrated in the previous section, “Printing a
Chapter 10 – Page 30
Report Based on Records in a Record Listing Screen.” Biota presents the Quick
Report Editor.
4.
Follow the instructions in the section “Exporting Custom Flatfiles” in Chapter 27.
Keyboard Shortcuts for Record Listing Screens
You can use keyboard shortcuts for most functions in Record Listing screens. Some are
always available and others must be enabled in the Preferences screen. (See also
“Keyboard Shortcuts for Input Screen Tabs” and “Keyboard Shortcuts for Input Screen
Buttons” in Chapter 7, summarized in Appendix C, “Keyboard Shortcuts.”)
Keyboard Shortcuts Always Available
The table below summarizes shortcuts that are always available in Records Listing
screens. The following section of this chapter, “Optional Keyboard Shortcuts,” describes
shortcuts available only if you enable them in the Shortcuts tab of the Preferences
screen (Special menu).
In the table below, shortcuts for on-screen buttons are indicated with a lavender
background, whereas shortcuts that do not correspond to an onscreen button are
indicated with a yellow background. Most of the button functions are described in
previous sections of this chapter, but a few are detailed in other chapters:
The “Aux Fields” button is described in Chapter 16, “User-Defined Auxiliary Fields
and the Project System.”
The “Scroll” and “Page” (“Display Images”) buttons are described in Chapter
19, “Images.”
FUNCTION
MAC OS
WINDOWS
“Done” button
RETURN
ENTER
“Print” button
COMMAND–P (
–P)
CTRL–P
“Sort” button
COMMAND–R (
–R)
CTRL–R
“Sub-Selection” button
COMMAND–N (
–N)
CTRL–N
Add Record button (e.g., “Add
Species")
COMMAND–J (
–J)
CTRL–J
“Aux Fields” button
(Core fields screens)
COMMAND–M (
–M)
CTRL–M
“Core Fields” button
(Auxiliary fields screens)
COMMAND–M (
–M)
CTRL–M
“Scroll” (Display Images) button
COMMAND–H (
–H)
CTRL–H
“Page” (Display Images) button
COMMAND–I (
Close screen (with Record Set Query
screen; same as “Done” button)
OPTION–W
Dismiss screen (bypassing the Record
Set Query screen)
COMMAND–HYPHEN (
HYPHEN)
–I)
CTRL–I
ALT–W
–
CTRL–HYPHEN
Chapter 10 – Page 31
Optional Keyboard Shortcuts
This section summarizes keyboard shortcuts for Record Listing screens that become
available only if you enable them in the Shortcuts tab of the Preferences screen (Special
menu), shown below. (See also Appendix B, “Setting Preferences”.)
In the “Keyboard shortcuts setting” panel, you indicate whether the shortcuts in
the table below are to be enabled (checkbox checked) or disabled (checkbox
empty).
In the “Scope of keyboard shortcuts settings” panel, you control the scope of
the setting in the “Keyboard shortcuts setting” panel.
◊
If you select the first option, “Keyboard settings for all users” (the default
setting), the keyboard shortcuts setting is saved between Biota sessions and
affects all users if you are running Biota4D under 4D Server.
◊
If you select the second option, “Keyboard settings for this user,” you must
reset your preferred keyboard shortcut setting each time Biota is launched, if it
differs from the setting most recently saved under the first option. With the
second option, any changes you make in the keyboard shortcuts setting will not
affect other users under 4D Server.
These optional shortcuts are not enabled when you first create a new Biota Data
File, so if you want to use them you must specifically enable them.
These shortcuts do not apply to the Record Listing screen for the Determination
History table.
FUNCTION
MAC OS
WINDOWS
Next record
DOWN ARROW
DOWN ARROW
Previous record
UP ARROW
UP ARROW
Last record
PAGE DOWN
PAGE DOWN
First record
PAGE UP
PAGE UP
Select or deselect highlighted record
SPACE BAR
SPACE BAR
Display selected record(s) in the Input
screen
SEMI-COLON (;)
SEMI-COLON (;)
Chapter 10 – Page 32
WARNING: With the optional keyboard shortcuts for Record Listing screens enabled, if
you use the mouse or another pointing device to select a record (single click) in the
second or higher page of records in the Record Listing screen, the clicked record
immediately scrolls to the top the display. (No scrolling occurs with the first page of
records.)
For this reason, if you use a mouse or another pointing device to open a record from the
Record Listing screen while the optional shortcuts are enabled, you must first select the
record with one mouse-click, wait for the record to scroll to the top of the list, then
double-click the record to open it in the Input screen. If you double-click a record without
waiting for the scrolling to occur, the second click may open the wrong record. Using the
semicolon key to open a selected record or records (details in the next section, “Using
the Optional Keyboard Shortcuts for Record Selection and Revision”) avoids this
problem entirely.
A warning regarding this behavior appears when you first enable the optional shortcuts
and, as a reminder, each time Biota is launched while the optional shortcuts are
enabled. Unfortunately, there is currently no way to alter this 4D behavior with
programming.
Using the Optional Keyboard Shortcuts for Record Selection and Revision
With the optional keyboard shortcuts for Record Listing screens enabled (see the
previous section, “Optional Keyboard Shortcuts”), you can select individual records or
groups of records in the Record Listing screen for a table without using the mouse or
other pointing device, then display the selected group of records in the record Input
screen for the table.
To highlight a record, use the up and down arrow keys to move one record at a
time.
To select a highlighted record, click the keyboard space bar. When you move the
highlight to another record, the selected record remains highlighted.
To add another record to the highlighted selection, move to that record and
click the keyboard space bar. You can create a highlighted selection including any
number of records, whether they are consecutive or on the screen or not.
To remove a record from the highlighted selection, move to that record and click
the keyboard space bar. No other record in the selection will be affected.
To display a highlighted record or a highlighted selection of records in the
Input screen, click the semicolon key on the keyboard. The highlighted record or
the first record in a highlighted selection
appears in the Input screen for the table.
The behavior of the navigation buttons
(“Navigate records”) in the Input screen
depends on how many records you highlighted
in the Record Listing screen before clicking the
semicolon key to display the Input screen.
◊
If only one record was highlighted, the navigation buttons operate just as they
do when the optional keyboard shortcuts are disabled, and you open a record in
the Input screen with a mouse double-click. The navigation buttons in the Input
Chapter 10 – Page 33
screen access all the records in the selection of records in the Record Listing
screen.
◊
If more than one record was highlighted, the navigation buttons in the Input
screen access only the records that were highlighted in the Record Listing
screen. In this case, other records in the full selection in the Record Listing
screen are not accessible with the navigation buttons. This behavior is quite
useful for viewing or editing a subset of the records in the current selection,
without using the “Sub-Selection” button and thereby losing view of the rest of the
full selection.
WARNING: With the optional keyboard shortcuts for Record Listing screens enabled (see
the previous section, “Optional Keyboard Shortcuts”), if you use the mouse or another
pointing device to select a record (single click) in the second or higher page of records in
the Record Listing screen, the clicked record immediately scrolls to the top of the
display. (No scrolling occurs with the first page of records.)
For this reason, if you use a mouse or another pointing device to open a record from the
Record Listing screen while the optional shortcuts are enabled, you must first select the
record with one mouse-click, wait for the record to scroll to the top of the list, then
double-click the record to open it in the Input screen. If you double-click a record without
waiting for the scrolling to occur, the second click may open the wrong record. Using the
semicolon key to open a selected record or records (details above in this section) avoids
this problem entirely.
A warning regarding this behavior appears when you first enable the optional shortcuts
and, as a reminder, each time Biota is launched while the optional shortcuts are
enabled. Unfortunately, there is currently no way to alter this 4D behavior with
programming.
Chapter 11
Input—Table by Table
As much as possible, all of Biota’s Input screens share the same features. These
common elements are discussed in Chapter 7, “Overview of Record Input Screens,”
Chapter 8, “Record Codes,” and Chapter 10, “Working With Records in Record Listing
and Input screens.” This chapter focuses on features restricted to one or a few Input
screens.
Specimen Input
You can enter a new record in the Specimen Input screen by selecting Specimen from
the Input menu or by clicking the “Add Specimen” button on the Specimen Record
Listing screen. The Specimen Input screen has seven tabs. Once you have entered a
Specimen Code, you can move to any tab. See “Keyboard Shortcuts for Input Screen
Tabs” in Chapter 7 for information on using keyboard shortcuts to move among the tabs.
This section describes how to enter data in the General, Determination, and Preparation
tabs of the Specimen Input screen.
Images tab. For information on entering and working with Specimen Images in the
Images tab, see Chapter 19, “Images.”
Chapter 11 – Page 2
Aux Fields tab. For information on entering Specimen Auxiliary Field data in the
Aux Fields tab, see Chapter 16, “User-Defined Auxiliary Fields and the Project
System.”
Notes tab. For information on entering Specimen Notes in the Notes tab, see
“Notes Input” later in this chapter.
Refs tab. For information on creating links to References in the Refs tab, see
Chapter 20, “References.”
Entering Specimen Data: The “General” Tab
1.
Enter a Specimen Code. You
can enter the Specimen Code by
typing it in the Specimen Code
entry area, by using the adjacent
“Assign” button (see “Assigning
New Record Codes Using an
“Assign” button: Step by Step” in
Chapter 8), by setting up the
Record Code Settings tool to enter it automatically (see “Assigning New Record
Codes Automatically During Data Entry” in Chapter 8, or by reading in a barcode
(see Appendix K, “Barcodes”).
The Specimen Code may be up to 30 characters in length. Because Specimen
Code is the Key field for the Specimen table, it is an obligatory entry, which must be
made first. All remaining entry areas are optional. The Specimen Code you enter
must not duplicate the Specimen Code of any existing Specimen record, or you will
receive an error message (see “Duplicate Key Errors” in Chapter 3). For help
understanding how Specimen Codes work, see Chapter 8, “Record Codes.”
2.
Enter a Species Code. The Species Code links this Specimen record with a record
in the Species table (see “Species Input” later in this chapter). There are five
alternative methods for entering a Species Code:
Method 1: Enter a complete Species Code manually or with a barcode reader.
◊
If a Species record exists with the Species Code you entered, the
Classification panel displays the Genus, Species (specific name), and Family.
The cursor moves on to the next entry area.
NOTE: Be sure to confirm that the correct Species record was found. If your
entry uniquely matches the first part of a different Species Code, the wrong
link will be made. See “Overriding Wildcard Input for Linking Fields” in
Chapter 7.
Chapter 11 – Page 3
◊
If no Species record exists with the Species Code you entered, Biota
offers you the option of creating a new Species record “on the fly” (using the
Species Code you entered) or accepting an orphan Specimen record. See
“‘On-the-Fly’ Creation of Linked Records” in Chapter 7 for details.
Method 2: Use the adjacent “Assign” button to create a new Species Code.
Biota offers you the option of creating a new Species record “on the fly,” with the
Code you entered, or accepting an orphan Specimen record. See “’On-the-Fly’
Creation of Linked Records” in Chapter 7 for details.
Method 3: Set up the Record Code Settings tool to enter a Species Code
automatically (see “Assigning New Record Codes Automatically During Data
Entry” in Chapter 8
Method 4: Enter the first letter or first few letters of a Species Code, then
press TAB (wildcard lookup). See “A Powerful Shortcut: Wildcard Data Entry for
Linking Fields” in Chapter 7.
◊
If only one existing Species Code matches the entry, Biota automatically
completes the entry.
◊
If more than one existing Species Code matches the entry, a scrollable
list of matching Species Codes for existing Species records appears, from
which you can choose the correct code by clicking it with the mouse.
Chapter 11 – Page 4
◊
If you enter the @ character (the wildcard character in Biota), and nothing
else, all Species codes appears in the scrollable list.
To sort the entries in the list by Genus or Species Name (specific name) or to
re-sort by Species Code, click the sort buttons at the top of the screen. When
you sort by Genus, records are sorted within Genus by Species Name. You
can change the width of the columns by dragging the green vertical lines with
the mouse.
◊
If no existing Species Code matches your entry, Biota offers you the
option of creating a new Species record “on the fly,” with the Species Code
you entered, or accepting an orphan Specimen record. See “‘On-the-Fly’
Creation of Linked Records” in Chapter 7 for details.
Method 5: Click the “Look Up” button in the Species Code panel of the
Specimen Input screen.
The Look Up Species window appears.
a. Enter a Genus, or the first letter or letters of a Genus and press TAB. If a
matching Genus record is found, all Species records for the Genus appear in the
scrollable area of the Lookup window. If more than one match is found, a list of
matches appears, from which you can select the correct Genus.
Chapter 11 – Page 5
b. If you find the Species you want, click it to enter the corresponding Species
Code.
c. To see the full Species record, once the Species Code has been entered, click
the “Show Species Record” button in the Species Code panel of the Specimen
Input screen.
3.
Enter a Collection Code. The Collection Code links this Specimen record with a
record in the Collection table (see “Collection Input” later in this chapter). You can
enter a Collection Code using any of five alternative techniques.
Method 1: Enter a complete Collection Code manually.
◊
If a Collection record exists with the Collection Code you entered, the
“Collection Data” panel displays the Collector’s name (“Collected By”), the
Date Collected (or date range), and the collection Locality (the Locality Name
field of the Locality record linked to the Collection record). The cursor moves
on to the next entry area.
NOTE: Be sure to confirm that the correct Collection record was found. If your
entry uniquely matches the first part of a different Collection Code, the wrong
link will be made. See “Overriding Wildcard Input for Linking Fields” in
Chapter 7.
◊
If no Collection record exists with the Collection Code you entered,
Biota offers you the option of creating a new Collection record “on the fly”
(using the Collection Code you entered) or accepting an orphan Collection
record. See “‘On-the-Fly’ Creation of Linked Records” in Chapter 7 for
details.
Chapter 11 – Page 6
Method 2: Use the adjacent “Assign” button to create a new Collection
Code. Biota offers you the option of creating a new Collection record “on the fly,”
with the Code you entered, or accepting an orphan Specimen record. See “‘Onthe-Fly’ Creation of Linked Records” in Chapter 7 for details.
Method 3: Set up the Record Code Settings tool to enter a Collection Code
automatically (see “Assigning New Record Codes Automatically During Data
Entry” in Chapter 8).
Method 4: Enter the first letter or first few letters of a Collection Code, then
press TAB (wildcard lookup). See “A Powerful Shortcut: Wildcard Data Entry for
Linking Fields” in Chapter 7.
◊
If only one existing
Collection Code matches the
entry, Biota automatically
completes the entry.
◊
If more than one existing
Collection Code matches the
entry, a scrollable list of
matching Collection Codes for
existing Collection records
appears, from which you can
choose the correct code by
clicking it with the mouse.
◊
If you enter the @ character
(the wildcard character in
Biota), and nothing else, all
Collection codes appear in the
scrollable list.
To sort the entries in the list by
Collector (“Collected By”) or to
re-sort by Collection Code,
click the sort buttons at the top
of the screen. You can change
the width of the columns by
dragging the green vertical lines with the mouse.
◊
If no existing Collection Code matches your entry, Biota offers you the
option of creating a new Collection record “on the fly,” with the Collection
Code you entered, or accepting an orphan Specimen record. See “‘On-theFly’ Creation of Linked Records” in Chapter 7 for details.
Chapter 11 – Page 7
Method 5: Click the “Look Up” button in the Collection Code panel of the
Specimen Input screen.
The Collections lookup options window appears.
a. Select a display option by clicking a button in the Collections lookup
options window. You can display All Collection Records (not the best
approach if there are hundreds or thousands of records) or restrict the
choices displayed to a certain value for Locality Name, Locality Code,
Collector (the “Collected By” field), Site, Source, or Method. Or, you can
launch the Query Editor (see “The Query Editor, a General-Purpose Tool
for Finding Records Based on Content” in Chapter 12) to find a record using
ad hoc criteria.
NOTE: If you have defined an Alias for the Site, Source, or Method fields of
the Collection table (see Chapter 18, “Renaming Fields”), the Alias appears in
the corresponding button text in the Look Up Collection window in place of
the Internal Field Name.
b. If you select the Locality Name, Locality Code, Collector, Site, Source,
or Method option, Biota creates a list of all unique values for the selected
field.
Chapter 11 – Page 8
◊
If there are only a few values, Biota displays the list in a popup list to
the right of the selected button. Click and hold the popup to display the
list of values, as shown below.
◊
If there are many values, Biota displays the
list in a separate window with a scrollbar, as
shown on the right.
c. Select the value you want from the popup list or
the scrolling list. Biota then shows the selected
value in the popup area.
d. Click the “OK” button in the Look Up
Collection window. The Look Up Collection
display screen appears, listing all Collection
records that match the option and criteria you
selected in steps a. and b. above (see the next
page).
Chapter 11 – Page 9
◊
If there are many records in the display screen, you may first want to
use the sort buttons at the top of each column to sort the records
displayed by the values for that column.
◊
If you want to try a different selection option or field value to display
records, click the “Try Again” button at the bottom of the Look Up
Collection selection screen.
e. When you find the record you want in the Lookup Collection display
screen, click it to enter its Collection Code in the Specimen Input screen.
f.
4.
To see the full Collection record, once the Collection Code has been
entered, click the “Show Collection Record” button in the “Collection Data”
panel.
Enter data for Stage/Sex, Medium, Storage, Deposited, Specimen Custom 1,
Specimen Custom 2, and Type Status. Enter each value and press TAB key to
advance to the next entry area.
Chapter 11 – Page 10
You can set any of the following options for each of these seven Specimen fields:
Aliases. Each field can be renamed using the “Core Field Aliases” tool from the
Special menu (see Chapter 18, “Renaming Fields”).
Field Value Defaults. You can ask Biota to enter a particular value in each new
record automatically using the “Field Value Defaults” tool from the Special menu
(see “Setting Default Entries: Field Value Defaults” in Chapter 17).
Entry Choice Lists. You can enable an Entry Choice List (pick list) for each field
using the “Entry Choice Lists” tool in the Special menu (see “Using Entry Choice
Lists” in Chapter 17).
NOTES:
5.
a.
The “Deposited” field in the Specimen table is used by the Specimen Loans
system in Biota. If you intend to use the Loans system do not use this field for
another purpose. See Chapter 21, “Specimen Loan System” for details.
b.
The Medium field also appears on the Preparation tab of the Specimen Input
screen. You can enter data in this field on either tab and the data will appear in
both locations.
Enter a value for Abundance. Biota enters a “1” as the default for the Abundance
field.
If this record is for a single physical specimen, leave the value at 1. Some
Biota tools sum the values in this field for sets of specimen records, so a record
representing a single physical specimen should read “1” for Abundance.
If this record represents more than one physical specimen, enter the total
number it represents. If the record for one physical specimen represents n
additional, unmounted specimens (a physical voucher), enter the value n + 1.
Chapter 11 – Page 11
Entering Specimen Data: The “Determination” Tab
In the “Last Determined By” and “Date Last Determined” fields of the Specimen table,
located in the Determination tab of the Specimen Input screen, Biota records the name
of the last person to identify (determine) the physical specimen referenced by the
Specimen record and the date the determination was made.
The Determination History for a Specimen record is also displayed in the Determination
tab of the Specimen Input screen. If you enable Biota’s Determination History system
before any subsequent changes in determination are made, Biota records each change
in determination, who made the change, when, and where (i.e., in the Specimen record
itself or through changes in the linked Species or Genus record). For full information on
the Determination History system, see Chapter 22, “Determination Histories.”
NOTE: You can set Field Value Default entries for the entry areas “Last Determined By”
and “Date Last Determined.” See “Setting Default Entries: Field Value Defaults” in
Chapter 17.
To enter determination data, take these steps.
1.
Enter the determiner’s “Short Name” in the “Last Determined By” entry area
on the Determination tab. Because this field is linked to the Short Name field of the
Personnel table, the entry area has a double border. You can use any of the
techniques for entering data in linking fields described in Chapter 7, “Overview of
Record Input Screens.”
If you know that the determiner has no existing record in the Personnel
table, enter a Short Name for the determiner in the “Last Determined By” entry
area (e.g., Albert B. Smith or A. B. Smith) and press the TAB key. If the entry you
Chapter 11 – Page 12
make does not match the Short Name field of any existing Personnel record,
Biota offers you a choice between creating a new Personnel record for that
name, “on the fly,” or accepting the Specimen record without creating a link to the
Personnel table (a “Personnel-orphan” Specimen record) (see “Entering Data in
Linking Fields” in Chapter 7).
NOTE: On Pin, Slide, Vial, and Herbarium labels, Biota uses the Short Name field
for the collector’s name (see Chapter 15, “Printing Labels”). Although the Short
Name may have up to 80 characters, it is best to make it substantially shorter
(20-30 characters is a good guideline) if you intend to use Biota to produce
specimen labels. Since determiners are very often also collectors and
preparators, be sure to choose a version of the determiner’s name that is
appropriate for collector’s names on labels—e.g., initials and last name, or first
name and last name. You can also use a “Group Name” in the “Determined By”
field, e.g., A. B. Smith & C. D. Jones (for help with Group Names, see “Entering
Personnel Data: The ‘Group’ Tab” later in this chapter).
If you think the determiner may already have a Personnel record, but you
are not sure what Short Name the record carries, enter the @ character and
press the TAB key. A scrollable list of all existing Personnel records appears
(below), from which you can choose the correct record by clicking it. You can sort
the records by Short Name, Last Name, or Institution by clicking the buttons
above the columns.
If you know the Short Name for the determiner’s existing Personnel record,
enter the first letter, the first few letters of the Short Name, or the full Short Name,
and press the TAB key. If a single match is found, Biota completes the name and
Chapter 11 – Page 13
the cursor moves into the next field. If more than one match is found, a choice list
like the one above appears, with all matches shown.
If the “Last Determined By” entry you make does not match the Short Name field
of any existing Personnel record, Biota offers you a choice between creating a
new Personnel record for that name, “on the fly,” or accepting the Specimen
record without creating a link to the Personnel table (a “Personnel-orphan”
Specimen record) (see “Entering Data in Linking Fields” in Chapter 7).
Note: If you are working with historical specimens, you may not want to create a
Personnel record for every Determiner, Preparator, or Collector—some of whom
may be long deceased and their particulars unknown.
2.
Enter the “Date Last Determined.” You can enter either a full date or a partial
date. See “Dates” in Chapter 9 for details on entering dates, date formats
(International vs. U.S.), partial dates, and how Biota handles dates in the Data File.
NOTE: If you have enabled the Determination History system and you change the
determination of a Specimen record in any way, Biota prompts you to complete the “Last
Determined By” and “Date Last Determined” fields of the Specimen record. For full
information on the Determination History system, see Chapter 22, “Determination
Histories.”
Entering Specimen Data: The “Preparation” Tab
The Preparation tab of the Specimen Input screen records the name of the preparator of
the physical specimen represented by the Specimen record, together with the date the
specimen was prepared (the “Date Prepared” field). For step-by-step help entering data
in these two fields, refer to the instructions for the “Last Determined By” and “Date Last
Determined” fields of the Determination tab (see “Entering Specimen Data: The
‘Determination’ Tab” earlier in this chapter).
In addition, the Medium field appears on the Preparation tab to record how the specimen
was prepared (e.g., “ethanol,” “exsiccatum,” “liquid nitrogen”) or what part of the
Chapter 11 – Page 14
specimen was prepared or preserved (e.g., “fruits,” “skin,” “skull,” “liver tissue,” “amplified
DNA”).
You can set any of the following options for the Medium field:
Alias. The Medium field can be renamed using the “Core Field Aliases” tool from
the Special menu (see Chapter 18, “Renaming Fields”).
Field Value Default. You can ask Biota to enter a particular value in the Medium
field for each new record automatically using the “Field Value Defaults” tool from the
Special menu (see “Setting Default Entries: Field Value Defaults” in Chapter 17).
Entry Choice List. You can enable an Entry Choice List (pick list) for the Medium
field using the “Entry Choice Lists” tool in the Special menu (see “Using Entry
Choice Lists” in Chapter 17).
NOTE: The Medium field also appears on the Preparation tab of the Specimen input
screen. You can enter data in this field on either tab and the data will appear in both
locations.
Entering Specimen Data: The “Images,” “Aux Fields,” “Notes,” and
“Refs” Tabs
Information on entering and working with data in these tabs appears elsewhere in the
Manual. Follow the links below:
Images tab. For information on entering and working with Specimen Images in the
Images tab, see Chapter 19, “Images.”
Aux Fields tab. For information on entering Specimen Auxiliary Field data in the
Aux Fields tab, see Chapter 16, “User-Defined Auxiliary Fields and the Project
System.”
Notes tab. For information on entering Specimen Notes in the Notes tab, see
“Notes Input” later in this chapter.
Refs tab. For information on creating links to References in the Refs tab, see
Chapter 20, “References.”
Chapter 11 – Page 15
Collection Input
You can enter a new record in the Collection Input screen by selecting Collection from
the Input menu, by clicking the “Add Collection” button on the Collection Record Listing
screen, or “on the fly” from the Specimen Input screen. The Collection Input screen has
seven tabs. Once you have entered a Collection Code, you can move to any tab. See
“Keyboard Shortcuts for Input Screen Tabs” in Chapter 7 for information on using
keyboard shortcuts to move among the tabs.
This section describes how to enter data in the General tab of the Collection Input
screen. For other tabs, follow the links below:
Host Record tab. For information on creating host record links in the “Host Record”
tab, see Chapter 24, “Host-Guest Relations.”
Georeference tab. For information on entering and working with spatial coordinates
in the Georeference tab, see “Spatial Coordinates” in Chapter 9.
Images tab. For information on entering and working with Specimen Images in the
Images tab, see Chapter 19, “Images.”
Aux Fields tab. For information on entering Specimen Auxiliary Field data in the
Aux Fields tab, see Chapter 16, “User-Defined Auxiliary Fields and the Project
System.”
Notes tab. For information on entering Specimen Notes in the Notes tab, see
“Notes Input” later in this chapter.
Refs tab. For information on creating links to References in the Refs tab, see
Chapter 20, “References.”
Chapter 11 – Page 16
Entering Collection Data: The “General” Tab
1.
Enter a Collection Code. You
can enter the Collection Code
by typing it in the Collection
Code entry area or by using the
adjacent “Assign” button (see
“Assigning New Record Codes
Using an “Assign” button: Step
by Step” in Chapter 8).
The Collection Code may be up to 30 characters in length. Because Collection
Code is the Key field for the Collection table, it is an obligatory entry, which must be
made first. All remaining entry areas are optional. The Collection Code you enter
must not duplicate the Collection Code of any existing Collection record, or you will
receive an error message (see “Duplicate Key Errors” in Chapter 3). For help
understanding how Collection Codes work, see Chapter 8, “Record Codes.”
NOTE: If you are creating a Collection record “on the fly” while working on a
Specimen record (see Step 3 of “Entering Specimen Data: The ‘General’ Tab”
earlier in this chapter), the Collection Code you entered in the Specimen Input
screen is already displayed and the cursor is in the next field (Locality Code).
2.
Enter a Locality Code. The Locality Code links this Collection record with a record
in the Locality table (see “Locality Input” later in this chapter). You can enter a
Locality Code using any of five alternative techniques.
Method 1: Enter a complete Locality Code manually.
◊
If a Locality record exists with the Locality Code you entered, the
“Locality data” panel displays the Locality Name and five other fields from the
related Locality record, and the cursor moves on to the next entry area.
NOTE: Be sure to confirm that the correct Locality record was found. If your
entry uniquely matches the first part of a different Locality Code, the wrong
link will be made. See “Overriding Wildcard Input for Linking Fields” in
Chapter 7.
Chapter 11 – Page 17
◊
If no Locality record exists with the Locality Code you entered, Biota
offers you the option of creating a new Locality record “on the fly” (using the
Locality Code you entered) or accepting an orphan Locality record. See “‘Onthe-Fly’ Creation of Linked Records” in Chapter 7 for details.
Method 2: Use the adjacent “Assign” button to create a new Locality Code.
Biota offers you the option of creating a new Locality record “on the fly,” with the
Code you entered, or accepting an orphan Collection record. See “‘On-the-Fly’
Creation of Linked Records” in Chapter 7 for details.
Method 3: Set up the Record Code Settings tool to enter a Locality Code
automatically (see “Assigning New Record Codes Automatically During Data
Entry” in Chapter 8).
Method 4: Enter the first letter or first few letters of a Locality Code, then
press TAB (wildcard lookup). See “A Powerful Shortcut: Wildcard Data Entry for
Linking Fields” in Chapter 7.
◊
If only one Locality Code matches the entry, Biota automatically
completes the entry.
◊
If more than one existing Locality Code matches the entry, a scrollable
list of matching Codes for existing Locality records appears, from which you
can choose the correct code by clicking it with the mouse.
Chapter 11 – Page 18
◊
If you enter the @ character (the wildcard character in Biota), and nothing
else, all Locality codes appear in the scrollable list.
To sort the entries in the list by Locality Name or re-sort by Locality Code,
click the sort buttons at the top of the screen. You can change the width of
the columns by dragging the green vertical lines with the mouse.
◊
If no existing Locality Code matches your entry, Biota offers you the
option of creating a new Locality record “on the fly,” with the Locality Code
you entered, or accepting an orphan Collection record. See “‘On-the-Fly’
Creation of Linked Records” in Chapter 7 for details.
Method 5: Click the “Look Up” button in the Locality Code panel of the
Collection Input screen.
The Look Up Locality window appears.
a. Select a display option by clicking a button in the Look Up Locality
window. You can display All Locality Records (an inefficient approach if there
are many Locality records in the database) or restrict the choices displayed to
a certain value for Locality Name, State/Province, or Country. Or, you can
launch the Query Editor (see “The Query Editor, a General-Purpose Tool
for Finding Records Based on Content” in Chapter 12) to find a record using
ad hoc criteria.
Chapter 11 – Page 19
NOTE: If you have defined an Alias for the Locality Name, District,
State/Province, or Country fields of the Locality table (see Chapter 18,
“Renaming Fields”), the Alias appears in the corresponding button text in the
Look Up Locality window in place of the Internal Field Name.
b. If you select the Locality Name, District, State/Province, or Country
option, Biota creates a list of all unique values for the selected field.
◊
If there are only a few values, Biota displays the list in a popup list to
the right of the selected button. Click and hold the popup to display the
list of values, as shown below.
◊
If there are many values, Biota
displays the list in a separate window
with a scrollbar, as shown on the right.
c. Select the value you want from the popup
list or the scrolling list. Biota then shows the
selected value in the popup area.
d. Click the “OK” button in the Look Up
Locality window. The Look Up Locality
selection screen appears, listing all Locality
records that match the option and criteria you
selected in steps a. and b. above.
◊
If there are many records in the
display screen, you may first want to
use the sort buttons at the top of each
column to sort the records displayed by
the values for that column.
Chapter 11 – Page 20
◊
If you want to try a different selection option or field value to display
records, click the “Try Again” button at the bottom of the Look Up
Locality selection screen.
e. When you find the record you want in the Lookup Locality display
screen, click it to enter its Locality Code in the Collection Input screen.
f.
3.
To see the full Locality record, once the Locality Code has been entered,
click the “Show Locality Record” button in the “Locality Data” panel.
Enter information on the collector and date(s) of collection.
NOTE: You can ask Biota to enter a particular value in each new record
automatically for the entry areas Collected By, Date Collected, and Date Collection
Complete using the “Field Value Defaults” tool from the Special menu (see “Setting
Default Entries: Field Value Defaults” in Chapter 17).
a. Enter the collector’s “Short Name” in the “Collected By” entry area on the
General tab. Because this field is linked to the Short Name field of the Personnel
table, the entry area has a double border. You can use any of the techniques for
entering data in linking fields described in Chapter 7, “Overview of Record Input
Screens.”
Chapter 11 – Page 21
◊
If you know that the Collector has no existing record in the Personnel
table, enter a Short Name for the Collector (e.g., Albert B. Smith or A. B.
Smith) and press the TAB key. If the entry you make in the “Collected By”
entry area does not match the Short Name field of any existing Personnel
record, Biota offers you a choice between creating a new Personnel record
for that name, “on the fly,” or accepting the Collection record without creating
a link to the Personnel table (a “Personnel-orphan” Collection record) (see
“Entering Data in Linking Fields” in Chapter 7).
NOTE: On Pin, Slide, Vial, and Herbarium labels, Biota uses the Short Name
field for the collector’s name (see Chapter 15, “Printing Labels”). Although the
Short Name may have up to 80 characters, it is best to make it substantially
shorter (20-30 characters is a good guideline) if you intend to use Biota to
produce specimen labels. Choose a version of the collector’s name that is
appropriate for specimen labels—e.g., initials and last name, or first name
and last name. You can also use a “Group Name” in the “Collected By”
field—e.g., A. B. Smith & C. D. Jones (for help with Group Names, see
“Entering Personnel Data: The ‘Group’ Tab” later in this chapter).
◊
If you think the collector may already have a Personnel record, but you
are not sure what Short Name the record carries, enter the @ character
and press the TAB key. A scrollable list of all existing Personnel records
appears (next page), from which you can choose the correct record by
clicking it. You can sort the records by Short Name, Last Name, or Institution
by clicking the buttons above the columns.
Chapter 11 – Page 22
◊
If you know the Short Name for the Collector’s existing Personnel
record, enter the first letter, the first few letters of the Short Name, or the full
Short Name, and press the TAB key. If a single match is found, Biota
completes the name and the cursor moves into the next field. If more than
one match is found, a choice list like the one above appears, with all matches
shown.
If the entry you make in the “Collected By” entry area does not match the
Short Name field of any existing Personnel record, Biota offers you a choice
between creating a new Personnel record for that name, “on the fly,” or
accepting the Collection record without creating a link to the Personnel table
(a “Personnel-orphan” Collection record) (see “Entering Data in Linking
Fields” in Chapter 7).
NOTE: If you are working with historical Collections, you may not want to
create a Personnel record for every Collector—some of whom may be long
deceased and their particulars unknown.
b. Enter date(s) of collection. To enter a single collection date, use the “Date
Collected”entry area and leave the “Date Collection Completed” entry area blank
(“TAB through” it). To enter a Date Range, use both areas. You can enter either a
full date, a Month-Year date, or a Year-only date in either date entry area.
NOTE: See “Dates” in Chapter 9 for full details on entering dates, date formats
(International vs. U.S.), Collection Date ranges, partial dates, and how Biota
handles dates in the Data File.
4.
Enter data for Collection Method, Site, and Source. Each field accommodates
entries up to 80 characters in length. Enter each value and press the TAB key to
advance to the next entry area.
You can set any of the following options for each of these three Collection fields:
Aliases. Each field can be renamed using the “Core Field Aliases” tool from the
Special menu (see Chapter 18, “Renaming Fields”).
Field Value Defaults. You can ask Biota to enter a particular value in each new
record automatically using the “Field Value Defaults” tool from the Special menu
(see “Setting Default Entries: Field Value Defaults” in Chapter 17).
Entry Choice Lists. You can enable an Entry Choice List (pick list) for each field
using the “Entry Choice Lists” tool in the Special menu (see “Using Entry Choice
Lists” in Chapter 17).
Chapter 11 – Page 23
Entering Collection Data: The “Host Record,” “Georeference,” “Images,”
“Aux Fields,” “Notes,” and “Refs” Tabs
Information on entering and working with data in these tabs appears elsewhere in the
Manual. Follow the links below:
Host Record tab. For information on creating host record links in the “Host Record”
tab, see Chapter 24, “Host-Guest Relations.”
Georeference tab. For information on entering and working with spatial coordinates
in the Georeference tab, see “Spatial Coordinates” in Chapter 9.
Images tab. For information on entering and working with Specimen Images in the
Images tab, see Chapter 19, “Images.”
Aux Fields tab. For information on entering Specimen Auxiliary Field data in the
Aux Fields tab, see Chapter 16, “User-Defined Auxiliary Fields and the Project
System.”
Notes tab. For information on entering Specimen Notes in the Notes tab, see
“Notes Input” later in this chapter.
Refs tab. For information on creating links to References in the Refs tab, see
Chapter 20, “References.”
Chapter 11 – Page 24
Specimen and Collection Combined Input
Biota’s structure (see Appendix A, “Biota Tables, Fields, and Relational Links”) allows
you to link any number of Specimen records to a single Collection record (a many-to-one
relation). This approach makes sense when a collector, collecting expedition, inventory,
or quadrat-based study gathers two or more distinct specimens, each requiring a
separate Specimen record, that nonetheless share the same Collection data.
Historical specimens in museum or herbarium collections, however, are often unique
with regard to collection data, each produced by a distinct collecting event (as far as a
particular museum or herbarium is concerned). For this reason, many museum
databases simply treat all collecting-event data (often including locality data as well) as
specimen attributes (fields in a specimen table). With such a design, however, any
many-to-one relationships between specimens and collecting events or between
collecting events and localities, for specimens produced by contemporary collecting
protocols, are either lost or must be recovered by laborious, text-based searches.
Biota allows you to freely mix records for unique historical specimens with Specimen
records that bear many-to-one-structured collecting event and locality data. The “Input
Specimen and Collection” tool speeds data entry for specimens (each with unique
Collection data) by automatically creating a linked Collection record for each Specimen
record. This approach preserves the option to later link additional Specimen records to
automatically-generate Collection records, if appropriate.
Specimen and Collection Combined Input: How It Works
Automatic creation of a linked Collection record. When you choose “Specimen
and Collection” from the Input menu, Biota creates a Specimen record (initially
blank), just as if you had selected “Specimen” from the Input menu. As soon as you
enter a valid Specimen Code manually, a linked Collection record is automatically
created, bearing a Collection Code identical to the Specimen Code for the linked
Specimen record. (Record Codes need not be unique if in different tables.)
Option to create Record Codes automatically. Alternatively, you can set up the
Record Code Settings tool to enter, automatically, a Specimen Code using one
prefix and a Collection Code for the linked Collection record, using a different prefix
(see Chapter 8, “Record Codes”). Or, you can enter Specimen codes manually and
set up the Record Code Settings tool to enter Collection codes, automatically, with a
prefix of your choice.
Save or Carry both records. When you click the “Save” button in the “Specimen
and Collection” Input screen, both records are saved. If you click Carry, a new
Specimen record is created, but it is automatically linked to the Collection record
created for the previous Specimen record. In addition, the same fields are
duplicated that the “Carry” button copies in the Input Specimen and Input Collection
screens.
Locality record. The “Input Specimen and Collection” screen does not
automatically create a Locality record linked to the automatically-created Collection
record. You must either create the Locality record “on the fly” from the Collection tab
of the “Input Specimen and Collection” screen, link the automatically-created
Collection record to an existing Locality record, or leave the Collection record
unlinked to any Locality record (“orphaned”). The next section provides details.
An input tool only. The “Input Specimen and Collection” screen is strictly an input
tool. When you finish a session of record entry using this screen, click the “Cancel”
Chapter 11 – Page 25
button to dismiss the screen and display the newly created Specimen records in the
standard Specimen Record Listing Screen. If you double-click one of the records in
this screen, it appears in the standard Specimen input screen, not the Input
Specimen and Collection screen. To enter additional records using the Input
Specimen and Collection screen, you must select “Specimen and Collection” from
the Input menu.
Based on the Specimen Input screen. The “Input Specimen and Collection”
screen is identical in overall design to the Specimen Input Screen. The only
differences are the automatic entry of the Collection Code for the automaticallycreated, linked Collection record, and the addition of a Collection tab for entering
data in the fields of the linked Collection record. The Collection tab duplicates the
General tab of the Collection Input screen.
Specimen and Collection Combined Input: Tabs of the Input Screen
You can enter a new Specimen record and a linked Collection record by selecting
“Specimen and Collection” from the Input menu. The “Specimen and Collection Input”
screen has eight tabs. Once you have entered a Specimen Code, you can move to any
tab. See “Keyboard Shortcuts for Input Screen Tabs” in Chapter 7 for information on
using keyboard shortcuts to move among the tabs.
This section describes or refers you to descriptions of how to enter data in the General,
Collection, Determination, and Preparation tabs of the Specimen Input screen.
Images tab. For information on entering and working with Specimen Images in the
Images tab, see Chapter 19, “Images.”
Chapter 11 – Page 26
Aux Fields tab. For information on entering Specimen Auxiliary Field data in the
Aux Fields tab, see Chapter 16, “User-Defined Auxiliary Fields and the Project
System.”
Notes tab. For information on entering Specimen Notes in the Notes tab, see
“Notes Input” later in this chapter.
Refs tab. For information on creating links to References in the Refs tab, see
Chapter 20, “References.”
Specimen and Collection Combined Input: The General Tab
1.
Enter a Specimen Code. You
can enter the Specimen Code by
typing it in the Specimen Code
entry area, by using the adjacent
“Assign” button (see “Assigning
New Record Codes Using an
“Assign” button: Step by Step” in
Chapter 8), by setting up the
Record Code Settings tool to enter it automatically (see “Assigning New Record
Codes Automatically During Data Entry” in Chapter 8, or by scanning in a barcode
(see Appendix K, “Barcodes”).
Once a Specimen Code has been entered, Biota automatically creates a linked
Collection record. Unless you have set up the Record Code Settings tool to enter
Collection Codes automatically (see “Assigning New Record Codes Automatically
During Data Entry” in Chapter 8), the Collection Code in the linked Collection record
duplicates the Specimen Code. Biota
displays the Collection Code in the
“Collection Code” panel of the “General”
tab.
NOTE: The Specimen Code may be up to 30 characters in length. Because
Specimen Code is the Key field for the Specimen table, it is an obligatory entry,
which must be made first. All remaining entry areas are optional. The Specimen
Code you enter must not duplicate the Specimen Code of any existing Specimen
record. Likewise, the Collection Code for the automatically created Collection record
must not duplicate the Collection Code of any existing Collection record, or you will
receive an error message (see “Duplicate Key Errors” in Chapter 3). For help
understanding how Record Codes work, see Chapter 8, “Record Codes.”
2.
Enter a Species Code. The Species Code links this Specimen record with a record
in the Species table (see “Species Input” later in this chapter). There are five
alternative methods for entering a Species Code. For details, refer to Step 2 in the
section “Entering Specimen Data: The ‘General’ Tab,” earlier in this chapter.
Chapter 11 – Page 27
3.
If you wish to enter data for the linked Collection record now, click the “Input
Collection Data” button in the Collection Code panel to move to the Collection tab of
the combined “Specimen and Collection Input” screen. (Remember, the Collection
Code had been entered automatically.) Alternatively, you can first complete the
General tab (Specimen fields), then move to the Collection tab.
4.
Enter data for Stage/Sex, Medium, Storage, Deposited, Specimen Custom 1,
Specimen Custom 2, and Type Status. Enter each value and press the TAB key to
advance to the next entry area.
You can set any of the following options for each of these seven Specimen fields:
Aliases. Each field can be renamed using the “Core Field Aliases” tool from the
Special menu (see Chapter 18, “Renaming Fields”).
Field Value Defaults. You can ask Biota to enter a particular value in each new
record automatically using the “Field Value Defaults” tool from the Special menu
(see “Setting Default Entries: Field Value Defaults” in Chapter 17).
Entry Choice Lists. You can enable an Entry Choice List (pick list) for each field
using the “Entry Choice Lists” tool in the Special menu (see “Using Entry Choice
Lists” in Chapter 17).
NOTES:
5.
a.
The “›” field in the Specimen table is used by the Specimen Loans system in
Biota. If you intend to use the Loans system do not use this field for another
purpose. See Chapter 21, “Specimen Loan System” for details.
b.
The Medium field also appears on the Preparation tab of the “Specimen and
Collection Input” screen. You can enter data in this field on either tab and the
data will appear in both locations.
Enter a value for Abundance. Biota enters a “1” as the default for the Abundance
field.
If this record is for a single physical specimen, leave the value at 1. Some
Biota tools sum the values in this field for sets of specimen records, so a record
representing a single physical specimen should read “1” for Abundance.
Chapter 11 – Page 28
If this record represents more than one physical specimen, enter the total
number it represents. If the record for one physical specimen represents n
additional, unmounted specimens (a physical voucher), enter the value n + 1.
Specimen and Collection Combined Input: The Collection Tab
The Collection tab of the combined “Specimen and Collection Input” screen shows the
Collection Code already entered at the top of the screen. Otherwise, the Collection tab is
identical in function and layout to the General tab of the “Collection Input” screen.
For full instruction on entering data in the Collection tab, refer to the section “Entering
Collection Data: The ‘General’ Tab” earlier in this chapter, and begin with Step 2 in that
section.
Specimen and Collection Combined Input: The “Determination,”
“Preparation,” “Images,” “Aux Fields,” “Notes,” and “Refs” Tabs
Information on entering and working with data in these tabs appears elsewhere in the
Manual. Follow the links below.
Determination tab. For information on entering and working with the field “Last
Determined By” and “Date Last Determined,” see “Entering Specimen Data: The
‘Determination’ Tab” earlier in this chapter. (Because the combined “Specimen and
Collection Input” screen is for data entry only, the Determination History panel does
not appear on the Determination tab of this screen.)
Preparation tab. For information on entering and working with the “Prepared By”
field on the Preparation tab, see “Entering Specimen Data: The ‘Preparation’ Tab”
earlier in this chapter.
Chapter 11 – Page 29
Aux Fields tab. For information on entering Specimen Auxiliary Field data in the
Aux Fields tab, see Chapter 16, “User-Defined Auxiliary Fields and the Project
System.”
Notes tab. For information on entering Specimen Notes in the Notes tab, see
“Notes Input” later in this chapter.
Refs tab. For information on creating links to References in the Refs tab, see
Chapter 20, “References.”
Locality Input
You can enter a new record in the Locality Input screen by selecting Locality from the
Input menu, by clicking the “Add Locality” button on the Locality Record Listing screen,
or by creating a new Locality record “on the fly” from the Collection Input screen. The
Locality Input screen has six tabs. Once you have entered a Locality Code, you can
move to any tab. See “Keyboard Shortcuts for Input Screen Tabs” in Chapter 7 for
information on using keyboard shortcuts to move among the tabs.
This section describes how to enter data in the General tab of the Collection Input
screen. For other tabs, follow the links below.
Georeference tab. For information on entering and working with spatial coordinates
in the Georeference tab, see “Spatial Coordinates” in Chapter 9.
Images tab. For information on entering and working with Specimen Images in the
Images tab, see Chapter 19, “Images.”
Chapter 11 – Page 30
Aux Fields tab. For information on entering Specimen Auxiliary Field data in the
Aux Fields tab, see Chapter 16, “User-Defined Auxiliary Fields and the Project
System.”
Notes tab. For information on entering Specimen Notes in the Notes tab, see
“Notes Input” later in this chapter.
Refs tab. For information on creating links to References in the Refs tab, see
Chapter 20, “References.”
Entering Locality Data: The “General” Tab
1.
Enter a Locality Code. You
can enter the Locality Code
by typing it in the Locality
Code entry area or by using
the adjacent “Assign” button
(see “Assigning New Record
Codes Using an “Assign”
button: Step by Step” in
Chapter 8).
The Locality Code may be up to 30 characters in length. Because Locality Code is
the Key field for the Locality table, it is an obligatory entry, which must be made first.
All remaining entry areas are optional. The Locality Code you enter must not
duplicate the Locality Code of any existing Locality record, or you will receive an
error message (see “Duplicate Key Errors” in Chapter 3). For help understanding
how Locality Codes work, see Chapter 8, “Record Codes.”
NOTE: If you are creating a Locality record “on the fly” while working on a Collection
record (see Step 3 of “Entering Collection Data: The ‘General’ Tab” earlier in this
chapter), the Locality Code you entered in the Collection Input screen is already
displayed and the cursor is in the next field (Locality Name).
2.
Enter Locality Name. The Locality Name may be very long, if necessary—up to
32,000 characters in length (the standard length of a “text” field in 4th Dimension).
Where possible, this entry might be an official geographical place name from a
geographical authority list or gazetteer. The Locality Code (Step 1 above), on the
other hand, can be any unique alphanumeric value, but in the absence of official
locality codes (which do exist in some countries), you may find it convenient to
make it either the same as Locality Name (if no more than 30 characters in length),
or an abridgement of the Locality Name.
Chapter 11 – Page 31
NOTE: Text fields in 4th Dimension, such as Locality Name, cannot be sorted or
indexed. (Indexing is an internal way of making sorts and queries faster.) Therefore,
Biota automatically and invisibly maintains a parallel “indexing field” for Locality
Name, called “Locality Name Index.” For each Locality record, Locality Name Index
contains the first 80 characters of the Locality Name field (80 characters is the
longest indexable field length in 4th Dimension). When you use the Sort Editor, use
the Locality Name Index to sort (Locality Name is not even listed). When you use
the Query Editor, you many search on either field, but the search will be faster if you
use Locality Name Index.
3.
Enter District, State/Province,
Country, and Elevation.
You can set any of the following
options for each of these four Locality
fields—as well as for the Locality
Name field (step 2 above):
Aliases. Each field can be
renamed using the “Core Field
Aliases” tool from the Special menu
(see Chapter 18, “Renaming
Fields”). For example, you might want to rename the District field County or the
Elevation field Depth.
Field Value Defaults. You can ask Biota to enter a particular value in each new
record automatically using the “Field Value Defaults” tool from the Special menu
(see “Setting Default Entries: Field Value Defaults” in Chapter 17).
Entry Choice Lists. You can enable an Entry Choice List (pick list) for each field
using the “Entry Choice Lists” tool in the Special menu (see “Using Entry Choice
Lists” in Chapter 17).
NOTES ON THE ELEVATION FIELD:
a.
The [Locality] Elevation field is an alphanumeric, not a numeric, field. This
design allows elevation ranges (as illustrated above) and non-metric units (e.g.,
feet) to be included in the entry.
b.
If you enter a numeral, with no units, Biota assumes that the elevation is in
meters, when printing Specimen locality labels, and automatically appends “m”
to the elevation (see Chapter 15, “Printing Labels”). Or, you can include “m” in
the field entry itself, if you wish.
c.
If you enter elevations or depths in feet instead of meters, be sure to
include the abbreviation “f” or “ft” (or anything with the letter “f” in it). In this
case, Biota prints the value on locality labels just as you entered it, without
adding “m.” If all your elevation data are in feet and you do not intend to
convert the values to meters, you may want to change the default name for the
[Locality] Elevation field from “Elevation (m)” to “Elevation (ft)” (see Chapter 18,
“Renaming Fields”).
d.
If the elevation entry is in feet and you wish to convert it to meters, click
the “Convert ft to m” button. The abbreviation “f” or “ft” (or anything with the
Chapter 11 – Page 32
letter “f” in it) must be present in the field, or the button does nothing and
presents an explanatory message.
If the entry is a single value, with or without a minus sign, it is directly
converted to meters and “m” is appended.
If the entry is a range, of the form “8000-8100 ft” or “8000 to 8100 ft,” the
range is converted to meters, in the same format (“2438-2469 m” or
(“2438 to 2469 m”)
If the entry is a range, and either value includes a minus sign, you
must use the “to” format (e.g., “-200 to -50 ft”) for the range to be
converted properly.
Entering Locality Data: Entering Latitude and Longitude in the
“Georeference” Tab
This section assumes you have already read the section “Spatial Coordinates” in
Chapter 9, which provides an overview of georeference options in Biota, including
settings in the Coordinates panel of the Preferences screen (Special menu).
1.
Enter Coordinates: Latitude and Longitude.
Biota stores Latitude and Longitude data in units of decimal degrees—the standard
system used in Geographic Information Systems (GIS) work. Nonetheless, Biota
offers three unit systems for the entry and display of latitude and longitude values in
the Locality table. You can enter data using any of the three systems and freely use
different systems for different records in the same data file. As you make an entry in
any of the systems, Biota instantly translates the value into the other two and
Chapter 11 – Page 33
displays all three versions in the Coordinates panel of the Georeference tab in the
Locality input screen.
NOTE: Biota validates entries for the Latitude and Longitude fields of the Locality
table. Latitude may not be less than –90 nor greater than +90, and Longitude may
not be less than –180 nor greater than +180, or the equivalents in
degree/minutes/seconds.
a. System 1: Degrees/Minutes/Seconds (DMS). This is the traditional system
found in most gazetteers and atlases—but see the important warning, in the
section “Latitude and Longitude (Locality Table),” in Chapter 9.
i.
Click the “1” button in the
Coordinates panel to select
System 1.
ii. Enter Degrees, Minutes, and
Seconds of Latitude, pressing
TAB after each entry.
iii. Continue with Degrees,
Minutes, and Seconds of
Longitude.
iv. Click the hemisphere buttons (N or S, E or W) if necessary. (The default
Hemispheres are N and W, reflecting Biota’s heritage.)
b. System 2: Integer Degrees, Decimal Minutes. This is the system used by
many Geographical Positioning System (GPS) instruments.
i.
Click the “2” button in the
Coordinates panel to select
System 2.
ii. Enter Integer Degrees and
Decimal Minutes of Latitude,
pressing TAB after each entry.
The Integer Degree value must
be negative for Latitudes in the Southern Hemisphere.
iii. Continue with Integer Degrees and Decimal Minutes of Longitude. The
Integer Degree value must be negative for Longitudes in the Western
Hemisphere.
WARNING: Beware! Some gazetteers list Latitude and Longitude values in DMS,
but use a format that looks like Integer Degrees with Decimal Minutes, e.g., 24°
48.39 actually means 24° 48’ 39” in these gazetteers. The easiest way to detect
this deceptive format is to see if you can find any values in the gazetteer to the
right of the ”decimal point” that exceed 59. If not, those values are Seconds, not
the decimal part of true Decimal Minutes.
Chapter 11 – Page 34
c. System 3: Integer Degrees, Decimal Minutes. This is the system used in
Geographical Information Systems (GIS).
i.
Click the “3” button in the
Coordinates panel to select
System 3.
ii. Enter Decimal Degrees of
Latitude and press TAB. The
value must be negative for
Latitudes in the Southern Hemisphere.
iii. Enter Decimal Degrees of Longitude. The value must be negative for
Longitudes in the Western Hemisphere.
d. Enter a code or description for the Accuracy of the Coordinates, once the
Coordinates have been entered.
e. To clear all Coordinate entry
areas, click the “Clear Coordinates”
button at the bottom of the
Coordinates panel.
NOTE: You can tell Biota to display,
print, and export only Degrees, Minutes, and Hemisphere for an individual record
by entering the value “Minutes” (or “Minutos,” for the Spanish interface) in the Lat
Long Accuracy field. (Do not enter the quotation marks.) See “Setting Latitude
and Longitude Display Resolution for Individual Locality Records” in Chapter 9
for details.
Entering Locality Data: Entering Alternate Coordinates in the
“Georeference” Tab
Please refer to the section “Alternate Coordinates (Locality Table)” in Chapter 9 for full
details on using Alternate Coordinate systems (e.g., UTM or Lambert coordinates, or the
U.S. Township-Range-Section system), translating alternate systems to latitude and
longitude, and Alternate Coordinate display settings in the Coordinates panel of the
Preferences screen (Special menu).
Entering Locality Data: The “Images,” “Aux Fields,” “Notes,” and
“Refs” Tabs
Information on entering and working with data in these tabs appears elsewhere in the
Manual. Follow the links below:
Images tab. For information on entering and working with Specimen Images in the
Images tab, see Chapter 19, “Images.”
Aux Fields tab. For information on entering Specimen Auxiliary Field data in the
Aux Fields tab, see Chapter 16, “User-Defined Auxiliary Fields and the Project
System.”
Notes tab. For information on entering Specimen Notes in the Notes tab, see
“Notes Input” later in this chapter.
Chapter 11 – Page 35
Refs tab. For information on creating links to References in the Refs tab, see
Chapter 20, “References.”
Species Input
You can enter a new record in the Species Input screen by selecting Species from the
Input menu, by clicking the “Add Species” button on the Species Record Listing screen,
or “on the fly” from the Specimen Input screen. The Species Input screen has eight tabs.
Once you have entered a Species Code, you can move to any tab. See “Keyboard
Shortcuts for Input Screen Tabs” in Chapter 7 for information on using keyboard
shortcuts to move among the tabs.
This section describes how to enter data in the Classification, Subsp/Names, and
Dist/Types tabs of the Species Input screen. For other tabs, follow the links below:
Synonymy tab. For information on designating a Species record as a synonym of
another Species record, or to learn how to display the synonyms of a valid Species
record, see Chapter 23, “Synonymy System.”
Images tab. For information on entering and working with Specimen Images in the
Images tab, see Chapter 19, “Images.”
Aux Fields tab. For information on entering Specimen Auxiliary Field data in the
Aux Fields tab, see Chapter 16, “User-Defined Auxiliary Fields and the Project
System.”
Notes tab. For information on entering Specimen Notes in the Notes tab, see
“Notes Input” later in this chapter.
Refs tab. For information on creating links to References in the Refs tab, see
Chapter 20, “References.”
Chapter 11 – Page 36
Entering Species Data: The “Classification” Tab
1.
Enter a Species Code. You can enter the Species Code by typing it in the Species
Code entry area, by using the adjacent “Assign” button (see “Assigning New Record
Codes Using an ‘Assign’ button: Step by Step” in Chapter 8), by setting up the
Record Code Settings tool to enter it automatically (see “Assigning New Record
Codes Automatically During Data Entry” in Chapter 8, or by reading in a barcode
(see Appendix K, “Barcodes”).
The Species Code may be up to 30
characters in length. Because
Species Code is the Key field for the
Species table, it is an obligatory
entry, which must be made first. All
remaining entry areas are optional.
The Species Code you enter must
not duplicate the Species Code of
any existing Species record, or you
will receive an error message (see “Duplicate Key Errors” in Chapter 3). For help
understanding how Species Codes work, see Chapter 8, “Record Codes.”
NOTE: If you are creating a Species record “on the fly” while working on a Specimen
record (see Step 2 of “Entering Specimen Data: The ‘General’ Tab” earlier in this
chapter), the Species Code you entered in the Specimen Input screen is already
displayed and the cursor is in the next field (Genus).
2.
Enter the Genus. The Genus entry links this Species record with a record in the
Genus table (see “Genus, Family, Order, Class, Phylum, and Kingdom Input” later
in this chapter). You can enter a Genus using either of two methods for entering
data in linking fields, as described in the section “Entering Data in Linking Fields” in
Chapter 7.
Method 1: Enter the full Genus name manually.
◊
If a Genus record exists with the Genus name you entered, the
“Classification” panel to the right of the Genus entry area displays the Family
name from the linked Genus record and the Order name from the linked
Family record, if any. The cursor moves on to the next entry area (Specific
Name).
NOTE: Be sure to confirm that the correct Genus record was found. If your
entry uniquely matches the first part of a different Genus name, the wrong
link will be made. See “Overriding Wildcard Input for Linking Fields” in
Chapter 7.
Chapter 11 – Page 37
◊
If no Genus record exists with the Genus name you entered, Biota offers
you the option of creating a new Genus record “on the fly” (using the Genus
name you entered) or accepting an orphan Species record. See “‘On-the-Fly’
Creation of Linked Records” in Chapter 7 for details.
Method 2: Enter the first letter or first few letters of a Genus name, then
press TAB (wildcard lookup). See “A Powerful Shortcut: Wildcard Data Entry for
Linking Fields” in Chapter 7.
◊
If only one Genus record matches the entry, Biota automatically
completes the entry.
◊
If more than one existing Genus record matches the entry, a scrollable
list of matching Genus names for existing Genus records appears, from
which you can choose the correct record by clicking it with the mouse. (If you
enter the @ character, and nothing else, all Genus records appear in the
scrollable list.)
NOTE: In two special circumstances, you might need to create a new Genus
record that legitimately duplicates an existing Genus name: (1) when genera in
two kingdoms have the same name and (2) when you want to record a generic
synonym. See “A Special Problem for Genera: Legitimate Duplicate Generic
Names” later in this chapter, if either case arises.
3.
Enter Specific Name (Specific Epithet).
Entry Choice List. You can enable an Entry Choice List (pick list) for the
Specific Name field using the “Entry Choice Lists” tool in the Special menu (see
“Using Entry Choice Lists” in Chapter 17).
Duplicate Specific Name checking. When you enter a Specific Name (the
Species Name field of the Species table), you can set Biota to check
Chapter 11 – Page 38
automatically for identical Species Name entries in existing records, disregarding
Genus. The purpose of this check is to prevent the accidental creation of two or
more Species records for the same species (albeit with distinct Species Codes).
The reason for disregarding Genus is to take into account changed or alternative
generic concepts.
To enable or disable checking for duplicate Specific Name values, choose
Preferences from the Special menu. Go to the “Other Settings” tab and find the
“Species Input screen settings” panel. Check or uncheck the setting for “Flag
duplicate specific epithets in Species Input screen.”
Here is how it works, with duplicate Specific Name checking enabled:
If the Specific Name you entered is unique among Species records in
the database, Biota automatically accepts your entry and moves on to the
next entry area (Species Author).
If the Specific Name you entered is any variation on sp., Biota accepts
your entry whether or not it is unique. Entries in this category include:
◊
sp without any additional characters.
◊
sp followed by a period or a space character, alone or followed by any
additional characters, including numbers (e.g., sp 1, sp. 3, sp. nov.).
◊
n. sp alone or followed by any additional characters.
If Biota finds another Species record with the same Species Name you
entered, an option window appears, shown below. (If more than one match
is found, the message gives the number of matches.)
Chapter 11 – Page 39
4.
◊
If you select the first option (the default), Biota accepts your entry and
moves on to the next entry area (Species Author).
◊
If you select the second option, Biota accepts your entry and moves
on to the next entry area, but a new window opens showing the existing
Species record (or records) that shares the same Species Name value.
Based on this information, it is then up to you whether to modify the
Species record you are working on, delete it, or save it as is.
◊
If you click Cancel in the option window, the entry you made in the
Specific Name entry area is cleared.
Enter Species Author (and Date). The Species Author field is an ordinary
alphanumeric field (up to 80 characters), not linked to the Personnel table. The date
(usually only the year), if you include one, is part of the entry in the Species Author
field and can therefore be in any format, without reference to the Biota date formats
described in the section “Dates” in Chapter 9.
Entry Choice List. You can enable an Entry Choice List (a pick list or authority
list) for the Species Author field using the “Entry Choice Lists” tool in the Special
menu (see “Using Entry Choice Lists” in Chapter 17). A Choice List can speed up
data entry when certain authors (and dates) apply to many Species records.
However, if you are entering a list of species that share the same entry in the
Species Author field, using the “Carry” button (see “Duplicating a Record
Displayed in the Input Screen Using the ‘Carry’ Button” in Chapter 10) may be
more efficient than using an Entry Choice List.
The parenthesis button. To place left and right parentheses around an entry in
the Species Author entry area, click the parenthesis button to the right and just
below the entry area.
5.
Enter Subgenus and Section. In Biota’s structure, Subgenus and Section are
attributes (field) of the Species table. See “Intermediate Taxonomic Levels (Subtaxa
and Supertaxa)” in Chapter 9 for details on how Biota handles Intermediate
Taxonomic levels (ranks).
Aliases. Each of the fields Subgenus and Section can be renamed using the
“Core Field Aliases” tool from the Special menu (see Chapter 18, “Renaming
Fields”).
Entry Choice Lists. You can enable an Entry Choice List (pick list) for the
Subgenus and/or Section fields using the “Entry Choice Lists” tool in the Special
menu (see “Using Entry Choice Lists” in Chapter 17).
Chapter 11 – Page 40
6.
Note the Valid Species Code and synonymy status summary in the Synonymy
panel at the bottom of the Classification tab. In a new record, the Valid Species
Code is automatically entered when you enter the Species Code and matches it
exactly. The synonymy status summary normally reads “A valid Species name with
no synonyms in the database.” (The only exception would be in the unusual case
that synonyms are already present.)
If you synonymize this Species record with another Species record, the Valid
Species Code is changed to the Species Code for the senior synonym. See Chapter
23, “Synonymy System” for details on the Synonymy panel of the Classification tab,
as well as the Synonymy tab itself.
Entering Species Data: The “Subsp/Names” Tab
The “Subsp/Names” tab records information on infra-specific classification and common
names for the taxon represented by the Species record. The rationale for including
infraspecific taxa—subspecies, varieties, cultivars, and the like—as attributes of the
Species table requires some explanation. Like other nonobligatory taxonomic ranks
(e.g., Subfamilies, Tribes, and Superorders) infraspecific taxa are defined for some
parent taxa (for some species, in this case) but not for others. By the logic presented in
Chapter 11 – Page 41
the section on “Intermediate Taxonomic Levels” in Chapter 9, infraspecific rank ought,
therefore, to be an attribute of Specimen records, not Species records, in a hierarchical
table structure like Biota’s, just as Subfamily membership is considered an attribute of a
Genus.
On the other hand, Specimen records are unique. They represent concrete entities—
physical specimens or material derived from them—whereas records in the Species,
Genus, Family, and higher taxon tables represent taxonomic concepts. In effect, records
in the Species table in Biota represent the lowest taxonomic concepts to which
Specimen records can be assigned, whether that level is in fact considered a species or
an infraspecific taxon. This structure permits Specimen determinations to be represented
by links to Species records, a key design feature of Biota’s structure, and essential to its
functioning.
For species that have infraspecific taxa, a separate record in Biota’s Species table is
required for each infraspecific taxon at the lowest level defined. For example, for a
species that has two subspecies, each in turn split into three recognized varieties, six
Species records would be required—one for each of the six varieties. Each of the six
records would also record the subspecies and species to which the variety belongs.
Field lengths. The Subspecies Author, Variety Author, and Common Name fields
each allow up to 80 characters. The Subspecies and Variety fields each allow up to
40 characters.
Entry Choice List. You can enable an Entry Choice List (a pick list or authority list)
for the Subspecies Author, Variety Author, and Common Name fields using the
“Entry Choice Lists” tool in the Special menu (see “Using Entry Choice Lists” in
Chapter 17).
The parenthesis button. To place left and right parentheses around an entry in the
Subspecies Author or Variety Author entry area, click the parenthesis button to the
right of the entry area.
Alias. The Common Name field can be renamed using the “Core Field Aliases” tool
from the Special menu (see Chapter 18, “Renaming Fields”).
Chapter 11 – Page 42
Entering Species Data: The “Dist/Types” Tab
The “Dist/Types” tab of the Species Input screen records information on the
geographical Distribution of the taxon represented by the Species record, the Type
Locality for the species, and the Type Depository (the institution in which the holotype is
deposited).
Field lengths. The Distribution field is a text field, allowing up to 32,000 characters.
The Type Locality and Type Depository fields each allow up to 80 characters.
Entry Choice Lists. You can enable an Entry Choice List (a pick list or authority
list) for the Distribution, Type Locality, and Type Depository fields using the “Entry
Choice Lists” tool in the Special menu (see “Using Entry Choice Lists” in Chapter
17).
NOTE: If you use an Entry Choice List to enter data in the Distribution field, each
entry is limited to no more than 80 characters. You can always enter a larger
number of characters manually for individual records.
Aliases. The Distribution, Type Locality, and Type Depository fields can be
renamed using the “Core Field Aliases” tool from the Special menu (see Chapter
18, “Renaming Fields”).
The “Display All Types” button. If you click this button, Biota finds and displays all
Specimen records linked to this Species record for which the [Specimen] Type
Status field contains either the string “type” (English) or “tipo” (Spanish), with or
without other characters, disregarding case (upper or lower). Thus, all Specimen
Chapter 11 – Page 43
records for this Species with “type,” “holotype,” “paratype,” “syntype,” etc., (or their
Spanish equivalents) in the Type Status field will be found.
WARNING: For Specimen records that do not represent types of any kind, do not
enter “Not a type,” “Non-type,” or any other entry containing the string “type” (or
“tipo”) in the Type Status field, or Biota will find and display them when you click the
“Display All Types” button.
The “Display Holotype” button. If you click this button, Biota finds and displays all
Specimen records linked to this Species record for which the [Specimen] Type
Status field reads (precisely) “holotype” (English) or “holotipo” (Spanish),
disregarding case (upper or lower). Presumably, there is at most one such record,
but if there are more, Biota displays them.
The “Display Specified Types” button. If you click this button, Biota presents a
request screen.
1. Enter the category of types you wish to find for this Species record by typing
in the entry area in the request window.
(The entry may be either singular or
plural. Biota strips terminal “s” before
the search.)
2. Click the “OK” button in the request
window. Biota finds and displays all
Specimen records linked to this
Species record for which the
[Specimen] Type Status field contains
exactly the string you entered (in
singular form), disregarding case
(upper or lower).
For all three buttons, any Specimen records found are displayed in the Specimen
Record Listing screen in a separate window, leaving the Species Input and screen
unchanged (although it may be hidden behind the Specimen Record Listing
screen).
Entering Species Data: Display, Printing, and Export of Infraspecific Taxon,
Distribution, and Type Information
In Record Listing screens and preformatted printed reports that display
Species information, the Species field displays Species Name (epithet), Subspecies
(if any), and Variety (if any). If both Subspecies and Variety names are present, they
are not likely to be fully displayed due to space limitations in Record Listing screens,
but all fields are fully visible in the Species Input screen. In preformatted printed
reports (e.g., the Species report, see Chapter 14, “Printing Reports”), sufficient
space is available for long Genus-Species-Subspecies-Variety tetranomials.
On pin, vial, and slide determination labels, full trinomials or tetranomials
appear, where appropriate, followed by the author field for the lowest level included
(e.g., Metrioptera roeseli subsp. roeseli var. diluta Charpentier). Authors for higher
levels are not included. See Chapter 15, “Printing Labels.”
On herbarium labels (following botanical convention), the Author fields for all
levels (species and below) are included (e.g., Beta vulgaris Linnaeus subsp. nivea
Jones var. odorata Lopez). See “Herbarium Specimen Labels” in Chapter 15.
Chapter 11 – Page 44
In the Create Web Pages sequence, a window entitled “Select Options and Fields
for Species Records” offers the option to treat subspecific authors in either the “pinvial-slide label” format or the “herbarium label” format, as described above. In
addition, checkboxes allow you to include Common Name, Distribution, Type
Locality, and/or Type Depository for each Species. See Chapter 33, “Exporting
Static Web Pages.”
If the Determination History option is enabled (see Chapter 22, “Determination
Histories”), Biota creates a Determination History record for each linked Specimen
when you add or update any infraspecific taxon fields (Subspecies, Subspecies
Author, Variety, or Variety Author) in a Species record.
To display infraspecific taxonomic, distribution, or type fields in the Species
Record Listing screen, see “Changing the Fields Displayed in an Record Listing
screen” in Chapter 10.
Entering Species Data: The “Synonymy,” “Images,” “Aux Fields,”
“Notes,” and “Refs” Tabs
Information on entering and working with data in these tabs appears elsewhere in the
Manual. Follow the links below:
Synonymy tab. For information establishing and managing species synonymies,
see Chapter 23, “Synonymy System.”
Images tab. For information on entering and working with Specimen Images in the
Images tab, see Chapter 19, “Images.”
Aux Fields tab. For information on entering Specimen Auxiliary Field data in the Aux
Fields tab, see Chapter 16, “User-Defined Auxiliary Fields and the Project System.”
Notes tab. For information on entering Specimen Notes in the Notes tab, see “Notes
Input” later in this chapter.
Refs tab. For information on creating links to References in the Refs tab, see
Chapter 20, “References.”
Genus, Family, Order, Class, Phylum, and
Kingdom Input
Data entry in the higher taxon (Genus, Family, Order, Class, Phylum, and Kingdom)
Input screens is virtually identical for all levels. You can enter a new record in one of
these screens by selecting the level from the Input menu, by clicking the Add Record
(Add Genus, Add Family, etc.) button on the Record Listing screen for that level, or “on
the fly” from the Input screen of a child table (for example, you can create a Genus
records “on the fly" from the Species Input screen).
Differences Among the Higher Taxon Input Screens
The Input screens for Genus, Family, and Order are identical in layout. The illustration
below shows the Genus Input screen as an example.
The Genus Input screen offers input areas for two intermediate taxon fields—Tribe and
Subfamily—and for three Custom fields—Genus Custom 1 through 3. Likewise, the
Family and Order Input screens also have entry areas for two intermediate taxon levels
(Superfamily and Suborder in the Family Input screen; Superorder and Subclass in the
Chapter 11 – Page 45
Order Input screen) and three Custom fields (labeled Family Custom 1–3 and Order
Custom 1–3).
The Input screens for Class and Phylum differ from this design by offering only a single
intermediate taxon field (Subphylum in the Class Input screen and Subkingdom in the
Phylum Input screen) and two Custom fields, instead of three. The Class Input screen is
shown below as an example.
Chapter 11 – Page 46
The Input screen for the Kingdom table, which has no parent table, is simplified by the
lack of the Classification panel at the lower left, but is otherwise like the Class and
Phylum Input screens. (The single intermediate taxon level is Superkingdom.)
Field lengths. You can enter up to 40 characters in each field of the higher taxon
tables.
Entry Choice Lists. You can enable an Entry Choice List (a pick list or authority
list) for the Tribe, Subfamily, and the Custom fields in the Genus table; the
Superfamily, Suborder, and Custom fields in the Family table; and the Superorder,
Subclass, and Custom fields in the Order table. You enable or disable the lists using
the “Entry Choice Lists” tool in the Special menu (see “Using Entry Choice Lists” in
Chapter 17).
Aliases. With the exception of Key fields (e.g., Genus in the Genus table, Family in
the Family table) and Linking fields (e.g., Family in the Genus table, Order in the
Family table), all fields in the higher taxon tables can be renamed using the “Core
Field Aliases” tool from the Special menu (see Chapter 18, “Renaming Fields”).
A Special Problem for Genera: Legitimate Duplicate Generic Names
The Genus field of each Genus record must contain a unique value within a Biota Data
File. There are two cases in which Biota’s use of generic names as the Key field (see
“Key Fields” in Chapter 3) for the Genus table may cause problems.
First, although the rules of nomenclature require unique names for Genera within
Kingdoms, the rules do not require unique generic names among Kingdoms, and a
number of cases exist in which the same name is legitimately used in two Kingdoms. For
example, Ammophila and Dryas are each valid genera of both plants and animals. The
uniqueness problem arises only if you need to use both names in the same Biota Data
File. Aside from general cross-Kingdom databases, host-parasite or herbivore-plant
databases provide potential examples.
Second, if you create Genus records to record generic junior synonyms, you will need to
handle duplicate names in the Genus field.
In these cases, you need to create two (or more) Genus records, with distinct values in
the Genus field. For synonyms within a Kingdom, appending the genus author in the
Genus field makes sense. For valid genera in different Kingdoms, you can add an
asterisk (*) or a pound (number or hash) sign (#) to distinguish the two records (e.g.,
Dryas and Dryas* or Dryas# and Dryas*). Or, you could add an explanatory suffix:
Dryas-Plant and Dryas-Butterfly.
NOTE: Biota looks for the characters * and # in Genus names when printing
determination labels and deletes the characters from the printed version (see Chapter
15, “Printing Labels”).
Entering Data in a Higher Taxon Input Screen: Step by Step
1.
Enter the taxon name (a Genus name, in this example), which may be up to 40
characters in length. Because Genus is the Key field for the Genus table, it is an
obligatory entry, which must be made first. All remaining entry areas are optional.
The Genus you enter must not duplicate the Genus of any existing Genus record, or
you will receive an error message (see “Duplicate Key Errors” in Chapter 3).
Chapter 11 – Page 47
NOTE: If you are creating a Genus (or other higher taxon) record “on the fly” while
working on a Species (or other lower taxon) record, the Genus name you entered in
the Species Input screen is already displayed and the cursor is in the next field
(Tribe, in the Genus Input screen).
2.
Enter intermediate taxon name or names (Tribe and Subfamily, in the Genus
Input screen).
You can enable an Entry Choice List (a pick list or authority list) for each
intermediate taxon field in the Genus, Family and Order tables, using the “Entry
Choice Lists” tool in the Special menu (see “Using Entry Choice Lists” in Chapter
17).
Each intermediate taxon field can be renamed using the “Core Field Aliases” tool
from the Special menu (see Chapter 18, “Renaming Fields”).
3.
Enter the parent taxon name (the Family name, in the Genus Input screen). You
can enter the parent taxon name using either of two methods for entering data in
linking fields, as described in the section “Entering Data in Linking Fields” in
Chapter 7.
NOTE: This step does not apply to the Kingdom Input screen, since the Kingdom
table has no parent.
Method 1: Enter the full parent taxon name manually.
◊
If a parent taxon record exists with the
name you entered, the “Classification” panel
in the lower left corner or the Input screen
displays the higher classification of the parent
taxon from the linked taxon record
(Superfamily, Suborder, and Order, in the case
of the Genus input screen). The cursor moves
on to the next entry area. The example here
show the Classification panel of the Genus
Input screen
NOTE: Be sure to confirm that the correct parent taxon record was found. If
your entry uniquely matches the first part of a different parent taxon name,
the wrong link will be made. See “Overriding Wildcard Input for Linking
Fields” in Chapter 7.
◊
If no parent taxon record exists with the name you entered, Biota offers
you the option of creating a new parent taxon record “on the fly” (using the
name you entered) or accepting an orphan record. See “‘On-the-Fly’ Creation
of Linked Records” in Chapter 7 for details.
Method 2: Enter the first letter or first few letters of a parent taxon name,
then press TAB (wildcard lookup). See “A Powerful Shortcut: Wildcard Data
Entry for Linking Fields” in Chapter 7.
Chapter 11 – Page 48
4.
◊
If only one parent taxon record matches the entry, Biota automatically
completes the entry.
◊
If more than one existing parent taxon record matches the entry, a
scrollable list of matching names for existing parent taxon records appears,
from which you can choose the correct record by clicking it with the mouse. (If
you enter the @ character, and nothing else, all records for the parent table
appear in the scrollable list.)
Enter data for the Custom fields.
You can enable an Entry Choice List (a pick list or authority list) for each Custom
field in the Genus, Family and Order tables, using the “Entry Choice Lists” tool in
the Special menu (see “Using Entry Choice Lists” in Chapter 17).
Each Custom field can be renamed using the “Core Field Aliases” tool from the
Special menu (see Chapter 18, “Renaming Fields”).
5.
Save or Carry the record.
Personnel Input
Through relational links, Biota uses records in the Personnel table to register the names
of Specimen collectors, preparators, determiners, and loan borrowers; Biota Project
managers and teams; and authors of Specimen, Species, Collection, Locality, and Loan
Notes (see Appendix A, “Biota Tables, Fields, and Relational Links”). By means of the
recursive Group system (see below), you can build multi-level Personnel hierarchies.
But Personnel records need not be linked to other records. You can also use the
Personnel table as an address book for colleagues and institutions you contact
frequently, if you wish.
The Personnel table holds four kinds of records:
Individual Personnel records. An Individual Personnel record generally registers
information for one person, but you can also create an Individual record in the
Personnel table to record contact information for an institution, organization, or
company.
Group Personnel records. A Group record in the Personnel table links together a
set of Individual Personnel records, a set of Group Personnel records (to build a
Personnel hierarchy), or a mixture of Individual and Group Personnel records. For
example, a collecting team needs a Group record linking the Individual Personnel
records of its members, so that all names in the group are linked to the appropriate
Collection records (see “Entering Collection Data: The ‘General’ Tab” earlier in this
chapter). Or, you might link all the individual records for your contacts at a museum
or herbarium to a Group record for the institution. (You can transform an Individual
record for an institution into a Group record at any time, see “Entering Personnel
Data: The 'Group' Tab,” later in this chapter.)
Project-linked Personnel records. In Biota, a single Data File can accommodate
any number of Projects, each of which is defined by a different record in the Project
table (see Chapter 16, “User-Defined Auxiliary Fields and the Project System”). Each
Project record may be linked (one-to-one) to a single Personnel record that provides
contact information for the Project.
Project-linked, Group Personnel records. A Project-linked Personnel record can
be a Group record, allowing any number of Individual or ordinary Group Personnel
records to be linked to identify a group of people associated with the Project.
Chapter 11 – Page 49
You can enter a new Personnel record by selecting Personnel from the Input menu; by
clicking the Add Record button on the Personnel Record Listing screen; or “on the fly”
from the Project, Specimen, Collection, or Notes Input screens. This section describes
how to enter data in the General, Group, and Note tabs of the Personnel Input screen.
Entering Personnel Data: The “General” Tab
1.
Enter a Short Name, Group Name, or Project Name (the Short Name field,
collectively). You can enter the Short Name for a Personnel record by typing it in
the entry area.
The Name may be up to 80 characters in length. Because Short name is the Key
field for the Personnel table, it is an obligatory entry, which must be made first. All
remaining entry areas are optional. The Short Name you enter must not duplicate
the Short Name of any existing Personnel record, or you will receive an error
message (see “Duplicate Key Errors” in Chapter 3).
Chapter 11 – Page 50
NOTE: If you are creating a Personnel record “on the fly” while working on a
Species, Specimen, Collection, Locality, Loan, or Project record, the Short Name
you entered in the linking field entry area is already displayed.
What should you assign for a Short Name? The Short Name you assign appears in
Specimen records in the Prepared By and Determined By fields, in Collection
records in the Collected By field, in Project records as the Project Short Name, in
Loan records as Borrower, and in Notes records in the Note By field.
On Pin, Slide, Vial, and Herbarium labels, Biota uses the Short Name field for the
collector’s name (see Chapter 15, “Printing Labels”). Although the Short Name may
have up to 80 characters, it is best to make it substantially shorter (20-30 characters
is a good guideline) if you are entering the name of a collector (or potential
collector) and you intend to use Biota to produce specimen labels. Choose a
version of the collector’s name that is appropriate for specimen labels—e.g., initials
and last name, or first name and last name. You can also use a “Group Name” in
the “Collected By” field—e.g., A. B. Smith & C. D. Jones (for help with Group
Names, see “Entering Personnel Data: The ‘Group’ Tab” later in this chapter).
2.
If the record is to be a Group Personnel record, check the Group checkbox in
the Short Name entry panel, then follow the instructions in the next section of this
chapter, “Entering Personnel Data: The ‘Group’ Tab.”
NOTE: You create a Project-linked Personnel record “on the fly” during creation of
Project record. When you open a Project-linked Personnel record in the Project
Input screen, the “Project Name” box is automatically checked and the “Show
Project Record” button is enabled. If you click this button, the linked Project record
is displayed in the Project Input screen in a separate window.
To ensure proper linking values, you cannot create a Project-linked Personnel
record directly in the Personnel input screen. See Chapter 16, “User-Defined
Auxiliary Fields and the Project System.”
3.
Complete the rest of the Personnel record. None of the remaining fields is
mandatory. For a Group record, you may wish to leave them all blank.
4.
Accept or Carry the Personnel record. The “Carry” button is particularly useful for
entering a series of records for people who share an address. See “Duplicating a
Chapter 11 – Page 51
Record Displayed in the Input Screen Using the ‘Carry’ Button” in Chapter 10 for
information on how the “Carry” button works.
Entering Personnel Data: The “Group” Tab
A Group record in the Personnel table links together a set of Individual Personnel
records, a set of Group Personnel records (to build a Personnel hierarchy), or a mixture
of Individual and Group Personnel records. (see the introduction to “Personnel Input,”
earlier in this chapter). Once you have created a Group record, you use the tools in the
Group tab to establish the membership of the Group.
1.
Create a Personnel record. See the previous section, “Entering Personnel Data:
The ‘General’ Tab.”
What should you assign for a Group Short Name? If you use a Group record to link
members of an institution, project team, or other organization, choose a Short Name
for the Group that best identifies the organization. If you use a Group record to
identify a group of individuals who were jointly responsible for collecting, preparing,
or determining certain specimens or for writing a Note, form the Short Name just as
you want it to appear on collection labels; in the Collected By field of Collection
records; in the Prepared By and Determined By fields of Specimen records; or in
the Note By field of Notes records. On herbarium labels, a Group Record is used to
create a list of collectors from the linked Individual records (see “Herbarium
Specimen Labels” in Chapter 15).
2.
Click the Group Name checkbox to declare this a Group record.
When you check the Group name box, the Group tab label changes from “Create
Group” to “Edit Group.” If you click the Group tab without first checking the Group
checkbox, Biota asks if you want to create a group, then checks the box for you if
you reply affirmatively.
3.
Click the “Edit Group” tab. A query window appears.
Chapter 11 – Page 52
4.
Click the “OK” button in the query window to proceed. The Group Editor appears.
The Group Editor screen has two scrollable panels. For a new Group record, the
lower panel (labeled “Not current members of this Personnel Group”) initially
displays all Personnel records, including other Group Personnel records and
Project-Linked Personnel records.
You can sort the records in the lower panel by Last Name, Institution or Short Name
using the buttons just above it.
The upper panel (labeled “Current members of this Personnel Group”), initially blank
in a new Group record, shows the members of the new Group once you form it.
5.
Use the “Append,” “Insert,” and “Remove” buttons in the Group Editor window
to establish and order the members of the Group in the upper panel.
“Append” button. To enter the first Individual record or to add an Individual to
the end of the “Current members” list in the upper panel, click the record you
want in the lower panel to select it, then click the “Append” button. Notice that the
record is “moved” to the upper panel—it is no longer listed in the lower panel.
Chapter 11 – Page 53
“Insert” button. To place an Individual record between two records already
listed in the upper panel, click the record in the upper panel that you want to
follow the record to be inserted. Click the record in the lower panel that you want
to insert, then click the “Insert” button.
“Remove” button. To remove an Individual record from the Group list in the
upper panel, click the record in the upper panel to highlight it, then click the
“Remove” button. Notice that the record now appears in the lower panel.
6.
Click the “Save Group” button in the Group
Editor tab to record the Group’s composition and the
order of its members. The General tab reappears
with the Group record displayed. Notice that both the
Group tab continues to read “Edit Group.” You can
change the Group composition in the future using this
tab.
7.
Complete additional fields (or none) in the Personnel record for this Group. For
an organizational Group record, you might record the address and contact
information for the organization. For a Group record that links specimen cocollectors, preparators, or determiners, you would probably leave the rest of the
record blank or possibly make an entry in the Notes tab with details of the
collaboration.
8.
Save the Group Personnel record.
Entering Personnel Data: The “Notes” Tab
Each Personnel record can include a single Personnel Note, up to 32,000 characters in
length.
Chapter 11 – Page 54
To create a Personnel Note, click the Note tab (which reads “Create Note” when
none is yet present), enter the Note text, and click the “Save” button for the record
to save it.
To edit an existing Personnel Note, click the Note tab (which reads “Edit Note”
when note text is already in the record), edit the Note text, and click the “Save”
button for the record to save it.
Displaying, Changing, or Reordering Group Membership for an Existing
Group Personnel Record
1.
Display the Group Personnel record in the Personnel Input screen.
2.
Click the Group tab, which reads “Edit Group” for a Group Record.
To display the members of the Group, click the “Show Group in Separate
Window” button at the bottom of the Group tab.
The records are displayed in a new window in the Personnel Record Listing
screen. Any number of Groups can be displayed simultaneously, each in its own
window. The original Personnel Record Listing screen from which you launched
the Group Record Lisitng screen(s) remains open also.
To change or reorder Group membership, use the “Append,” “Insert,” and
“Remove” buttons in the Group Editor. When you are done, click the “Save
Group” button in the Group Editor window to record the changes and return to
the General tab.
2.
Save the Group Personnel record, if you made any changes.
Notes Input
You can attach an unlimited number of Notes to each record in the Species, Specimen,
Collection, Locality, and Loans tables.
For each of these tables, a special Notes table (linked as a child table to the Species,
Specimen, Collection, Locality, or Loans table) accommodates these Notes records
(Appendix A, “Biota Tables, Fields, and Relational Links”).
This structure means you can import and export Notes records in the same way you
would any other records, using the Import (see Chapter 28, “Importing Data") and Export
Editors (see Chapter 27, “Exporting Data”). In addition, the special Export Notes tool
exports certain fields from each parent record, along with full records for each Note
(see “Exporting Notes” in Chapter 27).
When you create a new record in the Species, Specimen, Collection, Locality, or Loans
table, it has no Notes. When you delete a record from one of these five tables (or click
the “Cancel” button for a new record not yet saved), any associated Notes you have
created for it are deleted automatically (after Biota’s warning and your confirmation),
since they would otherwise be “orphaned.”
Chapter 11 – Page 55
The Personnel and Project tables accommodate notes in a simpler way. Each Personnel
or Project record has a Notes field. This means you can enter or update just one note for
each Personnel or Project record. The note can be up to 32,000 characters long. See
“Entering Personnel Data: The ‘Notes’ Tab” earlier in this chapter, and “Entering Project
Data: The ‘General’ Tab” in Chapter 16.
Entering a New Note in the Note Tab (Species, Specimen, Collection,
Locality, and Loans)
This section uses Collection Notes screens as an example, but all procedures are
identical and all screens analogous for Locality, Specimen, Species, and Loans Notes.
1.
Click the Notes tab in the Collection, Locality, Specimen, Species, or Loan Input
Screen. (You must first enter a valid Record Code.)
The Notes tab appears, with the insertion point (blinking cursor) in the Note By entry
area and today’s date (the date set in your computer’s internal clock) appearing in
the Note Date entry area. The “Save Note” button is enabled.
The Notes tab is used not only for creating new Notes and for displaying and editing
existing individual Notes, but also for listing Notes, in the same way a Record
Chapter 11 – Page 56
Listing screen lists records for Core tables. See “Viewing, Editing, or Deleting a
Note” later in this chapter.
2.
Enter the Note author’s Short Name in the “Note By” entry area.
Because this field is linked to the Short Name field of the Personnel table, the entry
area has a double border.
For step-by-step help entering a Short Name, refer to the instructions for the “Last
Determined By” field of the Specimen Input screen’s Determination tab (see Step 1
of “Entering Specimen Data: The ‘Determination’ Tab” earlier in this chapter).
The Note By field is optional. Just “TAB through” the field if you do not want to use it.
3.
Enter the Note Date. This field is obligatory, since Notes are sorted by Note Date.
To accept today’s date, just “TAB through” the date entry area, or click in the
Note Text area below.
To enter a different date, enter a full date. See “Dates” in Chapter 9 for details
on entering dates, date formats (International vs. U.S), full vs. partial dates, and
how Biota handles dates in the Data File.
4.
Enter the Note Text in the lower-right panel of the Notes screen. (Not required.)
If the length of the Note Text exceeds the size of the display panel, use the scroll
bar or the UP and DOWN arrow keys to scroll in the panel.
You can use line breaks (ENTER key in Windows, RETURN key in Mac OS) within the
Note Text field to organize the entry.
Chapter 11 – Page 57
NOTE: When exporting Notes using the Export Editor (see “Exporting Notes” in
Chapter 27), if you indicate carriage return (Mac OS) or carriage return plus line
feed (Windows) as the End of Record delimiter (see “Exporting by Tables and
Fields: Step by Step” in Chapter 27), line breaks within Note Text fields are replaced
by blanks to keep the Export Editor from interpreting them as End of Record
characters. To preserve internal line breaks in exported Notes records, specify a
different End of Record delimiter (one not used in Note Text fields), then change
this character globally to line breaks with a text editor in the exported records. (The
Export Editor automatically replaces your specified End of Record delimiter with
blanks within text and alphanumeric fields, regardless of which delimiter you
specify.)
5.
Click the “Save Note” button in
the Notes tab. The Note tab label
now shows the number of Notes
for this Species, Specimen,
Collection, or Locality record and
the “New Note” button is
enabled.
6.
To enter another Note, click
the “New Note” button in the
Notes tab and repeat Steps 2–4,
above.
NOTE: If you forget to click the “Save Note” button before going to a different tab, moving
to another record using the navigation buttons, Saving the record, or Carrying the
record, Biota asks if you would like to save the Note and does so, if you reply
affirmatively.
Viewing, Editing, or Deleting a Note
This section uses Collection Notes screens as an example, but all procedures are
identical and all screens analogous for Locality, Specimen, Species, and Loans Notes.
1.
Open an existing Collection, Locality, Specimen, Species, or Loans record.
The Notes tab shows the number of Notes already created for this record.
Chapter 11 – Page 58
2.
Click the Notes tab. The existing Notes for this record are displayed in the upper
panel (the “Collection Notes” panel in the example below), sorted by Note Date.
3.
To display an individual Note in full, click it in the Note listing panel. The Note By,
Note Date, and Note Text fields of the note you clicked appear in the Note display
(lower) panel. The “New Note,” “Save Note,” and “Delete Note” buttons are enabled.
If the length of the Note Text exceeds the size of the display panel, use the scroll
bar or the UP and DOWN arrow keys to scroll in the panel.
4.
To edit a Note, select it, make changes, then click the “Save Note” button in the
Notes tab.
5.
To delete a Note, select it, then click the “Delete Note” button in the Notes tab.
6.
To enter a new Note, click the “New Note” button in the Notes tab, then proceed as
in the previous section of this chapter (“Entering a New Note in the Note Tab
(Species, Specimen, Collection, Locality, and Loans)”.
Chapter 11 – Page 59
Carrying Notes
The “Carry” button in Biota Input screens allows you to use an existing record (or a
record you have just entered) as a template for a new record (see “Duplicating a Record
Displayed in the Input Screen Using the ‘Carry’ Button” in Chapter 10). As an option, you
can choose to Carry (copy) all Notes from the existing record to the new record (for the
tables that support Notes).
For example, a series of Collection records might share the same note describing
meteorological conditions or special equipment used at the time the collections were
made.
To enable or disable this option:
1.
Choose Preferences from the Special menu. The Preferences screen appears.
2.
Click the “Other Settings” tab.
3.
Click the “Carry Notes from the template records” checkbox to enable (check)
or disable (uncheck) the Carry Notes option. The default setting is disabled
(unchecked).
4.
Click the “Save” button in the Preferences screen.
PART
3
Finding and
Revising Data
Chapter 12
Finding and Updating Records
This chapter explains how to use tools from the Find menu and the Special menu to find
records already in a Biota Data File—and update them if you wish. Before using these
tools, you need to understand the ideas introduced in Chapter 3, “Key Concepts,”
especially the distinction between Selections and Record Sets, and the basic procedures
outlined in Chapter 10, “Working With Records in Record Listing and Input Screens.”
Biota offers several different kinds of tools for finding records, ranging from the general
to the specialized. This chapter follows the same organization, first presenting the more
general tools, then the more specialized ones. Like tools from the hardware store, a
specialized software tool applied to the task for which it was designed is almost
invariably more efficient and effective than a general-purpose tool applied to the same
task, even though the latter might work. Investing a few minutes learning how to use the
tools described in this chapter may save you much time in the long run.
Finding and Displaying All Records for a Table
You can find and display all existing records for any of Biota’s Core tables (see “Core
Tables” in Chapter 3) using the “All…” commands from the Find menu.
For example, for Specimen records, choose “All Specimens” from the Find menu. For
Locality records, choose “All Localities” from the Find menu, and so on for each Core
table.
If there are no records in the table, Biota displays a message like the one below
for the Kingdom table.
Chapter 12 – Page 2
If there are records in the table, Biota displays them in the standard Record
Listing screen for the table, where you can work with them using all the techniques
outlined in Chapter 10, “Working With Records in Record Listing and Input
Screens.”
When you click the “Done” button in the Record Listing screen, Biota displays the
standard Record Set options screen for the table (for the Order table, in the
illustration below). See “The Record Set Options Screen” in Chapter 3 for an
explanation of the options offered.
If you choose to create or modify the active Record Set for a table, you can display
the records in the new or changed Record Set using the command from the Display
menu for that table.
NOTE: Three special “Find All…” commands have special locations.
a.
The “All Loans” command is in the Loans menu. See “Displaying and Editing an
Existing Loan” in Chapter 21.
b.
The “All Determination Histories” command is in the Special menu. See
“Displaying, Editing, or Deleting Determination History Records” in Chapter 22.
c.
The “All Valid Species” command, in the Find menu, has a special function. See
Chapter 23, “Synonymy System.”
Finding Records Using the Taxonomic Hierarchy
A natural way to find records for taxa (or for Specimen records) in Biota is to use your
knowledge of the higher classification of the taxonomic (or Specimen) records you seek.
The Child Record button on the Input screen for each taxonomic rank allows you to
display all records for the next lower taxon in the Linnean hierarchy. In the Species Input
screen, the Child Record button displays all Specimen records linked to the Species
record displayed. (See “Moving Down the Table Hierarchies From an Input Screen: Child
Records Buttons” in Chapter 10.)
For example, suppose you want to find all records for genera of the plant family
Ericaceae. Here is how you might do it:
Chapter 12 – Page 3
1.
From the Find menu, select “All Families.”
2.
Find “Ericaceae” (scroll down if necessary) and open the record in the Family
Input screen. The Child Record button for the Family table is labeled “Show
Genera” and shows that there are 24 Genus records in the Data File for the plant
family Ericaceae.
3.
Click the “Show Genera” (Child Record) button. Biota displays the 24 records in
the Genus Record Listing screen.
You can continue down the hierarchy by opening a Genus record then clicking the
“Show Species” button to display the linked Species records in the Species Record
Listing screen. You could then repeat the procedure to show the Specimen records
linked to a particular Species record.
However, if your search requires finding broader sets of records linked across more than
a single level of the taxonomic hierarchy (such as finding all the Specimen records for a
Family), you need to use the “Lower Taxa for Higher Taxa” tool from the Find menu. See
“Finding Records for Lower Taxa Based on Higher Taxa” in the next section of this
chapter.
Special Tools for Finding Records in One Table Based
on a Set of Records in Another Table
Biota offers four special tools, with a common interface, for the
frequent task of finding related records up, down, and across the
taxonomic and place hierarchies. As an option, Biota will keep the
linking records for all intermediate tables as Record Sets for those
tables. These tools support rapid and intuitive query construction
and optimized, extremely fast search and display. They can be
used sequentially for complex searches. For most users, they are
among the most frequently used features of Biota.
Chapter 12 – Page 4
Finding Records for Lower Taxa Based on Higher Taxa
The “Lower Taxa for Higher Taxa” (“top-down”) taxon search tool finds all records for a
lower taxonomic rank (the target table) that belong to a higher taxon, or a selection of
higher taxa at a higher taxonomic rank (the criterion table). It does not matter whether
the two levels are adjacent in the taxonomic hierarchy or not—for example, you could
find all Specimens of a Family, or all Genera of three Orders (nonadjacent levels), or all
Specimens for a selection of Species, or all Classes for a Phylum (adjacent levels). For
nonadjacent levels, you can tell Biota to keep all related taxa at intermediate levels as
Record Sets.
This tool does exactly the opposite task from the “Higher Taxa for Lower Taxa” (“bottomup”) taxon search tool described in the next section (see “Finding Records for Higher
Taxa Based on Lower Taxa” later in this chapter).
1.
From the Find menu, choose “Lower Taxa for Higher Taxa.” The query setup
screen appears.
Chapter 12 – Page 5
2.
From the list of tables in the left panel (the panel
labeled “1. Select a Lower Taxon”), click the button
for the target table—the table containing the
records you seek. In the illustration here, the
Specimen table is being selected.
The query panel at the bottom of the screen
displays the beginning of the query.
3.
From the list of tables in the right panel (the panel labeled “2.
Select a Higher Taxon”), click the button for the table to be used
in the selection criterion (the criterion table).
If you choose Species and the Species Record Set is not
empty, the option window below appears.
◊
If you choose the first (default) option in this window
(“For one Species, to be selected”), Biota presents the “Look Up Species”
tool so you can look up a Species record according to its Genus. (See the
next pair of illustrations.)
◊
If you choose the second option (“For the Species Record Set”), Biota
automatically sets the Species Record Set option (see Step 4, below). The
Species Record Set may contain many records or only one.
If you choose Species and the Species Record Set is empty, the “Look Up
Species” tool appears. Enter a Genus name or the first few letters of a Genus
name in the “Enter Genus, select Species” entry area, then press TAB (wildcard
entry method) to display the Species records for that Genus. Click the Species
you are looking for to complete the search query.
Chapter 12 – Page 6
Here is a completed search query, using the illustration above.
If you choose a criterion table other than Species, the option panel (labeled
“3. Choose an Option or Use the Default”) will be set up for the next step. In the
example below, the user is asking Biota to find all Specimens for a Family.
4.
Specify whether Biota should use a single record or the current Record Set
from the criterion table in constructing the search query. You make this choice in the
option panel at the upper right, labeled “3. Choose an Option or Use the Default.”
Chapter 12 – Page 7
If you choose Species as the criterion table, the option you chose in Step 3
will already be set (one of the two options below).
If you choose a table other than Species as the criterion table, select the
individual record option (below, left) or the Record Set option (below, right). If you
choose the Record Set option, the Record Set for the criterion table may contain
many records or only one. The Family table was selected as the criterion table in
the illustrations below.
◊
If you choose the individual record option (above, left), you can use the
wildcard entry method to enter the name of the criterion taxon. (Enter the first
letter or first few letters of the taxon name and press TAB. See “A Powerful
Shortcut: Wildcard Data Entry for Linking Fields” in Chapter 7.)
◊
If you choose the Record Set option and there are no records in the
current Record Set for the criterion table, Biota will post a message like the
one below. If you like, you can leave the Lower Taxon for Higher Taxa screen
open while you create the appropriate Record Set in another window.
Chapter 12 – Page 8
The completed query appears in the search query panel.
5.
To create Record Sets automatically for the target records and for the linking
records in any intervening tables, click the checkbox.
You make this choice in the option panel
at the lower right, labeled “4. Create
Intervening Record Sets?”
For example, if you set up the query
“Find all Specimens for the Order
Hymenoptera” and check this option,
Record Sets for the Family, Genus, and Species tables are automatically created.
These Record Sets are composed of the records that link the “Hymenoptera” record
(in the Order table) with the Specimen records that Biota finds, based on the query.
If the box is checked, a Record Set is also automatically created for the Specimen
records found.
It is not necessary to check this option in order to find the target table (Lower
Taxon) records you are searching for, nor to create a Record Set for them. If you
want to create a Record Set for the target records without checking this option, you
may do so by means of the standard Record Set option screen (see “The Record
Set Options Screen” in Chapter 3) when leaving the Record Listing screen for the
target table (see Step 6, below).
WARNING: Creating Record Sets for intervening tables during the search replaces
any existing current Record Sets for those tables.
6.
To launch the search, click the “Find” button or
press the ENTER key (Windows) or RETURN key (Mac
OS).
If target table records matching the search query
are found, they are displayed in the standard Record
Listing screen for the target table, where you can
work with them using all the techniques outlined in Chapter 10, “Working With
Records in Record Listing and Input Screens.” When you click the “Done” button
in the Record Listing screen, Biota displays the standard Record Set options
screen (see “The Record Set Options
Screen” in Chapter 3 for explanation of
the options offered).
If no target table records match the
search query, Biota displays the
message screen at the right. If you
click the “Try Again” button, the search
setup screen reappears, with settings
as you left them.
Chapter 12 – Page 9
Finding Records for Higher Taxa Based on Lower Taxa
The “Higher Taxa for Lower Taxa” (“bottom-up”) search tool finds all records for a higher
taxonomic level (the target table) that belong to the active Record Set for a lower
taxonomic level (the criterion table). For example, you could find all Orders for the
Specimen Record Set (nonadjacent levels) or all Families for the Genus Record Set
(adjacent levels). For nonadjacent levels, you can tell Biota to keep all related taxa at
intermediate levels as Record Sets.
This tool does exactly the opposite task from the Lower Taxa for Higher Taxa (“topdown”) search tool described in the previous section (see “Finding Records for Lower
Taxa Based on Higher Taxa” above). In addition to working in the reverse direction along
the same set of linked tables, this tool also differs in requiring you to designate a Record
Set for the criterion table before setting up the search—an optional method in the
“Higher Taxa for Lower Taxa” tool. The Record Set for the criterion table may contain
many records or only one.
1.
From the Find menu, choose “Higher Taxa for Lower Taxa.” The query setup
screen below appears.
2.
From the list of tables in the left panel (the panel labeled “1. Select a Higher
Taxon”), click the button for the target table—the table containing the records you
seek. In the illustration on the next page, the Order table has been selected.
The query panel displays the beginning of the query.
Chapter 12 – Page 10
3.
From the list of tables in the right panel (the panel labeled “2. Select a Lower
Taxon”), click the button for the table to be used in the selection criterion (the
criterion table). In the illustration below, the Species table is being selected. The
Record Set for the criterion table may contain many records or only one.
The query panel displays the completed query.
4.
If there are no records in the current Record Set for the criterion table, Biota
posts a message. If you like, you can leave the Higher Taxon for Lower Taxa
screen open while you create the appropriate Record Set in another window.
5.
To create Record Sets automatically for the target records and for the linking
records in any intervening tables, click the checkbox.
You make this choice in the option panel at
the right, labeled “3. Create Intervening
Record Sets?”
For example, if you set up the query “Find
all Orders for the Species Record Set” and
check this option, Record Sets for the
Genus and Family tables are automatically created. These Record Sets are
composed of the records that link the Species records (the criterion Record Set)
with the Order records that Biota finds, based on the query. If the box is checked, a
Record Set is also automatically created for the Order records found.
It is not necessary to check this option in order to find the target table (Higher
Taxon) records you are searching for, nor to create a Record Set for them. If you
want to create a Record Set for the target records without checking this option, you
may do so by means of the standard Record Set option screen (see “The Record
Chapter 12 – Page 11
Set Options Screen” in Chapter 3) when leaving the Record Listing screen for the
target table (see Step 6, below).
WARNING: Creating Record Sets for intervening tables during the search replaces
any existing current Record Sets for those tables.
6.
To launch the search, click the “Find” button or press the ENTER key (Windows)
or RETURN key (Mac OS).
If target table records matching the search query are found, they are
displayed in the standard Record Listing screen for the target table, where you
can work with them using all the techniques outlined in Chapter 10, “Working
With Records in Record Listing and Input Screens.” When you click the “Done”
button in the Record Listing screen, Biota displays the standard Record Set
options screen (see “The Record Set Options Screen” in Chapter 3 for
explanation of the options offered).
If no target table records match the search query, Biota displays the message
screen below. If you click the “Try Again” button, the search setup screen
reappears, with settings as you left them.
Finding Place Records (Collection or Locality) for Specimens or Species
The “Places for Specimens or Species” search tool finds all Locality or Collection
records for the active Specimen or Species Record Set, or all Locality records for the
Collection Record Set, according to your query. For example, you could find all Locality
records for a group of Species (a cross-hierarchy query), to study their geographic range
in the database. You can tell Biota to keep the related Specimen and Collection records
(intermediate tables in the search) as Record Sets.
This tool does exactly the opposite task from the Specimens or Species for Places
search tool described in the next section (see “Finding Specimen or Species Records for
Places (Collections or Localities)” later in this chapter).
Chapter 12 – Page 12
1.
From the Find menu, choose “Places for Specimens or Species.” The query
setup screen below appears.
2.
From the list of tables in the left panel (the panel labeled “1. Select a Target
Table”), click the button for the target table—the table containing the records you
seek. In the illustration below, the Localities table has been selected.
The query panel displays the beginning of the query.
3.
From the list of tables in the right panel (the panel labeled “2. Select a Record
Set”), click the button for the table to be used in the selection criterion (the criterion
table). The Record Set for the criterion table may contain many records or only one.
In the illustration below, the Species table is being selected.
Chapter 12 – Page 13
The query panel displays the completed query.
4.
If there are no records in the current Record Set for the criterion table, Biota
posts a message like the one below. If you like, you can leave the “Places for
Specimens or Species” screen open while you create the appropriate Record Set in
another window.
5.
To create Record Sets automatically for the target records and for the linking
records in any intervening tables, click the checkbox.
You make this choice in the option panel
labeled “3. Create Intervening Record
Sets?”
For example, if you set up the query “Find
all Localities for the Species Record Set”
and check this option, Record Sets for the
Specimen and Collection tables are
automatically created. These Record Sets are composed of the records that link
selected Species records (the criterion Record Set) with the Locality records that
Biota finds, based on the query. If the box is checked, a Record Set is also
automatically created for the Locality records found.
It is not necessary to check this option in order to find the target table records you
are searching for, nor to create a Record Set for them. If you want to create a
Record Set for the target records without checking this option, you may do so by
Chapter 12 – Page 14
means of the standard Record Set option screen (see “The Record Set Options
Screen” in Chapter 3) when leaving the Record Listing screen for the target table
(see Step 6, below).
WARNING: Creating Record Sets for intervening tables during the search replaces
any existing current Record Sets for those tables.
6.
To launch the search, click the “Find” button or press the ENTER key (Windows)
or RETURN key (Mac OS).
If target table records matching the search query are found, they are
displayed in the standard Record Listing screen for the target table, where you
can work with them using all the techniques outlined in Chapter 10, “Working
With Records in Record Listing and Input Screens.” When you click the “Done”
button in the Record Listing screen, Biota displays the standard Record Set
options screen (see “The Record Set Options Screen” in Chapter 3 for
explanation of the options offered).
If no target table records match the search query, Biota displays the message
screen below. If you click the “Try Again” button, the search setup screen
reappears, with settings as you left them.
Finding Specimen or Species Records for Places (Collections or Localities)
The “Specimens or Species for Places” search tool finds all Specimen or Species
records for the active Collection or Locality Record Set, or all Collection records for the
Locality Record Set, according to your query. For example, you could find all Species
records for a group of Localities (a cross-hierarchy query) to create a regional fauna or
flora list. You can tell Biota to keep the related Collection and Specimen records
(intermediate tables in the search) as Record Sets.
This tool does exactly the opposite task from the “Places for Specimens or Species”
search tool described in the previous section (see “Finding Place Records (Collection or
Locality) for Specimens or Species” earlier in this chapter).
Chapter 12 – Page 15
1.
From the Find menu, choose “Specimens or Species for Places.” The query
setup screen below appears.
2.
From the list of tables in the left panel (the panel labeled “1. Select a Target
Table”), click the button for the target table—the table containing the records you
seek. In the illustration below, the Species table has been selected.
The query panel displays the beginning of the query.
3.
From the list of tables in the right panel (the panel labeled “2. Select a Record
Set”), click the button for the table to be used in the selection criterion (the criterion
table). The Record Set for the criterion table may contain many records or only one.
In the illustration below, the Locality table is being selected.
Chapter 12 – Page 16
The query panel displays the completed query.
4.
If there are no records in the current Record Set for the criterion table, Biota
posts a message like the one below. If you like, you can leave the Specimens or
Species for Places screen open while you create the appropriate Record Set in
another window.
5.
To create Record Sets automatically for the target records and for the linking
records in any intervening tables, click the checkbox.
You make this choice in the option panel at
the right, labeled “3. Create Intervening
Record Sets?”
For example, if you set up the query “Find
all Species for the Locality Record Set” and
check this option, Record Sets for the
Collection and Specimen tables are automatically created. These Record Sets are
composed of the records that link the Locality records (the criterion Record Set) with
the Species records that Biota finds, based on the query. If the box is checked, a
Record Set is also automatically created for the Species records found.
It is not necessary to check this option in order to find the target table (Higher
Taxon) records you are searching for, nor to create a Record Set for them. If you
want to create a Record Set for the target records without checking this option, you
may do so by means of the standard Record Set option screen (see “The Record
Chapter 12 – Page 17
Set Options Screen” in Chapter 3) when leaving the Record Listing screen for the
target table (see Step 6, below).
WARNING: Creating Record Sets for intervening tables during the search replaces
any existing current Record Sets for those tables.
6.
To launch the search, click the “Find” button or press the ENTER key (Windows)
or RETURN key (Mac OS).
If target table records matching the search query are found, they are
displayed in the standard Record Listing screen for the target table, where you
can work with them using all the techniques outlined in Chapter 10, “Working
With Records in Record Listing and Input Screens.” When you click the “Done”
button in the Record Listing screen, Biota displays the standard Record Set
options screen (see “The Record Set Options Screen” in Chapter 3 for
explanation of the options offered).
If no target table records match the search query, Biota displays the message
screen below. If you click the “Try Again” button, the search setup screen
reappears, with settings as you left them.
Sequential, Cross-Hierarchy Searches
If you want to find Collections or Localities for taxa above the level of Species, or
discover which higher taxa are represented in Collections or Localities, you can use the
appropriate pair of search tools sequentially, choosing among the tools introduced in the
preceding four sections of this chapter.
Finding Records for Lower Taxa Based on Higher Taxa
Finding Records for Higher Taxa Based on Lower Taxa
Finding Place Records (Collection or Locality) for Specimens or Species
Finding Specimen or Species Records for Places (Collections or Localities)
For example, to find all the Localities for an Order:
1.
Find all Species for the Order using the “Lower Taxa for Higher Taxa tool”
(Finding Records for Lower Taxa Based on Higher Taxa).
2.
Declare the group of Species records found to be the current Species Record
Set. (See “The Record Set Options Screen” in Chapter 3.)
Chapter 12 – Page 18
3.
Find all Localities for the Species Record Set using the Places for Specimens or
Species tool (Finding Place Records (Collection or Locality) for Specimens or
Species). The Locality records found will encompass all Localities in which any
Specimen of the original criterion Order has been found, as recorded in the Data
File.
The Query Editor, a General-Purpose Tool for Finding
Records Based on Content
When none of the specialized tools from the Find menu fits the record-finding task you
have in mind, the Query Editor may be the answer. The Query Editor is often the tool of
choice when you need to find records based on their content, although displaying all
records for a table (see “Finding and Displaying All Records for a Table” earlier in this
chapter), then using the Sort Editor (see the four sections beginning at “Sorting Records
in Record Listing Screens” in Chapter 10) is often just as efficient. The Query Editor is
restricted to finding Core table records, but the query can be based on fields and values
in virtually any Biota table.
Using the Query Editor: Step by Step
1.
From the Find menu, choose “Using the Query Editor.” A table selection
window appears.
2.
Click and hold the popup
list to select the table
containing the records you
seek—called the target
table. In the illustration
below, the Genus table is
being selected as the
target table for the search.
Chapter 12 – Page 19
When you have chosen a table, the search option buttons are activated.
3.
Choose a search option in the window (above).
Either: Search all records in the selected table.
Or: Search only in the active Record Set for the table.
If there are no records in the active Record Set for the table, the lower button is
disabled (dimmed). If there are no records in the table, Biota informs you with a
message, neither button is activated, and the search is canceled.
4.
Click the “Search” button or press the ENTER key (Windows) or RETURN key (Mac
OS) to launch the Query Editor. The Query Editor window appears.
Chapter 12 – Page 20
The Query panel of the Query Editor (initially blank) will display the search
query, once you have set it up. This is the upper panel in the window.
The “Available Fields” panel (the scrollable
panel on the center left) is used to display and
select fields (and tables), which are listed
alphabetically.
Field names in boldfaced type are indexed
fields. Searches for values in indexed fields
proceed faster than searches for values in
non-indexed fields—but you can search on
any field. (Indexes take up space in data files
and processor time to maintain, so not all
fields in Biota are indexed.)
When fields are displayed in the “Available Fields panel,” the icon to the left of
each field name indicates the field type, as follows:
◊
Alphanumeric field
◊
Text field
◊
Integer field
◊
Real number (decimal) field
◊
Date field
◊
Boolean field
(short)
(long)
The popup menu just below the panel title
“Available Fields” controls the display of fields.
The popup menu retains its setting between
uses of the Query Editor.
Chapter 12 – Page 21
The Comparisons panel (the scrollable
panel on the center right) is used to display
and select comparison operators for building
queries.
The Value entry area (running across the
window above the buttons) is the entry area
for field values used in search queries.
The logical operator buttons (And, Or, and Except) are used to create and
compound queries.
The line manipulation buttons (Clear All, Del Line, Insert Line, and Add Line)
are used to create and edit lines (criteria) for compound queries.
The “Save” and “Load” buttons allow you to save queries (which are
sometimes complex to set up) to disk file, then reload them at a later date.
The “Cancel” and “Query” buttons are used to dismiss the Query Editor and
launch a search, respectively.
The “Query in selection” button has no function in Biota. (The Query Editor is
a predefined 4D tool.) If you want to search in a particular selection of records,
declare them the current Record Set for the table (See “The Record Set Options
Screen” in Chapter 3) and choose the second
option in Step 3, above.
5.
If you have defined any Core Field Aliases
(see Chapter 18, “Renaming Fields”), the aliases
are displayed in the Query Editor instead of the
Internal Field Names.
In the example here, the fields Genus Custom 1
and Genus Custom 2 (Internal Field Names)
have been given the Aliases Genus Author and
Tribe Author, respectively.
6.
Set the popup menu to either “Related
Tables” or “Master Table.” All fields of the
target (= “master”) table will be shown in either
case.
7.
Click a field name from the “Available Fields”
panel to select it. When the Query Editor first
opens, this scrollable panel shows the names of
all fields for the table you selected in Step 2. (You
may have to scroll to see them all.) In the
Chapter 12 – Page 22
illustration above, the Family linking field in the Genus table is being selected for the
query. The field name you select appears in the query panel (see the illustration in
Step 8).
8.
Click an operator from the Comparisons
panel to add it to the query. In the illustration
below, the operator “is not equal to” is being
selected.
The operator you selected appears in the query
panel (see the second illustration in Step 9).
NOTE: The quantitative operators (is greater than, is greater than or equal to, and is
less than) can be used not only on numeric fields, but also on values in alphabetic
fields. When used on alphanumeric values, these operators evaluate the ASCII
code of the characters, left to right. Thus 01 is less than 10, but 1 is evaluated as
“greater than” 10. The digits 0–9 are “less than” the letters A–Z. In short, the order
of alphanumeric values is the same as their alphanumeric sort order.
9.
Enter a field value in the Value entry area to complete the query line.
The field value appears simultaneously in the query panel. In the illustration above,
the family name Ericaceae is the field value entered, completing the query line
“Family is not equal to Ericaceae.”
NOTE: Field values are not case-sensitive: Ericaceae, ericaceae, and ERICACEAE
would all have the same meaning in the query illustrated above.
Chapter 12 – Page 23
10. To create a compound query, take these steps:
a. Click the “Add Line” button to
start a new query line. (Or click the
“Insert Line” button to insert a new
line above the highlighted query line.)
b. Click a button in the logical operators panel. The
“And” button is being clicked in the illustration at the
right
c. Follow steps 7–9, above, to construct an additional query line.
d. Repeat as many times as necessary to complete the query.
In the completed example below, the compound query seeks all Genus records for
which the [Genus] Family field is neither Ericaceae nor Campanulaceae.
NOTE: Compound searches are performed in the order the lines appear in the
search query, top to bottom, regardless of the conjunction used (i.e., there is no
fixed precedence among the three conjunctions).
11. To launch the search, click the “Query” button in the
Query Editor.
If target table records matching the search query
are found, they are displayed in the standard
Record Listing screen for the target table, where you
can work with them using all the techniques outlined in Chapter 10, “Working
With Records in Record Listing and Input Screens.” When you click the “Done”
button in the Record Listing screen, Biota displays the standard Record Set
options screen (see “The Record Set Options Screen” in Chapter 3 for
explanation of the options offered).
If no records are found that match
the criteria in the search query,
Biota displays the message screen
below. If you click the “Try Again”
button, the Query Editor reappears,
set to search for records in the same
target table as before.
Chapter 12 – Page 24
Using Fields from Parent Tables in the Query Editor
Before consulting this section, please review the previous section, “Using the Query
Editor: Step by Step” and the section “Linking Fields: Parent and Child Records” in
Chapter 3.
When you open the Query Editor, you specify the table containing the records you
seek—the target table for the search (Step 2 in the previous section). In the previous
section, the search queries illustrated all relied solely on fields of the target table itself.
You can also use fields from linked tables in search queries you build with the Query
Editor. This section explains how to use fields from parent tables to build query criteria.
To learn how to use fields from child tables to construct query criteria, consult the
section “Using Fields from Child Tables in the Query Editor” later in this chapter.
1.
Launch the Query Editor following steps 1 through 4 in the previous section,
“Using the Query Editor: Step by Step.”
In the illustration here, the Collection table was
selected as the target table for the search.
2.
From the popup menu above the list of fields,
select “Related Tables.” To include a field from
a parent table in a query criterion, set the popup
(or leave it set) to “Related Tables.”
3.
Display the fields for a parent table by clicking
on the expansion triangle to the left of the name
of the parent-table linking field in the target table.
For example, if you want to search for Collection
records from Ecuador, you will need to set up a
query based on the Country field of the Locality
table. You can do this because Locality is a
parent table to the Collection table (each Locality
record may be linked to many Collection
records). Because the [Collection] LocalityCode
field is the linking field, click on the expansion
triangle next to that field.
All fields of the parent table (Locality) are
displayed, indented below the linking field name
(LocalityCode).
NOTE: There is an alternate way to display fields
from a parent table: Select “All Tables” from the
popup menu above the list of fields, then click the
parent table name to display its fields.
4.
Select a field from the parent table to use in the query criterion, and enter a
field value to search for. Once the fields for the parent table appear in the field list,
you can include these fields in search criteria, using the same techniques described
in the previous section, “Using the Query Editor: Step by Step.”
Chapter 12 – Page 25
Below, the Country field of the Locality table has been used to set up a query to find
Collection records linked to Localities in Ecuador. (Note that the table name,
“[Locality],” appears in the query window to make clear that a field from a linked
table has been used.)
NOTE: In the case of parent-child (many-to-one) links, you can reference fields from
a related table at any level up a hierarchy. For example, you could find all Genus
records linked to a specified Kingdom or to a specified value in any other field from
a higher taxon table. Or, you could find all Specimen records linked to Locality
records from a certain Country.
5.
When the query is ready, complete the search as described in Step 10 of the
previous section “Using the Query Editor: Step by Step.”
Chapter 12 – Page 26
Using Fields from Child Tables in the Query Editor
Before consulting this section, please review the sections “Using the Query Editor: Step
by Step” and “Using Fields from Parent Tables in the Query Editor,” earlier in this
chapter, and the section “Linking Fields: Parent and Child Records” in Chapter 3.
When you open the Query Editor, you specify the table containing the records you
seek—the target table for the search. The search queries illustrated in the section “Using
the Query Editor: Step by Step,” earlier in this chapter, all relied solely on fields of the
target table itself. You can also use fields from linked tables in search queries you build
with the Query Editor. The section “Using Fields from Parent Tables in the Query Editor,”
earlier in this chapter, explains how to use fields from parent tables to build query
criteria. This section explains how to use fields from child tables to construct query
criteria.
Here is the rule for using child tables in a query: If a query criterion refers to a field in a
child table, each record in the target table that is linked to at least one child record
meeting the search criterion will be found by the query.
For example, with Genus as the target table, you could use the “Number Images” field
from the Species table (which specifies the number of Image Archive records linked to
each Species record) to set up the search query “Number Images is greater than 0.”
This search would find all Genus records that are linked to at least one Species record
that has at least one linked Image Archive record.
1.
Launch the Query Editor following steps 1 through 4 in the section “Using the
Query Editor: Step by Step” earlier in this chapter.
In the illustration here, the Collection table was
selected as the target table for the search.
2.
From the popup menu above the list of fields,
select “All Tables.” To include a field from a child
table in a query criterion, you must set the popup (or
leave it set) to “All Tables.”
3.
Display the fields for a child table linked to the
target table by clicking on the expansion triangle to
the left of the name of the child table.
For example, if you want to search for Collection
records that have Collection Notes containing the
word “rain,” you can set up a query based on the
“Note Text” field of the Collection Notes table. You
can do this because Collection Notes is a child table
to the Collection table (each Collection record may be
linked to many Collection Notes).
4.
Select a field from the child table to use in the
query criterion, and enter a field value to search
for. Once the fields for the child table appear in the
field list, you can include these fields in the search
criteria, using the same techniques described in the
section “Using the Query Editor: Step by Step,”
earlier in this chapter. The “Note Text” field of the
Collection Notes table is being selected here.
Chapter 12 – Page 27
Below, the full query criterion appears for finding Collection records that have
Collection Notes containing the word “rain.” (Note that the table name, “[Collection
Notes],” appears in the query window to make clear that a field from a linked table
has been used.)
NOTE: In searching for records based on values in a child table, you can use fields only
from a directly linked child table. For example, you could not use a field of the Specimen
table in a search criterion for Genus records, because the Species table is interposed.
(In contrast, parent tables linked through intermediate tables may be used in queries.)
5.
When the query is ready, complete the search as in described in Step 10 of the
previous section, “Using the Query Editor: Step by Step.”
Using the Query Editor to Find Records Based on Notes
You can use the Query Editor to find records in the Locality, Collection, Specimen,
Species, or Loans table based on text in linked Notes records. You can search in the
“Note Date,” “Note By” (note author), or “Note Text” fields.
1.
From the Find menu, choose “By Using Query Editor.” A table selection window
appears.
Chapter 12 – Page 28
2.
Click and hold the popup list to select the Notes table you want to search. In the
illustration below, the Species Notes table is being selected.
The appropriate search options in the window are activated.
Chapter 12 – Page 29
3.
Choose a search option in the window (above).
Either: Search all records in the selected Notes table.
Or: Search only those Notes linked to records in the active Record Set for
the parent table.
If there are no records in the active Record Set for the parent table (the Species
table, in this example), the lower button is not activated.
4.
Click the “Search” button in the options window to launch the Query Editor. The
Query Editor window appears, displaying the fields of the Notes table (Species
Notes, in this example. Set up a query based on values in the Note Date, Note By,
and/or Note Text fields.
NOTE: If you are not familiar with the Query Editor, please consult the section “Using
the Query Editor: Step by Step” earlier in this chapter.
5.
Click the “OK” button to launch the search. Biota finds and displays all the
parent table records (Species records, in this example) for which the criteria you set
are true in the linked Species Notes records.
Chapter 12 – Page 30
NOTES:
a.
You can also include criteria from the parent table or any table linked to it, with the
same restrictions as for any other query. See “Using Fields from Parent Tables in
the Query Editor” earlier in this chapter.
b.
For any complex and time-consuming search, it is a good idea to create a Record
Set Pointer File to record the results for future reference or use. These files are very
small and very efficient. See “Record Set Pointer Files” in Chapter 3
Using the Query Editor with Auxiliary Field Values
You can use the Query Editor to search for Specimen, Species, Collection, or Locality
records based on values in Auxiliary Fields for those records.
WARNING: If you are not familiar with Auxiliary Fields in Biota, or you are not sure how
they work, be sure to consult Chapter 16, “User-Defined Auxiliary Fields and the Project
System,” before using the Query Editor with Auxiliary Field Values. If you are unfamiliar
with the Query Editor, please review the sections “Using the Query Editor: Step by Step”
earlier in this chapter.
Here are the steps to take:
1.
From the Find menu, choose “Using Query Editor.” The table selection window
appears.
NOTE: Notice the “Aux Field Search Help” button, which displays a succinct version
of these instructions, should you need help.
Chapter 12 – Page 31
2. Click and hold the popup list to select the table containing the records you seek—
called the target table. In the illustration below, the Species table is being selected as the
target table for the search.
If you choose a table that does not support Auxiliary Fields (e.g., Genus),
the “Use Auxiliary Field Values checkbox” remains disabled (dimmed).
If you choose one of the four tables that support Auxiliary Fields
(Specimen, Species, Collection, or Locality), the “Use Auxiliary Field Values”
checkbox is activated.
3.
Choose a search option in the window (above).
Either: Search all records in the selected table.
Or: Search only in the active Record Set for the table.
Chapter 12 – Page 32
If there are no records in the active Record Set for the table, the lower button is
disabled (dimmed). If there are no records in the table, Biota informs you with a
message, neither button is activated, and the search is canceled.
4.
Check (enable) the Use Auxiliary Field Values checkbox. If you do not want to
use Auxiliary Field Values in the search, leave the checkbox unchecked and
proceed according to the instructions in the section “Using the Query Editor: Step by
Step” earlier in this chapter.
5.
Click the “Search” button or press the
ENTER key (Windows) or RETURN key (Mac
OS) to launch the Query Editor. The Query
Editor window appears, with the “Available
Fields” panel displaying not the fields of the
target table (Species, in this example), but
rather the three fields of the corresponding
Auxiliary Field Value table (the Species Field
Value table, in this example).
6.
Set up a query based on both the “Field
Name” and the “Field Value” fields. For example, to find all Species records that
have the value “lanceolate” in a Species Auxiliary Field you have named “Leaf
Shape,” you would set up the query: “FieldName is equal to Leaf Shape And
FieldValue is equal to lanceolate,” as shown below.
7.
To launch the search, click the “Query” button in the Query Editor. Biota finds and
displays all the parent table records (Species records, in this example) for which the
criteria you set are true in the linked Auxiliary Field Value table.
WARNING: In a search based on Auxiliary Field Values, you must use only Auxiliary Field
Names and Auxiliary Field Values in the search criteria. You cannot use fields from the
parent table itself (the Species table, in the example) nor from any other table in such a
search. Moreover, you can search for only one Auxiliary Field based criterion at a time.
For more complex searches, see the next section of this chapter, “Using the Query
Editor with Auxiliary Field Values in Combination with Other Criteria.”
Chapter 12 – Page 33
Using the Query Editor with Auxiliary Field Values in Combination with
Other Criteria
If you need to perform a search based on Auxiliary Field Values as well as values in
other fields, you must use a two- or three-step process.
WARNING: This section assumes you are thoroughly familiar with the previous section of
this chapter, “Using the Query Editor with Auxiliary Field Values,” with Auxiliary Fields
(see Chapter 16, “User-Defined Auxiliary Fields and the Project System,” and with the
Query Editor (see “Using the Query Editor: Step by Step” earlier in this chapter).
Case 1: Finding records for a target table based on values in Core fields as
well as Auxiliary Fields of the target table.
Suppose you have defined an Auxiliary Field named “Weather” for the Collection
table, to record conditions at the time of each collecting event. Possible values for
Weather might include “Fair,” “Overcast,” “Rain,” and so on. Now suppose you wish
to find all Collection records for which the “Collected By” field of the Collection table
shows that the collection was made by C. Darwin, the “Country” field of the linked
Locality record shows that the collection was made in Ecuador, and the linked “Coll
Field Value” (Collection Auxiliary Field Value) record for “Weather” indicates an
“Overcast” day.
For this example, you would use the following strategy:
1. Use the Query Editor to find all records in the target table that meet the
criteria based on Auxiliary Field Values. In this example, you would select the
Collection table in the field selection window (see step 2 in the previous section,
“Using the Query Editor with Auxiliary Field Values”), select “Search All
Collection Records,” and check the “Use Collection Auxiliary Fields” checkbox in
the window. When the Query Editor appears, set up the query, “FieldName is
equal to Weather And FieldValue is equal to Overcast,” and launch the search.
2. When the records Biota finds are displayed, declare them to be the current
Record Set for the target table. In the example, you would declare the
Collection records for overcast days to be the current Collection Record Set,
using the Record Set Options screen that appears when you click the “Done”
button in the Collection Record Listing screen (see “The Record Set Options
Screen” in Chapter 3).
3. Use the Query Editor to search within the Record Set according to the
remaining criteria. In the example, you would again select the Collection table
in the field selection window (step 2 in the previous section, “Using the Query
Editor with Auxiliary Field Values”), but then choose the “Search in the Collection
Record Set” option. This time, do not check the “Use Collection Auxiliary Fields”
checkbox in the window. When the Query Editor appears, set up the query,
“CollectedBy is equal to C. Darwin And [Locality]Country is equal to Ecuador,”
and launch the search. (See “Using Fields from Parent Tables in the Query
Editor,” earlier in this chapter, if you need help using fields from the Locality table
in this example.)
Chapter 12 – Page 34
Case 2: Finding records for a target table based on values in Core fields as
well as Auxiliary Fields of a parent table.
What if you need to find records in one table based on Auxiliary Field Values linked
to a different (parent) table? Building on the previous example, what if you need to
find all Specimen records for specimens collected on overcast days by Darwin in
Ecuador?
In this case, you must add a new step to the strategy outlined above.
1. Use the Query Editor to find all records in the parent table that meet the
criteria based on Auxiliary Field Values and Core field values. In this
example, the Collection table is the parent table of the target table (Specimen).
Proceed exactly as in the previous example, finding all Collection records for
overcast days made by Darwin in Ecuador.
2. When the records Biota finds are displayed, declare them to be the current
Record Set for the target table. In the example, you would declare the
Collection records for overcast days to be the current Collection Record Set,
using the Record Set Options screen that appears when you click the “Done”
button in the Collection Record Listing screen (see “The Record Set Options
Screen” in Chapter 3).
3. Find all records in the target table that are linked to the Record Set in the
parent table, using the tools of the Find menu for finding records in one table
based on a Record Set for another table (see “Special Tools for Finding Records
in One Table Based on a Set of Records in Another Table” earlier in this
chapter). In this example, you would use the “Specimen or Species for Places”
tool (Find menu) to find all Specimen records linked to the Collection record set.
These Specimen records are the ones you are looking for.
More complex cases. You can use Biota’s capability for manipulating Record Sets
(see “The Record Set Options Screen” in Chapter 3) to carry out more complex
searches involving Auxiliary Field Values from two different tables or two different
Auxiliary Field Value criteria for the same target table.
Building again on the previous example, suppose you had also defined a Specimen
Auxiliary Field named “Condition” to record the current condition of mounted
specimens. Now suppose you need to find all Specimen records for specimens
collected on overcast days by Darwin in Ecuador, for which the Condition is “Good.”
To do so, you would first carry out a search just as described in the previous
section, finding all Specimen records for specimens collected on overcast days by
Darwin in Ecuador. Then declare these Specimen records to be the current
Specimen Record Set. Next, carry out a search, using the Query Editor, for all
Specimen records for which the “Condition” Auxiliary Field Value is “Good.” Click
the “Done” button in the Specimen Record Listing screen. When the Record Code
Options screen appears, click the “More Choices” button on it, then click the button
labeled “Make shared records the new Record Set” to find the intersection of the set
of records for specimens in good condition and the Record Set of specimens collected
on overcast days by Darwin in Ecuador. The resulting set of records meets all
criteria.
NOTE: For any complex and time-consuming search, it is a good idea to create a Record
Set Pointer File to record the result for future reference or use. These files are very small
and very efficient. See “Record Set Pointer Files” in Chapter 3.
Chapter 12 – Page 35
Finding Records by Record Codes
Because Record Codes uniquely identify each record in the Specimen, Collection,
Locality, and Species tables (see Chapter 8, “Record Codes”), finding a record in one of
these tables by its Record Code is sometimes the fastest way to retrieve, display, and—
if necessary—edit an existing record. If you use barcodes (see Appendix K, “Barcodes”)
for Specimen Codes or other Record Codes, these tools are especially fast to use.
Four commands from the Find menu (“By Specimen Code,” “By Collection Code,” “By
Locality Code,” and “By Species Code”), all with the same interface, take care of this
straightforward task. A fifth “Find” command with a different interface, “By Specimen
Code Series,” is covered in Chapter 13, “Creating, Finding, and Updating Specimen
Series.”
1.
From the Find menu, choose “By Specimen Code,” “By Collection Code,” “By
Locality Code,” and “By Species
Code.” The Record Code query screen
appears (illustrated below for the
Specimen table).
2.
In the entry area of the request window,
enter the full Record Code (Specimen
Code, Collection Code, Locality Code, or
Species Code) for the record you want to
find, manually or with a barcode reader.
NOTE: You cannot use the wildcard entry method with these tools.
3.
Click the “OK” button in the request window to launch the search.
If the record is found, it is displayed in the standard Input screen for the target
table, where you can work with it using the techniques outlined in Chapter 10,
“Working With Records in Record Listing and Input Screens.”
Chapter 12 – Page 36
When you click the “Cancel” button in the target table Input screen, above, Biota
displays the standard Record Set options screen for the target table. See “The
Record Set Options Screen” in Chapter 3 for explanation of the options offered.
If the record is not found, Biota displays a message like the one below
(illustrated for the Specimen table). If you click the “Try Again” button, the Record
Code request screen for the same target table reappears.
Finding Host and Guest Specimens and Collections
Four commands in the Find menu (“Host Specimens & Collections,” “Guest Specimens
& Collections,” “Host Specimens for Guest Specimens,” and “Guest Specimens for Host
Specimens”) find and display Specimen and Collection records linked through the Host
Specimen Code field in the Collection table to the Specimen Code field in the Specimen
table.
These commands are discussed in Chapter 24, “Host-Guest Relations.”
Finding Childless and Orphan Records
The section “Linking Fields: Parent and Child Records” in Chapter 3 introduces the
concepts of child and parent records. For example, as a consequence of the many-toone relation between the Species and Genus tables, a Species record (if linked) is a
child record of a particular Genus record; the Genus record is the parent record of the
Species record (and perhaps the parent of other Species records as well).
The metaphor is carried further in the concepts of orphan records (those that are not
linked to any record in the parent table) and childless records (those not linked to any
record in the child table, for a particular database relation). For example, a Genus record
not linked to any Family record is an orphan record. A Genus record not linked to any
Species record is a childless record. Orphan records, especially, and childless records,
to a lesser extent, tend to be “invisible” in relational searches. (In relational database
terminology, orphan records compromise the referential integrity of the database.) This
section explains how to use Biota’s search tools for finding and displaying orphan and
childless records.
Chapter 12 – Page 37
Finding Childless Records
1.
From the Find menu, select “Find Childless Records.” A table selection window
appears.
2.
Using the mouse, select a parent table from the popup list. The Species table is
being selected in the illustration below.
3.
When the table has been selected, click the “Find” button in the table selection
window to launch the search. The progress indicator appears during the search,
which may be lengthy if there are many records in the tables.
You can click the “Cancel” button in the progress indicator at any time to halt the
search.
NOTE: You can carry on other Biota tasks during the search, as long as you do not
edit records, delete records, or add new records to either of the two tables involved
in the search.
Chapter 12 – Page 38
If no childless records are found, Biota displays a message like the one below.
If one or more childless records are found, Biota displays the records in the
standard Record Listing screen for the parent table, where you can work with
them using all the techniques outlined in Chapter 10, “Working With Records in
Record Listing and Input Screens.”
Finding Orphan Records
1.
From the Find menu, select Find Orphan Records. A table selection window
appears.
2.
Using the mouse, select a child table from the popup list. The Specimen table,
with the Species table as parent, is being selected in the illustration below.
Notice that the popup includes two options for the Specimen table, since it is a child
of both the Species and the Collection tables. A Specimen record can be an orphan
of either table or of both.
NOTE: For information on finding Orphan Junior Synonyms, see “Finding Orphan
Junior Synonym Records” in Chapter 23.
Chapter 12 – Page 39
3.
To limit the search to child records that have an entry in the linking field,
uncheck the checkbox in the table selection window. (By default all Orphan records
are included in the search, even those with no entry in the linking field.) If you
uncheck the checkbox, the search will gather only those child records for which the
(nonblank) entry in the relating field matches no Key value (see the section “Key
Fields” in Chapter 3) in the parent table.
4.
Click the “Find” button in the table selection window to launch the search. The
progress indicator appears during the search, which may be lengthy if there are
many records in the tables.
You can click the “Cancel” button in the progress indicator at any time to halt the
search.
NOTE: You can carry on other Biota tasks during the search, as long as you do not
edit records, delete records, or add new records to either of the two tables involved
in the search.
If no orphan records are found, Biota displays a message like the one below.
Chapter 12 – Page 40
If one or more orphan records are found, Biota displays the records in
the standard Record Listing screen for the child table, where you can work with
them using all the techniques outlined in Chapter 10, “Working With Records in
Record Listing and Input Screens.”
Automatically Updating Child Records by Changing a
Parent Record
Sometimes, you need to change the Key field in a record (for background see “Key
Fields” in Chapter 3). For example, you may discover that a Genus name is misspelled
in your database, or perhaps the name of a Genus is changed for nomenclatural
reasons and you want to update the record. If the Genus record to be changed has any
linked Species records, however, the new version of the generic name must also replace
the old version in the [Species] Genus linking field. Otherwise, the Species records will
be orphaned (they will no longer be linked to any Genus record).
Biota takes care of updating child records for you. If you confirm the change, Biota
updates the relating field in all child records when you change the value in the Key field
of the parent record. This feature applies to all relations between Core tables. In
contrast, updates of relating values in child tables are made automatically, without
confirmation, when the child table is a Peripheral table (for example, Images, Notes,
Determination History, and Auxiliary Field Value tables). (See “Peripheral Tables” in
Chapter 3.)
Updating All Child Records by Changing a Parent Record
To illustrate, suppose you need to correct the misspelled genus name “Cavendishius” to
Cavendishia.
1.
Find the parent record to be changed and display it in the Input screen for the
parent table.
Chapter 12 – Page 41
2.
Edit the Key field, then click the “Save” button in the Input screen to register the
changes. If the record is linked to child records, Biota offers two options, explained
in the screen below.
If you choose to update the child records (the default option), all relating fields
in linked child records are updated to match the change in the parent record Key
field.
If you choose to change the Key field in the parent record without updating
the relating field in the child records (the second option), Biota offers you
another chance to change your mind.
As suggested in the warning above, if you want to take a look at the child records
that will be orphaned before severing their link with the parent record, click the
“Cancel” button in the warning screen above. Then use the Child Records button
(see “Displaying Records with a Child Records Button” in Chapter 10)—the
“Show Species” button in the Genus Input screen illustrated in Step 1—to display
the child records in a separate window.
Chapter 12 – Page 42
NOTE: If the Determination History
system has been enabled (see
Chapter 22, “Determination
Histories”), and you change a
Genus name in the Genus table,
Biota also posts a message
warning that the Genus change
will create a new Determination
History record. This message
appears only for the Genus table.
“Splitting” a Taxon: Linking a Subset of the Child Records
to a New Parent Record
If you need to “split” a taxon, leaving some child records linked to an existing parent
record (an old name) while reassigning other child records to a new parent record, you
can speed the process and avoid errors by using the following procedure:
1.
Display all child records for the old parent record, using the Child Records
button (see “Displaying Records with a Child Records Button” in Chapter 10).
2.
Create a Sub-Selection of the child records to be assigned to the new parent
record (see the section “Creating a Sub-Selection of Records” in Chapter 10).
3.
Declare the Sub-Selection a Record Set (see “The Record Set Options Screen” in
Chapter 3).
4.
Change the linking field in the child table Record Set to the new parent record
name using the Find and Replace tool (see “Updating Records Using the Find and
Replace Tool” later in this chapter).
5.
Create the new parent record.
6.
Click the Child Record button in the new parent record to check the new links.
Updating Records Using the Find and Replace Tool
The Find and Replace tool (in the Special menu) is a powerful—and therefore
dangerous—utility for correcting errors or updating records in any table in the Biota
structure. Not only Core tables but Peripheral tables can be accessed with this tool. The
search can be restricted to the records of a current Record Set (for tables that have
them) or limited to a selection of records you find using the Query Editor (see “The
Query Editor, a General-Purpose Tool for Finding Records Based on Content” earlier in
this chapter), or the search can encompass all records in a table.
Because of the potential for massive changes in your Data File, this tool can be used
only by a user with Administration access privileges, if you have enabled Biota’s user
password system (see Chapter 26, “Security: Passwords and Access Privileges”). If you
have not enabled the user password system, anyone can use this tool. In any case, be
sure you understand how it works and be sure to make a backup copy of your Data File
before you use the tool, just in case (see Appendix I, “Data File Backup, Recovery,
Compacting, and Segmenting”).
Chapter 12 – Page 43
WARNING: Changes made with this tool cannot be undone, except by using the tool in
reverse to change records back to their previous values.
The Find and Replace tool searches for and replaces field values in one field at a time.
Like the Replace command in a text processing application, the Biota tool looks for a
“current value” that you specify. When Biota finds the current value in a record, it
replaces it with the “new value” that you specify.
Using the Find and Replace Tool: Step by Step
In the example below, suppose that a botanist has replaced the fluid in which 23 plant
specimens are stored, and he or she needs to update the Specimen records to reflect
the change. The entry “FAA” (for formalin and acetic acid) will be replaced by the entry
“90% Ethanol” in the “Medium” field of the Specimen table, in all records in which “FAA”
currently appears in the active Specimen Record Set.
1.
Create a Record Set for the records to be searched, if necessary.
If you want to restrict the search to certain records in a Core table or the
Determination History table, create a Record Set for the records to be changed
(see “Core Tables” in Chapter 3; see “Displaying, Editing, or Deleting
Determination History Records” in Chapter 22).
If you want the search to encompass all records in a table, or the table
does not support Record Sets (among Peripheral tables, only the
Determination History table supports Record Sets), proceed to Step 2.
If you want to use the Query Editor to find the records to be searched by the
Search and Replace tool, proceed to Step 2.
2.
From the Special menu, choose Find & Replace. The screen below appears.
Chapter 12 – Page 44
3.
Choose a table from the popup list in the top panel. Table names are listed
alphabetically.
The text of the search option button in the second panel is updated to reflect the
choice of table. The field list in the third panel is created for the table you choose.
4.
Select a search option from the second panel.
The Record Set option is enabled only if the table you chose in Step 3 is a
table that supports Record Sets and the current Record Set for the table is not
empty. Otherwise, Biota posts a message highlighting the other two options in
this panel.
The “all records” option is always enabled and is the default when the Record
Set option is unavailable (dimmed).
The Query Editor option is always enabled. If you select it, the “Launch Query
Editor” button is enabled.
If you click the button, the
Query Editor is displayed
for selecting records for
the Find and Replace
operation. (The Find and Replace tool will nonetheless replace values only in
records in which the Current Value matches, not in all records found by the
Query Editor.) See “The Query Editor, a General-Purpose Tool for Finding
Records Based on Content,” earlier in this chapter, if you need help using the
Query Editor.
5.
Choose a field from the popup list in the third panel. Field names are listed
alphabetically.
Chapter 12 – Page 45
6.
Using the “Field Name/Alias” Button. The button below the field name popup list
controls whether Biota lists strictly Internal Field Names (as given in Appendix A) or
substitutes a Field Alias for the corresponding Internal Field Name for each field you
have given an Alias. (See Chapter 18, “Renaming Fields.”)
If no Aliases have been defined, the button is disabled. The caption to the right
of the button reads “Internal Field Names appear in the lists above. No Field
Aliases have been defined.”
If any Aliases have been defined, when you first open the Find and Replace
screen, the button is enabled and reads “Show Internal Names.” The caption to
the right of the button reads “Field Aliases you have defined are currently
included in the lists above in place of the corresponding Internal Field Names.”
If you click the “Show Internal Names” button, the button text changes to
“Show Field Aliases” and the caption reads “Internal Field Names appear in the
lists above. Click the button to the left to include the Field Aliases you have
defined.”
7.
Enter the Current Value to be replaced and press the TAB key. In the illustration
below, “FAA” has been entered as the Current Value to be found.
Biota now searches in the field you selected in Step 5, within the selection of
records indicated in Step 4, for records with the Current Value. In the example,
Biota looks for “FAA” in the Medium field of the Specimen records in the current
Specimen Record Set.
Chapter 12 – Page 46
If no records are found that
meet these criteria, a message
like the one at the right appears,
and the “Find & Replace” button
remains disabled.
If you click the “Try Again” button
in the message window, the
Current Value entry area is
cleared for a new value. If you
click the “Cancel” button, the
Find and Replace screen is
dismissed.
If records are found that meet the criteria, the “Find & Replace” button is
enabled and the cursor moves to the New Value entry area.
NOTE: For Alphanumeric or Text fields (only), you can use the wildcard character,
@, in the Current Value entry area. For example, entering [email protected] finds all records
(among those you have designated) that have a value beginning with the letter b
(either lower or uppercase) for the field indicated in Step 5. Entering [email protected] finds
values that begin with Bal, and so on. If you enter only the wildcard character @, all
values for the field are found.
The wildcard character, @, cannot be used to search in Numeric (Integer or Real
Number), Date fields, or Boolean fields. See Appendix A, “Biota Tables, Fields, and
Relational Links,” if you are uncertain of the field type for a field you want to search.
If you want to replace all values in a Numeric, Date, or Boolean field (or for that
matter, in an Alphanumeric or Text field), you can use the Import Editor to update
them (see the next section, “Updating Records Using the Import Editor”).
8.
Enter the New Value to be substituted for the
Current Value and press the TAB key. In the
illustration here, “90% Ethanol” has been entered as
the New Value to be substituted for “FAA.”
Chapter 12 – Page 47
Note: If you leave the New Value field blank, the Current Value is replaced with a
blank entry in each record found.
9.
If you want to save the Find and Replace
setup, click the checkbox.
10. Click the “Find & Replace” button to launch the search and replacement
process. Biota asks you to confirm
the proposed changes.
Notice that the default button is
“Cancel,” for safety’s sake.
The changed records are displayed in
the standard Record Listing screen for
their table.
Using the Find and Replace Tool for Auxiliary Fields and Notes Tables
The example in the previous section, “Using the Find and Replace Tool: Step by Step”
focused on replacing values in a field from a Core table. You can also use the Find and
Replace tool to change field values in Peripheral tables. Because Biota does not support
Record Sets for Peripheral tables (with the exception of the Determination History table),
you must define the scope of certain key Peripheral tables in terms of the Parent table
Record Set.
These tables are the Notes tables (Species Notes, Specimen Notes, Collection Notes,
Locality Notes, or Loans Notes tables) and the Auxiliary Field Value tables (Species
Field Value, Specimen Field Value, Collection Field Value, or Locality Field Value
tables).
If you need to “Find and Replace” values in a Notes table or an Auxiliary Field Value
table, and the parent table currently has a Record Set designated, the Find and Replace
tool automatically offers the option of searching and replacing values in the child records
(Notes or Auxiliary Field Value records) that are linked to the parent table Record Set.
Chapter 12 – Page 48
Suppose, for example, that you have created Species Auxiliary Fields named “Leaf
Shape” and “Bract Shape.” You could instruct the Search and Replace tool to replace
the value “Pointed” with the value “Acuminate” each time it occurs in a Species Field
Value record linked to any record in the current Species Record Set. Each occurrence of
“Pointed” in a Species Field Value record linked to any record in the active Species
Record Set will be changed to “Acuminate,” whether the value occurs in the “Leaf
Shape” or the “Bract Shape” Auxiliary Field.
Updating Records Using the Import Editor
By selecting the “Update existing records” option in the Import Editor (the “Import by
Tables and Fields” tool in the Special menu), you can use the Import Editor to update
fields in existing records in a Biota data file (see Chapter 28, “Importing Data”).
The Import Editor can update data in any Biota table using input from free-format,
delimited text (ASCII) files, such as the column-by-row text files you can create with a
spreadsheet application or export as text flatfiles from database management
applications.
There is no search for “current values” when you use the Import Editor to update
records. When you use the Import Editor to update a record in a Core table, Biota
matches the Key field in the text file with the Key field in the existing Biota record, then
replaces field values in the existing record with the corresponding values from the text
file record, regardless of field values.
The complete process is described in detail in Chapter 28, “Importing Data by Tables
and Fields,” which you should consult before attempting to update records with the
Import Editor.
Chapter 13
Creating, Finding, and Updating
Specimen Series
Biota’s origin as a data management system for a biodiversity inventory involving large
numbers of new specimens (see the “Preface”) is nowhere more apparent than in the
tools of the Series menu. The “industrial strength” Series tools are designed to carry out
several kinds of repetitive operations on groups of Specimen records, with an absolute
minimum of human effort.
The Series menu offers four special tools for efficient
entry, updating, and retrieval of groups of Specimen
records. Although all four tools can be used efficiently
with manual Specimen Code entry, they are optimized
for use of Specimen barcodes (see “Setting Default
Prefixes for Recognizing Specimen and Species Record
Codes” in Chapter 8 and Appendix K, “Barcodes”).
Input Specimen Series creates groups of new Specimen records—with consecutive
Specimen Codes—that share the same Collection data.
Input and Identify Specimen Series creates groups of new Specimen records—
with consecutive Specimen Codes—that share the same Collection data, the same
identification data (Species Code and determination information), or both collection
and identification data.
Find Specimen Series (also in the Find menu as “By Specimen Code Series”) finds
groups of existing Specimen records. The Specimen Codes for these records can be
consecutive or in random order.
Find and Identify Specimen Series finds groups of existing Specimen records and
adds identification data (Species Code and determination information) and/or
updates other Specimen fields (Stage/Sex, Storage, Type Status) in these records.
The Specimen Codes for these records can be consecutive or in random order.
NOTE: In spite of the verb “Identify” in the name of this tool, implying the addition or
updating a Species Code link, the “Find and Identify Specimen Series” tool serves
as a general-purpose updating tool for virtually any field or fields in groups of
Specimen records.
Using the “Input Specimen Series” and “Input and
Identify Specimen Series” Tools
In the field collection of specimens, it is common for a group of specimens to be
collected in the same “collecting event”—from the same site, quadrat, trap, trawl,
extraction, host, or modular organism—on the same day by the same collector(s). In the
Biota data model (Appendix A, “Biota Tables, Fields, and Relational Links”), the
Specimen records for such a group of specimens share the same Collection Code,
uniquely identifying a single Collection record that shows the details of the collecting
event.
Chapter 13 – Page 2
In some situations, a group of new specimens not only share the same Collection Code,
but also have been identified as representatives of the same species (or infraspecific
entity)—and thus require the same Species Code in their Specimen records.
It is certainly possible to create individual Specimen records for each specimen in a
group in either of these situations using the ordinary Specimen Input screen (see
“Specimen Input” in Chapter 11), accelerated by using the “Carry” button (see
“Duplicating a Record Displayed in the Input Screen Using the ‘Carry’ button” in Chapter
10), but Biota offers a much more efficient way to do the job.
With the “Input Specimen Series” tool, you set up the Input screen, shown below, by
entering the first and last of a series of consecutive Specimen Codes for a group of
records, plus the Collection, preparation, and related data that the Specimen records
share. Biota then creates all the records automatically when you are ready.
The “Input and Identify Specimen Series” tool, shown on the next page, is identical to the
Input Specimen Series tool above, except for the addition of the Species Code and
Determination input areas, familiar from the standard Specimen Input screen.
NOTE: Using the “Input and Identify Specimen Series” tool without entering a Species
Code or determination information is exactly equivalent to using the “Input Specimen
Series” tool for the same information. The latter is simply a subset of the former.
Chapter 13 – Page 3
Specimen Series Input: Step by Step
Before using these tools, you should read “Specimen Input,” in Chapter 11, and Chapter
8, “Record Codes,” especially “Using Alphanumeric Specimen Codes With the Series
Tools.”
1.
From the Special menu, select “Record Code Prefixes” to confirm that the
Specimen Code settings are correct (see “Setting Up for Automatic Record Code
Prefix Recognition” in Chapter 8).
In the Assignment tab, check that the Specimen settings are correct. These
settings control the number of digits that the “Series Input” tools generate for new
Specimen Codes. The settings also specify the “Alphanumeric Prefix” for these
codes, if you use the “Default Prefix” approach (see “Assigning New Record
Codes Using an ‘Assign’ Button: Step by Step” in Chapter 8).
Chapter 13 – Page 4
In the Recognition tab, check that the “Alphanumeric Prefix” (both “Original”
and “Substitute,” which are normally identical) and the “Number of Digits in
Integer Counter” settings match the values for your barcodes. (Note that two
different barcode prefixes and counter settings can be recognized.)
The same settings specify the prefixes and number of digits the “Find Specimen
Series” tools expect for recognizing existing Specimen Codes. See the next
section, “Finding (or Finding and Identifying) Specimen Series: First Steps.”
NOTE: The settings in the “Record Code Settings” screen for tables other than
Specimen are irrelevant to the operation of the Series tools.
2.
Click the “Save” Button in the “Record Code Prefixes” screen to record any
changes and dismiss the screen.
3.
From the Series menu, choose Input Specimen Series or Input and Identify
Specimen Series. The Input screen appears (screens for both commands are
illustrated in the previous section, “Using the ‘Input Specimen Series’ and ‘Input and
Identify Specimen Series’ Tools”).
4.
In the Specimen Code Series panel:
Either: In the “First Specimen Code” entry area,
manually enter the Integer Counter for the numerically
lowest Specimen Code in the series for which you want
to create Specimen records, then press the TAB key.
To begin the Specimen Series with the next Integer
Counter available (as specified in the Record Code
Settings screen, Special menu), use the “Next Integer
Counter Value” displayed in the “Records Created on”
panel at the lower right of the Series input screen.
Chapter 13 – Page 5
NOTE: If the counter has any leading zeros, omit them (left illustration, below).
Biota prefixes leading zeros (right illustration, below), if necessary, to complete
the number of digits you specified in the Record Code Prefixes screen. (If you
enter leading zeros in the “First Specimen Code” or “Last Specimen Code” entry
areas, Biota posts an error message.)
Do not enter any alphabetic characters in these entry areas. If you do, Biota
posts an error message.
Or: Read in the barcode for the “First Specimen
Code” in the series for which you want to create
Specimen records. Then press the TAB key if your
barcode reader is not set to enter an end-of-line
character automatically.
If the alphanumeric prefix correctly matches the barcode prefix setting in the
“Recognition” tab of the “Record Code Prefixes” screen, Biota accepts the
barcode. Otherwise, you will see the alphabetic character error message
mentioned in the Note above.
5.
In the “Specimen Code Series” panel, repeat step 3 for the “Last Specimen
Code” entry area. If there is only one specimen in the series, you can skip this
step. (Integer Counter entry is illustrated on the left, barcode entry on the right,
below.)
6.
If you entered an Integer Counter manually, and wish
to insert a Specimen Code Prefix to complete the
Specimen Codes, click the “Prefix” button. (If you entered a
barcode, the “Prefix” button has no effect.)
The Insert Specimen Prefix window appears.
Chapter 13 – Page 6
7.
In the Prefix window:
Either: Enter an ad hoc prefix in the Enter Prefix area (in the illustration
above, the prefix HMSB has been entered) and click the “Accept Prefix” button.
Or: Click the “Default Prefix” button to enter the prefix displayed next to the
button (SPM in the illustration;
see Step 1 to change the default
prefix). Biota completes the
“First Specimen Code” and “Last
Specimen Code” entries by
inserting the prefix.
NOTE: If you prefer, you can use the “Prefix” button to set a prefix first, then enter
the Integer Counters for the First and Last Specimen Codes. In this case, the codes
are completed as you enter them.
8.
Enter links to Parent tables:
“Input Specimen Series” tool. Complete the Collection Code link, following
instructions at Step 3 in the section “Specimen Input” in Chapter 11.
“Input and Identify Specimen Series” tool. Complete the Species Code and
Collection Code links, following instructions in Steps 2 and 3 of the section
“Specimen Input” in Chapter 11.
9.
Enter data for “Stage/Sex,” “Medium,” “Storage,” “Deposited,” “Specimen Custom
1,” “Specimen Custom 2,” and “Type Status,” following the instructions for the
standard Specimen Input screen (see “Specimen Input” in Chapter 11). Notice that
some of these fields in the “Input Series” tools are on a second tab, “Other Fields.”
All records in the range of codes
you specified in the “Specimen
Code Series” panel will include
the entries you make on either
tab.
You can set any of the following
options for each of these seven
Specimen fields:
Aliases. Each field can be
renamed using the “Core Field
Aliases” tool from the Special
menu (see Chapter 18,
“Renaming Fields”).
Field Value Defaults. You
can ask Biota to enter a
particular value in each new record automatically using the “Field Value Defaults”
tool from the Special menu (see “Setting Default Entries: Field Value Defaults” in
Chapter 17).
Entry Choice Lists. You can enable an Entry Choice List (pick list) for each field
using the “Entry Choice Lists” tool in the Special menu (see “Using Entry Choice
Lists” in Chapter 17).
Chapter 13 – Page 7
NOTE: The “Deposited” field in the Specimen table is used by the Specimen Loans
system in Biota. If you intend to use the Loans system do not use this field for
another purpose. See Chapter 21, “Specimen Loan System” for details.
10. Click the Save or “Carry” button to create the series of Specimen records.
If you use the “Carry” button, all entries except for the “First Specimen Code”
and “Last Specimen Code” are carried forward. You can edit entries in any field,
if necessary, for the next series.
If the records were created successfully, the
“Last Code Used” display area (below) now
shows the former “Last Specimen Code” entry,
to guide your input for the next series. The
Sequence Number display (step 4) is updated.
If you have requested the creation of more than 20 records, a confirmation
screen appears.
If the password system has been enabled (see Chapter 26, “Security:
Passwords and Access Privileges”) and you have requested the creation of more
records than the limit set in the “Admin Settings” tab of the Preferences screen
(Special menu; illustrated here), a message appears explaining that you cannot
complete the action. (A user with administration access privileges can change
the limit. See “The
‘Admin Settings’ Tab”
in Appendix B.)
11. Create additional series of records if you wish, following steps 4 through 9.
12. To examine the records created, click the “Cancel” Button in the Series Input
screen. The series you have created appear in a special version
of the Specimen Record Listing screen. In place of the standard
“Add Specimen” button, an “Add New Series” button is present.
13. To create another series of Specimen records, click the “Add New Series” button
(above). An option screen appears.
You can choose to carry forward all entries except the First and Last Specimen
Code entries (exactly the equivalent of having clicked the “Carry” button after the
last series you created), or start fresh.
14. Select an option and click OK. The Specimen Series Input screen you were using
before reappears.
Chapter 13 – Page 8
15. When you are finished creating series, click the “Done” Button in the Record
Listing screen to present the standard Record Set option screen (see “The Record
Set Options Screen” in Chapter 3).
Using the “Find Specimen Series” and “Find and
Identify Specimen Series” Tools
The tools of the Find menu offer many ways to find existing records, based on their
content or their linkage to other records, and several ways to update records if
necessary, once found (Chapter 12, “Finding and Updating Records”). The “Find
Specimen Series” and “Find and Identify Specimen Series” tools have the specialized
purposes of finding Specimen records based strictly on Specimen Code and updating
the records found, if you wish.
Specimen Codes may be entered in any order. Neither
tool requires that Specimen Codes be sequential,
although they may be.
These two tools share a common interface for entering
individual Specimen Codes or Specimen Code series.
The “Find Specimen Series” tool (below) simply finds a group of Specimen records,
based on Specimen Code. One common use for the tool is to gather Specimen records
into a Record Set to record those specimens as a Specimen Loan or to record their
return from an existing Specimen loan. (The “New Loan” screen has additional tools for
gathering Specimen records to record a new loan.) See Chapter 21, “Specimen Loan
System.”
In addition to finding Specimen records based on Specimen Code, the “Find and Identify
Specimen Series tool” (next page) automatically updates the Species Code and other
fields you specify, in all records found.
NOTE: In spite of the verb “Identify” in the name of this tool, implying the addition or
updating a Species Code link, the “Find and Identify Specimen Series” tool serves as a
general-purpose updating tool for virtually any field or fields in groups of Specimen
records.
Chapter 13 – Page 9
This tool is ideal for efficiently updating information in groups of existing Specimen
records, whether or not their Specimen Codes are numerically sequential. Some
common uses include:
Recording or changing the determination data (Species Code, Last Determined
By, Date of Determination) in the records for a group of specimens that have been
determined to represent the same species (whether named or not).
Recording or changing “Stage/Sex,” “Storage,” or “Type Status” data for a
group of records. For example, the “Storage” field could be updated for a group of
duplicate specimens or vouchers that have been moved to an auxiliary storage
location. The “Type Status” field could be updated when a type series is designated.
All three of these fields can be renamed for other uses. (See Chapter 18, “Renaming
Fields.”)
Finding (or Finding and Identifying) Specimen Series: First Steps
Before using these tools, you should read “Specimen Input,” in Chapter 11, and Chapter
8, “Record Codes,” especially “Using Alphanumeric Specimen Codes With the Series
Tools.”
1. From the Special menu, select “Record Code Prefixes,” and click the
“Recognition” tab to confirm that the Specimen Code recognition settings are
correct (illustrated on the next page). These settings specify the prefixes and
number of digits the “Find Specimen Series” tools expect for recognizing existing
Specimen Codes. check that the “Alphanumeric Prefix” (both “Original” and
“Substitute,” which are normally identical) and the “Number of Digits in Integer
Counter” settings match the values for your barcodes. (Note that two different
barcode prefixes and counter settings can be recognized.)
Chapter 13 – Page 10
NOTE: The settings in the “Assignment” tab and the settings for Species Codes in
the “Recognition” tab are irrelevant to the operation of the “Find Specimen Series”
tools.
2.
Click the “Save” Button in the “Record Code Prefixes” screen to record any
changes and dismiss the screen.
3.
From the Series menu, choose “Find Specimen Series” or “Find and Identify
Specimen Series.” The Input screen appears (full screens for both commands are
illustrated in the previous section, “Using the ‘Find Specimen Series’ and ‘Find and
Identify Specimen Series’ Tools”).
In “Find Specimen Series”: Choose a search option in the upper panel,
labeled “Enter Specimen Codes to be Found.”
◊
Option 1: “In any order.” With this option selected, you enter complete
Specimen Codes, in any order. Continue with steps in the next section of this
chapter, “If You Choose ‘In Any Order.’”
◊
Option 2: “In consecutive order.” If you select this option, you enter the
Integer Counter portion of the “First Specimen Code” and “Last Specimen
Code” of a consecutive series, then add a Prefix if necessary. Continue with
the section “If You Choose ‘In Consecutive Order,’” later in this chapter.
Chapter 13 – Page 11
In “Find and Identify Specimen Series”: Choose a search option in the
upper panel, labeled “Enter Specimen Codes to be Found,” or select the third
option, “Use the Specimen Record Set.”
◊
Option 1: “In any order.” With this option selected, you enter complete
Specimen Codes, in any order. Continue with steps in the next section of this
chapter, “If You Choose ‘In Any Order.’”
◊
Option 2: “In consecutive order.” If you select this option, you enter the
Integer Counter portion of the “First Specimen Code” and “Last Specimen
Code” of a consecutive series, then add a Prefix if necessary. Continue with
the section “If You Choose ‘In Consecutive Order,’” later in this chapter.
◊
Option 3: “Use the Specimen Record Set.” To use this option, you must
first have found the records to be updated and declared them the active
Specimen Record Set. Continue with the section “If You Choose ‘Use the
Specimen Record Set’”, later in this chapter.
If You Choose “In Any Order”
1.
Enter a complete Specimen Code for an existing Specimen record, manually or
using a barcode reader, in
the “Any Specimen Code”
entry area, illustrated here.
2.
Press TAB. Biota searches
immediately for the record.
NOTE: You need not press TAB if you are using a barcode reader that has been set
to enter an end-of-line character (RETURN [Macintosh] or ENTER [Windows])
automatically after each read.
If the record is found, the Specimen Code remains entered in the input area.
If the record cannot be found, an error message appears and the Specimen
Code entry area is cleared.
3.
If you are using the “Find and Identify Specimen Series” tool, complete as
many of the remaining entries in the screen as you wish, following the instructions
for the standard Specimen Input screen in the section “Specimen Input” in Chapter
11, with the following guidelines:
Chapter 13 – Page 12
Enter the Species Code link in the panel labeled “Species Code to be Entered
in Specimen Records Found,” following instructions in Step 2 of the section
“Specimen Input” in Chapter 11.
Once the link to a Species
record is made, Biota posts the
message on the right. If you
enter a value for Species Code,
then “Last Determined By” and
“Date Last Determined” are
required entries, to make sure
that changes in determination
can be tracked.
Enter data for “Last Determined By,” “Date Last Determined” (if not already
entered automatically), “Stage/Sex,” “Medium,” “Storage,” “Deposited,”
“Specimen Custom 1,” “Specimen Custom 2,” and “Type Status,” following the
instructions for the standard Specimen Input screen (see “Specimen Input” in
Chapter 11). Notice that some of these fields in the “Find and Identify Specimen
Series” tool are on a second tab, “Other Fields.”
Chapter 13 – Page 13
NOTE: Any or all of the fields “Stage/Sex,” “Medium,” “Storage,” “Deposited,”
“Specimen Custom 1,” “Specimen Custom 2,” and “Type Status” may have been
renamed using the “Core Field Aliases” tool from the Special menu (see Chapter
18, “Renaming Fields”).
Existing values that will be replaced: The Specimen record with the Specimen
Code you just entered—and any additional records whose Specimen Codes you
enter after using the “Carry” button—will be updated with the entries you make in
the “Find and Identify Specimen Series” screen for these fields, regardless of the
existing values in the fields.
Existing values that will not be replaced: Existing values in any field that you
leave blank in the “Find and Identify Specimen Series screen” will not be altered
in the Specimen records found. (In the case of the numerical field “Abundance,”
located in the “Other Fields” tab, a zero in the “Find and Identify Specimen Series
screen” indicates no change in existing records.)
4.
To find the first Specimen record and clear the Specimen Code entry area for the
next record, you have three options.
Option 1: Click the “Find” button (“Find Specimen Series,” below left) or the
“Save” button (“Find and Identify Specimen Series,” below right) if you want to
make another manual entry.
Option 2: Click the “Auto Find” button (“Find Specimen Series,” below left) or
the “Auto Carry” button (“Find and Identify Specimen Series,” below right), if
you want to set up for automatic Specimen Code entries.
These are toggle buttons. Click once to turn on “Auto Save” or “Auto Carry,” click
the button again to turn it off.
Chapter 13 – Page 14
Option 3: Click the “Carry” button
(“Find and Identify Specimen Series”
only).
If you click “Auto Carry” or “Carry” in the
“Find and Identify Specimen Series”
screen, any entries you made in the
update fields are carried over to the next
record to be updated.
Regardless of which approach you use to find the first record, the “Last Specimen
Code” entry from the previous series is
displayed in the “Last Code Found” panel
(upper right corner of the screen), for both the
“Find and Identify Specimen Series” and the
“Find and Identify Specimen Series” screens.
5.
If you clicked the “Auto Find” or “Auto
Carry” button to toggle it on, you can now proceed to enter additional Specimen
Codes without having to click any buttons on the screen.
Each time you enter a new Specimen Code and press TAB (or the barcode reader
reads a Specimen barcode and enters an end-of-line character), the Specimen
record is found automatically. If you are using the “Find and Identify Specimen
Series” screen, the record is not only found automatically, but also updated
automatically.
With a barcode reader set to append the end-of-line character, the entire process
requires neither keyboard nor mouse once the Auto Find or Auto “Carry” button is
toggled on. You can use both hands, uninterrupted, to handle specimens.
6.
Follow the steps in the section entitled “Finding (or Finding and Identifying)
Specimen Series: Final Steps,” later in this chapter.
If You Choose “In Consecutive Order”
1.
In the “In consecutive order” panel:
Either: In the “First Specimen Code” entry area, manually enter the Integer
Counter for the numerically lowest Specimen Code in the series you want to find
(or find and update). If the counter has any leading zeros, omit them. Press the
TAB key.
Biota prefixes leading zeros, if necessary, to complete the number of digits you
specified in the “Recognition” tab of the “Record Code Prefixes” screen (see Step
1 of the section “Finding (or Finding and Identifying) Specimen Series: First
Steps” earlier in this chapter.)
Chapter 13 – Page 15
◊
If you enter leading zeros, Biota posts this error message:
◊
If you entered an alphabetic character, Biota posts this error message:
Or: Read in the barcode for the “First Specimen Code” in the series for the
numerically lowest Specimen Code in the series you want to find (or find and
update). If the counter has any leading zeros, omit them. Then press TAB if your
barcode reader is not set to enter an end-of-line character automatically.
If the alphanumeric prefix correctly matches the barcode prefix setting in the
“Recognition” tab of the “Record Code Prefixes” screen, Biota accepts the
barcode. Otherwise, you will see the alphabetic character error message
illustrated in the previous paragraph.
2.
Repeat Step 1 for the “Last Specimen Code” entry area in the “In consecutive
order” panel. If there is only one specimen in the series, you can skip this step.
3.
If you entered an Integer Counter manually, and
wish to insert a Specimen Code Prefix to
complete the Specimen Codes, click the “Prefix”
button. (If you entered a barcode, the “Prefix” button
has no effect.)
Chapter 13 – Page 16
The Insert Specimen Prefix window
appears.
4.
In the Prefix window:
Either: Enter an ad hoc prefix in
the Enter Prefix area (in the
illustration on the right, the prefix
HMSB has been entered) and
click the “Accept Prefix” button.
Or: Click the “Default Prefix”
button to enter the prefix
displayed next to the button (SPM
in the illustration on the right; see
Step 1 of the section “Finding (or
Finding and Identifying) Specimen
Series: First Steps,” earlier in this chapter, to change the default prefix). Biota
completes the “First Specimen Code” and “Last Specimen Code” entries by
inserting the prefix.
NOTE: If you prefer, you can use the “Prefix” button to set a prefix first, then enter
the Integer Counters for the First and Last Specimen Codes. In this case, the
Codes will be completed as you enter them.
5.
If you are using the Find and Identify Specimen Series tool, complete as many
of the rest of the entries in the screen as you wish, following the instructions in Step
3 of the previous section of the chapter, “If You Choose ‘In Any Order.’”
6.
Click the “Find” button (“Find and Identify Specimen Series” tool) or click the
“Save” or “Carry” button (“Find and Identify
Specimen Series” tool) to accept the first series of
consecutive Specimen Codes.
The “Last Specimen Code” entry is displayed in the
“Last Code Found” panel (upper-right corner of the
screen), and Specimen Code entry areas are cleared
for the next series.
If you asked Biota to find (left, below) or find and update (right, below) more
than 20 records, a confirmation screen appears.
Chapter 13 – Page 17
If the password system has been enabled (see Chapter 26, “Security:
Passwords and Access Privileges”) and you have requested the updating of
more records than the limit set in the Preferences screen (see Appendix B,
“Setting Preferences”), a message appears explaining that you cannot complete
the action. (A user with Administration privileges can change the limit.)
NOTE: The “Auto Find” or “Auto Carry” toggle button is disabled when you choose
the “Consecutive order” option (or the “Use the Specimen Record Set” option in the
“Find and Identify Specimen Series” tool), since these buttons are used only for
single Specimen Code entry.
7.
Follow the steps in the section entitled “Finding (or Finding and Identifying)
Specimen Series: Final Steps,” later in this chapter.
If You Choose “Use the Specimen Record Set”
This third option for identifying a group of specimen records in the “Find and Identify
Specimen Series” screen allows you to use any tool in the Find menu to bring together
the group of records to be updated.
1.
Create a Specimen Record Set composed of the Specimen records you want to
update, using any of the tools of the Find menu.
2.
Choose the option “Use the Specimen Record Set” in the “Find and Identify
Specimen Series” screen.
3.
Complete as many of the rest of the entries in the screen as you wish,
following the instructions in Step 3 of the section “If You Choose ‘In Any Order,’”
earlier in this chapter.
4.
Click the “Save” or “Carry” button to find the records that compose the active
Specimen Record Set and make the changes you have set up.
The “Last Specimen Code” entry is displayed in
the “Last Code Found” panel (upper-right corner
of the screen), and Specimen Code entry areas
are cleared for the next series.
If you have asked Biota to find and update
more than 20 records, a confirmation screen
appears.
Chapter 13 – Page 18
If the password system has been enabled (see Chapter 26, “Security:
Passwords and Access Privileges”) and you have requested the updating of
more records than the limit set in the Preferences screen (see Appendix B,
“Setting Preferences”), a message appears explaining that you cannot complete
the action. (A user with Administration privileges can change the limit.)
NOTE: The “Auto Carry” toggle button is disabled when you choose the “Use the
Specimen Record Set” option in the “Find and Identify Specimen Series” tool, since
this button is used only for single Specimen Code entry.
5.
Follow the steps in the section entitled “Finding (or Finding and Identifying)
Specimen Series: Final Steps,” next in this chapter.
Finding (or Finding and Identifying) Specimen Series: Final Steps
This section specifies the final steps for using the “Find Specimen Series” and “Find and
Identify Specimen Series” tools. These steps are the same for the “In any order,” “In
consecutive order,” and (for the “Find and Identify Specimen Series” tool) the “Use
Specimen Record Set” options described in the previous three sections.
1.
Create additional series of records if you wish, following the steps in the
appropriate preceding section. (See “If You Choose ‘In Any Order,’” “If You Choose
‘In Consecutive Order,’” or “If You Choose ‘Use the Specimen Record Set,’” earlier
in this chapter.)
2.
To examine the records found (or found and updated), click the “Cancel” button
in either the “Find Specimen Series” or “Find and Identify Specimen Series” Input
screen. The records appear in a special version of the Specimen Record Listing
screen. In place of the standard “Add Specimen” button, an “ID or Find More” button
is offered.
3.
To find (or find and update) another series of Specimen records, click the “ID
or Find More” button (above).
If you are using the “Find and Identify Specimen Series” tool, an option screen
appears.
You can choose to carry forward all entries except the “First Specimen Code” and
“Last Specimen Code” entries (exactly the equivalent of having clicked the “Carry”
button after the last series you created), or start fresh. (There is nothing to “carry”
with the “Find Specimen Series tool,” so this option screen does not appear.)
Chapter 13 – Page 19
4.
If the option screen (below) appears, select an option and click OK. The
Specimen Series screen you were using before reappears.
5. When you are finished using the Series tool, click the “Done” Button in the
Record Listing screen to present the standard Record Set option screen (see “The
Record Set Options Screen” in Chapter 3).
PART
4
Printing Reports
and Labels
Chapter 14
Printing Reports
Biota offers printed reports for individual records as well as groups of records.
For an individual record from any Core table, Biota offers a standard, preformatted report form. (To print an Image record linked to the Species, Specimen,
Collection, or Locality table, use the "Print" button in the "This Image record" panel
of the Images tab for the parent record.)
For the records displayed in a Record Listing Screen (whether or not they have
been declared a Record Set), you can use the “Print” button on the Record Listing
Screen or the Print command from the File menu to print a list of the records
displayed. You can choose a preformatted Biota report or use the Quick Report
Editor, instead, to design your own printed report forms. You can save and reload
the formats you create in the Quick Report Editor. (See “Designing and Printing
Reports with the Quick Report Editor” later in this chapter).
WARNING: All Biota preformatted reports use the Geneva font (Mac OS) or the Arial
font (Windows). If you do not have the appropriate font installed (in the printer’s
memory as well as on your computer, for some printers), the layout of reports will
probably not be correct, depending on what font is substituted for Geneva or Arial.
Because these fonts are automatically installed with their respective operating
systems, this problem is unlikely to arise.
Printing and Previewing Procedures
for Reports and Labels
For all printed reports and labels, Biota presents the same series of screens and options
when you are ready to preview and print. This section outlines the steps to take once
you have chosen the report or label options you want. See the section that applies to the
report (this chapter) or labels (see Chapter 15, “Printing Labels”) you are printing, before
using the steps below.
Chapter 14 – Page 2
1.
Launch the printing process by clicking a “Print” button (Reports), selecting the
Print command from the File menu (Record Listing Reports), or clicking the “OK”
button (Label Option screen), after setting up any options for the report or labels.
The “Print Setup” (Windows) or “Page Setup” (Mac OS) window for your active
printer appears. (Because these windows vary greatly among printers and between
operating systems, none is illustrated here.)
2.
Check or adjust any settings in the “Print Setup” (Windows) or “Page Setup” (Mac
OS) window, then click the “OK” button. The “Print” window for your active printer
appears. (Because “Print” windows vary greatly among printers and between
operating systems, none is illustrated here.)
3.
Choose a Preview option. Look for a “Print preview”
(Windows) or “Preview on screen” (Mac OS) checkbox in the
lower-left corner of the Print window. If you don’t see the
checkbox, look for a popup menu of print
options and select “4D x.x.x” (where “x.x.x” is
the version number of 4th Dimension used to
compile the current version of Biota), then locate
the checkbox.
If you leave the Preview checkbox
unchecked, reports or labels or go directly to
your printer.
If you click the Preview checkbox, you can check the labels or report onscreen
and then Print or Cancel.
4.
Click the “OK” button (Windows) or “Print” button (Mac OS) in the Print
window. If you checked the Preview box, the first page of the report or the first
page of labels appear in a Preview window with a column of icon buttons at the left,
illustrated here. Using these buttons you can check the labels or report onscreen
and then Print or Cancel.
The “X” icon dismisses the screen, or stops a print job already
underway.
The printer icon sends the report or labels to the printer.
The page-with-arrow icons move the view forward or backward
one page in the print job.
The magnifying glass icon zooms the page image and changes
the cursor to a “hand” icon that can be used to move the page
image within the window.
NOTE: If you do not have a printer attached to your computer, the computer may
lock up if you click the OK or “Print” button in Print screen. If you are working
without a printer, you can avoid this behavior if you remember to click the
“Stop/Hand” icon button when you are through with the preview.
Printing an Individual Record
To print a copy of an individual record from a Core table, follow these steps.
Chapter 14 – Page 3
1.
Display the record you want to print in the Input screen for its table. Use the
techniques described in Chapter 10, “Working With Records in Record Listing and
Input Screens” to find and display the record.
2.
Click the “Print” button in the Input screen to
print the standard report for the table.
The “Print Setup” (Windows) or “Page Setup” (Mac
OS) window for your active printer appears.
3.
To preview the printed record, see “Printing and
Previewing Procedures for Reports and Labels”
earlier in this chapter.
Printing a Report Based on a Selection of Records
Printing a Report Based on the Active Record Set for a Table
To print a report listing all the records in the active Record Set (see “Record Sets” in
Chapter 3) for a Core table or for the Determination History table:
1.
Display the Record Set in the standard Record Listing Screen for the table.
For Core tables: From the Display menu, choose the command for the table.
For the Determination History table: From the Special menu, choose “Display
Determination Histories.” If you have enabled the password system, only the
Administrator can use this command.
2.
Follow the directions in the section “Printing a Standard or Custom Report Based
on the Records in a Record Listing Screen” later in this chapter.
Printing a Report Based on a Record Set Pointer File
To print a report listing all the records in a Record Set pointer file (see “Record Set
Pointer Files” in Chapter 3:
1.
Load the Record Set Pointer File from disk to display the records in the Record
Listing Screen for the table.
2.
Follow the directions in the next section, “Printing a Standard or Custom Report
Based on the Records in a Record Listing Screen.”
Printing a Standard or Custom Report Based on the Records in a
Record Listing Screen
For each Core table and the Determination History table, Biota offers a preformatted
report that you can print, listing all records in the current Selection, including fields from
related tables where appropriate. Each table has its own, specially designed report.
Rather than attempt to display them in this book, the best way to evaluate these report
formats is to print some records from your own Data File or from the Biota Demo Data
File (see Chapter 6, “A Brief Tutorial With the Demo Database”), or preview reports on
the screen (see “Printing and Previewing Procedures for Reports and Labels” earlier in
this chapter).
If the preformatted report for a table does not suit your needs, you can print the records
using a custom report layout that you design yourself using the Quick Report Editor (see
“Designing and Printing Reports With the Quick Report Editor” later in this chapter).
Chapter 14 – Page 4
Here are the steps to follow for printing a standard report:
1.
Display the records to be printed in the Record Listing Screen. See the
preceding two sections of this chapter (“Printing a Report Based on the Active
Record Set for a Table” and “Printing a Report Based on a Record Set Pointer File”)
and consult Chapter 10, “Working With Records in Record Listing and Input
Screens” and Chapter 12, “Finding and Updating Records” for help, if you need any.
2.
Click the “Print” button at the base of
the Record Listing Screen.
Alternatively, you can select “Print” from
the File menu while the records are
displayed in the Record Listing Screen.
3.
Choose a print option. A print option window appears offering two or three
choices, depending on the table for which you are printing records. (The
Determination History table has no options.) Three different option windows are
illustrated below.
Sort by Record Code before printing. Use this option to print a report with the
records sorted by Record Code (Species Code, Specimen Code, Collection
Code—illustrated above, or Locality Code). The Loans report can be sorted by
Loan Code.
Print using the existing order. If you have used the “Sort” button (the “Order
by” Editor) to create a special order for the records that you want maintained in
the report, choose this option.
Design and print a special report. If you choose this option, Biota presents the
4th Dimension “Quick Report Editor,” which you can use to design, save, and/or
load custom report formats that you create yourself. The report will be based on
the Selection of records in the output layout when you clicked the “Print” button
or selected Print from the File menu. See “Designing and Printing Reports With
the Quick Report Editor” later in this chapter.
Chapter 14 – Page 5
Sort taxonomically before printing. For records from taxonomic tables
(Species, Genus, Family, etc., and Specimen as well), this option prints the
records for the table in alphabetical order within taxonomic levels (ranks) in a
hierarchical report organized by rank (as in the table in the section, “The
Relational Model” in Chapter 2).
Include Host data in the report. For the Specimen table, an additional option is
offered. If the “Include Host data in the report” checkbox is checked, the report
will include, for each Specimen record, the Specimen Code of the Host for that
specimen (see Chapter 24, “Host-Guest Relations”).
NOTE: This option is automatically checked if any Specimen records in the
current selection have host data. Otherwise, it appears unchecked. In either
case, you can override the setting manually. The host data checkbox is disabled
when the “Design and print a special report” option is clicked.
4.
Click the “OK” button in the print option screen.
If you chose the standard Biota report, see “Printing and Previewing
Procedures for Reports and Labels” earlier in this chapter.
If you chose “Design and Print a Special Report,” see “Designing and
Printing Reports with the Quick Report Editor” later in this chapter.
Printing a Specimen Count by Taxon Report
The Specimen Count by Taxon report provides
quantitative information on the taxonomic breakdown of
a Specimen Record Set. The report computes and
displays the number of Specimen records for each taxon
and rank.
To use this tool, follow these steps:
1.
Choose “Specimen Count by Taxon” from the Special menu. An option screen
appears.
Chapter 14 – Page 6
2. Choose a summation option.
Option 1. “For subtotals and totals, count Specimen records.” If you check
this option (the default), values in the Abundance field of the Specimen table are
ignored, and the Specimen records are simply enumerated.
Option 2. “For subtotals and totals, sum the [Specimen] Abundance field.”
If you check this option, values in the Abundance field of the Specimen table are
summed for Specimen records in each taxonomic category.
NOTE: For information on the Abundance field of the Specimen table, see Step 5 of
the section “Entering Specimen Data: The ‘General’ Tab” in Chapter 11.
3.
Click the “OK” button. You can use the screen preview option to display the report
on the screen before (or instead of) printing it (see “Printing and Previewing
Procedures for Reports and Labels” earlier in this chapter).
Designing and Printing Reports with the
Quick Report Editor
The 4D Quick Report Editor is an “off the shelf” 4th Dimension utility described in
Appendix E, “The 4D Quick Report Editor.” But first, read the section below, “Launching
the 4D Quick Report Editor,” to get started.
NOTES:
a.
You can use the 4D Quick Report Editor to create reports for records in any Core
table (see “Core Tables” in Chapter 3), specifying fields from that table and any of
its parent tables. Fields in child tables cannot to be used. Because there may be
many child records linked to each parent record, the Quick Report Editor has no
way to determine which record to access.
b.
The Quick Report Editor can also be used to export text flatfiles. See “Exporting
Custom Flatfiles” in Chapter 27. If you wish to create a graph from a Quick Report,
export the report as a flatfile, then use another application (e.g., Microsoft Excel) to
create the graph.
Chapter 14 – Page 7
Launching the 4D Quick Report Editor
To launch the Quick Report Editor for printing a report, see “Printing a Standard or
Custom Report Based on the Records in a Record Listing Screen,” earlier in this
chapter. For detailed help in setting up the Quick Report Editor, see Appendix E, “The
4D Quick Report Editor.”
Left Margins in Quick Reports
In the Quick Report Editor, you can explicitly control the size of Headers and Footers
(see “Adding Page Headers and Footers” in Appendix E), but there is no obvious way to
leave a wide left margin (for binding, for example). To do, simply insert a blank first
column of the desired width.
Special Biota Date, Georeference, and Agent Formats in Quick Reports
When you use the Quick Report Editor to create custom reports (using the “Print” button,
with the “Design and print a special report” option, in Record Listing screens) or to export
custom flatfiles (using the “Export Custom Flatfile” tool in the Im/Export menu), you may
wish to include certain data in special Biota formats. These formats include Partial Dates
(month and year only, or year only), Collection Date Range, and Latitude/Longitude in
Degrees/Minutes/Seconds format.
In addition, linking to the Personnel table from the Specimen or Collection table requires
special commands to allow Personnel records linked to “agent” fields
([Specimen]PreparedBy, [Specimen]DeterminedBy, and [Collection]CollectedBy) to be
included in reports based on the Specimen or Collection table.
You can do all these things easily by inserting very simple commands in the Formula
Editor. You access the Formula Editor by adding a new column to a Quick Report, or by
double-clicking an existing column. Here is an example for the special Biota command
“ReportCollectionDateRange.”
Chapter 14 – Page 8
Here are the special commands:
Georeference commands
◊
ReportLatitude
◊
ReportLongitude
Date commands
◊
ReportCollectionDateRange
◊
ReportDateCollected
◊
ReportDateDetermined
◊
ReportDatePrepared
NOTE: The format of all Date commands (International vs. U.S. format), is controlled
by the Date setting in your operating system. See “Date Formats in Biota: U.S. and
International Formats” in Chapter 9.
Agent commands
◊
ReportPreparatorFirstName
◊
ReportPreparatorLastName
◊
ReportDeterminerFirstName
◊
ReportDeterminerLastName
◊
ReportCollectorFirstName
◊
ReportCollectorLastName
◊
ReportCollectorLink. This special command can be entered in the Formula Editor
in a hidden column (choose “Hide” from the Edit menu in the Quick Report
Editor) to give full access to all fields of the Personnel record for a Collector in
subsequent columns (to the right of the hidden column).
Chapter 15
Printing Labels
Biota provides several special tools (in the Labels menu) for producing labels for
specimens, collections, and species. You can print labels directly from Biota on plain,
acid-free paper or, for slide labels, adhesive-backed, acid-free paper. Alternatively, you
can export label data to text files, where you can format and duplicate the label text with
a word processing or spreadsheet application to suit your personal or institutional
preferences.
WARNING: Biota preformatted labels use the Arial and Helvetica fonts, depending on the
label type. If you do not have the appropriate font installed (in the printer’s memory as
well as on your computer, for some printers), the layout of labels will probably not be
correct, depending on what font is substituted for Arial or Helvetica.
Printing and Previewing Procedures for Labels
For all printed labels, Biota presents the same series of screens and options when you
are ready to preview and print. Because the procedures are identical for Reports, please
consult “Printing and Previewing Procedures for Reports and Labels” in Chapter 14,
“Reports.” That section outlines the steps to take once you have chosen the label
options you want, following the instructions in the appropriate section of this chapter.
Label Option Windows
Each Label tool in Biota presents an option window, giving you control over certain
features of the labels to be produced. Because most of the option sets recur in option
windows for several different label tools, it makes sense to describe them just once, in
this section.
Options that apply to only one or two kinds of labels are discussed in the section on the
particular tool or tools to which they apply.
Sort Options
Option 1: Sort selection by Record
Code or Key field. This is the default
option for all label tools. For all
Specimen labels (both locality and
determination labels), you can
choose to sort by Specimen Code
before printing them. For Collection labels, you can sort by Collection Code. With
the Custom Label tool, which prints labels for any Core table, you can choose to
sort by Key field (see “Key Fields” in Chapter 3).
Option 2: Sort the selection taxonomically. For all specimen determination
labels, you have the option of sorting Specimen records taxonomically before
Chapter 15 – Page 2
printing the labels. The Specimen records are sorted by Specimen Code within
species. Groups of records for the same species are sorted alphabetically by
specific name, then these groups are sorted by genus, and so on. This option does
not apply to locality labels or collection labels.
Option 3: Use the Sort Editor to sort the records. For all label tools, you can
choose to sort the records using the Sort Editor (see “Sorting Records in Record
Listing Screens” in Chapter 10).
Data Options
Include Specimen Code on
each label. A checkbox for this
option is offered for both locality
and determination labels of all kinds. It is not exclusive of any other option, where
offered.
Month format options.
◊
Option 1: Use three-letter
English abbreviations for
Months (Jan, Feb, Mar, Apr,
etc.). This is the default option
for all label tools.
◊
Option 2: Use Roman numerals for Months (I, II, III, IV… for Jan, Feb, Mar,
Apr…). In some disciplines, this style is preferred.
In either case, partial dates (Month-Year or Year-only) and “intelligent” collection
date ranges are exported or printed (see “Collection Date Ranges on Labels and in
Exported Text Files” in Chapter 9).
Include Host Specimen name on
each label. A checkbox for this
option is offered for collection
labels (Host Specimen Code is an attribute of the Collection table; see Chapter 24,
“Host-Guest Relations”) and for pin, slide, and vial Specimen locality labels. It is not
exclusive of any other option, where offered. If you choose this option, Host
Specimen data are checked case by case and are included only if present in
individual Collection records. The data included in Host Specimen name are the
host genus, specific name, and family.
Include Family on each label. A
checkbox for this option is offered
for slide and vial specimen
determination labels (but not for pin determination labels, on which Family is not
traditionally included) and for herbarium specimen labels. It is not exclusive of any
other option, where offered.
Output Options
Send labels to printer. With this
option selected, you can preview
and then print the labels (or
cancel printing if the preview
shows any problems.) Follow the directions in the section “Printing and Previewing
Procedures for Reports and Labels” in Chapter 14.
Chapter 15 – Page 3
Save labels as a text file. This option sends label data to a text file, where you can
work with it in a word-processor. Biota exports some kinds of labels to tab-delimited
text files and others to ordinary text files; see the individual sections for details.
Collection Labels
Labels produced from Biota Collection records (with fields from the parent Locality
record) have several uses. When mass collections are made, such as with quadrats,
traps, trawls, extractors, foggings, sweeps, and so on, many specimens share the same
collection data. In whatever manner the collection (or lot) is stored until sorted and
identified, it needs a collection label. Often, “residual” specimens need to remain in mass
storage or in smaller groups, properly labeled, even after focal groups have been
removed and specimens labeled individually.
In entomology, locality labels attached to specimens traditionally contain no information
about the individual specimen (such as a Specimen Code or the equivalent) and provide
only approximate geographical information. They are usually printed in large sets and
applied to all specimens from a broadly defined locality (broadly, that is, compared with
GIS/GPS standards, see “Spatial Coordinates” in Chapter 9).
Using Biota’s ability to export standard locality data (from Collection and parent Locality
records) to disk file, entomologists (and others) can fine-tune the format, delete
unwanted fields, and then produce as many copies of each label as needed for each set
of data exported, using a word processing or spreadsheet application. The labels can
then be printed on a laser printer or master sheets can be sent to a commercial printing
service.
Information Included on Collection Labels
When you use the Collection Label tool, as described in the next section, Biota exports
or prints the following fields from the Collection and Locality tables, for each record in the
active Collection Record Set. The intention in choosing these fields for the tool was to be
fairly inclusive, since you can delete extra information easily in a text file, whereas
looking it up in the database to add it manually to label text is time-consuming.
Fields from the Collection record (see “Collection Input” in Chapter 11)
◊
Collection Code
◊
Collected By
◊
Date Collected or collection date range (see “Collection Date Ranges on Labels
and in Exported Text Files” in Chapter 9)
◊
Method
◊
Optional: Site.
◊
Optional: Host Genus, specific name (Species Name field), and Family (optional)
(see “Data Options,” earlier in this chapter)
Fields from the linked Locality record (see “Locality Input” in Chapter 11)
◊
Country
◊
State/Province
◊
Locality Name
◊
District
◊
Elevation
Chapter 15 – Page 4
◊
Geographic coordinates: Latitude and Longitude in Degree/Minutes/Seconds
(see “Latitude and Longitude (Locality Table)” in Chapter 9) and/or Alternate
Coordinates (see “Alternate Coordinates (Locality Table)” in Chapter 9)
Below are three examples. In the second (a collection record for hummingbird flower
mites taken from a plant specimen), Host Specimen data are included. An entry for
District is included in the third label (Sarapiquí).
ECUADOR:
Galápagos Islands
Floreana Island
Elev 10 m
1°17'0"S90°26'0"W
coll. C. Darwin
24 Sep 1832
Shotgun
Collection Code:
CD002
PERU: Cajamarca
Cajamarca-Celendin rd.
Elev 3080m
7°5'0"S78°25'0"W
coll. J. L. Luteyn
12 Feb 1985
Search
Ex Siphocampylus
sanguineus
(Campanulaceae)
Collection Code:
JLL11314H
COSTA RICA:
Heredia
Sarapiquí
La Selva
Elev 150 m
10°26'0"N84°1'0"W
coll. J. T. Longino
9 Oct 1989
Search
Collection Code:
JTL03621
(The examples above are not actual labels, just the data that are printed or exported for
each Collection record.)
If you choose the print option, rather than exporting to a text file, the printed labels carry
the information shown above. Here is the middle example in printed format, shown at
actual size.
PERU: Cajamarca
Cajamarca-Celendin rd.
Elev 3080m
7°5'0"S78°25'0"W
coll. J. L. Luteyn
12 Feb 1985
Search Ex Siphocampylus
sanguineus
(Campanulaceae)
Collection Code: JLL11314H
Printing or Exporting Collection Labels: Step by Step
1.
Find the Collection records for which you wish to print labels or export label
data, using any of the tools in the Find menu (Chapter 12, “Finding and Updating
Records”).
2.
Declare these records to be the current Collection Record Set (see “The
Record Set Options Screen” in Chapter 3).
3.
From the Labels menu, choose “Collection Labels.” The Collection label option
screen appears.
Chapter 15 – Page 5
4.
Choose a Sort Option. See “Sort Options” earlier in this chapter for details.
5.
Choose Data Options.
Month format option. See “Data Options” earlier in this chapter for details on
Month formats.
Geographic coordinates options. You can include Latitude and Longitude in
Degree/Minutes/Seconds (see “Latitude and Longitude (Locality Table)” in
Chapter 9) and/or Alternate Coordinates (see “Alternate Coordinates (Locality
Table)” in Chapter 9) on each label.
NOTE: If you have defined Aliases for the Alternate Coordinate fields, the Aliases
will appear in the option screen by the checkboxes, instead of the default
Alternate Coordinate field names.
Host Specimen name option. See “Data Options” earlier in this chapter for
details.
Include Site data on each label. A checkbox for this option is offered for
collection labels
NOTE: If you have defined an Alias for the Site field, the Alias will appear in the
option screen by the checkbox instead of the default field name.
6.
Choose an Output Option. See “Output Options” earlier in this chapter. Exported
text files for Collection labels can be opened with any word-processing application.
7.
Click the “Sort & Output” Labels button in the options window.
Chapter 15 – Page 6
8.
Follow the instructions in “Printing and Previewing Procedures for Reports and
Labels” in Chapter 14.
Pin and Vial Specimen Locality Labels
Using tools from the Labels menu, Biota can print standard locality labels for pinned
insect specimens as well as slightly larger (“vial”) locality labels for fluid-preserved
specimens of arthropods, plants, and other taxa.
With the advent of GPS technology (see “Spatial Coordinates” in Chapter 9), individual
specimen barcodes (Appendix K, “Barcodes”), and high quality laser and ink-jet printers,
locality (or “collecting-event”) labels with information pertaining to individual specimens
are now practical, if still not yet widely used in many disciplines.
Information Included on Pin and Vial Locality Label Text
When you use the Pin or Vial Locality Label tools, as described in the section “Printing or
Exporting Pin or Vial Specimen Locality Labels: Step by Step” below, Biota prints the
following fields from the Specimen, Collection, and Locality tables, for each record in the
active Specimen Record Set.
Field from the Specimen record (see “Specimen Input” in Chapter 11)
◊
Optional: Specimen Code
Fields from the linked Collection record (see “Collection Input” in Chapter 11)
◊
Collected By
◊
Date Collected or collection date range (see “Collection Date Ranges on Labels
and in Exported Text Files” in Chapter 9)
◊
Optional: Host Genus, specific name (Species Name field), and Family (optional)
(see “Data Options,” earlier in this chapter)
Fields from the linked Locality record (see “Locality Input” in Chapter 11)
◊
Country
◊
State/Province
◊
Locality Name
◊
Elevation
◊
Geographic coordinates: Latitude and Longitude in Degree/Minutes/Seconds
(see “Latitude and Longitude (Locality Table)” in Chapter 9) or Alternate
Coordinates (see “Alternate Coordinates (Locality Table)” in Chapter 9).
Here are some examples of pin locality labels, at their normal printed size. They have no
printed borders, so they can be trimmed if you want. To make them even smaller, some
printers have a setting for size reduction in “Print Setup” (Windows) or “Page Setup”
(Mac OS) window.
COSTA RICA: Heredia
La Selva
Elev 150 m 10°26'0"N84°1'0"W
coll. J. T. Longino 22 Jan 1991
INBIOCRI001B459857
COSTA RICA: Heredia
La Selva
Elev 150 m 10°26'0"N84°1'0"W
coll. J. T. Longino 9 Oct 1989
INBIOCRI001459864
Below are vial locality labels, at their normal printed size, for the same collection data.
They have printed borders.
Chapter 15 – Page 7
COSTA RICA: Heredia
La Selva
Elev 150 m 10°26'0"N84°1'0"W
coll. J. T. Longino 22 Jan 1991
INBIOCRI001B459857
COSTA RICA: Heredia
La Selva
Elev 150 m 10°26'0"N84°1'0"W
coll. J. T. Longino 9 Oct 1989
INBIOCRI001459864
Printing or Exporting Pin or Vial Specimen Locality Labels: Step by Step
1.
Find the Specimen records for which you wish to print labels or export label
data, using any of the tools in the Find menu (Chapter 12, “Finding and Updating
Records”).
2.
Declare these records to be the current Specimen Record Set (see “The
Record Set Options Screen” in Chapter 3).
3.
From the Labels menu, choose:
Either: “Pin Labels: Locality”
Or: “Vial Labels: Locality”
In either case, Biota’s response depends on the current setting of the “Coordinate
Display” option in the Coordinates tab of the Preferences screen (Special menu). If
the “Show Alternate Coordinates” is active in the Preferences screen, an Alternative
Coordinates option screen appears (see “Latitude/Longitude and Alternate
Coordinates on Labels or Reports and in Exported Text Files” in Chapter 9),
followed by the screen below. With any other “Coordinate Display” settings, the
screen below appears immediately.
(The Label Options screen illustrated above is for Pin Locality labels. The Options
screen for Vial Locality labels is identical.)
4.
Choose a Sort Option and Data Options. See the section “Label Option
Windows” earlier in this chapter.
Chapter 15 – Page 8
5.
Choose an Output Option. See “Output Options” earlier in this chapter. Exported
text files for Pin or Vial Locality labels can be opened with any word-processing
application.
6.
Click the “Sort & Output Labels” button in the options window.
7.
Follow the instructions in “Printing and Previewing Procedures for Reports and
Labels” in Chapter 14.
Pin and Vial Specimen Determination Labels
Once determinations (identifications) have been entered in Biota for uniquely labeled
specimens (identified by barcodes or by more traditional means), automatically printed
determination labels are easy to produce. Using tools from the Labels menu, Biota can
print standard determination labels for pinned insect specimens as well as slightly larger
(“vial”) labels for fluid-preserved specimens of arthropods, plants, and other taxa.
Information Included in Pin and Vial Determination Label Text
When you use the Pin or Vial Determination Label tools, as described in the section
“Printing or Exporting Pin or Vial Specimen Determination Labels: Step by Step” below,
Biota prints the following fields from the Specimen, Species, and Genus tables, for each
record in the active Specimen Record Set.
Fields from the Specimen record (see “Specimen Input” in Chapter 11)
◊
Optional: Specimen Code
◊
Determined By
◊
Year of “Date Determined” field
Fields from the linked Species record (see “Species Input” in Chapter 11)
◊
Genus
◊
Specific name
◊
Species Author (unless subspecies and/or variety recorded)
◊
Subspecific name (if any)
◊
Subspecies Author (if any, unless variety recorded)
◊
Variety (if any)
◊
Variety Author (if any)
Fields from the linked Genus record (see “Genus Input” in Chapter 11)
◊
Family (optional for vial labels, not available for pin labels)
Here are some examples of pin determination labels, at their normal printed size. They
have no printed borders, so they can be trimmed if you want.
Strumigenys
godmani
Forel 1899
det. J. T. Longino 1992
INBIOCRI001B459857
Procryptoceros
impressus
Forel 1899
det. J. T. Longino 1992
INBIOCRI001459864
Chapter 15 – Page 9
Below are vial determination labels, at their normal printed size, for the same specimen
data. They have printed borders. The Family option has been included.
Strumigenys
godmani
Forel 1899
det.
J. T. Longino 1992
INBIOCRI001B459857
FORMICIDAE
Procryptoceros
impressus
Forel 1899
det. J. T. Longino 1992
INBIOCRI001459864
FORMICIDAE
Printing Pin or Vial Specimen Determination Labels: Step by Step
1.
Find the Specimen records for which you wish to print labels or export label
data, using any of the tools in the Find menu (Chapter 12, “Finding and Updating
Records”).
2.
Declare these records the current Specimen Record Set (see “The Record Set
Options Screen” in Chapter 3).
3.
From the Labels menu, choose:
Either: “Pin Labels: Determination”
Or: “Vial Labels: Determination”
In either case, the option screen that appears looks like the one below (with the
appropriate window title).
4.
Choose a Sort Option and Data Options. See the section “Label Option
Windows” earlier in this chapter.
5.
Choose an Output Option. See “Output Options” earlier in this chapter. Exported
text files for Pin or Vial Determination labels can be opened with any wordprocessing application.
6.
Click the “Sort & Output Labels” button in the options window.
7.
Follow the instructions in “Printing and Previewing Procedures for Reports and
Labels” in Chapter 14.
Chapter 15 – Page 10
Slide Specimen Labels
Using tools from the Labels menu, Biota can print standard locality and determination
labels for slide-mounted specimens. The precise format of these labels follows the
acarological tradition (revealing Biota’s ancestry), but this format may prove adequate for
other small arthropods or parasites, and for organ or tissue specimens.
Individual locality labels have a long history for slide-mounted specimens in acarology
and parasitology. With the advent of GPS technology (see “Spatial Coordinates” in
Chapter 9), individual adhesive specimen barcodes (see Appendix K, “Barcodes”), laser
and ink-jet printers, and high quality paper with permanent adhesive backing, printing
precise locality slide labels for individual specimens—automatically, using Biota—saves
an enormous amount of time over traditional methods.
Once determinations (identifications) have been entered in Biota for uniquely labeled
specimens (identified by barcodes or by more traditional means), automatically printed
determination labels are easy to produce and add to slides. (Barcoding the slides first
makes it easy to match up labels and specimens by Specimen Code.)
Information Included in Slide Specimen Label Text
Slide Locality Labels. When you use the Slide Label Locality tool, as described in the
“Step by Step” section below, Biota prints the following fields from the Specimen,
Collection, and Locality tables, for each record in the active Specimen Record Set:
Field from the Specimen record (see “Specimen Input” in Chapter 11)
◊
Optional: Specimen Code
Fields from the linked Collection record (see “Collection Input” in Chapter 11)
◊
Collected By
◊
Date Collected or collection date range (see “Collection Date Ranges on Labels
and in Exported Text Files” in Chapter 9)
◊
Optional: Host Genus, specific name (Species Name field), and Family (optional)
(see “Data Options,” earlier in this chapter)
◊
Source. The Source field is included only if the Host Specimen option is not
checked, or if the Host Specimen option is checked, but a Specimen has no host
record. The Source field is intended to be used for information such as “From soil
core,” “Blacklight sample,” “In leaf litter.” (There is not enough space on slide
labels for both the Source field and the Host Specimen data.)
Fields from the linked Locality record (see “Locality Input” in Chapter 11)
◊
Country
◊
State/Province
◊
Locality Name
◊
Elevation
◊
Geographic coordinates: Latitude and Longitude in Degree/Minutes/Seconds
(see “Latitude and Longitude (Locality Table)” in Chapter 9) or Alternate
Coordinates (see “Alternate Coordinates (Locality Table)” in Chapter 9).
Chapter 15 – Page 11
Here are two pairs of slide locality labels, shown at normal printed size, that include Host
Specimen information. The left pair are full-sized; the right pair leave room on the slide
for a barcode label (see “Printing or Exporting Slide Specimen Labels: Step by Step,”
below).
Slide Determination Labels. When you use the Slide Determination Label tool, as
described in the section “Printing or Exporting Slide Specimen Labels: Step by Step”
below, Biota prints the following fields from the Specimen, Species, and Genus tables,
for each record in the active Specimen Record Set.
Fields from the Specimen record (see “Specimen Input” in Chapter 11)
◊
Optional: Specimen Code
◊
Stage/Sex
◊
Determined By
◊
Year of “Date Determined” field
Fields from the linked Species record (see “Species Input” in Chapter 11)
◊
Genus
◊
Specific name
◊
Species Author (unless subspecies and/or variety recorded)
◊
Subspecific name (if any)
◊
Subspecies Author (if any, unless variety recorded)
◊
Variety (if any)
◊
Variety Author (if any)
Fields from the linked Genus record (see “Genus Input” in Chapter 11)
◊
Family (optional for vial labels, not available for pin labels)
Here is a pair of slide determination labels, with the Specimen Code and Family options
included, shown at normal printed size.
Chapter 15 – Page 12
Printing or Exporting Slide Specimen Labels: Step by Step
1.
Find the Specimen records for which you wish to print labels or export label
data, using any of the tools in the Find menu (Chapter 12, “Finding and Updating
Records”).
2.
Declare these records the current Specimen Record Set (see “The Record Set
Options Screen” in Chapter 3).
3.
From the Labels menu, choose:
Either: “Slide Labels: Locality.” Biota’s response depends on the current
setting of the “Coordinate Display” option in the Coordinates tab of the
Preferences screen (Special menu). If the “Show Alternate Coordinates” is active
in the Preferences screen, an Alternative Coordinates option screen appears
(see “Latitude/Longitude and Alternate Coordinates on Labels or Reports and in
Exported Text Files” in Chapter 9), followed by the screen below. With any other
“Coordinate Display” settings, the screen below appears immediately.
Chapter 15 – Page 13
Or: “Slide Labels: Determination.” The option screen below appears.
4.
Choose a Sort Option and Data Options. See the section “Label Option
Windows” earlier in this chapter.
5.
Choose an Output Option. See “Output Options” earlier in this chapter. Exported
text files for Slide Locality or Determination labels can be opened with any wordprocessing application.
6.
For slide Locality labels, choose a Size Option:
Either: Make full-sized labels (22 mm by 22 mm).
Or: Leave space for barcode labels. In this case, the printed labels measure 22
mm by 16.5 mm, leaving room for a 22 mm by 8 mm barcode label (see
Appendix K, “Barcodes”) spanning the end of the slide, with the specimen
centered on the slide.
7.
Choose a Layout Option.
Either: Use layout for plain label stock. With this option checked, label layout
is edge-to-edge, with unscored paper. Acid-free, permanent-adhesive-backed
laser or inkjet printer paper is ideal (Avery 5165 or the equivalent).
Or: Use layout for address label stock. With this option checked, label layout
is designed so that groups of three or four labels (the number depends on the
Size Option) fit within each address label on prescored, adhesive-backed,
address label stock for laser or inkjet printers (Avery 5160 or 5260 or the
5
equivalent, 30 labels per sheet, each 1 in. by 2 /8 in., 3 columns by 10 rows).
Chapter 15 – Page 14
NOTES:
a.
Address label stock is expensive. Print out a draft set of labels on ordinary
paper first to check the text and layout and to make sure the labels fit properly
on the label stock. (Hold the stock in front of the paper-printed label sheet
against a strong light to check the alignment.)
b.
If you want to try out both layouts before buying special paper in quantity, most
stationery and photocopy stores will sell you a few sheets of each kind.
WARNINGS:
a.
In a laser printer, never use any adhesive label stock not specifically intended
for laser printers.
b.
Use the single-sheet (manual) feed tray on your printer to feed label stock.
c.
Be sure to open the “face up tray”—the direct exit tray of the printer. Label
stock can cause serious (and very sticky) paper jams if forced to exit by the
normal, “face-down” route.
8.
Click the “Sort & Output Labels” button in the options window.
9.
Follow the instructions in “Printing and Previewing Procedures for Reports and
Labels” in Chapter 14.
Herbarium Specimen Labels
Biota can print standard herbarium specimen labels for dried, sheet-mounted
specimens. Elements on the labels include both locality and determination data, as
customary for herbarium labels. Numerous options allow flexibility regarding which
elements are included on the labels, and for some elements, the fields they represent in
the database. Multiple copies of each label can be printed for duplicate specimens.
Information Included in Herbarium Specimen Label Text
When you use the Herbarium Label tool, as described in the section “Printing Herbarium
Specimen Labels: Step by Step” below, Biota prints the following fields from the
Specimen, Collection, Locality, Species, Genus and Project tables, for each record in the
active Specimen Record Set:
Fields from the Specimen (and Specimen Note) record (see “Specimen Input” in
Chapter 11)
◊
Optional: Specimen Code
◊
Determined By
◊
Date Determined
◊
Options for Collector’s field number: Specimen Code, Stage/Sex, Medium,
Storage, Specimen Custom 1, Specimen Custom 2
◊
Optional fields to include: Determined By, Date Determined, Prepared By,
Stage/Sex, Medium, Type Status, Specimen Custom 1, Specimen Custom 2
◊
Optional: Text field of the first Specimen Note linked to the Specimen record,
containing a field description of the plant (optional). See details below.
Chapter 15 – Page 15
Fields from the linked Collection (and Collection Note) record (see “Collection
Input” in Chapter 11)
◊
Collected By (See details in the Note below for treatment of Individual and Group
Personnel records.)
◊
Date Collected or collection date range (See “Collection Date Ranges on Labels
and in Exported Text Files” in Chapter 9.)
◊
Options for Collector’s field number: Collection Code, Method, Source, Site
◊
Optional fields to include: Collection Method, Site, Source
◊
Optional: Site, as a component of Locality description, or as Collector’s Field
Number
◊
Optional: Text field of the first Collection Note linked to the Collection record,
containing details on the collecting site or locality. See details below.
Fields from the linked Locality (and Locality Notes) record (see “Locality Input”
in Chapter 11)
◊
Country
◊
State/Province
◊
Optional: District (as label header)
◊
Locality Name
◊
Elevation
◊
Geographic coordinates: Latitude and Longitude in Degree/Minutes/Seconds
(see “Latitude and Longitude (Locality Table)” in Chapter 9) or Alternate
Coordinates (see “Alternate Coordinates (Locality Table)” in Chapter 9).
◊
Optional fields to include: Locality Code, Alternate Coordinates 1-3
◊
Optional: Text field of the first Locality Note linked to the Locality record,
containing details on the Locality. See details below.
Fields from the linked Species record (see “Species Input” in Chapter 11)
◊
Genus
◊
Specific name
◊
Species Author (unless subspecies and/or variety recorded)
◊
Subspecific name (if any)
◊
Subspecies Author (if any, unless variety recorded)
◊
Variety (if any)
◊
Variety Author (if any)
◊
Optional fields to include: Species Code, Subgenus, Section, Common Name
Fields from the linked Genus record (see “Genus Input” in Chapter 11)
◊
Optional: Family
Fields from the linked Project record (see “Project Input” in Chapter 16)
◊
Project Name. This area displays the “Document Heading” field of the Active
Project record.
Chapter 15 – Page 16
NOTE:
The “Collected By” field is treated as follows for herbarium labels:
An individual collector: If the [Personnel] Short Name entered in the [Collection]
Collected By field represents an Individual Personnel record (see “Personnel Input”
in Chapter 11), the Short Name itself is used for the “collector” element of the
labels.
A group of collectors: If the Short Name entered in the [Collection] Collected By
field represents a Group Personnel record (see “Personnel Input” in Chapter 11),
the Short Name for each member of the Group is included in the collector element
of the labels. The order of individual names on the label follows the order displayed
in the Group Editor when you click the “Edit Group” button in the Personnel input
screen while the Group record is displayed. The names can be reordered using the
Group Editor (see “Displaying, Changing, or Reordering Group Membership for an
Existing Group Personnel Record” in Chapter 11).
An herbarium label produced by Biota is shown below, with all elements labeled. The
actual size of the label, when printed without reduction or enlargement, is 3 in. by 5 in.
(7.6 by 12.is also available as an option.)
Printing or Exporting Herbarium Specimen Labels: Step by Step
1.
Find the Specimen records for which you wish to print labels or export label
data, using any of the tools in the Find menu (Chapter 12, “Finding and Updating
Records”).
2.
Declare these records to be the current Specimen Record Set (see “The
Record Set Options Screen” in Chapter 3).
Chapter 15 – Page 17
3.
From the Labels menu, choose “Herbarium Labels” from the Labels menu.
The herbarium label option screen appears with the “Sort Options” tab displayed.
4.
Choose a Sort Option. See the section “Sort Options” earlier in this chapter.
Chapter 15 – Page 18
5.
Click the “Data Options” tab. The tab is shown below.
6.
Choose Data Options. (Each is independent of the others, and none need be
checked.)
Use {COUNTRY} as principal label heading. You
can choose the principal heading for the labels from
the popup list (indicated by curly brackets here) from
the following fields in the Locality table: Country,
State/Province, District, or Locality Name (all
uppercase or mixed case). Don’t forget to check the
checkbox as well as making a selection from the
popup list.
Include Specimen Code. See “Data Options” earlier in this chapter.
Include Family. See “Data Options” earlier in this chapter.
Append the first {Locality Note} to the Locality
Description. This option accommodates long locality
descriptions and/or habitat descriptions on herbarium
specimen labels. If you check this option, Biota will
include the “Note Text” field from the first Note for the either the Locality record,
the Collection record, or both. (The first Note for a record is the Note with the
Chapter 15 – Page 19
earliest Note Date). Don’t forget to check the checkbox as well as making a
selection from the popup list.
In all cases, the Note Text is appended to the string: [Locality] State/Province +
[Locality] District + [Locality] Locality Name.
NOTE: In Biota 2.x, the “Locality Name” field itself can accommodate very long
descriptions (up to 32,000 characters). This option and the next one are available
in Biota 2 primarily to maintain backward compatibility with Biota 1.x Data Files,
although you may find other reasons to use them.
Append [Collection] Site field to the Locality description. If you check this
option, whatever has been entered in the Site field of the Collection record will be
appended to the State/Province, District, Locality Name string on the label.
If you check this option and also “Append the first {Locality Note} to the Locality
Description” (see above), the order of Notes and the Site information depends on
the Note selection.
◊
If you select “Locality Note” and also check “Append [Collection] Site field
to the Locality Description,” the [Collection] Site value follows the Locality
Note text.
◊
If you select “Collection Note” the [Collection] Site value precedes the
Collection Note text, to maintain the correct hierarchy of information.
◊
If you select “Loc & Coll Notes” and also check “Append [Collection] Site
field to the Locality Description,” [Collection] Site value is placed between the
Locality Note text and the Collection Note text in the text string.
NOTE: In Biota 2.x, the “Locality Name” field itself can accommodate very long
descriptions (up to 32,000 characters). This option and the previous one are
available in Biota 2 primarily to maintain backward compatibility with Biota 1.x
Data Files, although you may find other reasons to use them.
Use the first Specimen Note as field description of plant. To accommodate
the inclusion of a field description of the living material for each Specimen (habit,
colors of floral structures, etc.), you can record the description as a Specimen
Note for that Specimen record (see “Notes Input” in Chapter 11). Since each
Specimen record can have any number of attached Notes (e.g., comments on
the specimen by different botanists who have studied it), Biota needs some way
to tell which note contains the field description in its Note Text field.
The convention Biota uses is a natural one: the earliest Specimen Note, by Note
Date, for each Specimen is assumed to contain a field description in its Note Text
field. Since field descriptions normally carry the date the specimen was collected,
no earlier Note Date could be legitimate, in any case.
If you leave this option unchecked, if there are no Notes for a Specimen, or the
earliest Note has a blank Note Text field, the field description of the plant is
simply left blank on the label. If you need to print labels for a mixture of
specimens, some of which have field descriptions in the earliest Specimen Note
and some of which have other information in the earliest Note, you can either (1)
print them in two sets, with this option checked for the set with field descriptions;
Chapter 15 – Page 20
or (2) enter a Note with the collection date in the Note Date field but no entry in
the Note Text field, for the specimens with that lack field descriptions.
Use {[Specimen] Specimen Code} as the
Collector’s Number. The Collector’s Field
Number for the specimen is the link between the
specimen and the collector’s field notes. There
are nine alternative fields you can use for the
collector’s number for the specimen, which Biota
will include on herbarium labels if you check this
option. Where you decide to keep track of
Collector’s Field Numbers in Biota depends on
your collecting practices and data entry decisions.
Don’t forget to check the checkbox in addition to making a selection from the
popup list.
The options offered are:
◊
Fields in the Specimen record: Specimen Code, Stage/Sex, Medium,
Specimen Custom 1, and Specimen Custom 2.
◊
Fields in the linked Collection record: Collection Code, Method, or Site.
NOTE: You can change the name of any of these fields except Specimen Code
and Collection Code to Collector’s Number using a Field Alias. The Alias will
appear in the popup list in place of the default field name. See Chapter 18,
“Renaming Fields.”
7.
Choose Variable Field Options. Using the popup
field lists labeled “Field 1” and “Field 2” in this
panel, you can add up to two fields of your choice
to each specimen label, or leave the areas blank
by selecting “[Leave blank].” The field options are
illustrated at the right.
The fields you specify will appear just above the
Project Name and just below the Collector’s name
(Field 1) and Date Collected (Field 2) in the
herbarium labels, as illustrated in the introduction
to the section “Herbarium Specimen Labels.”
Once you select a field from the list in the Variable
Field popup, you can instruct Biota to insert the
name of the field before its value on each
specimen label by checking the checkbox next to
the Field 1 or Field 2 popup list in the Variable
Field Options panel, as illustrated below for the
Medium field selected as Field 2.
Chapter 15 – Page 21
NOTE: If you have defined an Alias (see Chapter 18, “Renaming Fields”) for any of
the fields in this list, the Alias will appear in place of the default field name in the
field selection list shown above, as well as on the labels (as Field Name Labels) if
you check the checkbox.
8.
Choose Field Label Options. In this panel, you can choose field labels you wish to
include on the herbarium specimen labels for the fields “Collector’s Name,”
“Collection Date,” and for the field you have designated as the Collector’s Number—
or select “[Nothing]” to omit field labels and print only the values for these fields. The
options are illustrated in the popup lists, below.
NOTE: If you have enabled the Spanish option in the Language tab of the
Preferences screen (Special menu), a series of Spanish field label options appears
along with the English options illustrated above.
9.
Click the “Format Options” tab. The tab is shown below.
Chapter 15 – Page 22
10. Choose a Collector’s Number Placement Option.
Option 1: Print Collector’s Number in it own field. With this option selected,
the Collector’s Number appears, with the label specified in Step 6, above, in a
special field just below the Collection Date (as illustrated on the example label in
the section, “Information Included in Herbarium Specimen Label Text,” earlier in
this chapter.)
Option 2: Append Collector’s Number to Collector’s name. If you choose this
option, the Collector’s Number (specified in Step 6, above) appears after the
Collector’s name in the Collector or Collector Group field on the label, preceded
by the field label specified in Step 8, above.
11. Choose Font Options. The settings in this panel control the appearance of the
herbarium specimen labels.
The “Project Name” settings control font, font size, and style for the herbarium,
collection, or other name that appears at the bottom of each label. You enter the
text for the Project Name field in the “Document Heading” field of the Active
Project record. (See “Entering Project Data: The General Tab” in Chapter 16.)
The “Label Text” setting controls the font used for the rest of the label layout.
You can choose a sans serif font or a serif font. In either case, a 9-point font size
is used, except that “Principal label heading” (see Step 6, above) is set in 10point bold (uppercase), Family is set in 10-point bold, and the Project Name is
formatting is controlled separately (see above).
12. Click the “Output Options” tab. The tab is shown below.
Chapter 15 – Page 23
13. Choose a Duplicate Label Option.
Option 1: Print one herbarium label per Specimen record in the active
Specimen Record Set.
Option 2: Print [Specimen] Abundance duplicate labels per Specimen
Record. With this option selected, Biota looks at the Abundance field for each
record in the current Specimen Record Set. If the Abundance value in the record
is 1 (the default for all new Specimen records, see “Specimen Input” in Chapter
11), one label is printed for that Specimen record. If the Abundance value is the
number n, then n identical, duplicate labels are printed for the record.
NOTE: If no label is printed for a record in the current Specimen Record Set,
under Option 2, the record probably has a zero in the Abundance field. Change it
to 1 for one label, or to the number n for n labels.
14. Choose an Output Option. See “Output Options” earlier in this chapter. Exported
text files for Herbarium Specimen labels are in tab-delimited format. They can be
opened with any spreadsheet or word-processing application.
NOTE: You can use Microsoft Word Mail Merge tools (or the equivalent in another
application) to design your own labels, using the exported delimited text file to
provide the input fields.
15. Choose a Layout Option.
Option 1: Print labels 4 to a page (7.6 x 12.5 cm, landscape). This option
offers maximum space for long locality names and field descriptions.
Option 2: Print labels 6 to a page (8.1 x 9.6 cm, portrait). This option allows
less space for long locality names and field descriptions.
NOTE: You can also increase the amount of text that will fit on herbarium labels
by reducing the Font Size in the Font Options panel of the Format Options tab
(see Step 11, above).
16. Choose a Border Option.
Option 1: Print labels with border lines. If you choose this option, Biota prints
a simple, fine line border around each label.
Option 2: Print labels with tick marks, but no border lines. If you choose this
option, Biota prints very fine tick marks outside the area of the labels as a guide
for cutting the labels apart after printing.
17. Choose a Preview option. If you check the “Preview labels before printing”
checkbox, Biota automatically sets the Preview option in the “Print” window for your
active printer. See “Printing and Previewing Procedures for Reports and Labels” in
Chapter 14.
18. Choose a Save settings option. If you check the “Save Herbarium Settings
between sessions” checkbox, Biota saves your current option settings not only
between uses of the Herbarium Labels tool within the current Biota work session,
but stores them (transparently) in your Data File until changed in a later session.
Chapter 15 – Page 24
19. Click the “Sort & Print Labels” button in the options window.
20. Follow the instructions in “Printing and Previewing Procedures for Reports and
Labels” in Chapter 14.
Species Labels
Species Labels are used to identify conspecific sets of specimens in collections. They
may be used to label unit trays in entomological collections or species folders in
herbaria, for example.
Information Included on Species Labels
When you use the Species Label tool, as described in the next section, Biota prints the
following fields from the Species table.
Fields from the Species record (see “Species Input” in Chapter 11)
◊
Species Code
◊
Genus
◊
Specific name
◊
Species Author (unless subspecies and/or variety recorded)
◊
Subspecific name (if any)
◊
Subspecies Author (if any, unless variety recorded)
◊
Variety (if any)
◊
Variety Author (if any)
Field from the Personnel table. As an option, you can include an additional line to
show who determined the particular set of specimens that you intend to label with a
Species label:
◊
Personnel Short Name field for the determiner (optional)
Here are three examples of Species labels (determination option not included).
Cactospiza
heliobates
(Snodgrass & Heller)
1901
Sp. Code: cactheli
Strumigenys
godmani
Forel 1899
Sp. Code:
Cavendishia
crassifolia
(Bentham) Hemsley
Sp. Code:
Chapter 15 – Page 25
Printing Species Labels: Step by Step
1.
From the Labels menu, choose Species Labels. The Species Labels setup
screen appears.
2.
Define the set of Species records for which to print labels. There are three
different ways to specify which species to include in a print run of Species Labels.
These methods can be used in any combination.
Species Record Set method.
a. Find the Species records for which you wish to print labels, using any of the
tools in the Find menu (see Chapter 12, “Finding and Updating Records”).
b. Declare these records the current Species Record Set (see “The Record
Set Options Screen” in Chapter 3).
c. Click the “Include
Species Record Set”
checkbox in the Species
Labels setup screen to
set this option.
Chapter 15 – Page 26
Species Code entry method.
a. In the Enter Species Code box,
enter a Species Code. You can enter
a full Species Code—manually or with
a barcode reader (see Appendix K,
“Barcodes”), or enter a partial code
and use the wildcard entry method
(see “A Powerful Shortcut: Wildcard
Data Entry for Linking Fields” in
Chapter 7).
b. Press the TAB key. The “Last Code Entered” display area now shows the
Species Code you entered and the Classification panel shows information for
the record found.
c. Repeat with additional Species Codes.
“Look Up Species” method.
a. Click the “Look Up” button.
Use the techniques described
for this tool in Step 2, Method 5
of the section “Entering
Specimen Data: The ‘General’
Tab” in Chapter 11, to find and enter a Species Code.
b. Repeat with additional Species Codes. After each entry, the previous Code
will be displayed in the “Last code entry” box.
3.
Enter a determiner’s name (optional).
Use the techniques described in Step 1 of
“Entering Specimen Data: The
‘Determination’ Tab” in Chapter 11 to find
and enter the Short Name of a
determiner. The name will be included on every Species label in this print run.
4.
Choose an Output Option. See “Output Options” earlier in this chapter. Exported
text files for Species labels are in tab-delimited format. They can be opened with
any spreadsheet or word-processing application.
Chapter 15 – Page 27
NOTE: You can use Microsoft Word Mail Merge tools (or the equivalent in another
application) to design your own labels, using the exported delimited text file to
provide the input fields.
5.
Click the “Sort & Print Labels” button in the Species Labels window. The labels
will be sorted taxonomically (see “Sort Options” earlier in this chapter).
6.
Follow the instructions in “Printing and Previewing Procedures for Reports and
Labels” in Chapter 14.
Designing and Printing Custom Labels
Inevitably, the format of the standard labels produced by the tools of the Labels menu
will not meet everyone’s specialized label needs. In many cases, you may be able to
meet your requirements using the “Save labels as a text file” Output Option (see “Output
Options” earlier in this chapter) to export the label date to a text file, where you can
format, modify, or delete label text as you wish, or include additional data.
More generally, you can use the Export Editor (see Chapter 27, “Exporting Data by
Tables and Fields”) to export data to a text file from any one table at a time, or the Quick
Report Editor (see “Exporting Custom Flatfiles” in Chapter 27) to export data for fields
from related tables. Microsoft Word or other applications have tools you can use to edit
and format the data in the exported text file, as you require, before you print the labels.
For specialized labels of any kind, including those that require fields from related (child
or parent) tables, consider The 4D Label Wizard, the “off the shelf” 4th Dimension utility
described in Appendix D, “The 4D Label Wizard.” But first, read the section below,
“Launching the 4D Label Wizard,” to get started.
NOTE: You can use the 4D Label Wizard to make labels for records in any Core table
(see “Core Tables” in Chapter 3), specifying fields from that table and any of its parent
tables. Fields in child tables cannot to be used, because there may be many child
records linked to each parent record so the Label Wizard has no way to determine which
record to access.
Launching the 4D Label Wizard
1.
Find the records for which you want to print labels, and declare them the
Record Set for that table (see “The Record Set Options Screen” in Chapter 3).
2.
From the Labels menu, choose “Design & Print Custom Labels.” A table
selection and option screen appears.
Chapter 15 – Page 28
3.
Click and hold on the table selection popup list, then select the table for which
you want to print labels.
4.
Choose a Sort Option (See “Sort Options” earlier in this chapter).
5. Click the “Ready” button in the table selection window. A message appears
regarding a popup setting in the 4D Label Wizard that must be left set to the default.
To bypass the warning for the rest of the current Biota session, click the “Don’t
show this message again today” checkbox.
Chapter 15 – Page 29
6.
Click the “OK” button in the message screen. The 4D Label Wizard appears.
7.
Follow instructions in Appendix D, “The 4D Label Wizard.”
NOTE: Because Appendix D is based on a generic 4D document, the examples
used in it do not refer to Biota.
PART
5
Customizing Biota
Chapter 16
User-Defined Auxiliary Fields
and the Project System
As your experience with software of other kinds will doubtless confirm, an application
that is too narrow and inflexible is frustrating, whereas one that tries to do everything is
ponderous and confusing. Biota is an attempt to strike the right balance between a lean,
fast application that suits perfectly the needs of a few, and a jack-of-all trades application
that suits no one well.
A relational database, by its nature, is confined within the limits of whatever relational
structure the designer gives it. The challenge is to choose a structure that can
accommodate a broad spectrum of uses, without greatly compromising the efficiency of
the most common operations that users need to carry out.
This chapter and the next two in this Part explain in detail how you can customize Biota
to meet special needs by adding Auxiliary Fields and defining Projects (this chapter),
setting up Default Entries and Entry Choice Lists (pick lists) for data entry (Chapter 17),
and renaming existing fields (Chapter 18). See also Chapter 8, “Record Codes,” which
explains how to set up custom prefixes for Record Codes.
Core Fields and Auxiliary Fields
In designing Biota’s relational structure (see Appendix A, “Biota Tables, Fields, and
Relational Links”), the goal was to place essential and commonly used fields, called
Core fields, in the Core tables (see “Core Tables” in Chapter 3). Inevitably, however,
different people with different needs will find some existing fields needless and some
needed fields lacking. Biota’s ability to re-name many Core fields with Field Aliases can
solve some of these problems (see Chapter 18, “Renaming Fields”), but if you require
more fields than exist in the Core tables (plus linked records in child tables, such as
Notes and Images), you will need to create Auxiliary Fields.
Auxiliary Fields, in contrast to Core fields, are special fields that you create and name as
you like. Core fields, however, are much faster to sort and to query. For this reason, in
planning the way you will use Biota, wherever possible, it is better to use Core fields, renamed or not, in preference to Auxiliary Fields.
Any number of Auxiliary Fields can be created for the Species, Specimen, Collection,
and Locality tables. The potential uses for Auxiliary Fields are endless, but here are just
a few actual examples:
Chapter 16 – Page 2
Systematists use Species or Specimen Auxiliary Fields to record values for a
character matrix. Biota can export Auxiliary Fields in the NEXUS format for direct
use in MacClade1 or PAUP2.
Ecologists use Collection Auxiliary Fields to record the habitat features or
meteorological conditions of collection sites or live-organism observation sites. Plant
ecologists use Specimen Auxiliary fields to record individual plant age and
morphometric data (e.g., diameter at breast height).
Ethnobotanists use Species Auxiliary fields to record uses of each species in
matrix format.
Museums, herbaria, and reserves use Species Auxiliary fields to record such
ancillary data as conservation status and provenance.
How Auxiliary Fields Work
NOTE: Please do not skip this section. Auxiliary Fields are not complicated, but if you fail
to understand how they work you will likely cause yourself needless problems.
Auxiliary Field Value Tables
Biota’s Auxiliary Field system does not actually create “hard-wired” new fields in the
Core tables. (There is no way to do that in a compiled database application.) Instead,
data entered in an Auxiliary Field are kept in a special “triplet” format in a linked
“Auxiliary Field Value Table” (either the Specimen Field Value table, the Species Field
Value table, the Collection Field Value table, or the Locality Field Value table).
Suppose you create two Specimen Auxiliary Fields, one called “Bill Length” and the
other called “Wing Length” for a Project on birds. Each time you enter a Bill Length or
Wing Length value for a Specimen record, Biota creates a new record in the Specimen
Field Value table, in the format: Specimen Code, Field Name, Field Value. (The
Specimen Field Value table has only these three fields, hence the term triplet.)
Here are the records for Bill Length and Wing Length in the Specimen Field Value table,
linked to the three parent Specimen records through the Specimen Code:
1
Specimen Code
Field Name
Field Value
SPM00634
Bill Length
0.86
SPM00634
Wing Length
6.31
SPM00635
Bill Length
0.78
SPM00635
Wing Length
6.63
SPM00636
Bill Length
0.82
SPM00636
Wing Length
6.57
Maddison, W. P., and D. R. Maddison. 2000. MacClade 4: Analysis of Phylogeny and
Character Evolution. Sunderland, MA: Sinauer Associates.
2
Swofford, D. L. 2002. PAUP*: Phylogenetic Analysis Using Parsimony (and Other
Methods) 4.0. Sunderland, MA: Sinauer Associates.
Chapter 16 – Page 3
If you use statistical applications, you are probably already familiar with this alternative
way of representing tabular data: Row Index, Column Index, Value. Even though it
requires three entries for each Value, this format is a more memory-efficient way than
setting out a full table for storing “sparse matrices”—tables that are mostly blanks or
zeros. For this reason, you need not hesitate to add a new Auxiliary Field that will be
used for only a small subset of the records in a Core table, for fear of adding
unnecessarily to the size of the Data File. An Auxiliary Field “triplet” record is created
only when you actually enter a value for an Auxiliary Field. Furthermore, using the
Project system, you can control which Auxiliary Fields are available for input, displayed
in output, or exported.
Auxiliary Field Name Tables
Linked to each Auxiliary Field Value table (e.g., the Specimen Field Value table) is a
separate table that simply keeps a list of Auxiliary Field Names (e.g., the Specimen Field
Name table; see Appendix A, “Biota Tables, Fields, and Relational Links”). Each of the
four Auxiliary Field Name tables (the Specimen Field Name table, the Species Field
Name table, the Collection Field Name table, or the Locality Name Value table) includes
an Index field to keep track of the Auxiliary Field order you specify. Except for importing
or exporting Auxiliary Field Names, you never need to bother with these tables; Biota
does all the record-keeping automatically.
The “Auxiliary Fields” Field in Parent Tables
To keep track of how many Auxiliary Field Values are linked to each parent record, the
Species, Specimen, Collection, and Locality tables each have a field called “Auxiliary
Fields.” Biota automatically updates this field with the number of Field Value records
currently linked to the parent record, for all Projects combined (see “Projects” later in this
chapter. You cannot edit the “Auxiliary Fields” field directly.
Sorting Parent Records Based on Auxiliary Fields
Unfortunately, there is currently no tool for sorting parent records in the parent table
Record Listing screen based on linked Auxiliary Field values. However:
You can sort parent records according to the number of linked Auxiliary Field
Values, simply by selecting the “Auxiliary Fields” field in the Sort Editor. (See
“Sorting Records in Record Listing Screens” in Chapter 10 and “The ‘Auxiliary
Fields’ Field in Parent Tables” earlier in this chapter.)
You can use the Query Editor to search for parent records based on linked
Auxiliary Field values. See “Using the Query Editor with Auxiliary Field Values” and
“Using the Query Editor with Auxiliary Field Values in Combination with Other
Criteria” in Chapter 12.
Chapter 16 – Page 4
Creating, Editing, and Ordering Auxiliary Field Names
This section tells you how to create new Auxiliary Fields, change the order or name of
existing Auxiliary Fields, and how to delete Auxiliary Field Names when you no longer
want them. The next section explains how to enter, edit, and delete values in Auxiliary
Fields.
Opening the Field Name Editor
You use the Field Name Editor to create, change, or delete Auxiliary Fields.
You can access the Field Name Editor directly from the “Aux Fields” tab of the Input
screen for each Core table that supports Auxiliary Fields (Specimen, Collection, Locality,
and Species). This method is described in the following section, “Using the Field Name
Editor.”
Alternatively, you can open the Field Name Editor from the “Auxiliary Field Set” tab of
the Project Input screen (see “Entering Project Data: The ‘Auxiliary Field Set’ Tab” later
in this chapter).
Using the Field Name Editor
In this section, Species Auxiliary Fields will be used as an example, but the procedures
are identical for Specimen, Collection, or Locality Auxiliary Fields.
1.
From the Input menu, choose Species (or Specimen, Collection or Locality,
depending on which table’s Auxiliary Fields you want to work with). The Species
Input screen appears.
2.
Enter a Species Code. Any value will do. You can even Cancel the Species record
when you are finished modifying Species Auxiliary Field Names without losing the
changes in Auxiliary Field Names.
3.
Click the Aux Fields (Auxiliary Fields) tab in the Species Input screen.
The Auxiliary Fields tab screen appears showing all Species Auxiliary Fields
currently defined, together with spaces on the right for recording their value for this
record. (No Species Auxiliary Fields are already defined if you are working with your
own Data File and have not yet defined any.)
NOTE: If the Global Project is not currently selected as the Active Project, you will
see only those Auxiliary Fields associated with the Active Project. To learn how to
select the Global Project, see “Using the Active Project Floating Window” later in
this chapter.
Chapter 16 – Page 5
4.
Open the Field Name Editor by clicking the “Edit Field Names” button, as shown
above.
5.
Edit, append, insert, delete, re-order, or sort Field Names.
To edit an existing Field Name, select the Field Name in the list, then edit it in
the entry area at the bottom of the Field Editor window.
Chapter 16 – Page 6
To add a new Field Name at the end of the list, click the “Append” button, then
enter the new Field Name in the entry area at the bottom of the Field Editor
window, as shown below.
Auxiliary Field Names must be unique, within the set of Auxiliary Field Names for
each Core table. If you try to enter a duplicate Auxiliary Field Name in the Field
Name Editor, Biota displays the message shown here, and the name is not
accepted.
NOTE: Although you cannot create two Species Auxiliary Fields, both named
Size, you could create a Species Auxiliary Field and a Specimen Auxiliary Field,
both named Size. Of course, there is no restriction on repeated values for
Auxiliary Fields in different records. For example, any number of Species can
have the value Large for the Size field.
Chapter 16 – Page 7
To insert a new Field Name in the middle of the list, select the existing Field
Name you want to follow the new Field Name, then click the “Insert” button and
enter the new Field Name in the entry area at the bottom of the Field Editor
window, as shown below.
To delete an existing Field Name, select it in the list, then click the “Delete”
button.
WARNING: Biota will post a warning when you attempt to delete a Field Name. If
you confirm the deletion, not only the Field Name, but all Auxiliary Field Values
for that Field, for all records that have them, will also be deleted. There is no way
to undo this process.
Chapter 16 – Page 8
To sort the Field Names alphabetically, click the “Sort and Renumber” button.
The Sort Option screen appears. Accept the default (“Sort Fields by Field Names
& renumber”) by clicking the “OK” button.
To change the order of the Field Names to a different (non-alphabetic
order), edit the sort order numbers to match the desired order in the Number
Entry Area of the Field Editor.
NOTE: You need not use consecutive numbers, or even integer numbers, as the
fields are renumbered consecutively in the next step, based on the rank order of
whatever temporary numbers you enter.
Chapter 16 – Page 9
Now click the “Sort and Renumber” button. The Sort Option screen appears.
Choose “Sort Fields by Field Numbers & renumber” then click the “OK” button.
The fields are re-ordered and renumbered.
6.
Click the “Save Changes” button in the Field Name Editor to accept the list of
fields.
The Field Name Editor disappears, leaving the Aux Fields tab screen of the Species
Input screen showing the new fields you created, edited, or re-ordered, ready for
Auxiliary Field data entry for this Species record.
Chapter 16 – Page 10
Entering and Displaying Data in Auxiliary Fields
Once you have defined the Auxiliary Field Names you want by using the Field Name
Editor (see “Creating, Editing, and Ordering Auxiliary Field Names” earlier in this
chapter), you are ready to enter Auxiliary Field Values (data) in your Auxiliary Fields.
This section uses Collection Auxiliary Fields as an example, but the procedures are
identical for Species, Specimen, or Locality Auxiliary Fields.
Entering New Data or Editing Data in Auxiliary Fields
1.
Display a new or existing Species, Specimen, Collection, or Locality record in
the input screen, using any tools from the Input menu (Chapter 11, “Input—Table
by Table”) or the Find menu (Chapter 12, “Finding and Updating Records”).
2.
Click the Aux Fields tab.
The Aux Fields tab screen appears showing all Collection Auxiliary Fields currently
defined, together with spaces on the right for recording their value for this record.
(To add or modify Auxiliary Field Names, see “Creating, Editing, and Ordering
Auxiliary Field Names” earlier in this chapter.)
Chapter 16 – Page 11
NOTE: If the Global Project is not currently selected as the Active Project, you will
see only those Auxiliary Fields associated with the Active Project. To learn how to
define Projects, see “The Project System and Auxiliary Fields” later in this chapter.
To learn how to switch between Projects, see “Using the Active Project Floating
Window” later in this chapter.
3.
Click anywhere on the line for the field for which you want to enter (or edit) a
value. (The “Habitat” field has just been clicked in the example, above.) The Field
Value entry window appears.
4.
Enter a value (or edit the existing value), then click OK (or press the Return
key). (The value “Lower montane forest” has been entered for the Habitat Auxiliary
Field, in the example above.) The Field Value entry dialog reappears, ready for the
Field Value for the next field in the Field Name list (the “slope” field in the example
below).
5.
If you want to enter or edit a value for this field, do so and click OK. This cycle
continues until you reach the bottom of the Field Name list or until you click Cancel
in the Field Value entry dialog.
NOTE: For non-sequential value entry, click on the line you want, make the entry or
edit the existing value, then click Cancel when asked for a value for the next field.
6.
When you have completed the entries and they appear as you wish in the Field
Value list, click the “Save Changes” button in the Aux Fields tab screen.
Chapter 16 – Page 12
NOTE: If you forget to click the “Save Changes” button before going to a different
tab, moving to another record using the navigation buttons, Saving the record, or
Carrying the record, Biota saves the new or revised Auxiliary Fields automatically.
Therefore, if you make any changes you do not want to keep, be sure to click the
“Cancel Changes” button on the Aux Fields tab screen.
7.
If you have finished working with the record, click
the “Save” button for the parent record (the Collection
record, in the example here).
Carrying Auxiliary Fields
The “Carry” button in Biota Input screens allows you to use an existing record (or a
record you have just created) as a template for a new record (see “Using an Existing
Record as a Template for a New Record” in Chapter 10). As an option, you can choose
to Carry (copy) all Auxiliary Field Values from the existing record to the new record (for
the tables that support Auxiliary Fields).
To enable or disable this option:
1.
Choose Preferences from the Special menu. The Preferences screen appears.
2.
Click the “Other Settings” tab in the Preferences screen.
Chapter 16 – Page 13
3.
In the “Other Settings” screen, click the checkbox labeled “Carry Auxiliary
Field Values from template records” to enable (check) or disable (uncheck) the
Carry Auxiliary Field Values option. The default setting is disabled (unchecked).
4. Click the “Save” button in the Preferences screen.
Displaying Auxiliary Fields and Their Values for a Selection of Records
1.
Display a selection of records for the Specimen, Collection, Locality, or
Species table in the Record Listing screen for that table (see Chapter 12,
“Finding and Updating Records”).
In this section, Collection records will be used as an illustration, but the procedures
are identical for the other three tables.
The numbers in the “Aux” column (illustrated below) show how many Auxiliary Field
Values have been entered from each parent table record (5 for each Collection
record, in the example).
Aux Column
Chapter 16 – Page 14
2.
Click the “Aux Fields” button at the bottom of the Record Listing screen.
An option window appears, offering two alternative display formats for the Auxiliary
Fields for these Collection records.
3.
Choose a display option.
The Standard option (the default) displays the Auxiliary Fields in the same
orientation as ordinary (Core) fields in the Record Listing screen—in the
example, Collection records as rows, Auxiliary Fields as columns. See
“Displaying Auxiliary Fields in the Standard Format: Records as Rows, Auxiliary
Fields as Columns” later in this chapter.
The Transposed option (right option button) displays the same information in a
transposed format—in the example, it would display Auxiliary Fields as rows,
Collection records as columns. See “Displaying Auxiliary Fields in the
Transposed Format: Auxiliary Fields as Rows, Records as Columns” later in this
chapter.
Although these Auxiliary Field display formats are limited to 25 columns, you will be
able to examine all your data, regardless of the number of Auxiliary Fields you have
defined and regardless of the number of records in the selection.
If you have defined 25 or fewer Auxiliary Fields and there 25 or fewer
records in the current selection, choose the option that makes more sense for
the information you want to find or compare. (You may have to experiment a bit
to know which is better for your purposes.)
If you have defined fewer than 25 Auxiliary Fields but there are more than
25 records in the current selection, you will usually want to choose the
Standard Auxiliary Fields display (the left option button). See “Displaying
Auxiliary Fields in the Standard Format: Records as Rows, Auxiliary Fields as
Columns” later in this chapter.
Chapter 16 – Page 15
If you have defined more than 25 Auxiliary Fields, but there are fewer than
25 records in the current selection, you will usually want to choose the
Transposed Auxiliary Fields display (the right option button). See “Displaying
Auxiliary Fields in the Transposed Format: Auxiliary Fields as Rows, Records as
Columns” later in this chapter.
If you have defined more than 25 Auxiliary Fields and there are more than
25 records in the current selection, choose the option that makes more sense
for the information you want to find or compare.
Displaying Auxiliary Fields in the Standard Format: Records as Rows,
Auxiliary Fields as Columns
1.
Follow the instructions in the section “Displaying Auxiliary Fields and Their
Values for a Selection of Records” earlier in this chapter.
2.
In the display options window, make sure the Standard (left button) option is
selected, and then click the “OK” button.
The selection of parent table records (Collection records, in the example) appears,
with the corresponding values for Auxiliary Fields in labeled columns.
Chapter 16 – Page 16
In the example above, notice that only the first three Auxiliary Fields are visible (for
Habitat, Slope, and Aspect).
3.
To see the next set of Auxiliary fields (columns), click in the horizontal scroll
bar (where the cursor arrow appears, above), or use the horizontal scroll arrows or
“thumb-slider” to move to the right. The next set of fields appears (Temperature and
Precipitation, in the example), along with the Record Code (Collection Code, in the
example).
4.
If not all Auxiliary Fields have been revealed, continue to move to the right in
the display, using the horizontal scroll bar tools. Up to 25 Auxiliary Fields can be
displayed.
NOTE: If you have a monitor wider than the display window, you can expand the
window horizontally to see more Auxiliary Fields all at once, as shown below.
5.
To view all Auxiliary Fields for a record (or to edit them), double-click a row (a
Collection record, in the example) in the Record Listing screen. The individual
record appears in the standard Input screen (the Collection Input screen, in the
Chapter 16 – Page 17
example). To edit or add Auxiliary Field values to the record displayed, follow the
instructions in the section “Entering New Data or Editing Data in Auxiliary Fields”
earlier in this chapter.
NOTE: With the parent record (Collection record, in the example) displayed in the
Input screen, you can view (and edit) all Auxiliary Field Values for that record by
clicking the Auxiliary Fields tab in the Input screen, even if you have defined more
than 25 Auxiliary Fields.
6.
When you are through using the Auxiliary
Fields display screen, you can either dismiss
the selection by clicking the “Done” button, or
return to the normal Core Fields Record Listing
screen to display the current selection of
records by clicking the “Core Fields” button on
the Auxiliary Fields display screen.
Displaying Auxiliary Fields in the Transposed Format: Auxiliary Fields as
Rows, Records as Columns
1.
Follow the instructions in the section, “Displaying Auxiliary Fields and Their
Values for a Selection of Records” earlier in this chapter.
2.
In the display options window, click the button for the “Transposed” format
option, then click the “OK” button.
The selection of parent table records (Collection records, in the example) appears,
with Auxiliary Field Names labeling the rows of the display and identifiers of the
parent table records as column headings. (The identifier fields vary appropriately
among for Species, Specimen, Collection, and Locality Auxiliary Fields.)
Chapter 16 – Page 18
3.
If not all columns (records) in the selection are visible, use the horizontal
scroll bar to see additional columns.
NOTE: If you have a monitor wider than the display window, you can open the
window wider to see more Auxiliary Fields all at once, as shown below.
4.
To view the Values for all Core records in the selection, for a given Auxiliary
Field, double-click a row (a Collection Auxiliary Field, in the example). The Auxiliary
Field expansion screen appears listing the Value for that Auxiliary Field (“Habitat” in
the example below) for each parent table record (each Collection record, in the
example) in the current selection, even if there are more than 25 parent table
records in the selection.
Chapter 16 – Page 19
NOTES:
5.
a.
This screen is available only with Transposed display format for Auxiliary
Fields, not with the Standard format.
b.
Auxiliary Field Values and Auxiliary Field Names cannot be edited in this
screen. See “Entering New Data or Editing Data in Auxiliary Fields” earlier in
this chapter for instructions on editing of adding Auxiliary Field data.
If an Auxiliary Field Value or an identifier field is too long to read fully in the
display, you can double-click the record in the screen above, to display the
information in full.
Chapter 16 – Page 20
6. Click the “Done” button at the bottom of the Auxiliary Field expansion screen,
when you are through examining the values.
7.
When you are through using the Auxiliary Fields display screen, you can either
dismiss the selection by clicking the “Done” button, or return to the Core Field
display for the current selection of records by clicking the “Core Fields” button on
the Auxiliary Fields display screen.
Printing Auxiliary Fields
You can print Auxiliary Fields and their values for a selection of parent table (Specimen,
Species, Collection, or Locality) records in any of four formats: in matrix (row-by-column)
format, either Standard or Transposed (see below); or in triplet format, either Standard
or Transposed. (For details on these formats see “Displaying Auxiliary Fields in the
Standard Format: Records as Rows, Auxiliary Fields as Columns” and “Displaying
Auxiliary Fields in the Transposed Format: Auxiliary Fields as Rows, Records as
Columns” earlier in this chapter).
Printing Auxiliary Fields in Matrix (Row-by-Column) Format
The most flexible method for printing Auxiliary Field data is to export the Auxiliary Field
Values to a text file in full matrix format (either Standard or Transposed), open the text
file using a spreadsheet application (such as Microsoft Excel) or a text processing
application (such as Microsoft Word), then format and print the data to suit your own
needs. This is the method to use if you want to print Auxiliary Field data and Core Field
data together for the same records.
Biota does not provide a preformatted, printed report for Auxiliary Field data in matrix
format. For help exporting Auxiliary Fields, see the section “Exporting Auxiliary Field
Values” later in this chapter. For help exporting Core Field data, see Chapter 27,
“Exporting Data by Tables and Fields.”
Chapter 16 – Page 21
Printing Auxiliary Fields in Standard Triplet Format (Record Code, Auxiliary
Field Name, Auxiliary Field Value)
1.
Display Auxiliary Fields and their values in the Standard Auxiliary Fields Record
Listing screen, following the steps in the section “Displaying Auxiliary Fields in the
Standard Format: Records as Rows, Auxiliary Fields as Columns” earlier in this
chapter.
2.
Click the “Print” button at the bottom of the screen (see above). A warning
message appears, explaining that the data will be printed in triplet format.
3.
Click the “OK” button in the warning window to proceed. The Page Setup
window appears. (The appearance and options available in the Page Setup window
depends on the printer and operating system you are using.)
4.
Click the “OK” button in the Page Setup window. The Print window appears.
(The appearance and options available in the Print window depends on the printer
and operating system you are using.)
Chapter 16 – Page 22
5.
If you want to preview the printed report, click the “Preview on screen” checkbox
in the lower-left corner of the Print window. (With some printers, you will need to
select “4th Dimension” or “4D Engine” from a popup menu to find the “Preview on
screen” checkbox.)
Printing Auxiliary Fields in Transposed Triplet Format (Auxiliary Field
Name, Record Code, Auxiliary Field Value)
1.
Display Auxiliary Fields and their values in the Standard Auxiliary Fields Record
Listing screen, following the steps in the section “Displaying Auxiliary Fields in the
Transposed Format: Auxiliary Fields as Rows, Records as Columns” earlier in this
chapter.
Chapter 16 – Page 23
2.
Click the “Print” button at the bottom of the display (see above). A warning
window appears, explaining that the data will be printed in triplet format.
3.
Follow Steps 3 through 5 in the section “Printing Auxiliary Fields in Standard
Triplet Format (Record Code, Auxiliary Field Name, Auxiliary Field Value)” earlier in
this chapter. The report appears in the preview screen or is printed on paper.
Exporting Auxiliary Field Values
Like data in any other table in Biota, the data in the four Auxiliary Field Value tables
(Spcm Field Value, Spp Field Value, Coll Field Value, and Loc Field Value) can be
exported directly to a text file using the Export Editor (see Chapter 27, “Exporting Data
by Tables and Fields”). In fact, if you are moving Auxiliary Fields data between Biota
Data Files, you must use this method to create a text file in a format suitable for the
Import Editor to import the text file into another Biota Data File.
The information in Auxiliary Fields appears internally in triplet format rather than in
columns and rows (see “How Auxiliary Fields Work,” earlier in this chapter, and
Appendix A, “Biota Tables, Fields, and Relational Links”). Therefore Biota offers special
tools for exporting Auxiliary Field Values in matrix form, with a choice among several
different formats, as detailed below.
Chapter 16 – Page 24
1.
Establish a Record Set composed of the parent table records whose Auxiliary
Field Values you wish to export. (See “Record Sets” in Chapter 3 if you need help
declaring Record Sets.)
Suppose, for example, that you want to export values for the Collection Auxiliary
Fields records used as an illustration earlier in this chapter, and you have already
declared the parent Collection records as the current Collection Record Set.
2.
From the Im/Export menu, choose Export Auxiliary Fields. An option screen
appears.
3.
In the option window, click and hold on the table name popup list.
4.
Select the name of the Core table for which you want to export Auxiliary Field
Values. (“Collection” is selected, above.)
5.
Select the output format you want, using one of the three option buttons:
Standard format (Records as rows, Auxiliary Fields as columns).
Transposed format (Auxiliary Fields as rows, records as columns).
NEXUS format (see “Exporting Auxiliary Fields in the NEXUS Format” later in
this chapter.
6.
Click the “OK” button in the option window. The Save File window for your
operating system appears.
Chapter 16 – Page 25
7.
Enter a name for the text file and click the “Save” button (Macintosh) or “OK”
button (Windows) in the Save File window.
A progress indicator appears, then a notice that the text file has been created
successfully. (If an error comment appears, try again.)
Now you can view, edit, format, or print the text file using any spreadsheet or word
processing application. Here is how the example data, in Standard format, would
look in an exported text table:
COLLECTION\FIELD Habitat
JLL14697
Lower
montane wet
forest
JLL5020
Lower
montane forest
JLL13393
Degraded
cloud forest
JLL12327
Lower
montane forest
JLL14587
Montane forest
JLL10573
Second growth
montane forest
Slope Aspect
35%
E
Temperature Precipitation
24°C
None
30%
SSW
23°C
None
10%
ESE
16°C
Rain
15%
SSW
21°C
Heavy rain
10%
40%
SSW
NE
16°C
18°C
Light drizzle
None
Exporting Auxiliary Fields in the NEXUS Format
Systematists can use Biota Auxiliary Fields to create character matrices for Species or
Specimens, then export the matrices in NEXUS format. (Biota can also export matrices
in NEXUS format for the Collection and Locality Auxiliary Fields).
Biota exports NEXUS files using the “STANDARD” NEXUS datatype only (not to be
confused with Biota’s Standard Auxiliary Fields format). NEXUS files exported by Biota
can be used without modification as input for MacClade3 PAUP4, or any other application
that supports NEXUS input. You may want to edit the NEXUS documents that Biota
exports, however, to modify the way they are used by these applications.
To export a NEXUS file, just follow the directions in the previous section (“Exporting
Auxiliary Field Values” earlier in this chapter), but in step 4, click the “NEXUS” button in
the Export Auxiliary Fields option window.
Below is an example of a NEXUS file exported by Biota for several Species records for
hummingbird flower mites, from the BiotaDemo Data File that is distributed with Biota.
Notice that any internal space characters in Auxiliary Field Names are automatically
filled with the underline character, as required in the NEXUS standards. Please consult
the NEXUS data standards documentation for an explanation of the various components
of the file.
3
Maddison, W. P., and D. R. Maddison. 2000. MacClade 4: Analysis of Phylogeny and
Character Evolution. Sunderland, MA: Sinauer Associates.
4
Swofford, D. L. 2002. PAUP*: Phylogenetic Analysis Using Parsimony (and Other
Methods) 4.0. Sunderland, MA: Sinauer Associates.
Chapter 16 – Page 26
NOTE: There is one important restriction. To export Auxiliary Field Values in NEXUS
format, all Auxiliary Field Values in the set must be single-digit integers (0 through 9) or
single alphabetic characters (A through Z).
If you attempt to export a longer value or a value with other characters in NEXUS format,
Biota posts an error comment. Please note that this restriction does not apply to
Auxiliary Field values in general, only to those exported in NEXUS format
#NEXUS
BEGIN TAXA;
DIMENSIONS NTAX=5;
TAXLABELS rhinrich rhinhaplo troperio tropfuent
tropkressi;
END;
BEGIN CHARACTERS;
DIMENSIONS NCHAR=11;
FORMAT
DATATYPE=STANDARD
SYMBOLS=” 0 1 2”
CHARSTATELABELS
1 metapodal_plates,
2 opisthoventral_setae,
3 exopodal_plates,
4 genital_shield,
5 genital_setae,
6 anal_shield,
7 dorsal_shield,
8 peritrematic_plates,
9 setae_z1,
10 podonotal_setae,
11 coxa_IV_spur;
MATRIX
rhinrich 1 1 1 1 1 0 2 1 1 1 1
rhinhaplo 1 0 1 1 1 0 2 1 0 1 1
troperio 1 1 0 0 0 0 2 0 0 0 0
tropfuent 1 1 0 0 0 0 2 0 0 0 1
tropkressi 1 0 0 0 0 0 1 0 0 0 0 ;
END;
Chapter 16 – Page 27
The Project System and Auxiliary Fields
Biota’s Project System allows you to create, view, and edit different sets of Auxiliary
Fields for different Projects that share the same Biota Data File. For example, a
database for a protected area or reserve might include records for birds, plants, and
other groups of organisms. The bird Species records might require Auxiliary Fields for
“Egg Size,” “Egg Length,” and “Clutch Size,” whereas the plant Species records might
need Auxiliary Fields for “Breeding System,” “Pollination Type,” and “Habit.” Obviously,
the Bird Auxiliary Fields are meaningless for plant records, and Plant fields are
meaningless for Bird records.
To handle this problem you can create a “Birds” Project and a “Plants” Project for the
same Data File. Each Project specifies its own set of Auxiliary Fields that are visible only
when the corresponding Project is chosen as the Active Project. Here is an outline of
how the Project System works:
The Project Table holds a record for each Project you create. The Project table is a
Core Table (see “Core Tables” in Chapter 3) with its own Input screen and Record
Listing Screen (see “Project Input” later in this chapter).
The AuxIndex Table contains records that link Project records to Auxiliary Field
Name records, to keep track of which Auxiliary Fields are used in which Projects.
Biota creates and maintains these records automatically, based on the Auxiliary
Fields you designate for each Project.
The Global Project record, a special record that cannot be deleted, automatically
includes all Auxiliary Fields. To include a particular Auxiliary Field in a Project or
your own, you select it from the Global Project.
There is always one Active Project. The Active Project specifies which Auxiliary
Fields are visible in Species, Specimen, Collection, and Locality records. You can
designate any Project (including the Global Project) as the Active Project, and easily
activate a different Project in a floating window (see “Using the Active Project
Floating Window” later in this chapter).
You can link each Project to a Personnel record to record Project management
or other personnel and to record contact information for the Project. See “Personnel
Input” in Chapter 11 for information on Project-linked Personnel records, which may
double as Group Personnel Records to link the individual Personnel record for
Project participants.
NOTES TO USERS OF BIOTA 1.X:
a.
When you first open a Biota 1.x Data File with Biota 2.x, the Global Project record is
automatically created, with all pre-existing Auxiliary Fields (if any) automatically
included in it.
b.
If you designated a particular Personnel record in a Biota 1.x Data File as the
Project Record, Biota 2 automatically creates a Project record with the same name
(in addition to the Global Project record), with all pre-existing Auxiliary Fields (if any)
automatically assigned to both the Global Project and to your Biota 1.x Project.
Chapter 16 – Page 28
Project Input
You can enter a new record in the Project Input screen by selecting Project from the
Input menu or by clicking the “Add Project” button on the Specimen Project Listing
screen. The Project Input screen has two tabs. Once you have entered a Project Short
Name (the Key field, see “Key Fields” in Chapter 3), you can move between tabs. See
“Keyboard Shortcuts for Input Screen Tabs” in Chapter 7 for information on using
keyboard shortcuts to move between the tabs.
This section describes how to enter data in the General and Auxiliary Field Set tabs of
the Project Input screen.
Entering Project Data: The “General” Tab
1.
Enter a Project Name. The Project Name may be up to 80 characters in length.
When you tab to the
Project Short Name
field (or click in it),
the Project Name
you entered is
copied there. The
Project Name is an
obligatory field.
2.
Shorten or alter the Project Short Name as you wish, or leave it the same as the
Project Name. (The Project Short Name may be up to 80 characters in length.)
Chapter 16 – Page 29
Because Project Short Name is the Key field for the Project table, it is an obligatory
entry. All remaining entry areas (except Project Name) are optional.
The Project Short Name you enter must not duplicate the Project Short Name of
any existing Project record, or you will receive an error message (see “Duplicate
Key Errors” in Chapter 3 and Chapter 8, “Record Codes”).
Because this field is linked to the Short Name field of the Personnel table, the entry
area has a double border. You can use any of the techniques for entering data in
linking fields described in Chapter 7, “Overview of Record Input Screens.” Unless a
Personnel record already exists with a Personnel Short Name that matches the
Project Short Name you have entered, Biota offers to create a linked Personnel
record to record Project Personnel or contact data for the Project.
3. Enter Project Notes if you wish, up to 32,000 characters in length.
4. Enter a Project Document Heading if you wish, up to 100 characters in length. The
Document Heading appears on Reports (see Chapter 14, “Printing Reports”), on
Herbarium Labels (see “Herbarium Labels” in Chapter 15), and on Loan invoices
(see “Previewing, Printing, and Exporting Loan Records” in Chapter 21).
Chapter 16 – Page 30
5.
To make the Project displayed in the Project Input screen the Active Project,
check the “Activate this Project” checkbox at the bottom of the screen.
NOTE: You can also control which Project is activated using the popup list in the
Active Project floating window itself. See “Using the Active Project Floating Window”
later in this chapter.
6.
To Display the Active Project floating window, click the “Display Active Project
Window” button at the bottom of the screen. If the Active Project floating window is
already being displayed, the button is disabled.
NOTE: You can also display or dismiss the Active Project floating window using the
“Display Active Project Window” command in the Special menu.
Entering Project Data: The “Auxiliary Field Set” Tab
The Auxiliary Field Set tab of the Project Input screen manages the assignment of
Auxiliary Fields to Projects.
In addition, by clicking the “Edit Project Field Names”
button on the Auxiliary Field Set tab (the button reads “Edit
Global Field Names” for the Global Project), you can
access the Field Name Editor from this tab to create new
Auxiliary Fields or to re-name, re-order, or delete existing
Chapter 16 – Page 31
Auxiliary Fields. (For instructions on using the Field Name Editor, see “Creating, Editing,
and Ordering Auxiliary Field Names” earlier in this chapter.)
1.
Select a parent table from the popup list in the top panel of the tab: Species,
Specimen, Collection or Locality.
The Global List of Field Names for that table, if there are any, appears in the left
panel, regardless of which Project record is open.
2.
To sort fields in the “Global List of Field Names”
panel by Number or by Field Name, click the
appropriate button in the “Sort Global Field Names
By…” panel.
3.
To display a list of existing Projects that use a
particular Field Name, select the Field Name in the
“Global list of Field Names” panel, then click the “Show
Projects for a Field” button.
Chapter 16 – Page 32
4.
To add an existing Auxiliary Field to the current Project, select it in the left
panel (“Global List of Field Names”), then click the “Append” button. The Auxiliary
Field name is copied (not moved) from the left panel to the right panel (“Field
Names for this Project”). The next Auxiliary Field in the Global list is highlighted.
5.
Continue using the “Append,” “Insert,” “All,” and “Remove” buttons to add
more Auxiliary Fields to the Project or remove unwanted Fields. (To use the “Insert”
button, first select the Field in the right panel before which you want to insert a
selected Field from the left panel.)
Henceforth, when this Project is selected, only those fields (and their values) that you
have associated with this Project will appear in Record Listing Screens and Input
Screens for the appropriate Parent Table (Specimen, Species, Collection, or Locality).
Using this method, you can add or remove Field Names from any Project (except the
Global Project) without affecting data for those fields.
Chapter 16 – Page 33
Using the Active Project Floating Window
The Active Project specifies which Auxiliary Fields are visible in Species, Specimen,
Collection, and Locality records.
Unless you have dismissed it or turned it off in the Preferences
screen (see “To Dismiss or Hide the Active Project Floating
Window” later in this chapter), the tiny Active Project Window is
displayed in the upper left corner of your screen as a floating
window (in front of any other open windows).
The Active Project Floating Window specifies which of the existing Project
records is currently activated. The Active Project specifies which Auxiliary Fields are
visible in Species, Specimen, Collection and Locality records, and which Project
name appears on certain reports and labels (see “Entering Project Data: The
‘General’ Tab” earlier in this chapter.
There is always one Active Project.
You can designate any Project as the Active Project (including the Global
Project).
To Declare a Different Project to be the Active Project
1.
Click the small “Change” button in the Active Project
Floating Window.
The Project selection dialog appears.
2.
From the popup list, select the Project you want to activate.
Chapter 16 – Page 34
NOTE: You can also control which Project is activated using the “Activate this
Project” checkbox at the bottom of the General tab in the Project input screen. See
“Entering Project Data: The ‘General’ Tab” earlier in this chapter.
To Dismiss or Hide the Active Project Floating Window
To dismiss the Active Project Floating Window, click its
close box. The window will reappear next time you launch
Biota. If you want to re-display it in the current session, see
“To Display the Active Project Floating Window” later in this
chapter.
To hide the Active Project Floating Window on startup, choose Preferences
from the Special menu, go to the “Other Settings” tab, then un-check the “Display
the Active Project floating window on startup” checkbox and Save the Preferences.
To Display the Active Project Floating Window
To display the Active Project Floating Window
during the current Biota session, choose
“Display Active Project Window” from near the
bottom of the Special menu.
Chapter 16 – Page 35
To display the Active Project Floating Window on startup, choose Preferences
from the Special menu, go to the “Other Settings” tab, then check the “Display the
Active Project floating window on startup” checkbox and Save the Preferences.
Maintaining and Repairing the Auxiliary Fields and
Project Systems
Under normal operations, Biota correctly maintains links between parent records in the
Specimen, Species, Collection, and Locality tables and records in the tables that contain
information on Auxiliary Fields (the FieldValue and FieldName tables). In addition, Biota
normally prevents duplication of RecordCode/FieldName combinations (ambiguous
records) and correctly maintains the number of (non-blank) Auxiliary Field Values for
each parent record in the AuxiliaryFields field of each parent record.
Power failures, system crashes, and incorrectly imported data, however, can produce
anomalies. A record in a FieldValue table may become orphaned (either the
RecordCode field or the FieldName field contains a nonexistent parent record value), a
blank entry for FieldValue may appear, FieldValue records may be duplicated, or the
AuxiliaryFields field of a parent record (a Specimen, Species, Collection, or Locality
record) may indicate the wrong number of Auxiliary Field Values. In addition, the
AuxIndex records that specify the Auxiliary Fields associated with each Project may
sometimes be duplicated.
You can correct all these problems, without in any way affecting legitimate records, by
running the Auxiliary Field/Project Maintenance Utility. Whereas none of these problems
are very serious, it is recommended that you run this utility from time to time if you work
with Auxiliary Fields and Projects (especially if you suspect problems) to “clean up” any
orphan Field Value records and other anomalies.
1.
To run the Auxiliary Field/Project Maintenance Utility, choose “Maintenance
Utilities” from the Special menu. The option screen appears (next page).
Chapter 16 – Page 36
2.
Activate the option “Find and delete blank, orphan, and duplicate Auxiliary
Field Value records.”
3.
Click the “Launch” button. The utility presents a series of reports on its activities.
Here is an example of a report from the Auxiliary Field Maintenance tool.
Chapter 17
Default Entries and Entry Choice
Lists (Pick Lists)
This chapter explains how to set default values for data entry (see “Setting Default
Entries: Field Value Defaults” later in this chapter), and how to set up Entry Choice Lists
(pick lists) for data entry (see “Using Entry Choice Lists” later in this chapter). For
automatic entry of Record Codes, see also Chapter 8, “Record Codes,” which explains
how to set up custom prefixes and counters for Record Codes.
Setting Default Entries: Field Value Defaults
Some fields in your database may require the very same entry for many or even all the
records in a Data File. For fields likely to require default entries in the Specimen,
Collection, and Locality tables, you can assign a Field Value Default that is entered in
the data entry area for that field automatically whenever you create a new record. (You
can select or erase the entry and replace it with an ad hoc one if you need to.)
If you need to select from several repetitive values for data entry in a field, see “Using
Entry Choice Lists” later in this chapter
To Set Field Value Defaults
1.
Choose “Field Value Defaults” from the Special menu. Screen 1 of the Set Field
Value Defaults tool appears, showing default entries, if any, for fields in the
Specimen table.
Chapter 17 – Page 2
Enter or edit the values for any listed fields in the Specimen table for which you
want to enter default values.
Please note these important points:
If you have renamed any fields, using the Core field Alias editor (see Chapter
18, “Renaming Fields”), then the Aliases, not the Internal Field Names, appear in
the “Set Field Value Defaults” screens.
The “Prepared By” and “Determined By” entry areas, with the double
borders, are standard Biota wildcard lookup entries, linked to the Personnel
table. (See “A Powerful Shortcut: Wildcard Data Entry for Linking Fields” in
Chapter 7 for information on wildcard entry techniques.)
The “Date Prepared” and “Date Determined” fields each accept either full
(DD/MM/YYYY) or partial (MM/YYYY or YYYY) dates. (See “Partial Dates” in
Chapter 9.)
WARNING: Be careful how you use the “Deposited” field. If you use the Loans
system, this field is used to store the Loan Code for specimens you have lent or
borrowed. Entering your own collection name or institution name as a default entry
value often makes sense for the entry of original data, however. If you later lend the
specimens, the Loans system will automatically replace your collection name with
the Loan Code for the new loan.
2.
Display the second screen of fields if necessary. If you click the “Second Screen
of Fields” button, the screen for Collection and Locality default entries appears.
Chapter 17 – Page 3
Please note these important points:
Entering a default Locality Code for Collection records (the [Collection]
Locality Code field) links all Collection records created while this default is set to
the Locality record indicated in the default entry.
The “Collected By” entry area, with the double borders, is a standard Biota
wildcard lookup entry, linked to the Personnel file. (See “A Powerful Shortcut:
Wildcard Data Entry for Linking Fields” in Chapter 7 for information on wildcard
entry techniques.)
The “Date Collected” and “Date Collection Completed” entry areas each
accept either full (DD/MM/YYYY) or partial (MM/YYYY or YYYY) dates. (See
“Partial Dates” in Chapter 9.)
3.
Click the “Save” button on either screen to record the defaults in your Data File
for both screens, once you are done entering default values in both screens.
NOTE: Field Value Defaults are recorded in the Lists table in your Biota Data File.
See Appendix A, “Biota Tables, Fields, and Relational Links”
4.
To clear all Field Value Defaults, click the “Clear Default Values” button at the
bottom of either screen.
Using Entry Choice Lists
Some fields in your database will probably have a limited number of repetitive entries.
Here are some common examples.
Authors of Species, Subpecies, or Varieties.
Storage localities or Type designations for Specimens.
Sex, life stage, or growth habit for Specimens.
Collection Methods or Site characteristics for Collection records.
Political entities (Districts, States or Provinces, Countries) for Locality input.
For most non-linking fields in Biota you can activate and enter values in an Entry Choice
List or Pick List (usually called simply a Choice List in this manual) that presents entry
options in a floating window during data entry. Since Choice Lists eliminate misspellings,
they are especially useful when someone else assists you in entering data.
Once you activate a Choice List for a field, the Choice List window appears automatically
whenever you TAB or click into the entry area for that field during data input or revision.
When the window appears, you can simply click an item on the List to enter it—or
dismiss the List window (by pressing TAB or clicking the “Cancel” button in the Lists
window) and then make a manual entry.
Chapter 17 – Page 4
You construct each List by entering items with the List Editor, which is accessed from
the List window itself by clicking the “Modify” button, as detailed below.
Between Biota sessions, the Lists you have created are kept as part of your Biota Data
File in the List Items table (see Appendix A, “Biota Tables, Fields, and Relational Links”),
not in the Biota application file. Saved Lists are preserved whether currently activated or
not, until you change or erase them.
Each time you launch Biota, all activated Lists are loaded automatically from the Data
File into the Biota application file. If you activate an existing List during a Biota session,
the List is loaded and made available immediately.
Activating or Deactivating Choice Lists
1.
Choose “Entry Choice Lists” from the Special menu. The List settings screen
appears.
2.
Set the activation state for each List.
Click the empty checkbox next to the name of each field for which you want
to activate an Entry Choice List. Table names appear in square brackets,
followed by the field name.
Click checked boxes to uncheck any List you wish to deactivate.
Note: Deactivating a List does not erase or change its entries. If you later reactivate
the List, the entries appear just as they were last time the List was edited and
saved.
Chapter 17 – Page 5
3.
For additional tables and fields, click the
“Second Screen of Fields” button.
The second screen of options appears.
To return to the first screen of fields, click the “First Screen of Fields…” button.
4.
Click the “Save List Settings” button to register the settings you have
checked. Newly activated Lists will appear (and newly deactivated Lists stop
appearing) the next time you use the appropriate Input screen. Input screens
already open are not affected. Close any open Input screens and reopen them to
activate changes in List settings. (It is not necessary to quit and restart Biota).
5.
To deactivate all Lists, click the “Turn Off All Lists” button. This action does not
affect the content of the Lists.
6.
To restore all settings to their status when you opened the “Set Entry Choice
Lists” screen, click the “Revert to Saved” button.
Chapter 17 – Page 6
Adding, Deleting, Editing, or Re-ordering Items in a Choice List
Open the Input screen for the table that includes the List (field) you want to work on. You
can do this by selecting the appropriate command from the Input menu (e.g., Input
Specimens) or opening an existing record from an Record Listing screen (see Chapter
10, “Working With Records in Record Listing and Input Screens”).
1.
Click in the entry area for the field. The existing List, or an empty one, appears in
a window titled with the name of the field (“Stage/Sex” in the example below).
NOTE: If no List appears, either the List has not been activated (see “Activating or
Deactivating Choice Lists” earlier in this chapter), or the field does not support Entry
Choice Lists.
2.
To open the List Editor, click the “Modify” button in the Choices
window (above).
The buttons of the List Editor appear at the right side of the List window.
Chapter 17 – Page 7
You use the buttons in the List Editor to Sort, Insert, Append, Edit, or Delete items
in the Choice List for this field. You can change the order of List items by dragging
and dropping them in the List Editor window.
Each field for which a List can be activated in the Entry Choice List screen (see
“Activating or Deactivating Choice Lists” earlier in this chapter) has it own set of List
items.
NOTE: To edit Lists, you must have
Administrative access privileges.
Otherwise, Biota posts an explanatory
message when you click the “Modify”
button.
3.
To add a new item at the end of the
existing List, click the “Append”
button. Alternatively, you can use the keyboard shortcut,
CTRL–N (Windows) or COMMAND–N ( –N) (Mac OS).
The List Item editing window appears.
4.
Enter the text for the new item and click the “OK” button in the List Item editing
window.
Chapter 17 – Page 8
The item is added at the end of the List.
NOTE: Each List may have one blank list item. The blank item can be useful as a
default (first) entry. Placing a blank item in the first position in the List makes it easy
to enter a blank as the default (if that is something you often need to do), or to enter
a blank and then change it to an ad hoc entry for which there is no List item. On the
other hand, if you don’t want blanks or ad hoc entries in your records, don’t offer a
blank item.
5.
To insert a new item between two existing items, select the
item in the existing list that you want to follow the new item, then
click the “Insert” button. Alternatively, you can use the keyboard
shortcut, CTRL–i (Windows) or COMMAND–i ( –i) (Mac OS).
The List Item editing window appears.
6.
Enter the text for the new item then click the “OK” button in the List Item editing
window to insert the item in the list.
Chapter 17 – Page 9
7.
To edit an existing item, select the item to be modified, then
click the “Edit” button to display the item to be edited in the
List Item editing window. Edit the item then click the “OK”
button.
NOTE: The List Editor is not case-sensitive. Thus, if you want to change the case of
an existing item in the ListItems table, you must delete the old version of the item
(e.g., “canada”) before entering the new or corrected item (e.g., “Canada”).
Otherwise, Biota will consider the new item to be a duplicate, and will not accept it.
8.
To delete an existing item or a new item you don’t want,
click on the item to be deleted to select it, then click the
“Delete” button. Alternatively, you can use the keyboard
shortcut, CTRL–D (Windows) or COMMAND–D ( –D) (Mac OS).
(A blank item can also be deleted.)
9.
To sort the items alphabetically, click the “Sort” button. An option screen appears
offering alphabetical or reverse alphabetical order.
10. To change the order of List items non-alphabetically, drag and drop items to reorder them as you wish.
Chapter 17 – Page 10
11. To undo changes made in a List and dismiss the List Editor, without recording
any changes you have made, click the “Cancel” button in the List Editor. The List
Editor disappears and the List is restored to its previous state.
12. When a List is set as you wish, click the “Done” button in the List
Editor window to record the changes. The List Editor buttons
disappear.
Using an Entry Choice List to Enter Data in a Record
Once you have activated an Entry Choice List (see “Activating or Deactivating Choice
Lists” earlier in this chapter) and entered the items you want in the List (see “Adding,
Deleting, Editing, or Re-ordering Items in a Choice List” earlier in this chapter), you are
ready to use the List to enter values in records.
Open the Input screen for the table that includes the List (field) you want
to work on. You can do this by selecting the appropriate command from
the Input menu (e.g., Input Specimens) or opening an existing record
from a Record Listing screen (see Chapter 10, “Working With Records
in Record Listing and Input Screens”).
1.
Display a new or existing record in the Input Screen for a table. (See Chapter
10, “Working With Records in Record Listing and Input Screens.”)
2.
Tab into or click on a field for which an Entry Choice List has been enabled. The
List window appears, titled with the name of the field (“Stage/Sex” in the example
below).
3.
To enter an item from the Choices window:
If the item you want is already highlighted, simply press the ENTER key
(Windows) or the RETURN key (Mac OS), or click the “OK” button in the Entry
Choice List window. The Entry Choice List window is dismissed and the value is
entered in the Input screen.
To choose an item from the list:
◊
Either: In the List, click on the item you want. The Entry Choice List
window is dismissed and the value is entered in the Input screen.
Chapter 17 – Page 11
◊
Or: Type the first letter or first few letters of the item in the entry area at
the top of the Entry Choice List window (labeled “Type to match or select
from the list”) until the item you want is highlighted in the list.
(In the example above, the letter a has been typed, which automatically
highlights the first entry that begins with a: “Adult female.”)
Now press the ENTER key (Windows) or the RETURN key (Mac OS), or click
the “OK” button in the Entry Choice List window. The Entry Choice List
window is dismissed and the selected value is entered in the Input screen.
4.
To manually enter an item not shown in the Entry Choice List window, click the
“Cancel” button in the Entry Choice List window (not the “Cancel” button of the Input
Screen!) to dismiss the Entry Choice List window, then enter the special item
manually in the field.
NOTE: Each List will accept one blank List Items entry. If you have a field (that
supports Lists) for which blank entries are common, consider making the blank List
Item the first (default) entry in the List.
5.
To stop an Entry Choice List from appearing, you must deactivate the Choice
List. See “Activating or Deactivating Choice Lists” earlier in this chapter.
Deleting All the Items in an Entry Choice List or Lists
Sometimes you may wish to delete all the items in an Entry Choice List at once. For
example, you might first export all the items in the List to a text file (using the Export
Editor, see Chapter 27, “Exporting Data by Tables and Fields”), delete them all from the
Biota Data File, then edit them in the text file in some way and re-import the edited items
to the same Biota Data File.
Chapter 17 – Page 12
1.
Choose “Entry Choice Lists” from the Special menu. The List settings screen
appears.
2.
Set the deletion status for each List.
Click the empty checkbox next to the name of each field for which you want to
delete the entire contents of its Entry Choice List. Table names appear in square
brackets, followed by the field name.
Click checked boxes to uncheck any List you want to leave unchanged.
3.
For additional tables and fields, click the “Second Screen of Fields…”
button.
Chapter 17 – Page 13
The second screen of options appears.
To return to the first screen of fields, click the “First Screen of Fields…” button.
4.
To permanently delete the entire contents of all
checked Entry Choice Lists, click the “Delete Checked
Lists” button. Biota requests confirmation and warns you
that the action cannot be undone, even using the
“Revert to Saved” button.
5.
To permanently delete the entire contents of all
Entry Choice Lists, whether checked or not, click the
“Delete All Lists” button. Biota requests confirmation and
warns you that the action cannot be undone, even using
the “Revert to Saved” button.
6.
To dismiss the List settings screen without changing the previous activation
status of Lists, click the “Cancel” button.
Importing Choice List Data From a Text File
Sometimes data that you would like to place in a Biota Entry Choice List are available as
text files (e.g., lists of geographical names or authors of taxa) that you would like to
import into Biota. Or, for a long Entry Choice List that you create yourself, it may be
more convenient to create the List items in a spreadsheet application, then import the
data into Biota.
This section explains how to format and import data to populate Entry Choice Lists using
Biota’s Import Editor (see Chapter 28, “Importing Data by Tables and Fields”).
Chapter 17 – Page 14
All List items are stored in Biota in a table called (appropriately enough) “ListItems.” (The
activation status of Entry Choice Lists, on the other hand, is recorded in a separate
table, called “Lists.” (See Appendix A, “Biota Tables, Fields, and Relational Links.”)
The ListItems table has four fields. To import data into the ListItems table, you must
prepare a delimited text file (in Excel, for example) with four columns that match these
fields. Here are the fields, in alphabetical order.
FieldName (required, alphanumeric): In this field, you must enter the name of
the field for which you want to import List items. The field name must correspond
to a field name in the Lists table, Appendix A, “Biota Tables, Fields, and
Relational Links.”
Do not add any spaces to the field name (e.g., enter “CommonName” not
“Common Name”). Do not include the table name. If the FieldName entry does
not match a legitimate field, Biota posts an error message.
NOTE: You must use the “internal” field name, as indicated in the Lists table,
Appendix A, “Biota Tables, Fields, and Relational Links.” If you have set up any
Aliases, and are not sure which internal field name corresponds to an Alias,
select “Core Field Aliases” from the Special menu, then click the “Display Current
Aliases” button. (See Chapter 18, “Renaming Fields” for details.)
Item (required, alphanumeric): In this field, you enter the value of each List
item (e.g., geographical names). Each entry may be up to 80 characters in
length.
Each item should be unique. If you try to import two or more duplicate items, or
an item in the file to be imported matches an item already in the Lists table (for
the same field in the same table), Biota simply skips the duplicate item and does
not import it.
NOTE: The Import Editor is not case-sensitive. Thus, if you want to change the
case of an item in the ListItems table, you must delete the old version of the item
(e.g., “canada”) before importing (or manually entering) the new or corrected item
(e.g., “Canada”). Otherwise, Biota will consider the new item to be a duplicate,
and will not import it (or accept it, if entered manually.)
ItemNumber (required, integer): In this field, you may enter an integer to
indicate the order in which you want the List items to appear in the Entry Choice
List. ItemNumber entries need not be consecutive or even unique, but you must
include this field as a column in the text file to be imported.
Table (required, integer): In this field, you must enter a code number for the
table to which the field designated in FieldName (above) belongs. The table code
numbers appear below. If you try to import a FieldName and Table number that
do not correspond to a field that supports Entry Choice Lists, Biota posts an error
message.
Chapter 17 – Page 15
Table Table Name
Number
0
Species
1
Specimen
2
Collection
3
Locality
4
Genus
5
Family
6
Order
7
Class
8
Phylum
9
Kingdom
10
ImageArchive
Here is an example of a small, mixed-table text file set up for import into the ListItems
table.
FieldName
Item
ItemNumber
Table
SpeciesAuthor
E. W. Baker
1
0
SpeciesAuthor
A. Berlese
2
0
StageSex
Adult female
1
1
StageSex
Adult male
2
1
Method
Tullgren extractor
1
2
Method
Hand collected
2
2
Country
Colombia
1
3
Country
Ecuador
2
3
NOTE: The column headings in the text file are not required. If you use them, be sure to
check the “Column Headings: Ignore first record of text file” checkbox in the Import
Editor.
Once the text file is read for importing into Biota, follow the instructions in Chapter 28,
“Importing Data.” (Select “ListItems” as the table, then click the “All” button to set up the
fields in the order indicated above.)
Chapter 17 – Page 16
Transferring Choice Lists to a Different Biota Data File
If you have only a few short Entry Choice Lists, it will not take long to recreate them in a
new or existing Biota Data File. Long or complex Lists, however, are worth transferring
all at once.
Two different tables are involved in keeping track of Entry Choice Lists:
The Lists table. In the Lists table, Biota keeps track of the activation status of each
Entry Choice List: enabled or not enabled. This requires only a single record in the
Lists table, which has a field corresponding to each List-capable field in the Biota
data structure.
NOTE: The Lists table has exactly three records at all times, even in a new, “empty”
Biota Data File. The first two records contain long and short Core Field Aliases
(respectively), if any have been established, for re-namable fields in the data
structure (see Chapter 18, “Renaming Fields” and Appendix A, “Biota Tables,
Fields, and Relational Links”).
The third record contains the activation settings for Entry Choice Lists. Thus, if you
transfer the records of the Lists file from one Biota Data File to another, all Aliases
will be transferred, along with the Lists activation status record.
The ListItems table. In the ListItems table, Biota keeps track of the values for all
Entry Choice Lists, along with information on which field and table they apply to and
their ordering within list. See “Importing Choice List Data From a Text File,” earlier
in this chapter, for details.
You cannot view or edit the Lists or ListItems tables directly, but they can easily be
exported and imported between Biota Data Files. Here is how to do it:
1.
Launch Biota and open the “donor file”—the existing Biota Data File from which
you want to transfer Entry Choice Lists and List Settings. Press and hold the ALT
key (Windows) or the OPTION key (Macintosh) while launching Biota to display the
Open File window so you can select the correct Data File. If the user password
system has been activated, press and hold the key while clicking the “Connect”
button in the Password window, to display the Open File window for your operating
system.
2.
From the Im/Export menu, choose Export by Tables and Fields. The Export
Editor appears. (See Chapter 27, “Exporting Data by Tables and Fields” for a
detailed introduction to the Export Editor.)
3.
Choose Lists or ListItems from the Table Name popup list. The fields for the
selected table appear in the “Biota Field Names or Aliases” list in the lower-left
panel of the Export Editor.
4.
Click the “All>>>” button. All fields appear in the Text File
Fields list on the lower right.
5.
Click the “Export” button to launch the export. The Save File
window for your operating system appears.
6.
Place and name the text file that Biota will create for the Lists or ListItems table
records.
Chapter 17 – Page 17
7.
Edit the text file if necessary. If you wish, you can now edit the exported Lists
records using a text processing or spreadsheet application. Be sure to save the file
as Tab-delimited Text if you edit it.
8.
Open the “receiving file”—the new or existing Biota Data File into which you want
to import the Lists and/or ListItems records. If you are using BiotaApp (not Biota4D)
and you have sufficient available memory, you can open the receiving file using a
duplicate copy of BiotaApp, if you have made one. Otherwise, close down the donor
file and relaunch Biota.
Note: Be sure to press and hold the ALT key (Windows) or the OPTION key
(Macintosh) while launching Biota, to bring up the Open File window. Otherwise,
Biota will open the donor file again, if you have re-launched Biota.
If you want to create a new, blank Biota Data File, click the “New” button in
the Open File window (see “Creating an Empty Biota Data File” in Chapter 3).
Otherwise, find the receiving file and open it.
9.
From the Special menu, choose Import by Tables and Fields. An option screen
appears.
10. Click OK to accept the default option “Import new records.” The Import Editor
appears. See Chapter 28, “Importing Data” for full details on using the Import Editor.
11. Choose Lists or ListItems from the Table Name popup list. The fields for the
Lists table appear the “Biota Field Names or Aliases” list in the lower-left panel of
the Export Editor.
WARNING: If you import the three records for the Lists table, Biota replaces the three
existing Lists records with the ones you import—an action unique to Lists table
importation. (For all other tables, existing records are never deleted using any
import option.)
12. Click the “All>>>” button to enter all fields into the Text File
Fields list on the lower right.
Chapter 17 – Page 18
13. Click the “Import” button to launch the import. If you are importing the Lists
table, a warning message appears. (The warning does not appear if you are
importing records to the ListItems table.)
14. Find the text file you created for exported Lists or ListItems records and open
it. The Import progress indicator appears.
15. If problems arise or Biota posts an error message, see “Displays and Error
Messages During Record Importing or Updating” in Chapter 28. If all else fails,
repeat the steps in this section.
Chapter 18
Re-naming Fields
This chapter explains how to re-name fields in Biota, by creating Core Field Aliases.
Biota displays and prints these Aliases in virtually every context, once you establish
them, instead of the default (internal) name for the corresponding fields.
Core fields in Biota include all fields that belong to Biota’s Core tables: Specimen,
Collection, Locality, Species, and all higher taxon tables—plus Personnel, Projects,
References and Loans (see “Core Tables” in Chapter 3).
Auxiliary Fields, in contrast to Core fields, are special fields that you create and name as
you like (see Chapter 16, “User-Defined Auxiliary Fields and the Project System”). Core
fields, however, are much faster to sort and query, so you should always use Core fields,
renamed or not, in preference to Auxiliary Fields, wherever possible.
Each Core field has a default or Internal Field Name. An easily recognized version of
each Internal Field Name is used to label input areas on Input screens and output
columns on Record Listing screens, as well as in printed reports. For example, the
Internal Field Name [Specimen] Specimen Code appears on the screen as “Specimen
Code.” The internal field [Locality] State Province appears on the screen in two forms.
Where space permits, Biota displays “State/Province.” Where space is tight, you will see
“State/Prov.” (Notice the convention used for writing Internal Field Names: [TableName]
FieldName.)
If your data entry, display, and reporting needs would be better served by renaming
certain Core fields, you can use Biota’s Core Field Alias system to do so very easily. For
example, a plant ecologist, with no use for the [Species] TypeLocality field might want to
rename the field “Growth Form.” The new field name, Growth Form, is then called a
Core field Alias (or just an Alias). It is an alias because Biota must still use the Internal
Field Name “behind the scenes.”
Core Field Aliases do not affect the data in the fields that aliases describe. You can
change the field name later to something else (or back to the Internal Field Name) at any
time without affecting Core Table record data.
Renaming Core Fields: Setting Aliases
To re-name fields in Biota, take the following steps:
1.
From the Special menu, select “Core field Aliases.” The “Set Core field Aliases”
window appears.
Chapter 18 – Page 2
2.
Locate the field you want to rename. Notice that the Internal Field Names (the
left-hand column in the screen) follow the format: (TableName) FieldName.
3.
Click once on the field you want to rename in the list of fields. The field name
now appears in the entry areas in the lower panel of the window. (If you can’t see
the field you want, use the scroll bar to move down the list.)
The selected Internal Field Name (“Type Locality” in the exampled above) now
appears in the entry areas in the lower panel of the window.
4.
Edit the Long Alias and Short Alias entries in the lower panel. In Biota’s
screens and reports, the Long Alias (25–30 characters) appears where space
permits, and the Short Alias (13–15 characters) otherwise. Be sure to define both.
Chapter 18 – Page 3
NOTE: You may have to experiment with the length of the Aliases after you see
them in context in other screens. The number of characters that will fit depends on
the exact letters used—e.g., “tillage” and “maximum” are each seven letters long,
but differ substantially in the space they occupy in proportional fonts.
5.
When you have finished setting up all the Aliases you want,
click the “Save” button in the “Set Core field Aliases” window.
Checking Field Aliases
1.
From the Special menu, select “Core field Aliases.” The “Set Core field Aliases”
window appears.
2.
Click the “Display Current Aliases” button.
If any Aliases have been defined and saved, a floating window appears, listing all
current Core field Aliases and their Internal Field Name equivalents. (If no Aliases
have been defined and saved, a message appears instead.)
3.
To close the floating window, either click in the close box in the upper left corner
or click the “Save” or “Cancel” button in the Set Core field Aliases window.
Clearing All Aliases and Resetting to Defaults
1.
From the Special menu, select “Core field Aliases.” The “Set Core field Aliases”
window appears.
2.
Click the “Reset to Defaults”
button.
Chapter 18 – Page 4
A confirmation dialog appears.
3.
Click the “OK” button if you want to proceed. All Aliases will be reset to the
defaults that Biota uses when you first create a new Data File. These default values
correspond closely with the Internal Field Names.
PART
6
Special Tools and
Features
Chapter 19
Images
Biota incorporates a powerful and flexible set of tools for acquiring or importing, editing,
archiving, comparing, and exporting images. You can link as many images as you wish
to each record in the Species, Specimen, Collection or Locality table.
How Biota Works With Images
Special Components: QuickTime and QPix
Biota’s image capabilities rely on two non-4D software components (the only non-4D
components in Biota).
QuickTime. Low-level image handling, including format conversions, compression,
depth adjustment, and display, is handled by Apple QuickTime.
NOTE: You must have a recent version of QuickTime installed on your computer to
use images in Biota. If you are not sure whether you have QuickTime or not, Biota
will tell you if you need it. If the version you have is too old, Biota will notify you
about that as well. Just click on the Image tab in the Input
screen for the Species, Specimen, Collection or Locality table.
You can also click the “Check QuickTime” button on any
Image Input screen.
The latest version of QuickTime is available, gratis, from Apple for both Windows
and Mac OS at www.apple.com/quicktime/download. Be sure to select the
“Recommended” installation option.
QPix. The second special image component is QPix (www.escape.gr), which
integrates QuickTime into Biota through a special set of programming tools. QPix is
automatically installed along with Biota (in the Win4DX or Mac4DX folder). If you use
BiotaApp (the stand-alone version of Biota), the purchase price you paid for Biota
includes a single-user license for QPix. In the case of Biota4D (the client-server
version of Biota), you must purchase a separate QPix license based on the number
of client connections you intend to use. (Write [email protected] for details on how
to purchase the QPix license for Biota4D.)
Chapter 19 – Page 2
How and Where Images Are Archived
Biota can archive images in either of two ways:
Either: Full image in an external file with a linked thumbnail in the Biota Data
File. With this approach, you can store images in individual files, in virtually any file
format you wish, compressed or not. When you link an image file to a Species,
Specimen, Collection or Locality record, Biota creates a small thumbnail copy of the
image and stores the thumbnail in the Biota Data File, along with path information to
the original image file. When you use Zoom or editing tools in Biota, the original
image is automatically accessed and displayed at full resolution.
NOTE: Biota keeps track of the location of linked external files by recording (in the
Biota Data File) the “path” to the image file. This means that, if you move the image
file to another folder, or relocate the folder that contains it, Biota will no longer be
able to find the original file (for zooming, editing, changing file format, etc.).
To help ensure that linked image files remain where Biota expects them, you must
place all linked image files somewhere inside the Biota application folder. You
can create as many folders as you like to organize your images, at any number of
levels, but all must be within the Biota Application folder.
Or: Full image in the Biota Data File. With this alternative, Biota stores images
directly in the Biota Data File, along with your text data. When you use Zoom or
editing tools in Biota, the stored image is displayed at full resolution. With this
option, if you import an image from an external image file, it does not matter where
the that file is located.
ADVICE: High color depth, high-resolution image files can be extremely large.
Storing many large images in a Biota Data File is not a good idea (even if they are
compressed.) Archiving a single, high-depth color image in the Data File itself may
enlarge the Data File more than saving hundreds of Specimen or Species records.
The first approach (Full image in an external file with a linked thumbnail in the Biota
Data File) allows you to leave image files of any size untouched, yet access them
transparently from within Biota. Unless you intend to store only a few, relatively
small images in the Biota Data File, it is strongly recommended that you use the
external file approach instead. The only drawback is that (for obvious reasons), you
cannot move the external image files to a different location and expect Biota to find
them. You can always create a copy elsewhere, however.
WARNING TO BIOTA 1 USERS: In Biota 1, all images were stored in the Biota Data
File. When you convert your Biota 1 Data Files to work with Biota 2, it is strongly
advised that you first export the Image records to individual image files, then reacquire them as thumbnails in the corresponding Biota 2 Data File. This process is
very easy using special tools provided. See Appendix F, “Updating Biota 1.x Data
Files to Biota 2 Format,” for full details.
Chapter 19 – Page 3
Image Sources
You can use images from a digital camera or download image files from Web pages or
from ftp sites. You can scan drawings, photographs, illustrations in books, herbarium
sheets, live plant specimens, or text documents using a flatbed scanner. You can
capture video frames directly from a video camera, from videotape played on a
VCR/VTR, or from other video storage technologies. If your image acquisition device is
TWAIN compatible, you can acquire images directly from the device using Biota (see
“Acquiring an Image From a TWAIN-compliant Digital Device” later in this chapter).
Some graphics and image editing applications store supplementary information with
image files that provide special instructions for output devices such as a PostScript
printer. This information “tags along” when you paste or import an image into Biota and
is used when printing the picture to an appropriate output device.
Image Size and Shape
Unless you use Biota’s image editing tools, images in Biota are never enlarged, cropped,
or changed in proportion.
Enlargement generally reduces image quality, cropping might remove an important
feature you intended to illustrate, and “stretch to fit” changes in proportion are a
surrealistic touch not usually approved by biologists attempting to document living
things. If you need to enlarge, crop, proportion, touch up, or change the palette for an
image, you can either use Biota’s onboard image editing tools (see “Editing an Image”
later in this chapter) or use an application designed for those purposes before storing the
image in a Biota Data File.
Image areas in Biota are uniformly about 3 by 4 in proportion, but they vary in absolute
size from thumbnail display areas (100 by 133 pixels) to large format zoom screens (768
x 576 pixels). If the original image is smaller than the dimensions of a display area, the
entire image is shown at its original size. If the original image is larger than a display
area, it is proportionally reduced to the largest size that can be displayed in the display
area, for display only. The digital archive retains the original resolution and size for the
image.
Image Color Depth
Biota Image records accept images of any bit depth, including black and white (1 bit),
gray scale (8 bit), or color (8, 16, 24, or 32 bit). As you know if you work with color image
files, the bit depth of a color image greatly affects the amount of memory required to
store the image on disk.
Image File Formats
An image file format specifies the algorithm used to translate the
pattern and color of pixels in a screen image into digital form in a
disk file. Many different image formats exist. Biota imports,
archives, edits, exports, and interchanges all still image formats
currently supported by QuickTime (see “Special Components:
QuickTime and QPix” earlier in this chapter).
Export formats currently available (in QuickTime 6) are listed in
the popup menu on the left. The list of import format supported by
QuickTime 6 is somewhat longer, since certain formats are
Chapter 19 – Page 4
proprietary, and may be read but not written. These additional import formats
currently include GIF, FlashPix and QDGX.
Image Compression
Image compression algorithms, or codecs (for compressor/decompressor),
allow image files to be stored in a fraction of the memory required by
uncompressed image files. Biota supports all codecs supported by QuickTime
(see “Special Components: QuickTime and QPix” earlier in this chapter),
although not all are relevant to still images. The current list appears on the right.
See “Compressing an Image” later in this chapter for instructions on image
compression.
Creating a New Image Record in Biota
When you archive an image in Biota, you can bring the image (or its thumbnail
representation and external link) into Biota by any of three different means: by
pasting the image into Biota from the Clipboard, by importing the image from an
image file, or by directly acquiring the image from an external device (scanner or
camera). In all cases, start by taking the steps in the section immediately below
(“Displaying an Image Input Screen”), then proceed to the appropriate section for the
image-acquisition method you intend to use.
Displaying an Image Input Screen
1.
From the Input menu, choose Specimen, Collection, Locality, or Species. The
Input screen appears for the table you selected. The Species Input screen is
illustrated here.
Chapter 19 – Page 5
(In the case of Species records, you may instead create a new Species record “on
the fly” from the Specimen Input screen. See “‘On-the-Fly’ Creation of Linked
Records” in Chapter 7. Likewise, Collection records may be created on the fly from
the Specimen Input screen, and Locality records from the Collection Input screen.)
NOTE: Of course, Images can also be added at any time to an existing Specimen,
Collection, Locality, or Species record (Chapter 12, “Finding and Updating
Records”).
2.
Enter a Record Code. If you need help with Record Codes, see Chapter 8,
“Record Codes.”
3.
Click the Images tab to display the Images Input screen for the table. The
keyboard shortcuts for the Image tab are CTRL–I for Windows or COMMAND–I ( –I)
for Mac OS.
The Images Input screen for the table appears.
Chapter 19 – Page 6
Importing an Image From an External File
NOTE: As an alternative to the method described in this section, you can also import
images using the Image Console. See “Acquiring and Editing Images in Biota Using the
Image Console,” later in this chapter.
1.
Display an Image Input screen, following the instructions in the section
“Displaying an Image Input screen” earlier in this chapter.
2.
From the “Get new Image” popup list in the Image
Input screen (illustrated on the right), choose “Import
from File.”
The Image Import options window appears (below).
Choose an option for importing the Image:
Either: Import a thumbnail image in the Biota Data File, with a link to the
image file.
Biota presents an Open Image screen. (The appearance of the screen depends
on your operating system.)
Chapter 19 – Page 7
a. Choose an image to import and click the “Open” button (above).
A thumbnail of the imported image appears in the Image display area, and
the name of the external file now appears automatically in the Image Name
entry area in the middle of the Image Input screen. The name also appears in
the Image List panel at the left side of the Image Input screen.
b. Change the name of the Image record in Biota if you wish, then click the
TAB key to enter the Image Name.
NOTE: The Image name that matches the file name is just a default
suggestion. You may name the Image in the Biota Data File anything you
want. It does not have to be the same as the corresponding external file to
maintain the linkage between the two.
Size and resolution data for the saved thumbnail image appear in the Image
Data display area on the right side of the Image Input screen, along with the
designation “Thumbnail” to indicate that these data apply to the thumbnail
image stored in the Biota Data File, not the image in the external file.
The “Path” button in the Image Data display area is enabled.
Chapter 19 – Page 8
c. Click the “Save” button in the
pane titled “This Image record.”
(Not the “Save” button for the
parent record, although this action
will also allow you to save the
Image.)
d. To display the path to the saved Image
file, click the “Path” button in the Image
Data display area. The path information is
displayed in a separate window. (You
might need this information to find the external file if you want to work with it
in another application.)
Or: Import the image itself into the Biota Data File.
Biota presents an Open Image screen. (The appearance of the screen depends
on your operating system.)
a. Choose an image to import and click the “Open” button (above).
Chapter 19 – Page 9
A thumbnail of the imported image appears in the Image display area, and
the name of the external file now appears automatically in the Image Name
entry area in the middle of the Image Input screen. The name also appears in
the Image List panel at the left side of the Image Input screen.
b. Change the name of the Image record in Biota if you wish, then click the
TAB key to enter the Image Name.
NOTE: The Image name that matches the file name is just a default
suggestion. You may name the Image in the Biota Data File anything you
want.
Size and resolution data for the saved full image appear in the Image Data
display area on the right side of the Image Input screen, along with the
designation “Full Image” to indicate that these data apply to the
characteristics of the full-sized image stored in the Biota Data File.
The “Path” button in the Image Data display area is not enabled, since no link
is maintained with the external image file that was the source of this image.
c. Click the “Save” button in the pane
titled “This Image record.” (Not the
“Save” button for the parent record.)
Chapter 19 – Page 10
Pasting an Image From the Clipboard
1.
Display an Image Input screen, following the instructions in the
section “Displaying an Image Input screen” earlier in this chapter.
2.
Copy an image to the Clipboard from any application.
3.
From the “Get new Image” popup list in the Image Input
screen (illustrated on the right), choose “Paste from
Clipboard.”
The Image Save Options window appears (below).
4.
Follow the instructions in the section “Saving and Naming a New Image” later in
this chapter.
Acquiring an Image From a TWAIN-compliant Digital Device
TWAIN is an image capture protocol (an industry standard that applies to both Windows
and Mac OS) used to control digital scanners, cameras or other image acquisition
devices from within an image-processing application, such as Biota or Adobe
Photoshop. This means that, instead of having to capture the digital image in a separate
program, save it and then re-open it in Biota, the TWAIN-compliant camera or scanner
delivers the image directly to Biota. Using Biota’s onboard image editing tools (see
“Editing an Image” later in this chapter), you can then correct color balance, size,
cropping, orientation, and so on before saving the image in any of the ways described in
the section “Creating a New Image Record in Biota” earlier in this chapter.
Although Biota supports TWAIN-compliant digital devices, it is up to you to install the
latest TWAIN driver specific to your device. (Check the device manufacturer’s website
for the latest driver.)
NOTE: According to www.twain.org, “The word TWAIN is from Kipling's ‘The Ballad of
East and West’—‘...and never the twain shall meet.…’ reflecting the difficulty, at the time
[TWAIN was established], of connecting scanners and personal computers. It was upcased to TWAIN to make it more distinctive. This led people to believe it was an
acronym, and then to a contest to come up with an expansion. None were selected, but
the entry ‘Technology Without An Interesting Name’ continues to haunt the standard.”
Chapter 19 – Page 11
1.
Display an Image Input screen, following the instructions in the section
“Displaying an Image Input screen” earlier in this chapter.
2.
Set up the connection to the digital device.
Either: From the “Get new Image” popup list in the
Image Input screen, choose “Set TWAIN Source.”
Or: From the “Get new Image” popup list in the
Image Input screen (illustrated on the right), choose
“Use Image Console.”
The Image Console appears. From the File menu in the
Image Console, choose “Twain source….”
If one or more TWAIN-compliant devices is connected to
your computer or local network, and the proper TWAIN
driver has been installed, a list of devices appears. If no
devices are connected, or the drivers are not installed,
Biota informs you.
NOTE: If you are using Mac OS 9, the first time you try to access a TWAIN device
Biota will post a message explaining how to enable this feature, which you need do
only once.
3.
Select the digital device from the popup list. The list of devices disappears, but
the device is now set as the default.
4.
Acquire the image.
Either: From the “Get new Image” popup list in
the Image Input screen, choose “Acquire from
TWAIN.” The Image Save Options window appears.
Or: From the File menu in the Image Console,
choose “Acquire….”
Depending on the device, either the captured image or
an interface dialog window appears.
5.
Name, edit if necessary, and save the Image.
Either: In the Image Input screen, the Image Save Options window appears.
Follow the instructions in the section “Saving and Naming a New Image” later in
this chapter, for naming and saving the image and Biota Image record. If you
want to edit the image, see the section “Editing an Image,” later in this chapter.
Chapter 19 – Page 12
Or: From in the Image Console, edit the image if
you wish (see “Editing an Image,” later in this chapter).
Then click the Close Box in the Image Console.
The Image Save Options window appears. Follow
the instructions in the section “Saving and Naming a New Image” later in this
chapter, for naming and saving the image and Biota Image record.
Saving and Naming a New Image
1.
Follow the instructions in one of the following sections: “Pasting
an Image From the Clipboard” or “Acquiring an Image From a
TWAIN-compliant Digital Device,” earlier in this chapter; or “Editing
an Image” or “Compressing an Image” later in this chapter.
The Image Save Options window appears (below).
2.
Choose an option for saving the Image:
Either: Save the image in an external file, with a thumbnail Image in the Biota
Data File.
If you choose this option, Biota presents the Export Image screen. (The
appearance of the screen depends on your operating system.)
a. Navigate to the folder that contains the Biota application (BiotaApp or
Biota4d). If you have established a special sub-folder for image files, within
the Biota application folder, open the image folder.
NOTE: To help ensure that linked image files remain where Biota expects
them, you must place all linked image files somewhere inside the Biota
application folder. You can create as many folders as you like to organize
your images, at any number of levels, but all must be within the Biota
Application folder.
Chapter 19 – Page 13
b. Enter a name for the file to be saved.
c. Select an image format from the “Format” popup list. See “Image File
Formats” earlier in this chapter. (Current Format settings are displayed in the
Format pane in Mac OS.)
d. If you need to change any options for the selected Format, click the
“Options” button to the right of the popup list (illustrated above).
e. Click the “Save” button in the Export Image
window.
A thumbnail of the imported image appears in
the Image display area, and the name you gave
the external image file now appears automatically in the Image Name entry
area in the middle of the Image Input screen. The name also appears in the
Image List panel at the left side of the Image Input screen.
f.
Change the name of the Image record, if you wish.
NOTE: The Image name that matches the file name is just a default
suggestion. You may name the Image in the Biota Data File anything you
want. It does not have to be the same as the corresponding external file to
maintain the linkage between the two.
g. Click the “Save” button in
the pane titled “This Image
record.” (Not the “Save”
button for the parent record,
although this action will also
allow you to save the Image.)
Chapter 19 – Page 14
Size and resolution data for the saved thumbnail image appear in the Image
Data display area on the right side of the Image Input screen, along with the
designation “Thumbnail” to indicate that these data apply to the thumbnail
image stored in the Biota Data File, not the image in the external file. The
“Path” button in the Image Data display area is enabled.
Image List panel
Image Name entry area
Image Data display area
h. To display the path to the saved Image file, click the “Path” button in the
Image Data display area (above). The path information is displayed in a
separate window. (You might need this information to find the external file if
you want to work with it in another application.)
Or: Save the Image in the Biota Data File.
If you choose this option, a thumbnail of the imported image appears in the
Image display area, with the reminder “[Enter new Image Name]” in the Image
Name entry area and in the Image List panel at the left side of the Image Input
screen.
a. Enter a name for the Image record.
Chapter 19 – Page 15
b. Click the “Save” button in the
pane titled “This Image
record.” (Not the “Save” button
for the parent record, although
this action will also allow you to
save the Image.)
Size and resolution data for the
saved full image appear in the
Image Data display area on the
right side of the Image Input screen, along with the designation “Full Image”
to indicate that these data apply to the characteristics of the full-sized image
stored in the Biota Data File.
The “Path” button in the Image Data display area is not enabled, since no link
is maintained with the external image file that was the source of this image.
Adding an Image Note
Each Image record may have an associated Image Note, up to 32K characters in length
(although short notes are expected, given the small size of the Note area).
1.
Enter the note in the Image Note area in the
Image Input screen.
2.
Click the “Save” button in the pane titled
“This Image record.” (Not the “Save” button
for the parent record, although this action will
also allow you to save the Image.)
Chapter 19 – Page 16
Exporting and Importing Images
Exporting Individual Images
1.
Display an Image Input screen, following the instructions in the section
“Displaying an Image Input screen” earlier in this chapter.
2.
Select an Image record from the Image List panel on the left side of the Image
Input screen. The Image is displayed in the adjacent thumbnail area.
3.
To place a copy of the image on the Clipboard, select
“Copy to Clipboard” from the “Send this image” popup list
in the Image Input screen.
The image on the Clipboard can be pasted into any
application that accepts images.
NOTE: The original image, not the thumbnail, is copied to the clipboard from the
linked external image file or from the Biota Data File, depending upon where you
have saved it. The original image format is maintained.
4.
To export the image to a new external file:
Either: Select “Export to File” from the
“Send this image” popup list in the Image
Input screen.
Or: Select “Export and Replace with
Thumbnail” from the “Send this image”
popup list in the Image Input screen. This option is intended to allow you to clear
large images out of the Biota Data File, replacing them with thumbnails linked to
newly exported external image files.
Biota presents the Export Image screen. (The appearance of the screen depends
on your operating system.)
Chapter 19 – Page 17
a. Navigate to the folder where you wish to save the new image file.
Either: If you do not intend to link the new image file to the Biota Data
File, you may place it in any folder.
Or: If you are replacing a full image with a linked thumbnail, or you
intend to link the new data file to the Biota Data File, you must place the
new image file in the folder that contains the Biota application (BiotaApp or
Biota4d). If you have established a special sub-folder for image files, within
the Biota application folder, open that image folder.
NOTE: To help ensure that linked image files remain where Biota expects
them, you must place all linked image files somewhere inside the Biota
application folder. You can create as many folders as you like to organize
your images, at any number of levels, but all must be within the Biota
Application folder.
b. Enter a name for the file to be saved.
c. Select an image format from the “Format” popup list. See “Image File Formats”
earlier in this chapter. (Current Format settings are displayed in the Format pane
in Mac OS.)
Chapter 19 – Page 18
d. If you need to change any options for the selected Format, click the “Options”
button to the right of the popup list.
e. Click the “Save” button in the Export Image
window.
Exporting Groups of Images
Biota has a special Export Images utility (in the Im/Export menu) for exporting groups of
images to individual, external image files. Biota names the files automatically and
creates a special log of the exports that can be used to import the same group of images
into another Biota Data File. (For full instructions for importing, see “Importing Groups of
Images” later in this chapter).
1.
Using Biota search tools (Chapter 12, “Finding and Updating Records”), create a
Record Set representing the Species, Specimen, Collection or Locality records for
which you wish to export Image files.
2.
From the Im/Export menu, choose “Export
Image Files.”
Biota presents the Export Images screen.
Chapter 19 – Page 19
3.
Select the Parent table name (Species, Specimen, Collection, or Locality) from the
popup list at the top of the options screen.
4.
Choose an export strategy.
Either: All Images for each [Species] record in the [Species] Record Set.
(The name of the table depends on which Parent table you chose in Step 3.)
Or: Only the first Image for each [Species] record in the [Species] Record
Set. (The name of the table depends on which Parent table you chose in Step 3.)
5.
Specify which images to export.
Either: Export full images and thumbnails. With this option, an external image
file is created for each Image record indicated in Step 4, including not only full
images stored in the Biota Data File, but also thumbnail images linked to external
image files.
NOTE: For full images from the Data File, the full image is exported. For
thumbnails linked to external image files, the thumbnails themselves are
exported, not the linked images.
Or: Export full images only; skip thumbnails. With this option, an external
image file is created for each Image record indicated in Step 4 for which the full
image is stored in the Biota Data File. The full image is exported.
Chapter 19 – Page 20
6.
Choose an image format for the exported image files from the popup list. See
“Image File Formats” earlier in this chapter.
7.
Click the “Set Folder” button.
A folder selection window appears.
NOTE: The window’s appearance depends on your operating system. The Mac OS
window, shown above, includes a “New Folder” button, should you wish to create a
new folder to hold the exported images. In Windows, there is no such button, so if
you need a new folder in Windows you will have to create it manually before
exporting the images.
8.
Choose the folder that will to hold the exported image files. Be sure you have
plenty of space on the drive you choose to hold the exported image files.
9.
Click the “OK” button in the Export Images
window to launch the image file export.
A progress indicator appears. When the export
process is complete, Biota confirms it.
Chapter 19 – Page 21
What Biota Exports. File names for the exported image files are assigned
automatically, in the form RecordCode_ImageName.Extension, where the Extension
identifies the image format that you specify in the popup list in Step 6, above. If the total
length of the file name, including the extension, exceeds 31 characters, it is truncated to
31 characters. If a proposed file name would duplicate an existing one in the Image
Folder, a numerical suffix is automatically added after the Image Name component of
the file name.
Two log document files are automatically created and placed in the Image Folder: an
Error Log and an Image File List. Both are plain text documents, which can be read with
any text editor. The initial exclamation point, which is part of the file name, forces the
Error Log and Image File List documents to appear first in the image folder.
1.
!ImageExportErrors.txt, the Error Log, lists any Image records that could not be
exported to image files, with an error code for each failure. If you get errors, try to
figure out why by looking at the offending Image record in the Biota Data File. (The
most common errors involve corrupted image records.) If you cannot figure out the
problem, try manually exporting the image following the instructions in the section
“Exporting Individual Images” (earlier in this chapter), a tool that provides additional
diagnostics.
2.
!ImageFileList.txt, the Image File List, records all images exported and the file
names assigned. If you want to import the image files into a different Data File, as
detailed in the section “Importing Groups of Images” later in this chapter, Biota will
use this list to link the external image files with corresponding thumbnail images that
it creates in the recipient Biota Data File. (You may choose, instead, to import the
full images into the recipient Biota Data File.)
The format for the Image File List (!ImageFileList.txt) is as follows:
Column 1: The name of the parent table in Biota (Species, Specimen,
Collection, or Locality).
Column 2: The Record Code (Species Code, Specimen Code, Collection Code,
or Locality Code) for the parent record.
Column 3: The Image Name for this image.
Column 4: The full name (including extension) of the external image file
created.
Importing Individual Images
Please see the section “Importing an Image From an External File” earlier in this
chapter.
Importing Groups of Images
Biota offers a special Import Images utility (in the Im/Export menu) for importing groups
of images from individual, external image files in “batch mode.” To do this automatically,
Biota needs to know where to look for the image files to import, what to name the Image
records in the recipient Biota Data File, and where to link the new Image records in the
recipient Biota Data File. For all this information, Biota looks for a special Image File List,
which by convention is named “!ImageFileList.txt.”
Chapter 19 – Page 22
1.
Set up the Image File List to guide the import.
NOTE: If you are importing images that you exported automatically following the
directions in the section “Exporting Groups of Images” earlier in this chapter, the
Image File List, named “!ImageFileList.txt,” has already been created in the proper
format. Proceed directly to Step 3, below.
The name of the Image File List may be any name you wish, but the
convention is: !ImageFileList.txt (including the exclamation mark at the
beginning, which causes the file to sort at the top of its folder).
The Image File List must be a tab-delimited, plain text file. (To create such a
file in Microsoft Excel, save the file as file type “Tab-Delimited Text.”)
The Image File List may be placed anywhere, but it is conventional to place it
inside the Image Folder (see Step 2, below).
The format for the Image File List must be exactly as follows, with a row for
each image file to be imported:
◊
Column 1: The name of the parent table in Biota (Species, Specimen,
Collection, or Locality).
◊
Column 2: The Record Code (Species Code, Specimen Code, Collection
Code, or Locality Code) for the parent record.
NOTE: All parent records referenced in the Image File List must already exist
in the recipient Biota Data File. If not, Biota displays an error message.
◊
Column 3: The Image Name for this image.
◊
Column 4: The full name (including extension) of the external image file
to be used as a source for import.
NOTE: All external image source files must be placed in the same folder as
the Image File List.
2.
Set up the Image Folder. Each image to be imported must be in a separate image
file on your hard disk.
The image files can be in any image format supported by QuickTime. See “Image
File Formats” earlier in this chapter.
All image files to be imported must be contained in a single folder, called the
Image Folder.
If you intend to import thumbnail versions of each image (linked to the
original image files), the Image Folder must be inside the same folder (call it the
Data Folder) that contains the Biota Data File. Furthermore, in this case, the
Image Folder must remain within the Data Folder. This requirement allows the
Data Folder itself (containing both the Biota Data File and the Image Folder) to
be moved to any location without losing the links, since Biota addresses the
Image Files relative to the location of the Data File.
Chapter 19 – Page 23
If you will be importing the full images, instead of thumbnails, the Image
Folder can be in any location, because no links are recorded in this case.
3.
From the Im/Export menu, choose Import Images. The Import Images setup
screen appears.
4.
Choose an import strategy.
Either: Import a thumbnail image to the Biota Data File, with a link to the
image file. This option creates a thumbnail image in your Biota Data File for
each external image file in the Image File List, with a persistent link to the
external image file. The external image file remains unchanged.
NOTE: This option is highly recommended for any Biota Data File that has more
than a few images or any large images.
Or: Import the image itself into the Biota Data File. In this case, a full copy of
the image is imported to the Biota Data File for each image file in the Image File
List. The external image file remains unchanged.
Chapter 19 – Page 24
5.
Find the Image Folder containing the image files to be imported. Click the “Find
the Image Folder” button and locate the folder.
6.
Find and open the Image File List. Click the “Open the Image File List” button and
locate file.
7.
Click OK to launch the import. While displaying a
progress indicator, Biota automatically reads the file
names, Image Names, and Record Codes from the Image
File List.
If you chose the thumbnail option, Biota creates and saves a thumbnail image in the
Biota Data File, for each external image file. The path to the external image file is
also saved in the Biota Data File, allowing the full image from the external file to be
transparently displayed in zoomed views or edited within Biota.
8.
Test the images in Biota when the import process is complete.
Chapter 19 – Page 25
Displaying, Zooming, Reordering, or Deleting Images
in the Image Input screen
Displaying an Image in the Input Screen
1.
Display a Specimen, Collection, Locality, or Species record in the Input screen.
The Species Input screen is illustrated here.
The number of linked images is displayed in the parenthesis on the Image tab
(there are 5 in the example below).
2.
Click the Images tab to display the Images Input screen for the table. The
keyboard shortcuts for the Image tab are CTRL–I for Windows or COMMAND–I ( –I)
for Mac OS.
Chapter 19 – Page 26
The Images Input screen for the record appears, with the first Image displayed in
the central panel. A scrollable list of all linked Images for this parent record appears
on the left, an Image Note (if any) for the displayed Image appears in the upper
panel on the right, with data for the displayed image shown in the lower panel
(“Data for this image”) on the right.
Note: If you want to change the order of the Image records in the scrolling display
(which controls the order in other contexts as well), see “Changing the Order of
Linked Image Records in the Input Screen” later in this chapter.
Zooming Images in the Input Screen
1.
Display an Image in the Image Input screen. (See “Displaying an Image in the
Input Screen” earlier in this chapter.)
2.
Select an Image to zoom by clicking the Image Name in the scrolling list of Image
Names. An Image linked to a Species record is illustrated here.
Chapter 19 – Page 27
3.
To zoom the image, click the “Zoom” button on the
screen, located in the panel labeled “This Image.”
The image is displayed at full size in a new window.
NOTES:
a.
The original image is always displayed when you
zoom, not the thumbnail. If the original image is in an
external file, that file is accessed and the image
displayed.
b.
If the original image is smaller than 576 x 768 pixels,
the full Image is displayed, but is not initially enlarged (example below).
c.
If the original image is larger than 576 x 768 pixels, the Image is displayed at
full resolution, even it if is larger than the 576 x 768 pixel area.
Chapter 19 – Page 28
4.
To zoom in further or zoom out from the Image, select a zoom
percentage from the popup at the bottom left of the image display
window.
If the image is larger than the display area, select
a percentage less than 100. You can also use the
“Hand” tool, activated from a popup menu just to
the left of the zoom menu, to move the Image
around in the viewing area.
5.
To display the first 4 Images for a parent record in the Zoom 4 Screen, click the
“Zoom 4 Images” button on the screen. The
button is located in the panel labeled “This Image
record.”
NOTES:
a.
Original images are always displayed when
you use the Zoom 4 tool, not thumbnails. If
an original image is in an external file, that
file is accessed and the image displayed.
b.
If an original image is smaller than 340 x 240
pixels (Windows) or 359 x 255 pixels (Mac
OS), the full Image is displayed, but is not
enlarged.
c.
If an original image is larger than 340 x 240 pixels (Windows) or 359 x 255
pixels (Mac OS), the Image is displayed, without distortion, at the largest
magnification that will fit in the display area.
Chapter 19 – Page 29
6.
To zoom a single image from the Zoom 4
Screen, click the “Zoom” button in the upper right
corner of one of the four image panels.
Changing the Order of Linked Image Records in the Input Screen
When you create a new Image record for a Species, Specimen, Collection, or Locality
(see “Creating a New Image Record in Biota” earlier in this chapter), the Image Name is
added to the end of the scrolling list of Image records for that parent record. This section
explains how to change the order of the Images in the scrolling list for an individual
parent record.
The order of the Image Names in the scrolling Image list of the Image Input screen for a
parent record is important in three contexts in Biota.
The thumbnail image Record Listing screens use this order to display the first
four images for each parent record (see “Displaying Thumbnail Images in the
Record Listing Screens,” later in this chapter). To allow easy comparison of
analogous views of related species by scanning “columns” of the thumbnail image
screen, it is best to order images by view (and thus by Image Name) identically for
related species. The images for four ant species in the section “Displaying
Thumbnail Images in Record Listing Screens” later in this chapter are a good
example of this technique.
The Export Image Files tool can export either the first image for each selected
parent record, as ordered in the scrolling Image Name list in the Image Input
screen, or all images in the list for each selected parent record. See “Exporting
Groups of Images” earlier in this chapter.
The Create Web Pages tool exports the first image for each Species, as ordered in
the scrolling list in the Species input screen, and creates a hyperlink to the image
from the Species record in a Species Web page. See Chapter 33, “Exporting Static
Web Pages.”
If you want to change the order of the Images in the scrolling list for a parent record,
follow these steps.
1.
Display the Image tab of a Specimen, Collection, Locality, or Species record in
the Input screen, following directions in the section “Displaying an Image in the
Input Screen” earlier in this chapter.
2.
Click the “Reorder Images” button in the Image Input
screen. (If there are no Image records linked to this parent
record, the “Reorder Images” button is disabled.)
Chapter 19 – Page 30
The Image Order Editor appears (below), displaying the Image Names for the
parent record. The Image Names are ordered by Image Number, which is displayed
in the left column. The first Image Name is displayed at the bottom of the window,
with its Image Number highlighted in the Image Number editing area.
3.
To sort Images alphabetically by Image Name:
a. Click the “Sort” button in the Image Order Editor window.
A Sort option window appears.
b. Click the “OK” button in the option window to accept the default option, “Sort
Images by Image Name and renumber.”
The Image Names reappear in the Image Order Editor, sorted alphabetically.
c. Click the “Save” button in the Image Order Editor.
The list reappears in alphabetical order in the Species
input screen.
Chapter 19 – Page 31
4.
To reorder Images as you wish (non-alphabetically), you edit the Image
Numbers in the Image Order Editor to reflect the order you wish. You can skip
numbers and use decimal or negative numbers if you wish.
a. Click the Image Name of the Image you want to reorder. “Lateral” is clicked,
below. The Image Name you clicked appears at the bottom of the editor.
b. Change the Image Number (in the Image Number editing area at the lower left)
to place the Image in the desired position among the remaining Images in the list.
In this example, the Image Number for “Lateral” has been changed to 6, so this
Image will sort numerically at the end of the list.
c. To move an Image to the beginning of the list, enter a fractional or negative
Image number. The Image called “Male Faces” will be moved to the beginning of
the list in the example below.
Chapter 19 – Page 32
d. Click the “Sort” button in the Image Order Editor window. A Sort option window
appears.
e. Choose the second option, “Sort Images by Image Number and renumber.”
f.
Click the “OK” button in the option window.
The Image Names reappear in
the Image Order Editor, sorted
numerically according to the
edited Image Numbers, but
renumbered sequentially by
integers.
g. Click the “Save” button in the
Image Order Editor. The list
reappears in the new order in
the Species input screen.
NOTES:
a. When you click the “Save” button in the Image Order Editor, Biota automatically
reassigns Image Numbers in sequential, integer order, based on the Image
Numbers you have assigned. So if you want, you can skip the last steps, above,
and just click the “Save” button.
b. If you delete an Image record, Biota automatically reassigns Image Numbers in
sequential, integer order to the remaining Image records linked to the parent record,
without changing their order, to account for the deleted Image record.
Chapter 19 – Page 33
Deleting an Image Record From the Input Screen
1.
Display an Image in the Image Input screen. (See “Displaying an Image in the
Input Screen” earlier in this chapter.) An Image linked to a Species record is
illustrated here.
2.
Click the “Delete” button in the panel labeled “This Image record.” Do not click
the “Delete” button for the parent record (in the panel labeled “This Species record,”
in the example below.
Chapter 19 – Page 34
If the Image record is a linked thumbnail, only the thumbnail is deleted. The
external image file is not touched. Biota posts the following confirmation
message.
If the Image record is a full image in the Biota Data File, the image itself is
permanently deleted. Biota posts this message.
Chapter 19 – Page 35
Editing or Compressing Images Displayed in the Image
Input screen
Once an Image is displayed in the Image tab of the parent (Species, Specimen,
Collection, or Locality) Input screen, you can edit it in the Image Console using a variety
of image editing tools, and/or compress the image.
Editing an Image
1.
Display a Specimen, Collection, Locality, or Species
record in the Image Input screen (see “Displaying an
Image in the Input Screen” earlier in this chapter.) or
import a new Image (see “Creating a New Image Record
in Biota” earlier in this chapter).
2.
Click the “Edit” button in the panel labeled “This
Image.”
The Image is displayed in the Image Editing Console, at
its full, original resolution, regardless of whether it is
smaller or larger than the display area of the Console.
3.
Moving or changing the displayed size of the Image in
the display window.
For example, the Image shown below (the viceroy
butterfly shown in the Image Input screen, above) is much larger than the display
area, which by default shows the upper left corner of the original Image. The
butterfly is not visible.
Chapter 19 – Page 36
To view a different part of the image (e.g., to center the view on the butterfly,
in the example above), you can:
◊
Use the scroll bars in the display area of the Console.
◊
Select the “Hand” tool from the tool popup at the
lower left corner of the Console, then use it to move the
image.
To change the displayed size of the image, you can:
◊
Select the Zoom Out (or Zoom In) item from the View menu in the Image
Editing Console.
◊
Zoom out (or in), using the zoom selection popup at the
lower left corner of the Console (illustrated on the right).
◊
Select the “Zoom” (magnifying glass
icon) tool from the tool popup at the
lower left corner of the Console, then
depress the SHIFT key and Click to
zoom out (Click to zoom in).
Chapter 19 – Page 37
The image of the butterfly, above, is now displayed at 50% of its actual size (the
original image file is unchanged), and has been centered using the Hand tool.
4.
To Flip or Rotate an Image in the display window, select “Flip” or “Rotate” from the
Edit menu in the Image Editing Console.
Below, the “Image…Rotate…Arbitrary” tool has been used to rotate the butterfly
image.
5.
To Crop an Image in the display window:
a. Select the Crop (“cross-hairs”) tool from the tool popup
at the lower left corner of the Console.
b. Using the cursor, select the area you wish to keep after
cropping the image.
The butterfly is being selected below.
Chapter 19 – Page 38
c. Select “Crop” from the Edit menu in
the Image Editing Console window.
The cropped image remains.
Chapter 19 – Page 39
6.
To use QuickTime’s Adobe Photoshop-style tools to modify an Image:
a. Select “Filter” from the Image menu in the
Image Editing Console.
The Filter setup window appears, including a
preview image for effects.
b. Expand a category, select a tool, and adjust the settings, if appropriate. In
the example below, Brightness has been reduced to intensify the colors in the
butterfly image.
Chapter 19 – Page 40
NOTE: Instructions for using the many QuickTime effects tools in the Filters window
are beyond the scope of this Manual.
7.
The File menu includes tools for importing, exporting,
printing, reverting to the original image, or displaying
format information about the image.
NOTE: The Import and Export tools in the Image
Console File menu are identical to those in Biota’s
Image Input screen. See “Creating a New Image
Record in Biota” and “Exporting Individual Images”
earlier in this chapter. You can use the Image Editing
Console to carry out virtually all image processing, if
you wish. (The TWAIN tools are not enabled in the Image Console.)
8.
To save an edited Image, click the close box in the
Image Console window. (The Mac OS close box is
shown here.)
A save option window appears.
Either: Replace the original Image file with the edited Image.
Or: Create and name a new Image file for the edited Image. If you choose this
option, Biota presents the Save dialogue screen so you can name and place the
Image file. The save Image window appears. Follow the instructions for saving
and naming the Image file in the section “Saving and Naming a New Image”
earlier in this chapter.
NOTE: Be sure to place the edited Image in a folder positioned next to the active
Biota Data File. If you try to place it outside the folder that contains the Data File,
Biota warns you, and you may then place the edited Image correctly.
Chapter 19 – Page 41
Compressing an Image
For general information on Image compression, see the section “Image Compression”
earlier in this chapter.
By default, when Biota saves a new or edited Image, it compresses the Image using the
“Photo-JPEG” compression codec (with “normal” resolution), whether the Image is
stored in the Biota Data File or placed in external files. Images are transparently
decompressed before they are displayed on the screen. JPEG compression is both
efficient and ubiquitous in the world of computer imaging. But in some circumstances
(e.g., no compression for print publication of TIFF’s) you may wish to use other
compression codecs or image formats.
NOTE: Photo-JPEG compression is not the same as the JPEG image format (also the
default in Biota). Theoretically, an image in any format (e.g., TIFF, Photoshop, BMP, as
well as JPEG) can be compressed using any codec (Photo-jpeg and others). In practice,
certain combinations of codec and image file format are best used together: Photo-JPEG
compression with JPEG file format, BNP compression with BMP format.
1.
Display a Specimen, Collection, Locality, or Species record in the Image Input
screen (see “Displaying an Image in the Input Screen” earlier in this chapter.) or
import a new Image (see “Creating a New Image Record in Biota” earlier in this
chapter).
2.
Click the “Compress” button in the panel labeled “This
Image.”
The compression options screen appears.
3.
Choose a compression codec from the
upper popup list in the Compressor panel.
(Photo-JPEG is the default. Note that not all
codecs listed by QuickTime are useful for still
images.)
Chapter 19 – Page 42
4.
Choose a color depth from the lower popup list in the
Compressor panel. (“Best Depth,” is the default.)
Different codecs offer different option lists for color
depth.
5.
Choose a Quality setting using the slider in the lower
panel of the option screen.
6.
Click the “OK” button in the option screen to save the
settings, or the “Cancel” button to cancel them.
A confirmation screen appears, offering you one more
chance to change your mind.
7.
Click the “OK” button in the confirmation screen to compress the Image.
If the full Image you intend to compress is stored in the Biota Data File, the
Image is compressed and saved to the Data File.
If the full Image you intend to compress is stored in an external file, Biota
presents the standard save Image dialog. Follow the instructions for saving and
naming the Image file in the section “Saving and Naming a New Image” earlier in
this chapter.
NOTE: If the original Image is in an external file, you can either replace that file with
the compressed one, by assigning the compressed file the same name and placing
it in the same folder as the original, or you can save the compressed image as a
new file. In either case, a new thumbnail is created based on the compressed image
and a new link is established to the external file.
Chapter 19 – Page 43
Displaying Thumbnail Images in Record Listing Screens
If you want to compare images for several Species, Specimen, Collection, or Locality
records at once, you have three options:
You can launch separate processes and open the images simultaneously in
separate windows, using tools in the Image Input screen as described in the section
“Displaying, Zooming, Reordering, or Deleting Images in the Image Input screen”
earlier in this chapter.
You can use the Scroll option for displaying images in a Record Listing screen for
Species, Specimen, Collection, or Locality records.
You can use the Page option for displaying images in a Record Listing screen.
Using the Scroll Images Record Listing Screen
1.
Find the Species, Specimen, Collection, or Locality records for which you want
to display and compare images. To find the records, you can use any of the tools
described in Chapter 12, “Finding and Updating Records.”
The standard Species Record Listing screen is illustrated below as an example.
Notice that the Images column in the Species Record Listing screen shows the
number of linked Image records for each Species.
Chapter 19 – Page 44
2.
If you wish, sort the parent table (Species, Specimen, Collection, or Locality)
records by decreasing the number of linked images. (Of course, you can sort by
other criteria instead or in addition to number of images.)
To sort the Species records by number of images, follow these steps.
a. Click the “Sort” button at the bottom of the
parent table Record Listing screen.
The “Order by” window appears.
b. Click the “Number Images” field name in the “Available Fields” panel on the
left.
c. Click the “add field” button (blue horizontal triangle) in the middle
of the Order By window to add “Number Images” to the sort criteria
panel on the right (labeled “Ordered by Fields/Formulas”).
d. Click the sort order indicator (triangle) at the upper right to point it
downwards, for descending order.
Chapter 19 – Page 45
e. Click the “Order by” button at the bottom
of the Sort Species window (above).
The parent table records reappear, sorted by decreasing
number of linked images.
3.
Click the “Scroll” button in the “Display Images”
button at the bottom of the Record Listing screen.
The first four Image records for each record in the current parent table selection
(Species, in the example below) appear as a row of thumbnail images, one parent
record per row.
For each parent record, identifying information appropriate to the parent table
appears in a text bar above the horizontal group of images for that record. For
the Species table illustrated above, for example, Genus, specific name (Species
Name), Species Author, Species Code, and Family appear in the text band.
Chapter 19 – Page 46
The Image Name for each Image appears in a small inset at the base of each
image.
The order of the images, within rows, follows the order you have set for the
Image records in the parent table input screen. See “Changing the Order of
Linked Image Records in the Input Screen” earlier in this chapter.
To display a parent record in the parent table Input screen from the thumbnail
Record Listing display, double-click the row of images for the parent record. You
can then go to the Images tab to work with the images for that record.
To view Images for other parent records, use the vertical scroll bars, just as
you would for a text Record Listing screen.
To create a Sub-Selection of parent
records (thumbnail image rows), select
the rows you want to keep in the SubSelection, then click the “Sub-Selection”
button at the bottom of the screen.
To return to the standard (text) Record Listing screen, click the “Done” button
in the thumbnail display.
Using the Page Images Record Listing Screen
1.
Find the Species, Specimen, Collection, or Locality records for which you want
to display and compare images. To find the records, you can use any of the tools
described in Chapter 12, “Finding and Updating Records.”
2.
If you wish, sort the parent table (Species, Specimen, Collection, or Locality)
records by decreasing the number of linked images. For instructions, see Step
2 in the section “Using the Scroll Images Record Listing Screen” earlier in this
chapter. (Of course, you can sort by other criteria instead or in addition to the
number of images.)
3.
Click the “Page” button in the “Display Images”
panel at the bottom of the Record Listing screen.
An option screen appears for
setting the number of images
per parent record to be
displayed.
`
4.
Select the number of images per parent record that you want to display and click
the “OK” button.
On slower computers, a full page of images can take a few seconds to display, but
a smaller number per parent record displays faster. Once you set the number, Biota
remembers it until you change it or end the work session and quit Biota. Because
Chapter 19 – Page 47
the “OK” button in this screen is a default button, you can just “key past” this screen
with the ENTER key (Windows) or the RETURN key (Mac OS) once you have set it.
The first n (1, 2, 3, or 4) Image records for each record in the current parent table
selection (Species, in the example below) appear as a row of thumbnail images,
one parent record per row, for the first four parent records in the selection. (In other
words, if you asked for four images per parent record, Biota posts 16 images.)
The example below is for four species in the ant genus Pheidole, considered a very
“difficult” genus, with many very similar species. Notice that the images for each
Species records are ordered identically, to easily allow visual comparison of
analogous images among the species.
For each parent record, identifying information appropriate to the parent table
appears in a text bar above the horizontal group of images for that record. For
the Species table illustrated above, for example, Genus, specific name (Species
Name), Species Author, Species Code, and Family appear in the text band.
Chapter 19 – Page 48
To display a parent record in the parent table Input screen directly from the
Page Image display, click the “Record Zoom” button at the right end of the main
text bar for the parent record. You can then go to the Images tab to work with the
images for that record.
The Image Name for each Image appears in a text band at the base of each
image.
The order of the images, within rows, follows the order you have set for the
Image records in the parent table input screen. See “Changing the Order of
Linked Image Records in the Input Screen” earlier in this chapter.
To view Images for other parent
records, four records at time, click
the “Next 4 Records” button or the
“Prev 4 Records” button.
To create a Sub-Selection of parent
records (thumbnail image rows), select the rows you want to keep in the SubSelection by clicking the “Add Record to Sub-Selection” box (the “+” boxes in the
right margin of the screen, for a parent record).
Then click the “Sub-Select [Records]” button at the bottom of the
screen. (The button reads “Sub-Select Species,” in this
example.)
Chapter 19 – Page 49
NOTE: The Sub-Selection carries over between screens of Images. You can click
as many “Add Record to Sub-Selection” boxes (the “+” boxes in the right margin
of the screen) as you wish, on any number of screens within a selection of parent
records, before clicking the “Sub-Select [Records]” button.
To zoom an individual Image, click the “Image Zoom” button at the lower right
corner of any individual thumbnail image.
The zoomed Image (not an enlarged thumbnail) appears at full original size,
unless it is larger than the zoom viewing area. See “Zooming Images in the Input
Screen” earlier in this chapter for notes and instructions on further use of this
screen.
Chapter 19 – Page 50
To display any four images, from any combination of parent records in the
Zoom 4 Screen, take these steps:
a. Click the “Add Image to Zoom 4” box (the “+” box at the left lower corner
of an individual Image pane) for up to four Images, on any record on any
page of Images.
To simplify the illustration, four images from a single page have been
selected (the selected boxes are in yellow), below.
b. To display the selected Images in the Zoom 4 Screen, click the “Zoom 4
Images” button at the bottom of the Page Image window.
The selected images appear in a new window in the Zoom 4 Screen.
Chapter 19 – Page 51
c. To further zoom a single image from the Zoom 4
Screen, click the “Img” zoom button in the upper right
corner of one of the four image panels. (See “Zooming
Images in the Input Screen” earlier in this chapter for
notes and instructions on further use of this screen.)
d. To display the parent record for an Image in the
Zoom 4 Screen, click the “Rec” zoom button in the
upper right corner of one of the four image panels.
To return to the standard (text) Record Listing screen,
click the “Done” button in the thumbnail display.
Chapter 19 – Page 52
Deleting Images for a Species, Specimen, Collection, or
Locality Record Set
Occasionally, you might need to delete all the Image records linked to particular group of
parent records in the Species, Specimen, Collection, or Locality table.
NOTES:
a.
This operation deletes records in Biota’s ImageArchive table only. It does not affect
parent (Species, Specimen, Collection, or Locality) records, nor any external image
files in disk, even if they are linked to Biota.
b.
This operation cannot be undone, so if you have any doubts, make a fresh backup
of your Biota Data File first.
1.
Find the Species, Specimen, Collection, or Locality (parent) records for which
you want to delete all linked Image records. To find the parent records, you can use
any of the tools described in Chapter 12, “Finding and Updating Records.”
2.
From the Special menu, choose “Delete Images by Record Set.” A warning and
table selection screen appears.
3.
From the table popup, select the parent table for which you want to delete linked
Image records.
Chapter 19 – Page 53
4.
Click the “OK” button. Yet another warning and confirmation screen appears.
5.
Click the “OK to Delete” button. Biota confirms the deletions.
Chapter 19 – Page 54
Maintaining and Repairing Image Links
Under normal operations, Biota correctly maintains links between parent records in the
Specimen, Species, Collection, and Locality tables and Image records (records in the
Image Archive table).
Power failures, system crashes, and incorrectly imported data, however, can produce
orphan Image records,or the NumberImages field of a parent record (a Specimen,
Species, Collection, or Locality record) may indicate the wrong number of linked Images.
You can correct these problems, without in any way affecting legitimate records, by
running the Image Maintenance Utility. Whereas neither of these problems is very
serious, it is recommended that you run this utility from time to time if you work with
Images in Biota, especially if you suspect problems.
1.
To run the Image Maintenance Utility, choose “Maintenance Utilities” from the
Special menu. The option screen appears.
2.
Activate the option “Delete orphan Image records and update Number Image
fields.”
3.
Click the “Launch” button. The utility presents a series of reports on its activities.
Chapter 20
References
This chapter explains how to use Biota’s literature reference tools. Reference records
are stored in their own table (called References). Each Reference record can be linked
to any number of Species, Specimen, Collection, or Locality records. Likewise, each
Species, Specimen, Collection, or Locality record can be linked to any number of
Reference records. (This is called a “many-to-many” relationship.)
A separate table, called ReferenceLinks, keeps track of which Reference records are
linked to which Species, Specimen, Collection, or Locality records. There is one record
in the ReferenceLinks table for each link. You do not normally need to pay any attention
to the ReferenceLinks table, since its records are maintained transparently by Biota.
(The only reason you would ever need to deal with it would be to merge two Biota Data
Files.)
Reference Input
You can create a new record in the Reference Input screen by selecting “Reference”
from the Input menu, by clicking the “Add Reference” button on the Reference Record
Listing screen, or by clicking the “New Ref” button on the “Refs” tab of the Species,
Specimen, Collection, or Locality Input screen.
The Reference Input screen has two tabs. Once you have entered a Reference Code or
accepted the default, you can move to either tab. See “Keyboard Shortcuts for Input
Screen Tabs” in Chapter 7 for information on using keyboard shortcuts to move between
the tabs.
Chapter 20 – Page 2
Entering Reference Data: The “Reference” Tab
Biota handles four types of references: Journal Article, Book, Book Section, and Online
Source.
Except for Online Source, the fields, their attributes, and their use in Biota are
identical to the EndNote 4 format for the same information. (EndNote does not
have an Online reference type).
All four Reference Types have a URL Field and a “Go to URL” button that
launches your default Web browser and brings up the URL. The button is activated
when the URL Field is not blank.
Three fields (Author, Title, Editor, and JournalOrEditedBook) allow very long
entries. These fields are 4D Text fields, allowing entries up to 32K in length. Since
Text fields cannot be indexed or sorted, matching Index fields (80 characters,
maximum), maintained behind the scenes, allow rapid sorts and searches based on
the first 80 characters of each entry. The full Text fields are always displayed.
To create a new Reference record, take the following steps:
1. Create a new record in the Reference Input screen by one of the following
methods:
Select “Reference” from the Input menu.
Or: Click the “Add Reference” button on the Reference Record Listing
screen.
Or: Click the “New Ref” button on the “Ref” tab of the Species, Specimen,
Collection, or Locality Input screen.
2. Enter a Reference Number or accept the default Reference Number offered by
Biota.
NOTE: Unlike all other Record Codes in Biota, Reference Numbers (the Record
Code for the Reference table) are integer numbers, for compatibility with standalone reference management software, such as
EndNote.
Biota automatically generates a suggested
Reference Number: the next integer after the highest
numbered existing Reference Number in your Biota
Data File.
You can enter a different Reference Number
manually, if you prefer, by typing it in the Reference
Number entry area. (Biota ensures that whatever
number you enter is unique.)
To restore the suggested Reference Number, click
the “Assign” button in the Reference Number panel.
Chapter 20 – Page 3
3.
Click the Reference Type popup list (which by default has “Journal Article”
selected.)
4.
Select a Reference Type from the popup List.
Each Reference Type presents a different version of the Reference Input screen
(see the next step for illustrations).
5.
Fill in the input fields on the Reference screen. As you fill in the fields, the “Full
Reference” panel shows the reference in a typical (although of course not universal)
format.
Here are examples for all four Reference Types.
Journal Article (note URL at www.jstor.org).
Chapter 20 – Page 4
Book (with a URL for the text of this classic book).
Book Section (note that the “Go to URL” button is disabled when the URL field
is blank).
Chapter 20 – Page 5
Online Source.
NOTE: You can select text from the “Full Reference” pane and copy it to the
Clipboard. But changes made in this pane are not saved. To edit the Reference,
you must edit the fields themselves in the upper part of the screen.
6.
Save the Reference record.
Chapter 20 – Page 6
Examining or Deleting Reference Links: The “Links” Tab
The Links tab of the References Input screen displays a scrolling list of all Species,
Specimen, Collection, and Locality records that are currently linked to the Reference
displayed in the Input screen. For a new References record, therefore, the list of links
will be empty.
Reference Links are created from the Refs tab of individual Species, Specimen,
Collection, and Locality records. For instruction on creating Reference Links see “Linking
a Reference to Species, Specimen, Collection or Locality Record” later in this chapter.
When a Reference record that has been linked in this way is displayed in the Record
Input screen, the Links tab shows these links.
1.
Display a Reference record in the Reference Input screen (see Chapter 12,
“Finding and Updating Records”).
2.
Click the “Links” tab in the Reference Input
screen.
Note that the number of links between this
Reference record and Species, Specimen,
Collection, and Locality records appears on the tab.
The Links tab screen for this Reference record appears.
The scrolling list in the middle of the screen lists each Link for this Reference
record, showing the table (Species, Specimen, Collection, or Locality), Record
Code, and a brief identifying content summary for each Link.
Chapter 20 – Page 7
3.
To display a Species, Specimen, Collection, or Locality record linked to this
Reference record:
a. Click the Link in the scrolling list of Links to select it.
b. Click the “Show Record” button below the scrolling list of
Links.
The linked record appears in a new window.
Chapter 20 – Page 8
4.
To Unlink a Species, Specimen, Collection, or Locality record linked to this
Reference record:
a. Click the Link in the scrolling list of Links to select it.
b. Click the “Unlink Record” button below the scrolling list of
Links.
The Link is deleted and the linked record disappears from the
list of Links.
Chapter 20 – Page 9
Linking or Unlinking a Reference to a Species,
Specimen, Collection, or Locality Record
References are linked or unlinked from the Refs tab of individual Species, Specimen,
Collection, and Locality records. When a Reference record that has been linked in this
way is displayed in the Record Input screen, the Links tab of the Reference record
shows the link (see “Examining or Deleting Reference Links: The ‘Links’ Tab” earlier
in this chapter for details).
Linking a Reference to a Species, Specimen, Collection, or Locality Record
1.
Display a new or existing Species, Specimen, Collection or Locality record.
(See Chapter 11, “Input,” or Chapter 12, “Finding and Updating Records.”)
2.
Click the “Refs” tab in the Input screen.
The References tab screen for the record appears.
Chapter 20 – Page 10
3.
Click the “Link a Ref” button in the middle of the Refs
screen.
The References lookup options window appears.
a. Select a display option by clicking a button in the References lookup options
window. You can display All Reference Records (not the best approach if there
are hundreds of records) or restrict the choices displayed to a certain value for
Author, Year, Title, or Reference Type. Or, you can launch the Query Editor
(see “The Query Editor, a General-Purpose Tool for Finding Records Based on
Content” in Chapter 12) to find a Reference record using ad hoc criteria.
b. If you select the Author, Year, Title, or Reference Type option, Biota creates
a list of all unique values for the selected field.
◊
If there are only a few values, Biota displays the list in a popup list to the
right of the selected button. Click and hold the popup to display the list of
values, as shown below.
Chapter 20 – Page 11
◊
If there are many values, Biota displays the list in a
separate window with a scrollbar, as shown on the right.
c. Select the value you want from the popup list or the
scrolling list. Biota then shows the selected value in the
popup area.
d. Click the “OK” button in the References lookup options
window. The “Link a Reference” display screen appears,
listing all Reference records that match the option and
criteria you selected in steps a. and b. above (see below).
◊
If there are many records in the display screen (there
is only one match in the example below, but you might
have many for “Author” or “Year”) you may first want to
use the sort buttons at the top of each column to sort the
records displayed by the values for that column.
◊
If you want to try a different selection option or field
value to display records, click the “Try Again” button at
the bottom of the “Link a Reference” selection screen.
e. When you find the record you want in the “Link a Reference” display screen,
click it to create the link to the Species, Specimen, Collection, or Locality record.
Chapter 20 – Page 12
The linked Reference record now appears in the scrolling list of links in the
middle of the Refs tab window.
f.
To see the full, formatted Reference, click the Reference entry in any panel of
the scrolling list. The full reference appears in the “Full text for the selected
Reference” pane at the bottom of the screen.
NOTE: You can select text from the “Full text for the selected Reference” pane to
the Clipboard. But changes made in this pane are not saved. To edit the
Reference, click the “Edit Ref” button and follow the instructions in the section
“Editing a Reference Record On the Fly From a Species, Specimen, Collection or
Locality Record” later in this chapter.
Chapter 20 – Page 13
Unlinking a Reference from a Species, Specimen, Collection
or Locality Record
1.
Display the Species, Specimen, Collection or Locality record. (See Chapter 12,
“Finding and Updating Records.”)
2.
Click the “Refs” tab in the Input screen. Note that the number of linked
References is indicated on the tab.
The References tab screen for the record appears.
Chapter 20 – Page 14
3.
Select the Reference to be unlinked, from the scrolling list of links in the middle of
the Refs tab window. The full Reference appears in the “Full text for the selected
Reference” pane at the bottom of the screen.
4.
Click the “Unlink Ref” button in the middle of the screen.
The selected Reference link is removed.
Chapter 20 – Page 15
Editing a Reference Record “On the Fly” From a
Species, Specimen, Collection, or Locality Record
1.
Display the Species, Specimen, Collection or Locality record. (See Chapter 12,
“Finding and Updating Records.”)
2.
Click the “Refs” tab in the Input screen. Note that the number of linked
References is indicated on the tab.
The References tab screen for the record appears.
Chapter 20 – Page 16
3.
Select the Reference to be edited, from the scrolling list of links in the middle of
the Refs tab window. The full Reference appears in the “Full text for the selected
Reference” pane at the bottom of the screen.
In the example below, the word “southwestern” should be “northwestern.” Rather
than searching for the Reference record in the References table and correcting the
error there, you can simply edit the linked Reference record “on the fly” from (in this
example) the Species record.
4.
Click the “Edit Ref” button in the middle of the screen (see above).
The linked Reference record appears in a new window.
5.
Edit the Reference record as needed (see above).
6.
Click the “Save” button in the Reference Input screen.
The Reference Input screen closes and returns control to the
“Refs” tab of the Species, Specimen, Collection or Locality screen, with the edited
Reference data displayed.
Chapter 20 – Page 17
Importing and Exporting References
Importing References
It is likely that you already have many references in specialized reference management
software (e.g., EndNote, ProCite, etc.). Rather than start all over, entering them
manually into Biota, you can export them from your reference management application
and import them directly into Biota.
Note: Because EndNote is the most widely used reference management application, on
both Windows and Mac OS, and has a straightforward design, Biota’s Reference
management system was designed around EndNote fields and document types. Other
reference management applications (e.g., ProCite) can also be made to export citations
in a form that can be imported into Biota, with some modifications, but instructions for
applications other than EndNote are beyond the scope of this manual.
1.
In your application management software, select the references you want to
export to Biota.
2.
Set up the export tools in your application management software to export a
tab-delimited, plain text file, with the following fields (or their equivalents), with
comments on each field:
NOTE: You must know the order of these fields in the exported file, but they may be
in any order in the exported file.
Reference Number (ReferenceNo in Biota). This must be an integer; no
alphabetic characters are allowed.
Reference Type (ReferenceType in Biota). Biota accepts only four Reference
Types:
◊
Journal Article
◊
Book
◊
Book Section
◊
Online Source
NOTE: The text of ReferenceType field must exactly match one of these four
entries, including spaces. Biota flags any other entry in this field during import,
and offers to import the reference in “Book” format.
Author(s) (Author in Biota; Author in EndNote). Biota has only one field for
Author, but it may contain as long a list of authors as necessary (up to 32K).
Year of Publication (Year in Biota; Year in EndNote). This is an alphabetic field
(up to 20 characters), so you can use date ranges (e.g., “1996-1999”) or brief text
notations (e.g., “Unknown” or “Late 18th Century”).
Chapter 20 – Page 18
Article or Book Title (Title in Biota; Title in EndNote). The title may be of
virtually any length (up to 32K characters).
Editor (Editor in Biota; Secondary Author in EndNote). This field may be of
virtually any length (up to 32K characters).
Title of Journal or Edited Book (JournalOrEditedBook in Biota; Secondary Title
in EndNote). This field may be of virtually any length (up to 32K characters).
Place of Publication (PlacePublished in Biota; PlacePublished in EndNote).
This field may contain up to 60 characters.
Publisher (Publisher in Biota; Publisher in EndNote). This field may contain up to
80 characters.
Journal Volume (Volume in Biota; Volume in EndNote). This text field may
contain up to 10 characters.
Pages or Article or Book Section (Pages in Biota; Pages in EndNote). This text
field may contain up to 20 characters.
URL for Online Source (URL in Biota; no corresponding field in EndNote). This
text field may contain up to 32K characters.
Notes for EndNote Users:
a.
Set up the export file format by choosing “Tab Delimited” from the Style
Manager (choose “Output Styles” from the File menu to get to the Style
Manager).
b.
Edit the Tab Delimited style to export only the above fields (except for
“Record Number” and “Reference Type”). In the EndNote Style Editor, go to the
“Bibliography” theme, then click “Templates” and modify the “Generic”
Reference Type template to include the above fields, as shown below. Do not
specify anything for any other Reference Types.
c.
Click the “Layout” tab (still in the Bibliography theme) and confirm that
“Record Number” and “Reference Type” will be included in the export.
Chapter 20 – Page 19
3.
Export the text file from your application management software.
4.
Open the exported file (e.g., in Excel) to verify that: (a) the file begins with the
first record (there are no header rows), and (b) only the four Reference Types that
Biota supports are specified. (Change the Reference Type field to one of these four,
if any Reference Types appear in the exported file. For files exported by
applications other than EndNote, you will need to enter the appropriate
Biota/EndNote Reference Type.)
5.
Close the exported file, taking care to ensure that it saved as filetype “Text” (or
“Tab-delimited Text”).
6.
From the Im/Export menu in Biota, choose Import by Table and Fields. The
Import Options screen appears.
NOTE: For help with the Import Editor, refer to Chapter 28, “Importing Data.”
7.
Choose the default, “Import new records,” and click
the “OK” button. The Import Editor appears.
8.
Choose “Reference” from the “Table Name”
popup.
9.
Select and Append fields from the left panel (Biota
Field Name or Aliases) to create a list in the right panel
(Text File Fields) that precisely matches the order of
fields in the text file to be imported. (Use the “Skip”
button if necessary.)
Note: Do not select any of the “Index” fields:
AuthorIndex, TitleIndex, or JournalOrEditedBookIndex.
These fields are automatically filled by Biota, with the
first 80 characters of the corresponding Text fields:
Author, Title, and JournalOrEditedBook.
Chapter 20 – Page 20
10. Click the “Save Import Setup” box, in case you
need to come back and modify the setup or import
additional References.
11. Click the “Import” button. If error messages
appear, consult Chapter 28, “Importing Data by Tables and Fields.”
Exporting References
You can export Reference records from Biota, for the current Reference Record Set (see
“Record Sets” in Chapter 3) in either two ways:
Using the Export Editor. You can export any or all fields from the Reference table,
for the Reference Record Set for all Reference records, using the Export Editor, just
as you can for any other Core table in Biota. See “Exporting Data by Tables and
Fields” in Chapter 27.
Using the “Export References” tool from the Im/Export menu. This tool exports
all records for the current Reference Record Set, in American Naturalist format, to a
text file. This format was chosen as approximately representative of many journals
in ecology, evolutionary biology, and systematics, and because this leading journal
publishes papers in all these areas.
Maintaining and Repairing Reference Links
Under normal operations, Biota correctly maintains links between parent records in the
Specimen, Species, Collection, and Locality tables and Reference records, by means of
records in the ReferenceLinks table.
Power failures, system crashes, and incorrectly imported data, however, can produce
orphan ReferenceLinks records.
You can correct this problem, without in any way affecting legitimate records, by running
the Reference Links Maintenance Utility. Whereas this problem is not serious (orphan
ReferenceLink records simply take up space), it is recommended that you run this utility
from time to time if you work with References in Biota, especially if you suspect
problems.
1.
To run the Reference Link Maintenance Utility, choose “Maintenance Utilities”
from the Special menu. The option screen appears.
Chapter 20 – Page 21
2.
Activate the option “Delete orphan Reference Links.”
3.
Click the “Launch” button. The utility reports on its activities.
Chapter 21
The Specimen Loan System
The Loans menu contains the primary tools for managing Specimen Loans. Using these
tools, you can keep track of loans you make to others as well as specimens you borrow
from others. You can review existing Loan records and print or reprint Loan forms and
lists of Specimens loaned.
How Biota Keeps Track of Specimen Loans
To use the Loan system, it is essential to understand how Biota keeps track of Loans.
Each Specimen record in your Data File has a field called “Deposited.” Biota uses this
field to identify each group of Specimen records that constitute a Loan. You can view the
“Deposited” field in the standard Specimen Record Listing screen, as well as in the
individual Specimen records in the Specimen Input screen.
When you create new Specimen records for your own specimens, you should
enter a name or code in the Deposited field (up to 20 alphanumeric characters),
indicating that the physical specimens are presently in your custody. (You may wish
to set up this code as the default entry for the Deposited field, by using the Field
Value Defaults utility from the Special menu. See “Setting Default Entries: Field
Value Defaults” in Chapter 17.
When you lend a group of specimens from your collection to another institution or
individual, you create a new record in the Loans table to record the loan, with a
unique Loan Code to identify the Loan. Once you have indicated which Specimen
records will be included in the Loan, Biota changes the Deposited field of each
Specimen record in the Loan, replacing the existing value with the Loan Code.
When loaned specimens are returned to your collection, you use the Record
Returns tool to change the Deposited field of the corresponding Specimen records
back to your institutional or personal collection name or to some other meaningful
code.
NOTE: Since there is, as yet, no loan history capability in Biota to keep track of
previous (as opposed to current) loan status of Specimens, you could devise a
system of codes to indicate which returned specimens have been previously lent
and to whom, although there are obviously serious limitations to this approach if you
repeatedly lend the same specimens.
When you borrow a group of specimens from another institution or individual,
you can create a Loan Code for the group and use the New Loan screen to record
the specimens as a loan to your own institution or to your own collection.
When you return borrowed specimens, you can use the Record Returns tool to
change the Deposited field in the corresponding Specimen records of your Data File
to a new code, indicating that the physical specimens have been returned.
Chapter 21 – Page 2
Recording a New Loan
To create a Loan record for a new loan from your collection, or to record a loan you have
received from another collection, take the following steps:
1.
From the Loans menu, choose “New Loan.” The New Loan Input screen
appears.
2.
Enter a Loan Code. You can enter the Code
either by typing it in the Loan Code entry area or
by using the adjacent “Assign” button (see
“Assigning New Record Codes Using an ‘Assign’
button: Step by Step” in Chapter 8).
Loan Codes may be up to 80 characters in
length.
Loan Code, the Key field for the Loan table, is an obligatory entry, which must be
made first. All remaining entry areas are optional. The Loan Code you enter must
not duplicate the Loan Code of any existing Loan Record, or you will receive an
error message.
See “How Biota Keeps Track of Specimen Loans,” earlier in this chapter, for ideas
on how to set up a system of Loan Codes.
Chapter 21 – Page 3
If you use the “Assign” button, the Assign Loan Code window offers two options.
You can enter a prefix of your own choice, then click the “Accept Prefix”
button.
You can click the “Default Prefix” button to use the prefix “Loan.” (This default
is fixed and cannot be altered in the Record Code Prefix screen, unlike other
Record Code prefixes.)
In either case, Biota will format the Loan Code with the prefix (up to 14 characters in
the case of an ad hoc prefix) plus a four-digit integer counter derived from the Loans
table sequence number.
3.
Enter the Borrower’s “Short Name” in the
Borrower entry area. Because this field is
linked to the Short Name field of the
Personnel table, the entry area has a double
border. You can use any of the techniques
for entering data in linking fields described in Chapter 7, “Overview of Record Input
Screens.”
If you know that the Borrower has no existing record in the Personnel
table, enter a Short Name for the determiner in the “Borrower” entry area (e.g.,
Albert B. Smith or A. B. Smith) and press the TAB key. If the entry you make does
not match the Short Name field of any existing Personnel record, Biota offers you
a choice between creating a new Personnel record for that name, “on the fly,” or
accepting the Loan record without creating a link to the Personnel table (a
“Personnel-orphan” Loan record) (see “Entering Data in Linking Fields” in
Chapter 7).
NOTE: On Pin, Slide, Vial, and Herbarium labels, Biota uses the Short Name field
for the collector’s name (see Chapter 15, “Printing Labels”). Although the Short
Name may have up to 80 characters, it is best to make it substantially shorter
(20-30 characters is a good guideline) if you intend to use Biota to produce
specimen labels. Since Borrowers are often also collectors, be sure to choose a
version of the Borrower’s name that is appropriate for collector’s names on
labels—e.g., initials and last name, or first name and last name. You can also
use a “Group Name” in the “Determined By” field, e.g., A. B. Smith & C. D. Jones
Chapter 21 – Page 4
(for help with Group Names, see “Entering Personnel Data: The ‘Group’ Tab” in
Chapter 11).
If you think the Borrower may already have a Personnel record, but you are
not sure what Short Name the record carries, enter the @ character and
press the TAB key. A scrollable list of all existing Personnel records appears
(below), from which you can choose the correct record by clicking it. You can sort
the records by Short Name, Last Name, or Institution by clicking the buttons
above the columns.
If you know the Short Name for the Borrower’s existing Personnel record,
enter the first letter, the first few letters of the Short Name, or the full Short Name,
and press the TAB key. If a single match is found, Biota completes the name and
the cursor moves into the next field. If more than one match is found, a choice list
like the one above appears, with all matches shown.
If the Borrower entry you make in the Loan record does not match the Short
Name field of any existing Personnel record, Biota offers you a choice between
creating a new Personnel record for that name, “on the fly,” or accepting the
Loan record without creating a link to the Personnel table (a “Personnel-orphan”
Specimen record) (see “Entering Data in Linking Fields” in Chapter 7).
NOTE: Creating a “Personnel-orphan” Loan record is not recommended. If you do
so, none of the information on the Borrower’s institution or contact information
can be entered in the loan forms.
Chapter 21 – Page 5
4.
Enter the Date Loaned. When the New Loan screen
opens, today’s date (the date in your computer’s internal
clock) is entered in the Date Loaned entry area. If you
need to change it, enter a full date (see “Dates” in
Chapter 9). If you want to keep today’s date, just “TAB
through” the date entry areas.
5.
Enter the Loan Period. This alphanumeric entry can be
up to 20 characters.
6.
Indicate the Specimens Loaned. Although you can create a Loan record without
linking it to any Specimen records (e.g., for unmounted material not in the Data
File), normally a Loan record is linked to the Specimen records for the physical
specimens loaned (see “How Biota Keeps Track of Specimen Loans” earlier in this
chapter).
There are two, non-exclusive methods of indicating which Specimen Records are
included in the Loan.
Click the Include Specimen Record Set
checkbox in the Specimens Loaned panel.
To use this option, you must first have defined a
Specimen Record Set (see “Record Sets” in Chapter 3). You can find the
Specimen records using any of the tools of the Find or Series menus (see
Chapter 12, “Finding and Updating Records”).
Once you click the checkbox, the Specimen Code for the last record in the
Record Set appears in the Last Code Entered display area, showing the current
value of the [Specimen] Deposited field for that record in the Previous Deposition
display area (below).
The Number of Specimens display area (above) counts the number of Specimen
Records you have entered so far—including the number in the Specimen Record
Set plus any records entered using the “one by one” option described below.
Enter the Specimen Codes, one by one, in the Enter Specimen Code entry
area of the Specimens Loaned panel.
You can enter the Specimen Codes manually, pressing TAB after each entry,
enter them with a barcode reader, or use both methods for the same Loan. If the
Chapter 21 – Page 6
barcode reader is set to enter an end-of-line character after each read, you can
enter all Specimen Codes without touching the keyboard or mouse.
Once entered, each Specimen Code appears in the Last Code Entered display
area, showing the current value of the [Specimen] Deposited field for that record
in the Previous Deposition display area.
The “Number of Specimens” display area counts the number of Specimen
Records you have entered so far—including any in the current Specimen Record
Set if the Include Record Set checkbox has been checked.
7.
Make an entry in the “Loan Description or Conditions” text area. This optional
entry (up to 32,000 characters) will appear on the printed Loan Invoice (see
“Previewing, Printing, and Exporting Loan Records” later in this chapter). If the Loan
includes any specimens or other material not represented by Specimen records,
this is the place to describe that material. When you create a new Loan record, the
“Loan Description or Conditions” text area displays the default entry “See attached
list,” referring to the list of specimens that would usually be attached to the Loan
Invoice. You are of course free to delete or change this entry.
8.
Click the Notes tab to add a Loan Note (or Notes), if
you wish. Loan Notes should be used for any comments
on the loan that are not intended to appear on the Loan
Invoice itself. Any number of additional Loan Notes can
be added to the Loan record later, to document notices
sent to the Borrower, condition of returned specimens,
and so on. See “Notes Input” in Chapter 11 for detailed
instructions.
9.
Click the “Save and Continue” or the “Save and Close” button to save the
Loan record (or the ““Cancel” button to cancel it).
The “Save and Continue” button saves changes in the “Deposited” field of any
Specimens so far included in the new Loan and saves the Loan record itself. It
leaves the New Loan window open so you can include
additional Specimens or make other changes. If you are
entering a large number of specimens manually, or with
a barcode reader, it is a good idea to click this button
periodically.
The “Save and Close” button saves all changes in the
“Deposited” field of any Specimens included in the new
Loan, saves the Loan record itself, and closes the New
Loan window. If you want to add Specimens or make other changes to the Loan
later, you can do so by re-opening the Loan record. See “Displaying and Editing
an Existing Loan” later in this chapter.
Chapter 21 – Page 7
10. If you have clicked the “Save and Close” button, the next step depends on
whether or not any Specimen records have been included in the Loan in Step 6,
above.
If no Specimen Records are linked to the Loan record, the message below
appears.
If you click the “OK” button, the Loan form printing sequence begins. See
“Previewing, Printing, and Exporting Loan Records,” later in this chapter. You
might create a Loan record, for example, for a group of unsorted and unmounted
specimens.
If one or more Specimen Records are linked to the Loan record, the
Specimen Records appear in a special version of the Specimen Record Listing
screen entitled “Specimens in Loan.” Notice that the “Deposited” field of each
record in the new Loan has been changed to the Loan Code (“MNH0501” in the
example below).
Chapter 21 – Page 8
The purpose of this screen is to provide an opportunity to confirm that no errors
have been made in specifying the content of the Loan.
To sort the records, click the “Sort” button (see “Sorting Records in Record
Listing Screens” in Chapter 10).
To incorporate additional Specimens in the
Loan, click the “Add More Specimens” button. The
New Loan screen re-appears.
To examine a full Specimen record in the standard Specimen Input screen,
double click the record in the Record Listing screen.
NOTE: If you wish, you can re-size the
columns in the “Specimens in Loan”
Record Listing screen (above) by
dragging the column dividers in the
header area. The cursor changes to a
“splitter” icon.
11. If the Specimens have been displayed,
Either: Click the “Print Loan Forms” button to
print a Loan Invoice and, if you wish, print a list of
the Specimen records in the Loan and/or export a
text file with these records.
The “Print Setup” (Windows) or “Page Setup”
(Mac OS) window appears. Please continue with
the next section, “Previewing, Printing, and Exporting Loan Records.”
Or: Click the “Done” button to leave the New Loan procedure without printing
or exporting. The Record Set Options screen appears to allow you to declare the
Specimen records in the Loan to be the current Specimen Record Set, if you
wish (see “The Record Set Options Screen” in Chapter 3). (It is not necessary to
create a Specimen Record Set to complete the Loan process.)
NOTE: This is the place to stop if you are recording a loan made to you from another
individual or institution (see “How Biota Keeps Track of Specimen Loans,” earlier in
this chapter).
Previewing, Printing, and Exporting Loan Records
This section describes the procedures and options for printing Loan invoices, printing a
list of the Specimen records in a Loan, and exporting text files to disk for the Specimen
records in a Loan.
1.
Follow the instructions for “Recording a New Loan” (earlier in this chapter) or for
“Displaying and Editing an Existing Loan” (later in this chapter) until instructed to
proceed with this section.
2.
Check or adjust any settings in the “Print Setup” (Windows) or “Page Setup” (Mac
OS) window, then click the “OK” button. The “Print” window for your active printer
appears. (Because “Print” windows vary greatly among printers and between
operating systems, none is illustrated here.)
Chapter 21 – Page 9
3.
Choose a Preview option. Look for a “Print preview”
(Windows) or “Preview on screen” (Mac OS) checkbox in the
lower-left corner of the Print window. If you don’t see the
checkbox, look for a popup menu of print
options and select “4D x.x.x” (where “x.x.x” is
the version number of 4th Dimension used to
compile the current version of Biota), then
locate the checkbox.
If you leave the Preview checkbox
unchecked, the Loan invoice goes directly to your printer.
If you click the Preview checkbox, you can check the Loan invoice onscreen
and then Print or Cancel.
4.
To print the Loan invoice, click the “OK” button (Windows) or “Print” button (Mac
OS) in the Print window.
If you requested Print Preview, the Loan Invoice for the active Loan record
appears in the Preview screen.
Header
Lender block
Borrower block
◊
The header at the top of the Loan Invoice shows the [Project]Heading for the
Active Project. See “Entering Project Data: The ‘General’ Tab” in Chapter 16.
◊
The lender block displays address and contact information from the ProjectLinked Personnel record (if any) for the Active Project. (Each Project record
Chapter 21 – Page 10
may be linked, one-to-one, to a single Personnel record that provides contact
information for the Project. See “Personnel Input” in Chapter 11.)
◊
The remaining information on the Loan Invoice comes from the
corresponding fields of the Loan record, or from the Personnel record for the
Borrower (borrower block, above). (Loan Number on the Invoice is the Loan
Code for the record.)
To print the Invoice after previewing it, click the Printer icon in the
control panel at the top left of the Preview screen (see “Printing and
Previewing Procedures for Reports and Labels” in Chapter 14 for
details on the Preview screen).
To proceed without printing the Invoice, after viewing the Invoice
in the Preview screen, click the “X” icon in the control panel at the
top left of the Preview screen.
If you choose to Print without previewing the invoice, or you
clicked the “Print” button on the Preview screen, the Loan
Invoice is printed and the “Print and Export Options” screen
appears.
5.
Choose Print and Export options and click the “OK” button, or Cancel to
dismiss the rest of the procedure.
Either: Choose “Sort taxonomically before printing.” This option sorts
Specimen records taxonomically (see “Sort Options” in Chapter 15) before
printing, if you select the “Print a list of Specimens loaned” option in the lower
half of the Print and Export Options screen.
Or: Choose “Design and print a special report.” This option launches the
Quick Report Editor (see “Designing and Printing Reports with the Quick Report
Editor” in Chapter 14), with which you can create your own format for a report on
the Specimen records in the Loan. Fields from the Loan record are not available,
however, except for the Loan Code, which is reproduced in the [Specimen]
Deposited field.
If you chose “Sort taxonomically before printing,” the two checkboxes in the
Print and Export Options screen are enabled. You can check either or both.
Chapter 21 – Page 11
◊
If you click the “Print a list of Specimens loaned” checkbox, Biota prints
a special version of the standard Specimen report (see “Printing a Standard
or Custom Report Based on the Records in a Record Listing Screen” in
Chapter 14) that includes Loan information and lists all Specimen records in
the Loan (below).
◊
If you click the “Export the Specimen list to a text file” checkbox, Biota
presents the Export Specimen Flatfile tool. See “Exporting Specimen
Flatfiles” in Chapter 27 for instructions on using this tool. The text Specimen
flatfile exported for the Specimen records in the Loan includes a special
header with Loan information.
The exported Specimen flatfile can include virtually any selection of fields
from the Core tables that you wish, allowing you to provide the Borrower with
a complete archival electronic record of the loan (with or without a printed
version).
If the Borrower determines specimens in the Loan, he or she can add the
new determination to the same text file and return it to you for updating the
Specimen records, using the “Update records” option in the Import Editor
(see “Import Step 3: Set Up and Launch the Import or the Update” in Chapter
28).
Chapter 21 – Page 12
Displaying and Editing an Existing Loan
Records in the Loans table, like other Core tables in Biota, can be displayed in a Record
Listing screen and grouped as Record Sets, and Record Sets can be saved as Record
Set Pointer Files (see Chapter 3, “Key Concepts”). The commands “Display All Loans”
and “Display Loan Record Set,” however, are located in the Loans menu, rather than the
Find and Display menus, respectively, where the analogous commands for other Core
tables can be found.
To display an existing Loan record, follow these steps:
1.
From the Loans menu, choose “Display All Loans.” A list of all Loan records
appears in the Loans Record Listing screen.
The Loans Record Listing screen differs from the standard Record Listing screens
for other Core tables only in lacking a New Record button. (To create a new Loan
record, choose New Loan from the Loans menu; see “Recording a New Loan”
earlier in this chapter). The “Sort,” “Delete Selection,” and “Sub-Selection” buttons
work in the same way as the analogous buttons for other Core tables (see Chapter
10, “Working With Records in Record Listing and Input Screens.”).
2.
To print a list of the Loans displayed in the Record Listing screen, click the
“Print Loan List” button in the Record Listing screen, or select Print from the File
menu while the screen is displayed. A print options window appears.
Chapter 21 – Page 13
See Chapter 14, “Printing Reports,” for help using these options.
3.
To display an individual Loan record, double-click the record in the Record
Listing screen. The record appears in a special version of the Loan Records Input
screen.
This screen resembles the New Loan screen (see “Recording a New Loan” earlier
in this chapter) but has a different set of tabs, buttons, and functions. This is the
same screen used for recording Returns, by displaying the Returns tab (see
“Recording Specimen Returns,” later in this chapter).
In this screen you can edit the Date Loaned, Loan Period, Loan Description or
Conditions, add a Loan Note, or add more specimens to the existing loan. You can
also manually change the Number of Specimens Returned and Number of
Specimens Loaned, if necessary, but these numbers are normally (and preferably)
adjusted automatically when you record returns by the methods described in
“Recording Specimen Returns,” later in this chapter.
4.
To add more Specimens to this Loan record, click the
“Add More Specimens” button in the “Loan Records”
screen (above). See the next section of this chapter,
“Adding More Specimens to an Existing Loan” for details.
5.
To display the Specimen records linked to this Loan
record, click the “List Specimens” button in the screen above.
The Specimen records are displayed in a special Specimen
Record Listing screen entitled “Specimens in Loan.” (If the Loan
is not linked to any Specimen records, a message appears, instead.)
Chapter 21 – Page 14
This screen has two special buttons, “Returns” (see “Recording Specimen Returns”
later in this chapter) and “Reprint Loan Forms” (see the next step).
NOTE: If you wish, you can re-size the
columns in the “Specimens in Loan”
Record Listing screen (above) by
dragging the column dividers in the
header area. The cursor changes to a
“splitter” icon.
6.
To reprint the Loan Invoice, reprint the list of Specimens in the Loan, or export a
text file for the Specimen records in the Loan:
Either: Click the “Reprint Loan Forms” button in the
Loan Records Input screen.
Or: Click the “Reprint Loan Forms” button in the
Specimens in Loan Record Listing screen.
Biota offers the same sequence of options and functions
available for New Loans (see “Previewing, Printing, and
Exporting Loan Records” earlier in this chapter for examples).
7.
If you clicked either “Reprint Loan” button, please continue with “Previewing,
Printing, and Exporting Loan Records” earlier in this chapter.
Chapter 21 – Page 15
Adding More Specimens to an Existing Loan
If you wish, you can incorporate additional Specimens in an existing Loan. This
capability can be useful when you are preparing a complicated or extensive Loan over
several Biota sessions and need to save your progress in the meantime.
1.
Display the existing Loan record, following the instructions in the section
“Displaying and Editing an Existing Loan” earlier in this chapter.
2.
To add more Specimens to the Loan record, click the
“Add More Specimens” button in the “Loan Records”
screen. The “Loan Records” screen is replaced by a
special version of the New Loan screen, with the special
title “Add More Specimens to the Loan.”
Using this screen, you can incorporate additional Specimens into the existing Loan,
using all the tools described in the section “Recording a New Loan” earlier in this
chapter.
Note: The Loan Code and Borrower fields of the Loan record are not editable in the
“Add More Specimens to the Loan” screen (above). Once a Loan record has been
saved, these fields are protected from alteration, by design.
Chapter 21 – Page 16
Recording Specimen Returns
Biota offers three alternative methods of recording the return of physical specimens
represented by Specimen records in the Data File.
Using the Specimen Record Set to Record Returns
This is usually the most efficient method when a set of returned specimens represents
several different Loan records. For example, you may have made several Loans to the
same individual or institution, who then returns some or all of the specimens, determined
and sorted by species, but each conspecific group is a mixture of specimens from
several Loans.
1.
Gather the Specimen records for the returned specimens using any of the tools
in the Find or Series menus (see Chapter 12, “Finding and Updating Records”).
Probably the most useful tool for this purpose, especially when the specimens have
barcodes, is the “Find Specimen Series” tool (Series menu; the same tool is called
“By Specimen Code Series” in the Find menu). Use this tool with the “In any order”
option and the “Auto Accept” button enabled. See “Creating, Finding, and Updating
Specimen Series” in Chapter 13.
2.
Declare the Specimen records to be the current Specimen Record Set (see
“The Record Set Options Screen” in Chapter 3).
3.
From the Loans menu, select “Record Returns.” The Loan returns option screen
appears.
4.
Choose the second option, “Record the current Specimen Record Set as
returned,” then click the “OK” button in the option window. (If the Specimen Record
Set is empty, this option is disabled and the window displays a help message; see
Step 1 in the next section, for an
illustration.)
A window appears requesting a value to
be entered in the “Deposited” field of the
Specimen records returned.
Chapter 21 – Page 17
NOTE: If the Specimen Record Set is empty, the second option is disabled and the
window displays a help message.
5.
Type in the value and click OK.
If you are recording returns to your own collection, you would normally enter
its code or name.
If you are recording the return of specimens loaned to you, you would
normally enter the code or name for the collection to which they have been
returned.
A confirmation message appears.
6.
Click the “OK” button to confirm the changes, or Cancel to leave the records
unchanged.
If you click OK, Biota makes the changes in the Specimen records.
Chapter 21 – Page 18
If any of the Specimen records in the Record Set are not part of an existing
Loan, Biota posts a message, for each such record.
All records in the Record Set are then displayed in the Specimen Record Listing
screen, whether changed or not.
NOTE: When you use this method to record Returns, the “Number Returned” field
in the Loan record for each Loan involved in the return is automatically updated
to reflect the number of specimens returned.
Two Ways to Use the Loan Records Screens to Record Returns
With either of the methods described in this section, you record returns of specimens
from one Loan at time. If you need to record returned specimens mixed from several
Loans, see “Using the Specimen Record Set to Record Returns” earlier in this chapter.
1.
From the Loans menu, select “Record Returns.” The Loan Returns option
screen appears.
Chapter 21 – Page 19
NOTE: If the Specimen Record Set is empty, the second option is disabled and the
window displays a help message, which you may ignore, for this method.
2.
Choose the first (default) option, “Look up the Loan now, then select the
Specimens returned,” then click the “OK” button in the option window.
The Loans Record Listing screen appears, showing all Loan records.
3.
Double-click the Loan record for which you need to record returns (above).
The Loan record appears in the Loan Records Input screen.
Chapter 21 – Page 20
4. Click the Returns tab.
The Returns screen appears.
5.
To record returns by Specimen Code:
a. Enter the Specimen Code for a returned specimen in the “Enter Specimen
Code” area of the Returns screen.
b. Press TAB. (If you are using a barcode reader and Specimen barcodes, and the
reader is set to enter an end-of-line character automatically after each read, this
step is not necessary.)
Chapter 21 – Page 21
◊
If Biota determines that the Specimen Code is linked to this Loan
record, the Specimen Code appears in the Last Code Entered display area,
and the Enter Specimen Code area is cleared for the next Specimen Code.
The Number Returned field is incremented by 1.
◊
If Biota finds the Specimen Code, but it is not linked to this Loan, the
message below appears. The Specimen Code may be linked to a different
Loan record, or to no Loan record.
◊
If Biota determines that the Specimen record is not in the Data File, the
message below appears.
c. Enter the remaining Specimen Codes for the returned specimens in the
same way.
d. Click the “Save” button in the Loan Records Input
screen.
A window appears requesting a value to be entered in
the Deposited field of the Specimen records returned.
Chapter 21 – Page 22
e. Go to Step 6, below.
6.
To record returns by selecting them from a list of Specimen records:
a. Click the “List Specimens” button in the Loan tab of the
Loan Records Input screen.
The Specimen records will be displayed in the “Specimens
in Loan” Record Listing screen. (If the Loan is not linked to
any Specimen records, a message will inform you.)
b. Select from the list all records for the returned Specimens, using the mouse
(see “Creating a Sub-Selection of Records” in Chapter 10, for selection
techniques).
c. Click the “Returns” button at the bottom of the “Specimens in Loan” screen
(shown above).
A window appears requesting a value to be entered in the Deposited field of the
Specimen records returned.
Chapter 21 – Page 23
NOTES:
7.
a.
You can select a few Specimen records at a time, then click the “Returns”
button for each group, if more convenient. Each time, you will need to fill in the
request window, above.
b.
As with all methods for recording Returns, when you use this method the
“Number Returned” field in the Loan record for each Loan involved in the return
is automatically updated to reflect the number of specimens returned.
Type in the value for the Deposited field.
If you are recording returns to your own collection, you would normally enter
its code or name.
If you are recording the return of specimens loaned to you, you would
normally enter the code or name for the collection to which they have been
returned.
A confirmation message appears.
Chapter 21 – Page 24
8.
Click the “OK” button to confirm the changes, or Cancel to leave the records
unchanged. When you click OK, Biota makes the changes in the Specimen records
and displays them again in the Specimens in Loan Record Listing screen.
9.
Click the “Done” button in the “Specimens in Loan” Record Listing screen.
The Record Set Options screen appears (see “The Record Set Options Screen” in
Chapter 3).
10. Select a Record Set Option and click the “OK” button. The “Loan Records”
Record Listing screen reappears. (It has been open all along, but hidden by the
“Specimens in Loan” screen.) The “Loan Records” screen allows you to work with
another Loan now, if you wish.
11. When you are through, click the “Done” button in
the “Loan Records” screen and choose a Record
Set option for the Loans records displayed.
Chapter 22
Determination Histories
In the management of biological collections and in systematic revisions, the
determination of individual specimens often changes as knowledge increases,
nomenclature is corrected, or opinions shift. Botanists often record such changes right
on the herbarium sheet, vertebrate biologists annotate tags or add secondary tags,
whereas entomologists generally update determinations by adding secondary labels to
specimens.
In biotic surveys and inventories, information on the taxonomic identity of a specimen is
useful even when imprecise. A trained non-specialist assistant can correctly identify
most insects to order or family, for example. (See Chapter 25, “Temporary Taxa for
Approximate Determinations.”) A specialist may at first determine the same specimens
to genus, and later determine some of the same specimens to species while others
await description as types for new taxa.
If you enable the Determination History system (see “Enabling or Disabling the
Determination History System” later in this chapter), Biota keeps track of all sources of
change in specimen determination automatically.
Determination History Records
Determination History records have a child-parent (many-to-one) relation with Specimen
records (see Appendix A, “Biota Tables, Fields, and Relational Links”). Each
Determination History record (in the Determination History table) records the following
information:
The Specimen Code field of the parent record (the linking field for the childparent relation between a Determination History table and the Specimen table). If
you change the parent record’s Specimen Code, this field in the Determination
History table is automatically updated to keep the records linked.
The Determined By and Date Determined fields of the parent Specimen
record, at the time the determination change was recorded in the Determination
History record.
The Species Code, Species Name, and Species Author fields of the Species
record to which the Specimen record was linked at the time of the determination
change was recorded in the Determination History record.
The Genus field of the Genus record to which the Species record was linked, at
the time of the determination change was recorded in the Determination History
record.
A record of who entered the change (the Changed By field of the Determination
History table). The person entering the change may or may not be the same person
who changed the determination. This entry is made automatically based on who
signed on when Biota was launched. If the User Password system has not been
activated (see Chapter 26, “Security: Passwords and Access Privileges.”) Biota
records “Administrator” in the Changed By field of the Determination History record.
Chapter 22 – Page 2
NOTE: If it is important to know who entered each change in Specimen
determination, be sure to set up sign-on names and passwords for each user, with
appropriate privileges (see Chapter 26, “Security: Passwords and Access
Privileges”).
The date the change was entered (the Date Changed field of the Determination
History table), entered automatically from the computer’s internal clock.
A record of where the change was made. (See “How and When Changes in
Determination Are Recorded,” later in this chapter, for details.)
◊
In an individual Specimen record, by changing the Species Code linking field
of the Specimen record.
◊
In a series of Specimen records, by changing the Species Code linking field of
several Specimen records by means of the “Find and Identify Specimen Series”
tool (see “Using the ‘Find Specimen Series’ and ‘Find and Identify Specimen
Series’ Tools” in Chapter 13).
◊
In the linked Species record, by changing the Species Name field, the Species
Author field, or the [Species] Genus linking field, then choosing to update linked
Specimen records (see “Automatically Updating Child Records by Changing a
Parent Record” in Chapter 12).
◊
In the linked Genus record, by changing the [Genus] Genus field and choosing
to update linked Species records (see “Automatically Updating Child Records by
Changing a Parent Record” in Chapter 12).
◊
In the Synonymy screen, by reassigning Specimen records to a Species that
has been declared a senior synonym (see Chapter 23, “Synonymy System”).
The Sequence Number of the record in the Determination History table. The only
purpose for this field is to sort the records in the reverse order they were created
(see illustrations below).
NOTE: The sequence number is the number of records entered in the table since the
Data File was created. The number increases by one every time a record is created,
no matter how many records are later deleted. (The Date Changed field cannot be
used to sort by entry order since more than one change can occur on the same
date.)
Enabling or Disabling the Determination History System
NOTE: If the User Password System has been activated (see Chapter 26, “Security:
Passwords and Access Privileges”), you must have Administration access privileges to
enable or disable the Determination History system.
1.
From the Special menu, select Preferences.
2.
Click on the “Admin Settings” tab.
Chapter 22 – Page 3
The Admin Settings tab screen appears.
3.
Check to enable, or uncheck to disable the option “Record Determination
Histories automatically.”
4.
Choose an option for saving any changes in Preference settings made during
this Biota session.
If you want the changes to remain in force until altered regardless of how
many times Biota is launched in the meantime, choose the option “Use these
Preferences next time Biota is launched.”
If you want the changes to be in force only for this session, choose the
option “Reset Preferences to defaults next time Biota is launched.
The default setting for Determination Histories is unchecked (off).
5.
Click the “Save” button on the Preferences screen.
Displaying the Determination History for a Specimen
Record
You can display previously recorded Determination History records, whether or not the
system is currently enabled (see “Enabling or Disabling the Determination History
System” earlier in this chapter).
1.
Display a Specimen record in the Specimen Input screen (see Chapter 10,
“Working With Records in Record Listing and Input Screens”).
2.
Click the Determination tab.
Chapter 22 – Page 4
The Determination History tab screen for this Specimen appears, displaying a
record of all previous determinations for this Specimen (in reverse chronological
order, most recent to earliest). Each line (after the first) shows data from a separate
record in the Determination History table.
In addition, the Determination tab screen has a data entry area for “Last Determined
by” and “Date Last Determined.”
The Determination History Record list has two groups of columns:
◊
The “Historical Data” panel, on the left, shows the history of changes in
Species Code, Genus, Species (specific name), Author, Determined by, and
Date Determined.
◊
The “Record Change Data” panel, on the right, shows, for each line of
Historical Data, the table in which the determination in the left panel was
changed (Where), when the change was made (Date), and who made it (By
Whom).
Keep in mind the convention used in this screen: “Record Change Data” in the
right panel refers to changes made to the Historical Data on the same line in the
left panel. See the historical summary for this Specimen record, below, for an
illustration.
The first data row of the screen, labeled “Current Record” in the Record
Change Date panel, is not a Determination History record. It shows fields from
the parent Specimen record.
The rest of the data rows, which are Determination History records, are listed
from most recent to the earliest.
Chapter 22 – Page 5
In the illustration above, the Determination History of Specimen
INBIOCRI001248084 can be fully reconstructed, as follows:
On October 24, 1995, the Specimen was tentatively identified as “cf.
Lamrophyllum sp. 2” (Species Code AL1248074) by P. Naskrecki.
On October 26, 1995, Naskrecki determined the correct genus to be Steirodon.
He himself entered this information in Genus field in the Species record (Species
Code AL1248074) on the same date (shown on the last line of the display in the
Record Change Date panel).
On July 28, 1996, Naskrecki updated the determination again, by identifying the
species as Steirodon robertsorum Emsley, 1970. On July 29, 1996, R. Colwell
entered this change in the Species record, replacing “sp. 2” in the Species Name
field with Naskrecki’s definitive determination, “robertsorum,” adding the Author
(and date), “Emsley, 1970.”
3.
To display an individual Determination History record, double-click the row.
(Clicking the Current Record row has no effect.)
The record appears in a special, read-only Determination History Input screen. You
can use the navigation buttons to look at the sequence of Determination History
records for this Specimen.
In the illustration, for example, “cf. Lamprophyllum” is too long to fit in the Genus
column of the Determination listing pane, but can be read in the Input screen.
Chapter 22 – Page 6
NOTE: If you need to edit or delete a Determination History record, you must do so
using commands from the Special menu. See “Displaying, Editing, or Deleting
Determination History Records,” later in this chapter.
How and When Changes in Determination Are Recorded
Because Biota is a relational database, it records changes in Specimen determination
made not only in Specimen records but also in the parent Species and Genus records.
Changing a Determination in an Individual Specimen Record
Make sure you have enabled the Determination History system (see “Enabling or
Disabling the Determination History System,” earlier in this chapter).
1.
Display the existing Specimen record in the Specimen Input screen (see
“Viewing, Editing, Printing, or Deleting Individual Records from an Input Screen” in
Chapter 10).
2.
Change the existing Species Code in the Specimen record to a new value. See
“Entering Specimen Data: The ‘General’ Tab” in Chapter 11 for help in finding and
entering a Species Code in a Specimen record.
Biota enters today’s date automatically in the Date Last Determined area. You
can change the date if necessary. (See “Entering Specimen Data: The
‘Determination’ Tab” in Chapter 11.)
Biota prompts you to enter a new value for “Last Determined by.”
When you click the “OK” button in this window, Biota highlights the “Last
Determined by” entry area. If the new determination was made by the same
person as the previous one, you need not make an entry. See “Entering
Specimen Data: The ‘Determination’ Tab” in Chapter 11 for help in finding and
entering a “Last Determined by” value.
If you don’t want Biota to remind you to update the “Last Determined by” field
again during this session, check the “Don’t show me this message again today”
box.
Chapter 22 – Page 7
NOTE: If there was no previous Species Code entry in the Specimen record, no
Determination History record is created when you enter one, and the window above
does not appear.
3. Accept the revised Specimen record.
If you did not update the “Last Determined by” area after changing the
determination, Biota prompts you again.
If you updated the “Last Determined by” area or you click OK in the
window above, Biota creates a linked record automatically in the Determination
History based on information from the old Specimen determination. The new
information then replaces the old in the Specimen record.
4.
To check that the Determination History record was created, re-display the
Specimen record in the Input screen and click the Determination History tab
The “Where Changed” field for the new Determination History record will now read
“Spcmn Rec,” to indicate where the change was made.
Changing a Determination in a Specimen Record Series
Changing the determination for groups of specimens efficiently is the special function of
the “Find and Identify Specimen Series” tool. The group of specimens may have
sequential or non-sequential Specimen Codes. See “Using the ‘Find Specimen Series’
and ‘Find and Identify Specimen Series’ Tools” in Chapter 13.
Make sure you have enabled the Determination History system (see “Enabling or
Disabling the Determination History System” earlier in this chapter).
1.
From the Series menu, choose “Find and Identify Specimen Series.” Following
the instructions in “Using the ‘Find Specimen Series’ and ‘Find and Identify
Specimen Series’ Tools” (Chapter 13), set up the screen to find a group of
Specimen records.
2.
Set up the Species Code for the new determination. Follow the instructions in
“Changing a Determination in an Individual Specimen Record,” earlier in this
chapter.
3.
Accept the revisions to the Specimen series. Biota automatically creates a
Determination History record for each Specimen record in the Series.
4.
To check that the Determination History records were created:
a. Click the “Cancel” button in the “Find and Identify Specimen Series” screen to
dismiss it.
Chapter 22 – Page 8
b. Display a Specimen record in the Input screen and click the Determination tab.
The “Where Changed” field for the new Determination History record will read “ID
Spcm Ser,” to indicate where the change was made.
Changing a Determination in a Species Record
If you have enabled the Determination History system (see “Enabling or Disabling the
Determination History System” earlier in this chapter), any of the following changes in an
existing Species record generates a new Determination History record for all linked
Specimen records:
Changing the Species Code.
Changing the Genus field. (Changing the Genus field in a Genus record also
generates a Determination History record. See “Changing a Determination in a
Genus Record” later in this chapter.)
Changing the specific name (Species Name) or the Species Author field.
Changing the Subspecies or the Subspecies Author field.
Changing the Variety or the Variety Author field.
Biota posts the following confirmation message:
Chapter 22 – Page 9
The “Where Changed” field in the Determination History record will read “Species Rec,”
to indicate where the change was made.
Changing a Determination in a Genus Record
If you have enabled the Determination History system (see “Enabling or Disabling the
Determination History System” earlier in this chapter), the following action generates a
Determination History record for each Specimen linked to a Genus record through any
Species record:
Changing the Genus field in a Genus record.
Biota posts a confirmation message:
After you click the “OK” button, the “Where Changed” field in the Determination History
record will read “Genus Rec.”
Changing a Determination Using the Synonymy Tool
Using the Synonymy tool, you can automatically reassign Specimen records to a
Species that has been declared a senior synonym (see Chapter 23, “Synonymy
System”), unlinking those records from the junior synonym you specify.
If you have enabled the Determination History system (see “Enabling or Disabling the
Determination History System” earlier in this chapter), this action generates a
Determination History record for each Specimen affected.
The “Where Changed” field in the Determination History record will read “Species Syn.”
Displaying, Editing, or Deleting Determination
History Records
Generally, the purpose of Determination History records is to keep a complete “audit
trail” for all actions that affect the identification of Specimen records, including errors and
corrections of errors.
Nonetheless, circumstances may arise that require editing or deletion of Determination
History records. This section describes the tools available in Biota for working with
existing Determination History records directly. The creation of new Determination
History records occurs only through the mechanisms described in the previous section.
Chapter 22 – Page 10
NOTE: If the User Password system has been activated (see Chapter 26, “Security:
Passwords and Access Privileges”), you must have Administration access privileges to
use the tools described in this section. If the User Password system has not been
activated, any user will have Administration privileges, by default, and may use these
tools.
To display all Determination History records,
choose “All Determination Histories” from the
Special menu.
To display the Determination History records
linked to the Specimen records in the active
Specimen Record Set, choose “Determination Histories for the Specimen Record
Set” from the Special menu (abbreviated “Det Hists for the Spcm Rec Set” in the
menu).
In either case, the records are displayed in a standard Biota Record Listing screen,
with columns arranged in the same way as in the special Determination History
Record Listing screen used to display Determination History records for an
individual Specimen Record.
The screen includes all the standard Record Listing screen buttons except for the “Add
Record” button (see “Using the Add Record Button” in Chapter 10). You can Sort the
records, Print them, Delete a Selection, or create a Sub-Selection.
Chapter 22 – Page 11
To display an individual Determination History record, double-click the
record. The record appears in the Determination History Input screen.
In this screen, you can edit any field except Specimen Code. (Editing the Specimen
Code field in a Determination History record could create an orphan Determination
History record, an action that would render the record useless.)
To create a Determination History Record Set or Record Set Pointer File, click
the “Done” button in the Determination History Record Listing screen and choose an
option in the standard Record Set option screen (see “The Record Set Options
Screen” in Chapter 3).
To display the current Determination History Record Set, choose “Display
Determination Histories” from the Special menu.
To Save or Load a Record Set Pointer File for Determination History records, use
the appropriate command from the File menu. See the note below.
To use the Query Editor to find Determination History records by their
content, choose “Using the Query Editor” from the Find menu (see “The Query
Editor, a General-Purpose Tool for Finding Records Based on Content” in Chapter
12). See the note below.
Note: If the User Password system has been activated (see Chapter 26, “Security:
Passwords and Access Privileges”), the Determination History table is accessible to the
“Save Record Set Pointer File” and “Load Record Set Pointer File” tools and the Query
Editor only for users with Administration access privileges.
Chapter 22 – Page 12
Importing and Exporting Determination History Records
Determination History records can be exported to text files using the “Export by Tables
and Fields” tool from the Im/Export menu. There are no special considerations; just
follow the general instructions in Chapter 27, “Exporting Data by Tables and Fields.”
Determination History records can be imported from text files using the Import by Tables
and Fields tool from the Im/Export menu. Be sure to consult the section “Importing Data
to Notes Tables or the Determination History Table” in Chapter 28.
Chapter 23
Synonymy System
The Synonymy system can help you keep track of synonymies among Species records.
If your work is in systematics, you can use the system to record historical
synonymies from the literature. The same system is easily used in managing your
own specimen data: you can update Species and linked Specimen records, in your
own active database, when you conclude that two groups of specimens are
conspecific. Biota keeps a record of the junior synonym by synonymizing—but
retaining—its original Species record.
With your confirmation, Biota automatically switches the links for Specimen records
from the junior synonym to the senior synonym. If you have activated the
Determination History system (see “Enabling or Disabling the Determination History
System” in Chapter 22), the switch is recorded for each Specimen.
In biotic surveys and inventories, Biota’s Synonymy system can be used to
resolve and document the “synonymies” that often arise in pooling two or more
temporarily determined groups of Specimens, when each group was initially
identified as representing a different Species (which may well have only a
temporary name in the Species Name field; see Chapter 25, “Temporary Taxa for
Approximate Determinations”).
If you determine that both groups of Specimens represent the same Species, the
Synonymy system can “move” all Specimens from one of the two Species to the
other instantaneously. If you have enabled the Determination History system (see
“Enabling or Disabling the Determination History System” in Chapter 22), Biota
documents the move for each Specimen affected.
Biota’s Synonymy system is not designed to handle all the complexities that arise under
the rules of nomenclature, nor does Biota have an explicit system for synonymies at
higher ranks. But it does well with the commonest case: simple synonymies at the
Species level.
How Biota Keeps Track of Species Synonymies
Biota uses Species Codes to uniquely identify each record in the Species table (the
section “Why Does Biota Require Species Codes?” in Chapter 8 explains how and why).
In addition to the Species Code field, however, each Species record has a separate field
called Valid Sp Code (for Valid Species Code; see Appendix A, “Biota Tables, Fields,
and Relational Links”).
In each new or imported Species record, the Valid Sp Code field is automatically
initialized with the same value as the Species Code—each Species record thus begins
life as a valid Species record, defined in Biota as any record in which the Valid Sp Code
is the same as the Species Code.
When you synonymize Species Z with Species Y, Species Z becomes a junior synonym
record and Species Y becomes the senior synonym record. Biota replaces the Valid Sp
Code in the record for the junior synonym (Species Z) with the Species Code of the
Chapter 23 – Page 2
senior synonym (Species Y). No change is made in the record of the senior synonym,
which remains a valid Species record.
NOTE: Unfortunately there is no agreement between different Codes of Nomenclature
regarding what to call Species Z and Y in the previous sentence. With apologies to those
to whom these terms sound non-standard, this Manual uses them consistently in senses
defined above.
Thus Biota recognizes junior synonyms by the presence of a Valid Sp Code that does
not match the Species Code. Of course, the Valid Sp Code need not be unique; several
Species records may share the same Valid Sp Code when there are several junior
synonyms of the same senior synonym.
Biota recognizes senior synonyms by searching for junior synonyms—that is, searching
for other Species records that carry the Species Code of the senior synonym in their
Valid Sp Code field.
To summarize, there are three proper kinds of Species records, with regard to the
Synonymy system:
Species X is a valid Species with no synonyms in the database if its Valid Sp
Code matches its own Species Code, but the Valid Sp Code of no other Species in
the database matches Species X’s Species Code.
Species Y is a valid Species and a senior synonym if its Valid Sp Code matches
its own Species Code, and the Valid Sp Code for at least one other Species in the
database matches Species Y’s Species Code.
Species Z is a junior synonym if its Valid Sp Code does not match its own
Species Code, but instead matches the Species Code of a valid Species in the
database.
In addition, there are two improper kinds of Species records, with regard to the
Synonymy system. Biota safeguards against the inadvertent creation of either of these
categories of junior synonyms, while permitting you to do so intentionally anyway, if you
wish.
Species A is an orphan junior synonym if its Valid Sp Code matches neither its
own Species Code nor the Species Code of any other Species in the database.
When you change the Species Code of a senior synonym, the Valid Sp Code of all
its junior synonyms is automatically updated to prevent this anomaly.
Species B is a compound junior synonym if its Valid Sp Code does not match its
own Species Code, but instead matches the Species Code of a junior synonym in
the database. When you synonymize a Species record that was previously a senior
synonym using the “Synonymize This Species” button, Biota automatically updates
the Valid Sp Code of its former junior synonyms to the Species Code of the new
senior synonym. If you wish to create compound synonyms, intentionally, to keep
track of historical changes in nomenclature, you can do so by entering manual
changes in Valid Sp Code.
Chapter 23 – Page 3
Displaying the Synonymy Status of a Species Record
Each Species record falls into one of the five categories outlined in the previous section
(“How Biota Keeps Track of Species Synonymies” earlier in this chapter). To display
complete information for a Species record, follow these steps.
1.
Display the Species record in the Species Input screen (see “Viewing, Editing,
Printing, or Deleting Individual Records from an Input Screen” in Chapter 10).
Valid Species Code entry area
Synonymy Status display
The Classification (main) tab of the Species Input screen includes a “Synonymy”
panel at the bottom of the screen that includes two elements:
The Valid Species Code entry area. Although the Synonymy system normally
takes care of assigning values to the Valid Sp Code field, you can change the
value manually in this entry area if necessary (for example, to correct an orphan
or compound synonym anomaly).
The Synonymy Status display. This line summarizes the Synonymy Status of
the Species record. The degree of detail depends on the setting of the “Show full
Synonymy Status in Species Input screen” checkbox in the Preferences screen.
See the section “The Synonymy Status display” later in this chapter.
Chapter 23 – Page 4
2.
To display full synonymy information for the current Species record, click the
Synonymy tab in the Species Input screen.
The Synonymy tab screen appears.
The synonymy screen displays complete synonymy information for the Species.
There are no data entry areas—the screen is used only for display and to create
new synonymies using the “Synonymize This Species” button in the lower-left
corner of the screen (see the section “Declaring a Species Junior Synonym and
Transferring Its Specimens,” later in this chapter).
To indicate the Synonymy Status of the current Species record, a check appears
next to one of the three alternatives, completing the statement:
“The name…” [Genus, Specific Name, Author, Species Code]…
“Is a valid Species name with no synonyms in the database.” This
alternative is illustrated above.
Chapter 23 – Page 5
“Is a valid Species name with the following junior synonyms in the
database,” followed by a scrollable list of junior synonyms. This alternative is
illustrated below.
“Is a junior synonym of…” [Genus, Specific Name, Author, Species Code].
This alternative is illustrated below for a proper junior synonym
Chapter 23 – Page 6
The three alternatives correspond to the three proper forms of Synonymy Status,
detailed the section “How Biota Keeps Track of Species Synonymies,” earlier in this
chapter. The next three steps explain what happens if a Species record falls into the
improper categories of orphan junior synonym or compound junior synonym, or if it
has compound junior synonyms linked to it.
3.
If the Species is an orphan junior synonym, the junior synonym alternative is
checked, but the message indicates orphan status.
4.
If the Species is a compound junior synonym, both the first and second
checkboxes are checked. The first has the special legend “…which is itself a junior
synonym of…” followed by the Valid Species Code for the record of which the
current record is a junior synonym. The second checkbox legend details the Valid
Species of which the “linking” species is a proper junior synonym.
Chapter 23 – Page 7
5.
If the Species itself is a proper junior synonym, but has one or more
compound junior synonyms linked to it, both the first and second checkboxes
are checked. The first has the special legend “…which itself has the following
compound junior synonym…” followed by a scrollable list of compound junior
synonyms. The second checkbox legend details the Valid Species of which the
species is a proper junior synonym.
The Synonymy Status display
The small “Synonymy” display area in the “Classification” (primary) tab of the Species
Input screen, the Synonymy Status display, shows the Synonymy Status for the current
Species record. The five possible status alternatives are discussed in the section “How
Biota Keeps Track of Species Synonymies,” earlier in this chapter.
The level of detail shown in the Synonymy Status display depends on whether or not the
“Show full Synonymy Status in Species Input screen” checkbox in the Preferences
screen has been checked and on whether or not you have already used the Synonymy
tab for the current Species record. The only advantage of leaving the Full Synonymy
checkbox unchecked (disabled—the default setting) is a slightly faster display of Species
records in the Species Input screen.
NOTE: If you use the Synonymy system, it is recommended that you enable the Full
Synonymy Display. The slight cost in display time is worth it.
Chapter 23 – Page 8
To Enable or Disable Full Synonymy Display
1.
From the Special menu, select Preferences. The Preferences screen appears.
2.
Click the “Other Settings” tab.
3.
Check or uncheck the box labeled “Show full Synonymy Status in Species Input
screen.” The default setting is unchecked, to allow faster display of Species records
in the Species Input screen.
4.
Click the “Save” button in the Preferences screen.
NOTE: To keep the setting between Biota sessions, click the “Admin Settings” tab (if
you have Administrative privileges) and select “Use these Preferences next time
Biota is launched.”
If Full Synonymy Display Is Not Enabled
If you have not enabled the Full Synonymy option (see “To Enable or Disable Full
Synonymy Display” earlier in this chapter), Biota makes a preliminary check of
Chapter 23 – Page 9
Synonymy Status of each Species record just before it is displayed in the Species Input
screen and reports accordingly in the Synonymy Status display area.
If the Valid Species Code matches the Species Code for the record, the
Synonymy Status display reads “A valid Species name. Click the Synonymy tab to
check for synonyms.”
If the Valid Species Code does not match the Species Code for the record, the
Synonymy Status display reads “A junior synonym. Click the Synonymy tab for
details.” The message is in red type, to alert you not to link Specimen records to a
junior synonym (unintentionally).
If Full Synonymy Display Is Enabled
If you have enabled the Full Synonymy option (see “To Enable or Disable Full Synonymy
Display” earlier in this chapter), Biota investigates the full Synonymy Status of each
Species record just before it is displayed in the Species Input screen and reports
accordingly in the Synonymy Status display area.
If the Valid Species Code matches the Species Code for the record and no
junior synonyms are found, the Synonymy Status display reads “A valid Species
name with no synonyms in the database.”
If the Valid Species Code matches the Species Code for the record and n
junior synonyms are found, the Synonymy Status display reads “A valid Species
name with n junior synonyms in the database.” (Three were found in the example
below).
Chapter 23 – Page 10
To display the full list of junior synonyms, click the Synonymy tab. (See “Displaying
the Synonymy Status of a Species Record.” earlier in this chapter.)
If the Valid Species Code does not match the Species Code for the record but
matches the Species Code of a valid Species, the Synonymy Status display
reads “A junior synonym of [full name of the senior synonym].” The message is in
red type, to alert you not to link Specimen records to a junior synonym
(unintentionally).
To display the full list of junior synonyms, click the Synonymy tab. (See “Displaying
the Synonymy Status of a Species Record.” earlier in this chapter.)
If the Species is an orphan synonym, the Synonymy Status display reads “An
orphan junior synonym.” The message is in red type, to alert you not to link
Specimen records to an orphan junior synonym and to highlight the need to correct
this anomaly.
For more information, click the Synonymy tab. (See “Displaying the Synonymy
Status of a Species Record.” earlier in this chapter.)
If the Species is a compound junior synonym, the Synonymy Status display
reads “A junior synonym of a junior synonym.” The message is in red type, to alert
you not to link Specimen records to a junior synonym and to highlight the need to
correct this anomaly.
For more information, click the Synonymy tab. (See “Displaying the Synonymy
Status of a Species Record.” earlier in this chapter.)
The Synonymy Display after Using the Synonymy Screen
Regardless of whether you have enabled the Full Synonymy option (see “To Enable or
Disable Full Synonymy Display,” earlier in this chapter), Biota investigates the complete
Synonymy Status of a Species record when you click the Synonymy tab. (See
“Displaying the Synonymy Status of a Species Record.” earlier in this chapter.)
Chapter 23 – Page 11
When you return to the Classification tab of the Species Input screen, Biota displays full
information on synonymy, as described in the preceding section (“If Full Synonymy
Display Is Enabled” earlier in this chapter).
Declaring a Species a Junior Synonym and Transferring
Its Specimens
In systematics, you may need to record that two species names are synonymous. In
survey or inventory work, you may conclude that two groups of specimens linked to
different temporary Species (morphospecies) records are, in fact, conspecific.
Biota makes it easy to synonymize two Species records. As explained in detail earlier in
this chapter (see “How Biota Keeps Track of Species Synonymies”), Biota keeps a
record of the junior synonym by synonymizing—but retaining—its original Species
record.
With your confirmation, Biota automatically switches the links for Specimen records from
the junior synonym to the senior synonym. If you have activated the Determination
History system (see “Enabling or Disabling the Determination History System” in Chapter
22), the switch will be recorded for each Specimen (see “Changing a Determination
Using the Synonymy Tool” in Chapter 22).
Here are the steps to take to synonymize one Species record with another:
1.
Display the Species record in the Species Input screen (see “Viewing, Editing,
Printing, or Deleting Individual Records from an Input Screen” in Chapter 10).
2.
Click the Synonymy tab in the Species
Input screen.
The Synonymy tab screen appears, with
a complete report on the Synonymy
Status of the Species record. (See “Displaying the Synonymy Status of a Species
Record,” earlier in this chapter, for details.)
3.
Click the “Synonymize This Species” button in the
bottom left corner of the Synonymy screen.
The standard “Look Up Species” screen
appears. (See “Entering Specimen Data:
The ‘General’ Tab” in Chapter 11 if you
need help with this tool.)
4.
Enter the Genus (or the first letters of the
Genus) of the Species with which the
current Species is to be synonymized,
then press TAB.
The scrolling list in the Look Up Species
tool displays all specific names (Species
Names) linked to the Genus.
Chapter 23 – Page 12
5.
Click the specific name of the valid Species (senior synonym) of which the
current Species is to be declared a junior synonym.
If the Species you clicked is a valid Species, and the Species to be
synonymized has no junior synonyms of its own, Biota posts the report
below. “The name… [Genus, Specific Name, Author, Species Code]…Will be
made a junior synonym of… [Genus, Specific Name, Author, Species Code].”
If the Species you clicked is a valid species, and the Species to be
synonymized has one or more junior synonyms of its own, Biota posts the
report below. The species to be synonymized and all its own junior synonyms will
be declared junior synonyms of the designated valid species.
Chapter 23 – Page 13
If you attempt to make a Species record a junior synonym of an existing
junior synonym (i.e., if you attempt to create a compound junior synonym),
Biota posts the following message:
6.
Accept or Cancel the proposed changes by
clicking the appropriate button (“Accept New
Synonymy” or “Cancel New Synonymy”) in the
Synonymy screen.
7.
If you clicked “Accept the New Synonymy” and the Species destined to
become a junior synonym has linked Specimen records, Biota offers to update
the Species Code in the Specimen records to match the Species Code of the senior
synonym.
If you choose “Update the [Specimen] Species Code…,” Biota “moves” the
Specimens from the junior synonym to the senior synonym, automatically, by
changing the [Specimen] Species Code field in the Specimen records.
If you choose “Do not update the Species Code…,” no change will be made
in any Specimen record. The Specimens linked to the junior synonym’s Species
record will remain linked to it.
Chapter 23 – Page 14
NOTE: If you have enabled the Determination History system, and you choose the
first option above, Biota records the change in Specimen determination for each
Specimen record that was “moved” to the senior synonym. See “Enabling or
Disabling the Determination History System” in Chapter 22.
8.
Select an option and click OK.
Clearing All Synonymies
You can undo any synonymy by setting the Valid Species Code equal to the Species
Code for an individual Species record. In addition, Biota offers a tool to do this for every
Species record in a Biota Data File, all at once.
1.
From the Special menu, choose “Clear All Synonymies.” A warning appears.
2.
Understanding that this action cannot be undone, click OK to confirm the
proposed action or Cancel to dismiss it.
NOTE: If the User Password system has been enabled (see Chapter 26, “Security:
Passwords and Access Privileges”), only a user with Administration access privileges
can use this command.
Displaying Specimen Records for Junior Synonyms
When you display the Species record for a senior synonym (a Valid Species record with
one or more junior synonyms in the Data File), you can use the “Specimens” button to
display not only all Specimen records linked to the Species record for the senior
synonym, but (as an option) all Specimen records linked to the Species records for its
junior synonyms as well. You must first enable the “Full Synonymy” option.
1.
In the Preferences screen (Special menu), enable the “Show full Synonymy
status in Species Input screen ” checkbox (see “To Enable or Disable Full
Synonymy Display” earlier in this chapter).
Chapter 23 – Page 15
2.
Display the Species record for a senior
synonym and click the “Show Specimens”
button. The number shown on the button
includes all linked Specimens, both those linked to the Species displayed (if any),
plus any Specimens linked to junior synonyms.
An option screen appears.
3.
Choose an option:
Either: “Display only the Specimen records linked to this Species record.”
Normally, if a Species record has no linked Specimens, the “Show Specimens”
button is not enabled, but if one or more junior synonyms has linked specimens,
it is enabled whether or not the valid Species has linked Specimens (if you have
enabled this feature).
If you select this option, and only the junior synonyms have linked Specimens,
Biota displays this message.
Or: “Display all Specimen records linked to this Species record or to its
junior synonym.”
4.
Click the “OK” button in the option screen. Biota displays the Specimen records in
a new window.
Chapter 23 – Page 16
Finding Valid Species, Species With Synonyms, or
Junior Synonym Records
Sometimes you may want to work only with valid Species, rather than both valid Species
and junior synonyms. Or, you might want to work only with senior synonyms (valid
species that have junior synonyms) or just with junior synonyms.
In the Find menu, Biota offers special tools to find
valid Species records (with or without junior
synonyms), valid Species with junior synonyms, and
junior synonym Species records.
1.
If you want to search within a Species Record Set, establish the Record Set first
(see “Record Sets” in Chapter 3).
2.
From the Find menu, choose one of these commands:
“Valid Species.” This category includes all species for which the Species Code
is identical to Valid Sp Code, whether or not a Species has any Junior
Synonyms.
“Species With Junior Synonyms.” This category includes all Species for which
the Species Code is identical to Valid Sp Code that have at least one Junior
Synonym.
“Junior Synonyms.” This category includes all species for which the Species
Code differs from the Valid Sp Code, whether or not the Valid Sp Code matches
the Species Code of a senior synonym.
Biota presents an option
screen. The opening
statement differs
appropriately depending on
the command you chose,
but the options are the
same for all three
commands. If the Species
Record Set is empty, Biota
will inform you.
3.
Choose an option and click OK. Biota displays the requested records in the
Species Record Listing screen.
NOTE: If you need to find all valid Species that have no junior synonyms:
a.
Choose the command “Valid Species” from the Find menu.
b.
Establish the Species found as a Record Set.
c.
Choose the command “Species With Junior Synonyms” from the Find menu.
d.
In the Record Set Options screen, click “More Choices” then “Subtract it from the
Species Record Set” (the difference operation).
Chapter 23 – Page 17
Finding Orphan Junior Synonym Records
An orphan junior synonym is a Species record for which the Valid Sp Code value is
either blank or does not match the Species Code for any Species record in the
database. The “Orphan Records” command in the Find menu (see “Finding Orphan
Records” in Chapter 12) offers a tool to find such records.
1.
From the Find menu, choose “Orphan Records.”
The “Find Orphan Records” selection screen appears.
2.
Click the popup and choose “Junior Synonym.”
3.
Click the “Find” button. Biota displays the requested records in the Species
Record Listing screen.
Chapter 24
Host-Guest Relations
In the web of life, biological interactions link one species with another in myriad patterns.
A relational database offers a natural way to document these links, enriching the
biological information you record about specimens or living individuals.
In addition, organs, tissues, or molecules derived from whole-organism specimens are
specimens in their own right and often require their own records, but these records
should be linked to the master record for the whole-organism specimen.
How Biota Handles Links Between Specimens
Biota uses a host–guest metaphor to express linkage between two Specimen records—
whether the “guest” is a welcome one or not. The relationship may be an interspecific
one, such as between a host and a parasite, pathogen, commensal, or mutualist
(guests); or between a food plant (host) and an herbivore (guest). Alternatively, the
relationship may be intraspecific, such as between a parent (host) and its several
offspring (guests). Using the same metaphor, organ, tissue, or molecular specimens are
considered “guests” of the individual organism to which they belonged—the host
specimen.
Structurally, Biota handles relationships between Specimen records through a recursive
(circular) relationship mediated by the Collection table (see Appendix A, “Biota Tables,
Fields, and Relational Links”). The justification is simple: the collection site for a guest
specimen is its host specimen. Thus, Host Specimen Code appears as a field in the
Collection table, as illustrated in the “Host Record” tab of the Collection Input screen
below. (The field is abbreviated Host Spcm Code in Biota’s internal structure.)
Chapter 24 – Page 2
Host–Guest Relations: An Example
Suppose, for example, that a caterpillar (the guest specimen) has been collected from its
food plant (the host specimen), and a Specimen record has been created for each.
To begin with, you link the Specimen record for the plant (the host Specimen record) to
an ordinary Collection record (the host Collection record) through the Collection Code
field, defining details of the collecting event (collector, date collected, etc.). Of course,
additional Specimen records, such as duplicate plant specimens, may be linked to the
same Collection record. These are simply the normal procedures for data entry (see
“Specimen Input” in Chapter 11).
To use Biota’s Host-Guest system, you then link the Specimen
record for the caterpillar (the guest Specimen record), however,
to a separate Collection record (the guest Collection record).
The guest Collection record includes the Specimen Code for the
host plant in the [Collection] Host Specimen Code field
(illustrated here). If Specimen records exist for additional guest
specimens collected from the same plant host, you would link
them to the same guest Collection record. These links are
depicted in the illustration that follows the next paragraph.
Host–guest relations are recursive in Biota. Most often, you will need to use only a single
level of host–guest relations, but you can link Specimen records recursively to any level
necessary. For each level in a recursive host–guest relationship, a guest Collection
record—distinct from the host Collection record—must be created. The illustration below
shows the Specimen and Collection records necessary to link the Specimen records for
two host–guest levels: (1) a host plant and its caterpillar “guests”; and (2) one of those
caterpillars, now as a host, and its parasitic wasp “guests.” (Only the linking fields are
shown.)
Collection Records
Specimen Records
Specimen Description
Collection Code: CollL
Specimen Code: SpcmA
Locality Code: LocX
Species Code: SpeciesS
Plant: Host of caterpillar
specimens SpcmB and SpcmC
Host Spcm Code: (None)
Collection Code: CollL
Collection Code: CollM
Specimen Code: SpcmB
Locality Code: LocX
Species Code: SpeciesT
Host Spcm Code: SpcmA
Collection Code: CollM
Specimen Code: SpcmC
Species Code: SpeciesU
Collection Code: CollM
Collection Code: CollN
Specimen Code: SpcmD
Locality Code: LocX
Species Code: SpeciesV
Host Spcm Code: SpcmC
Collection Code: CollN
Specimen Code: SpcmE
Species Code: SpeciesV
Collection Code: CollN
Caterpillar: Guest of plant
specimen SpcmA
Caterpillar: Guest of plant
specimen SpcmA
and Host of parasitic wasp
specimens SpcmD and SpcmE
Parasitic wasp: Guest of
caterpillar SpcmC
Parasitic wasp: Guest of
caterpillar SpcmC
Chapter 24 – Page 3
Notice that, at each level in this hypothetical example, guest Specimen records
potentially bear a many-to-one relationship with the guest Collection record, and thus
also with the host Specimen record. Specifically, two caterpillar specimens (SpcmB and
SpcmC) are linked to a single guest Collection record (CollM), and thus to a single plant
host Specimen record (Spcm A). Likewise, two wasp specimens (SpcmD and SpcmE)
are linked to a single guest Collection record (CollN), and thus to a single caterpillar host
Specimen record (SpcmC). Moreover, multiple guests of a single host need not be
conspecific. In the illustration, caterpillar SpcmB has been identified as a representative
of SpeciesT whereas caterpillar SpcmC belongs to SpeciesU.
Notice, also, that all three Collection records in the illustration are linked to the same
Locality record (LocX).
Recording Information in the Guest Collection Record
If the guest specimen was collected by the same person at the same time and place as
the host specimen, then most of the fields of the host Collection record can be repeated
in the guest Collection record. Biota offers a quick way to transfer this information (see
“Creating Guest Collection Records Automatically” later in this chapter). Even so, you
may wish to add details in the Site or Source fields specifying the precise collection site
or collection method for the guest specimen: “Reared from host pupa,” “Under bark of
the host tree,” “Recovered by washing leaves,” “Attached to the third gill arch,”
“Extracted by centrifugation,” or “Amplified by PCR.”
On the other hand, the guest specimen may have been collected or extracted from the
host specimen at a later date by a different person than the collector of the host
specimen. In this case the appropriate place to record this collection information is in the
guest Collection record. Collection data for the host can still be located, if needed, by
first following the link from the guest Collection record (Host Record tab) to the host
Specimen record. Then follow the link from the host Specimen record to the host
Collection record.
Host Information in Guest Specimen Labels and Printed Reports
As an option, Biota will include host information on printed locality labels for guest
Specimens. See Chapter 15, “Printing Labels,” especially the section on “Data Options.”
In printed reports for Specimen records, you can choose to include host information for
each guest Specimen record. See Chapter 14, “Printing Reports,” especially the section
on “Printing a Standard or Custom Report Based on the Records in a Record Listing
Screen.”
Creating a Host Specimen Link
As explained and illustrated in the section “Host–Guest Relations: An Example,” earlier
in this chapter, to link a guest Specimen record to a host Specimen record, you enter the
Host Specimen Code in the Collection record for the guest. Here are the steps to take.
1.
Display a Collection record in the Collection Input screen.
Either: Create a new guest Collection record. You can do this by selecting
Collection from the Input menu, by clicking the “New Collection” button on the
Collection output (record listing) screen, or “on the fly” from the Specimen Input
screen (with the guest Specimen record displayed). See “Specimen Input” in
Chapter 11.
Chapter 24 – Page 4
Or: Find and display the existing, linked guest Collection record from a
Specimen record. You can do this by clicking the “Show Collection Record”
button in the Collection panel of the Specimen Input screen with the guest
Specimen record displayed (see “Moving Up the Table Hierarchies from an Input
Screen: Parent Record Buttons” in Chapter 10), or by using tools from the Find
menu (see Chapter 12, “Finding and Updating Records”).
2.
Complete or update the fields of the Collection record, except for the Host
Specimen Code tab, following the instructions in the section “Collection Input” in
Chapter 11.
3.
Click the “Host Record” tab.
The Host Record tab screen appears.
4.
Enter the Host Specimen Code.
Either: Enter the Host Specimen Code manually. When you press TAB to
complete the entry, the Genus, Species Name (specific name), and Family for
the host Specimen should appear in the Host Specimen display area, as
illustrated below.
◊
If the information is correct, click the “Save” button in the Collection Input
screen. You are done; skip the rest of the steps in this section.
◊
If the host specimen information does not appear or is incorrect, you
have probably entered the wrong Specimen Code. Try the alternative method
below.
Chapter 24 – Page 5
Or: Click the “Look Up Host by Species” button in the Host Specimen Code
panel of the Collection Input screen (illustrated above). The Look Up Host by
Species window appears (left illustration below).
a. Enter a Genus, or the first letter or letters of a Genus and press TAB
(above left illustration). If a matching Genus record is found, all Species
records for the Genus appear in the scrollable area of the Lookup window
(above, upper right illustration). If more than one match is found, a list of
matches appears from which you can select the correct Genus (not illustrated
here.)
b. When you find the Species you want, click it (above, upper right
illustration). A list of all Specimen records for that Species will appear (above,
lower right illustration).
c. Click the host Specimen record in the scrollable list (above, lower right
illustration).
The information for the selected host Specimen record appears in the Host
Specimen Code panel in the guest Collection record.
d. If the information is correct, click the “Save” button in the Collection Input
screen.
Chapter 24 – Page 6
Creating Guest Collection Records Automatically
Commonly, most fields of a guest Collection record require the same values as the
corresponding fields in the linked host Collection record. For example, if a collector
removes and preserves ectoparasites from a host when the host is collected, or collects
herbivores and food plant vouchers at the same time and place, then the Locality Code,
Collected By, Date Collected, Coordinates, and perhaps other fields of the host and
guest Collection records will share the same values.
Biota takes advantage of this circumstance to offer a quick way to create guest
Collection records, using the corresponding host Collection records as templates. For
this reason, you must first have linked each host Specimen record to a host Collection
record (through the Collection Code field) before using this tool, although Biota will warn
you if you fail to create the appropriate links.
Creating Guest Collection Records Automatically: Step by Step
NOTE: If the User Password system has been enabled, only a user with Administration
access privileges can use this tool (see Chapter 26, “Security: Passwords and Access
Privileges”).
Here are the steps to take to create guest Collection records automatically, based on
information in host Specimen and host Collection records.
1.
In the Specimen Record Listing screen, display only the host Specimen
records that will be referenced by the guest Collection records that you want
to create. You can use any of the tools of the Find menu to find the host Specimen
records. If other Specimen records are also displayed, select the host Specimen
records and use the “Sub-Selection” button (see “Creating a Sub-Selection of
Records” in Chapter 10) to dismiss the other records.
2.
Make a note of how many host Specimen records are displayed.
3.
Click the “Done” button and declare the host Specimen records the current
Specimen Record Set. See “The Record Set Options Screen” in Chapter 3 if you
need help.
4.
If you wish to confirm that a host Collection record already exists for each
host Specimen record, follow the lettered steps below. (If you are reasonably
confident that each host Specimen is linked to a host Collection record, proceed
directly to Step 5, instead. Biota checks for missing links in any case.)
a. From the bottom of the Find menu, choose
“Orphan Records.”
The query screen for this tool appears.
Chapter 24 – Page 7
b. From the popup, choose “Specimen Colls.”
If any of the records in the (host) Specimen Record Set appear in the list of
orphan records, it means they lack a linked Collection record.
NOTE: If there are many orphan records to scan, you could use the Record Set
Options screen (“More Choices,” then “Make shared records the new Record
Set”) to find the offending records. (Make a Record Set Point file for the host
Specimen records first, to recover the set after this procedure.) See “The Record
Set Options Screen” and “Record Set Pointer Files” in Chapter 3
5.
From the Special menu, choose “Make Guest
Collection Records.”
An instruction and warning message appears.
6.
Click the “OK” button to proceed, or Cancel to dismiss the procedure. (Notice
that Cancel is the default button, for safety.) If you click OK, Biota creates one new
Chapter 24 – Page 8
guest Collection record based on each host Specimen record in the current
Specimen Record Set, with the following characteristics:
The Collection Code of the new guest Collection record is composed of the
Specimen Code of the host Specimen record, with the letter H appended.
The Host Specimen Code field of the guest Collection record contains the
Specimen Code of the host Specimen record.
All other fields of the guest Collection record have the same value as the
corresponding fields of the host Collection record.
The new guest Collection records are displayed in the Collection Record Listing
screen.
Creating Guest Collection Records Automatically: Error Messages
Two error messages may appear during the process of creating new guest Collection
records.
No host Collection record. For each Specimen record in the current Specimen
Record Set that is not linked to any Collection record (through the Collection Code
field) Biota displays the message shown
here.
Make a note of the Specimen Code. The
creation of other new guest Collection
records proceeds when you click the “OK”
button.
When the process is complete, create the
missing link for each Specimen record
flagged for this error, declare them the
current Specimen Record Set, then repeat
the steps in the previous section to create
guest Collection records based on the
Specimen records that were flagged.
Host Specimen Code already maximum length. If the Specimen Code for any
host Specimen is already 30 characters in length (the maximum length allowed),
you cannot use this tool to create a corresponding guest Specimen record because
there is no room to append the H. If the
Specimen Code is already 30 characters long
for a host Specimen record, Biota displays
the alert shown here, but proceeds with the
rest of the records.
In this circumstance, you will have to create a
guest Collection record manually. You can
use the existing host Collection record as a
template and the “Carry” button (see “Using
an Existing Record as a Template for a New
Record” in Chapter 10) to speed the process.
Chapter 24 – Page 9
Duplicate Key Error. If Biota attempts to create a new guest Collection record
using a Collection Code that matches the Collection Code for an existing Collection
record, you will receive the warning below.
Make a note of the Collection
Code. The creation of other
new guest Collection records
proceeds when you click the
“OK” button.
A Duplicate Key Error probably
means that the guest
Collection record you want to
create already exists, perhaps
because you have
inadvertently used this tool
with the same host Specimen
record previously. In this case,
just ignore the warning.
Finding Host and Guest Records
You can find linked host and guest records by following, one link at a time, the links
shown in the illustration in the section “Host–Guest Relations: An Example,” earlier in
this chapter. However, the Find menu provides four tools to help trace host–guest links
much more efficiently.
Finding Host Specimens and Host Collections
1.
If you want to base the search for host Specimen and host Collection records
on a certain group of Specimen records (or even just one host Specimen record),
find the Specimen records and declare them the current Specimen Record Set (see
“Record Sets” in Chapter 3).
2.
From the Find menu, choose “Host Specimens & Collections.” An option
window appears. (See the next step.)
3.
Choose a search option.
If the active Specimen Record Set is not empty, the search option window
offers two alternatives (below).
Chapter 24 – Page 10
◊
All Specimen records. If you choose this option (the default) Biota finds and
displays : (1) All Specimen records in the Data File for which the Specimen
Code appears in the Host Specimen Code field of any Collection record (all
host Specimen records) and (2) the Collection records linked to those
Specimen records through the Collection Code field (all host Collection
records).
◊
The current Specimen Record Set. If you choose this option Biota finds and
displays (1) all Specimen records in the current Specimen Record Set (which
may contain only a single record, if you wish) for which the Specimen Code
appears in the Host Specimen Code field of any Collection record (host
Specimen records) and (2) the Collection records linked to those Specimen
records through the Collection Code field (host Collection records).
If the active Specimen Record Set is empty, the search option window offers
only the first alternative (below). The second alternative is disabled.
4.
Click the “OK” button in the search option window to launch the search. When
the search is complete, Biota reports the results and offers three display options.
You can choose to display Specimen and Collection records, only the Specimen
records, or only the Collection records.
5.
Click the “OK” button to display the records. The records appear in the standard
Record Listing screen for each table. When you click the “Done” button in the
Record Listing screen, the usual Record Set options are made available (see “The
Record Set Options Screen” in Chapter 3).
Finding Guest Specimens and Guest Collections
1.
If you want to base the search for guest Specimen and guest Collection
records on a certain group of Specimen records (or even just one guest Specimen
record), find the Specimen records and declare them the current Specimen Record
Set (see “Record Sets” in Chapter 3).
2.
From the Find menu, choose “Guest Specimens & Collections.” An option
window appears. (See the next step.)
Chapter 24 – Page 11
3.
Choose a search option.
If the active Specimen Record Set is not empty, the search option window
offers two alternatives (below).
◊
All Specimen records. If you choose this option (the default), Biota finds and
displays (1) all Collection records in the Data File that have a non-blank value
in the Host Specimen Code field (guest Collection records) and (2) all
Specimen records linked to those Collection records through the Collection
Code field (guest Specimen records).
◊
The current Specimen Record Set. If you choose this option, Biota finds
and displays (1) all Collection records in the Data File that have a nonblank
value in the Host Specimen Code field (guest Collection records) and are
linked through the Collection Code field to a record in the current Specimen
Record Set, and (2) the Specimen records linked to those Collection records
through the Collection Code field (guest Specimen records).
If the active Specimen Record Set is empty, the search option window offers
only the first alternative. The second alternative is disabled.
4.
Click OK in the search option window to launch the search. When the search is
complete, Biota reports the results and offers three display options.
You can choose to display Specimen and Collection records, only the Specimen
records, or only the Collection records.
Chapter 24 – Page 12
5.
Click the “OK” button to display the records. The records appear in the standard
Record Listing screen for each table. When you click the “Done” button in the
Record Listing screen, the usual Record Set options are made available (see “The
Record Set Options Screen” in Chapter 3).
Finding Host Specimens for Guest Specimens
This tool finds the host Specimen record linked to the Specimen record for a guest or the
host Specimen records linked to a group of guest Specimen records.
1.
Create a Specimen Record Set for a guest Specimen record or records (see
“Record Sets” in Chapter 3). If you wish, you can first ensure that all the putative
guests are linked to host records by using the Guest Specimens and Collections
tool (see “Finding Guest Specimens and Guest Collections” earlier in this chapter).
2.
From the Find menu, choose “Host Spcms for Guest Spcms.” An explanatory
message appears.
3.
Click the “OK” button. Biota finds the Host Specimen records and displays them
in the Specimen Record Listing screen. When you click the “Done” button in the
Record Listing screen, the usual Record Set options are made available (see “The
Record Set Options Screen” in Chapter 3).
Finding Guest Specimens for Host Specimens
This tool finds the guest Specimen records linked to the Specimen record for a host or to
a group of host Specimen records.
1.
Create a Specimen Record Set for a host Specimen record or records (see
“Record Sets” in Chapter 3). If you wish, you can first ensure that all the putative
hosts are linked to guest records by using the Host Specimens and Collections tool
(see “Finding Host Specimens and Host Collections” earlier in this chapter).
Chapter 24 – Page 13
2.
From the Find menu, choose “Guest Spcms for Host Spcms.” An explanatory
message appears.
3.
Click the “OK” button. Biota finds the Guest Specimen records and displays them
in the Specimen Record Listing screen. When you click the “Done” button in the
Record Listing screen, the usual Record Set options are made available (see “The
Record Set Options Screen” in Chapter 3).
Chapter 25
Temporary Taxa for Approximate
Determinations
In virtually any study that involves new collections, many specimens will initially be
undetermined (unidentified) to the species level, particularly if you work with highly
diverse or poorly known taxa or with groups that are unfamiliar to you. Nonetheless, it is
often useful to record approximate identifications of specimens that can later be made
more precise as new information or authoritative determinations become available.
A natural (and familiar) way to provide an approximate identification is to identify a
specimen accurately at a higher taxonomic rank—”Drosophila sp.,” “drosophilid fly”
(Family Drosophilidae), “fly” (Order Diptera), or simply “insect” (Class Insecta). In fact,
not recording known, accurate determinations at higher ranks, when specific identities
are unknown, means a loss of potentially useful information that is already in hand.
The problem with recording approximate determinations in a relational database, like
Biota, is that records for higher taxa must be linked to Specimen records through the
appropriate records at all intervening ranks. Otherwise, the Specimen record remains an
orphan record (see “Linking Fields: Parent and Child Records” in Chapter 3), invisible to
searches based on higher ranks, even though the physical specimen may have been
identified accurately at a higher rank.
The easiest solution to this dilemma is to link any Specimen record that you have
identified as representing a higher taxon (a taxon at a rank above species) to the record
for that taxon through temporary taxon records at all intervening ranks. (The term refers
to the temporary nature of the specimen determination. Temporary taxon records
themselves need not be temporary.)
Biota’s Convention for Temporary Taxon Records
Biota uses a specific convention to indicate a temporary taxon: its name is
enclosed in parentheses.
Suppose, for example, that you have identified a particular plant specimen as a
composite—a member of the Family Asteraceae—but you do not know its genus and
specific name. Using Biota’s convention, you would link it to a Species record (with any
unique Species Code) for the Species “(Asteraceae)” (with the parentheses but without
the quotation marks). The Species record would be linked to a Genus record for the
Genus “(Asteraceae),” which, in turn, would be linked to the Family record for
“Asteraceae” (no parentheses, since this is indeed a family). Subsequently, you would
link all Specimen records identified only as members of the Family Asteraceae the same
temporary taxon record in the Species table: the Species “(Asteraceae).”
With this approach, if you set up the query “Find all Specimens of the Family
Asteraceae” in the “Lower Taxon for Higher Taxa” search tool (see “Finding Records for
Lower Taxa Based on Higher Taxa” in Chapter 12), for example, Biota would find and
display not only all Specimens fully determined to Species within Genera of the Family
Asteraceae, but also all Specimen records identified only as “(Asteraceae).”
Chapter 25 – Page 2
Automatic Creation of Temporary Taxon Records
If you decide to use Biota’s convention for temporary taxa (see the previous section in
this chapter, “Biota’s Convention for Temporary Taxon Records”), you need not create
the temporary taxon records one by one, although there is nothing wrong with that
approach. Biota offers an option for the automatic creation of temporary taxon records,
either by manual input or importing of higher taxon “master” records.
Enabling or Disabling Automatic Creation of Temporary Taxon Records
NOTE: If the User Password System has been activated (see Chapter 26, “Security:
Passwords and Access Privileges”), you must have Administration access privileges to
enable or disable the Determination History system.
1.
From the Special menu, select Preferences.
2.
Click on the “Admin Settings” tab.
The Admin Settings tab screen appears.
3.
To enable the automatic creation of temporary taxon records, click the
checkbox labeled “Generate Temporary Taxa automatically” to check it. To disable
this option, click the checkbox to uncheck it (illustrated above).
4.
Choose an option for saving any changes in Preference settings made during
this Biota session.
Chapter 25 – Page 3
If you want the changes to remain in force until altered regardless of how
many times Biota is launched in the meantime, choose the option “Use these
Preferences next time Biota is launched.”
If you want the changes to be in force only for this session, choose the
option “Reset Preferences to defaults next time Biota is launched.
The default setting for Determination Histories is unchecked (off).
5.
Click the “Save” button on the Preferences screen.
How Biota Creates Temporary Taxon Records
If you have enabled the automatic creation of temporary taxon records (see the previous
section in this chapter, “Enabling or Disabling Automatic Creation of Temporary Taxon
Records”), each time you create or import a new record for any of Biota’s taxon tables
above the rank of Species (Kingdom, Phylum, Class, Order, Family, or Genus), a
temporary taxon record is created automatically for all tables of lower rank, including
Species.
For example, if you create or import a new record in the Order table for (Asterales), Biota
immediately creates each of the following records, automatically:
Table
Key
Field
Key Field
Value
Linking
Field
Linking Field
Value
Family
Family
(Asterales)
Order
Asterales
Genus
Genus
(Asterales)
Family
(Asterales)
Species
Species Code
Aster001234
Genus
(Asterales)
Biota assigns a Species Code for the Species record (in the table above) automatically,
prefixing the first five characters of the taxon name (Aster, in this example) to a six-digit
integer based on the Species table sequence number (0001234 is just an example; see
“The Format of Automatically Generated Record Codes” in Chapter 8 for information on
sequence numbers). The Species Name field of the automatically created Species
record is also assigned the temporary taxon name—(Asterales) in this example.
NOTE: There is a second option for the format of automatically created Species Code for
temporary taxa for imported records. See the next section of this chapter, “Automatic
Creation of Temporary Taxon Records for Imported Records.”
If instead or in addition, you create or import a Family record for Asteraceae, Biota
automatically creates the following records:
Table
Key
Field
Key Field
Value
Linking
Field
Linking Field
Value
Genus
Genus
(Asteraceae)
Family
Asteraceae
Species
Species Code
Aster009946
Genus
(Asteraceae)
Chapter 25 – Page 4
The Species Name field of the automatically created Species record is also assigned the
temporary taxon name—(Asteraceae) in this example.
Automatic Creation of Temporary Taxon Records for Imported Records
For manually created records, if the Temporary Taxon option is enabled (see “Enabling
or Disabling Automatic Creation of Temporary Taxon Records” earlier in this chapter),
Biota simply creates the records without confirmation.
To create temporary taxon records for imported higher taxon records, take the following
steps.
1.
Enable automatic creation of temporary taxon records in the Preferences
screen (Special menu), following the instructions in the section “Enabling or
Disabling Automatic Creation of Temporary Taxon Records” earlier in this chapter.
2.
Prepare a delimited text file for importing taxon records (Genus or above),
following instructions in Chapter 28, “Importing Data by Tables and Fields.”
3.
From the Im/Export menu, choose “Import by Tables and Field.” The Import
Option screen appears.
4.
Choose “Import new records” or “Merge imported records” (the “Update
existing records” option does not create temporary taxon records) and click the “OK”
button.
Biota displays the Import Editor.
5.
Set up the Import Editor to import the higher taxon records (Genus, Family,
Order, Class, Phylum, or Kingdom), following the instructions in Chapter 28,
“Importing Data by Tables and Fields.”
6.
Click the “Import” button in the Import Editor to launch the import process.
Biota displays an option screen for the creation of
temporary taxon records (see next page).
Chapter 25 – Page 5
The upper pair of options allows you to confirm or suppress the automatic
creation of temporary taxon records for each imported record.
◊
“Create Temporary Taxon records at all lower ranks for each [higher
taxon] record imported.” The name of the taxonomic rank you are importing
(Family, in the example above) appears in the option text.
◊
“Do not create any Temporary Taxon records based on the imported
records.” If you choose not to create the temporary taxon records, the lower
pair of buttons is disabled.
The lower pair of options controls the format of Species Codes in automatically
created Species records. (You must choose to create temporary taxon records,
as explained above, to enable these options.)
5.
◊
“For Species Codes use the first 5 letters of the [higher taxon] name
plus the Sequence Number.” The name of the taxonomic rank you are
importing (Family, in the example above) appears in the option text. This is
the same format Biota uses for automatically created Species records based
on manually entered higher taxon records. See “How Biota Creates
Temporary Taxon Records” earlier in this chapter.
◊
“For Species Codes use the first 20 letters of the [higher taxon] name.”
This option provides more alphabetic information, but leaves less room for
long sequence numbers. (The maximum number of characters allowed in a
Species code is 30.)
Click the “OK” button to proceed with the import, under the settings you have
selected. Or, click the “Cancel” button to abort the import.
Eliminating Unused Temporary Taxon Records
If you leave the option for the automatic creation of temporary taxon records enabled
over a long period, you may discover that some of the temporary taxon records that
Biota has created are not needed to link undetermined Specimen records with higher
taxa.
You can find all currently unused temporary taxon records quite easily with the Childless
Records tool in the Find menu (“Finding Childless Records” in Chapter 12).
Chapter 25 – Page 6
1.
From the Find menu, choose “Childless Records.” A table selection screen
appears.
2.
From the popup, select “Species.”
3.
Click the “Find” button. Biota finds and displays childless Species records.
Depending on your Preference settings, Species records may already be sorted by
Genus + Species Name. If not, use the “Sort” button in the Species Record Listing
screen to order the records in this way (see “Sorting Records in Record Listing
Screens” in Chapter 10 if you need help) or reset the Preferences (“Sorting” tab) to
do so. Temporary taxon Species records, for which both Genus and Species begin
with “(“ (the left parenthesis character) should sort at (or near) the top of the list.
4.
Delete all childless temporary taxon Species records that you do not
anticipate using to link records for undetermined specimens.
5.
Repeat the process with the Genus table, then the Family table, and so on up the
taxonomic hierarchy.
Chapter 25 – Page 7
Temporary Taxa on Determination Labels
If you follow Biota’s parenthesis convention for temporary taxon names (see “Biota’s
Convention for Temporary Taxon Records” earlier in this chapter), you can decide
whether or not you want to print temporary taxon names on determination labels (see
Chapter 15, “Printing Labels” for general information on printing determination labels of
various kinds).
1.
From the Special menu, select Preferences.
2.
Click on the “Admin Settings” tab.
The Admin Settings tab screen appears.
3.
To enable or disable the printing of temporary taxa parentheses on
determination labels, click the checkbox labeled “Include Temporary Taxa
parentheses on determination lables” to check it. To disable this option, click the
checkbox to uncheck it (illustrated above).
Biota looks for an initial left parenthesis in specific names (Species Name), Genus
names, and Family names (if you have checked the data option to include Family
on the labels, see “Data Options” in Chapter 15), and includes or suppresses the
opening and closing parentheses according to the setting of this preference.
4.
Choose an option for saving any changes in Preference settings made during
this Biota session.
Chapter 25 – Page 8
If you want the changes to remain in force until altered regardless of how
many times Biota is launched in the meantime, choose the option “Use these
Preferences next time Biota is launched.”
If you want the changes to be in force only for this session, choose the
option “Reset Preferences to defaults next time Biota is launched.”
The default setting for Determination Histories is unchecked (off).
5.
Click the “Save” button on the Preferences screen.
Chapter 26
Security: Passwords and Access
Privileges
Biota offers an optional User Password system that can be configured to your needs.
You can use the Password Editor to set up a system of user passwords for yourself and
other users and assign each user individualized access privileges. Each user can
change his or her own password, but the Administrator has “Super User” privileges to
change any password or access privileges. (See “Using the Password Editor” later in
this chapter.)
If your database requires extra security, the Administrator can also activate an optional,
secure link between your active copy of Biota and one or more Data Files (see “Using
the Data File Password Link” later in this chapter).
For the highest level of security, running Biota4D under 4D Server in a secure room with
password-protected access from remote clients is recommended (see “If You Need High
Security,” later in this chapter).
Activating and Deactivating the User Password System
When you first launch a new copy of Biota from the distribution disks, the User Password
system is not activated. Biota opens without displaying the Password screen, shown
here. You may choose to leave the User Password system deactivated if you are the
only user or if you have confidence that no one else with access to your computer will
launch Biota and alter a Data File in unintended or undesirable ways.
The cue Biota looks for to activate or deactivate the User Password system is the
current password of the Administrator.
If the Administrator’s current password is the null string (no characters at all—not one or
more space characters), the User Password system is deactivated. Assigning any other
value to the Administrator’s password activates the User Password system. You can
deactivate the system at any time by reassigning the null string as the Administrator’s
password.
Chapter 26 – Page 2
Activating the User Password System
1.
If Biota is not already launched, launch Biota,
opening any Data File. (If Biota is already launched,
proceed to Step 2 instead.) You have been automatically
signed on as “Administrator.”
2.
From the Special menu in Biota, choose “Change
User Password.”
The “Enter new password” request window appears
(illustrated in the next step).
3.
Enter a password and click the “OK” button. The password may consist of up to 15
characters, including letters, numbers, and symbols.
WARNINGS:
a.
This will be the Administrator’s password—don’t forget it!
b.
Passwords are case sensitive. If you create a password that includes
uppercase and/or lowercase letters, you must always reproduce the case of
each letter precisely.
Biota responds by requesting the new password a second time (illustrated in the
next step).
4.
Enter the same password again, carefully repeating the case of each letter.
Click the “OK” button.
Chapter 26 – Page 3
If the two entries match, Biota confirms the new password.
If the two entries do not match, Biota posts the message below. Your “old
password” in this case is the null string (no characters at all) and the User
Password system remains inactivated. To activate the User Password system,
begin again with Step 2, above.
Deactivating the User Password System
1.
If Biota is not already launched, launch Biota with any Data File. (If Biota is
already launched, proceed to Step 2 instead.)
When the Password screen appears, enter the Administrator’s User Name and
the Administrator’s current password, then click the “Connect” button.
NOTE: “Administrator” is the User Name assigned to the database Administrator
when you first activate the User Password system. You can change the
Administrator’s User Name (see “Editing a User’s Password and Profile” later in
this chapter).
Chapter 26 – Page 4
WARNING: Passwords are case sensitive. If the password includes uppercase
and/or lowercase letters, you must reproduce the case of each letter precisely.
User Names are not case sensitive.
If the Password screen does not appear during the launch, the User Password
system has not been activated. Skip the rest of this section.
2.
From the Special menu in Biota, choose “Change User Password.” The
Password screen appears.
3.
Enter the Administrator’s User Name and the Administrator’s current
password (as shown in Step 1, above), then click the “Connect” button. If the
password is correct, the “Enter new password” request window appears (illustrated
in the next step).
4.
Enter nothing at all and click the “OK” button.
Biota responds by requesting the new “password” a second time (illustrated in the
next step).
5.
Again, enter nothing at all and click the “OK” button.
If the two null entries match, Biota confirms the “new password” (the null
string), indicated by two sets of double quotation marks, with no character
between them.
Chapter 26 – Page 5
If you made a mistake, Biota posts the message below. The old Administrator’s
password is still in force and the User Password system is still activated. To
deactivate the User Password system, begin again with Step 2, above.
Launching a Password-Protected Copy of Biota
If the User Password system has been activated, you must launch Biota by following
these steps.
1.
Double-click the Biota icon or application name (Or in Windows, select it from
the Programs menu.) The Password screen appears.
2.
Enter your User Name and press TAB. User Names are not case sensitive.
3.
Enter your user password and press TAB. Passwords are case sensitive. If the
password includes uppercase and/or lowercase letters, you must reproduce the
case of each letter precisely.
Chapter 26 – Page 6
If you want to open the same Biota Data File used the last time this copy of
Biota was launched, click the “Connect” button in the Password window.
If you want to open a different Biota Data File (or verify that the correct file will
be opened), hold down the ALT key (Windows) or the OPTION key (Macintosh)
while you click the “Connect” button in the Password window. Use the navigation
window to find the correct Data File.
Changing Your User Password
If the User Password system has been activated, any user can change his or her own
password at any time by following these steps.
1.
If Biota is not already launched, launch Biota with any Data File. (If Biota is
already launched, proceed to the next step.)
2.
From the Special menu in Biota, choose Change Password. The Password
screen appears.
3.
Enter your User Name and your current password, then click the “Connect”
button. If the password is correct, the “Enter new password” request window
appears.
WARNING: Passwords are case sensitive. If the password includes uppercase
and/or lowercase letters, you must reproduce the case of each letter precisely. User
Names are not case sensitive.
Chapter 26 – Page 7
4.
Enter the same password again, carefully repeating the case of each letter.
Click the “OK” button.
If the two entries match, Biota confirms the new password.
If the two entries do not match, Biota posts the message below. Your “old
password” in this case is the null string (no characters at all) and the User
Password system remains inactivated. To activate the User Password system,
begin again with Step 2, above.
Using the Password Editor
The Password Editor (an off-the-shelf 4th Dimension utility) is easy to use, once
mastered, but the interface is not particularly intuitive. You will probably save time by
reading or at least skimming this section before using the Password Editor.
NOTE: Once the User Password system has been activated, only the database
Administrator can access the Password Editor.
Chapter 26 – Page 8
Users, User Names, Passwords, Access Levels, and Privileges
Biota’s implementation of the 4th Dimension User Password system is built on several
key concepts.
A user record is an individual record in the User Password system. (The User
Password system is not an ordinary database table but, rather, an internal one that
is not accessible to Biota’s import and export tools.)
Each user record has an assigned User Name, password, and Access Level.
The User Name can be any name the Administrator assigns to the user record, up
to 30 characters, including letters, numbers, and symbols.
The password can consist of up to 15 characters, including letters, numbers, and
symbols.
WARNING: Passwords are case sensitive. If you create a password that includes
uppercase and/or lowercase letters, you must always reproduce the case of each
letter precisely.
The Access Level. Biota offers five Access Levels, each with its own set of
privileges. The privileges and Access Levels are outlined below and detailed in the
table that follows. To assign an Access Level to a user, you assign the user to an
Access Group that has those privileges.
◊
Super User. The database Administrator, only, is assigned to the “Super User”
Access Level, which allows the Administrator to use the Password Editor and
enable or disable the Data File Password Link (see “Using the Data File
Password Link” later in this chapter). The Administrator also has all the privileges
of the Administration level (below).
◊
Administration. Any user assigned to the “Administration” Access Level can
find, display, print, export, create, modify, delete, or import records; change
master settings; and use all the tools of the Special menu, with the exception of
Edit Password System and Edit Data File Password Link. Only the Administrator
can assign passwords and Access Levels using the Password Editor and enable
or disable the Data File Password Link (see “Using the Data File Password Link”
later in this chapter). Other users assigned to the Administration Access Level do
not have these privileges.
◊
Read Write Export. A user assigned to the “Read Write Export” Access Level
can find, display, print, export, create, modify, or delete records, change certain
settings in the Preferences screen, and change his or her own password. The
Administrator, or another user with Administration privileges, can set limits on the
number of records that can be deleted or created (see Appendix B, “Setting
Preferences”) by users with Read Write Export privileges.
◊
Read Export. A user assigned to the “Read Export” Access Level can find,
display, print, or export records, change certain settings in the Preferences
screen, and change his or her own password.
◊
Read Only. A user assigned to the “Read Only” Access Level can find and
display records, change certain settings in the Preferences screen, and change
his or her own password.
Chapter 26 – Page 9
Privilege
Find records
Display records
Change password
Print records, reports, & labels
Use all export tools
Create records
Modify records
Delete records
Set Preferences for:
Determination Histories,
Temporary Taxa, “Record
Changed By” display, Record
Deletion and Record Series
Creation limits
All other Preference settings
Use Import Editor
Web Server settings
Use Find & Replace tool
Set Field Value Defaults
Enable/Disable Choice Lists
Set Core Field Aliases
Set default Record Code
Prefixes
Use Maintenance Utilities
Create Guest Collection
Records automatically
Clear All Synonymies
Delete Images by Record Set
Find, modify, or delete
Determination Histories using
tools of the Special menu
Use the Password Editor; Set
the Data File Password Link
Add a Data File Segment
Enter/view Biota License Code
Super
User
Administration
Read Write
Export
Read
Export
Read
Only
Chapter 26 – Page 10
Opening and Closing the Password Editor
1.
Launch Biota and sign on as Administrator. If you are already signed on as a
different user, you need not quit Biota. Choose “Change Password” from the
Special menu and sign on as Administrator without shutting down Biota. Be sure to
reenter the Administrator’s password correctly if you use this trick.
NOTE: “Administrator” is the User Name assigned to the database Administrator
when you first activate the User Password system. You can change the
Administrator’s User Name (see “Editing a User’s Password and Profile” later in this
chapter).
WARNING: Passwords are case sensitive. If a password includes uppercase and/or
lowercase letters, you must reproduce the case of each letter precisely. User
Names are not case sensitive.
2.
From the Special menu, choose Edit Password System. The Password Editor
appears.
The Password Editor consists of four scrollable lists: the “Users” list, the “Belongs
To” list, the “Groups” list, and the “Members” list. When you first display the
Password Editor, the lower two list panels are blank.
The Password Editor has its own menu bar with a Passwords menu.
When you first activate the User Password system (see “Activating the
User Password system” earlier in this chapter), Biota offers a set of
generic User Names (e.g., Collaborator, Browser, etc.), in addition to
Administrator, as shown above. These default user records have
different access privileges and startup Language settings that you can
use as models. You can use the Password Editor to change these
entries to suit your own needs, or leave them as they stand.
Chapter 26 – Page 11
3.
To close the Password Editor and save any changes, click the close box in the
Password Editor window. (There is no Save or Close command in the menus.)
Editing a User's Password and Profile
1.
Open the Password Editor (see the previous section, "Opening and Closing the
Password Editor").
2.
Double-click a User Name in the Users list or select a User Name and choose
"Edit User" from the Passwords menu. The "User" screen appears.
In the "User" screen, you can assign or modify the following settings:
User Name. A User Name can include up to 30 characters, including letters,
numbers, and symbols.
◊
You can change any of the default User Names to suit your needs.
◊
You cannot delete user records themselves, although you can add
additional user records (see "Adding a New User Record" later in this
chapter).
WARNING: You may change the User Name for the Administrator. However, the
first record in the User Password system, and only that record, is permanently
assigned the privilege of access to the Password Editor and Data File Password
Link. Furthermore, the first record must be assigned to the Super User group to
activate these privileges (see "Users, User Names, Passwords, Access Levels,
and Privileges" earlier in this chapter).
Password. A password can include up to 15 characters, including letters,
numbers, and symbols.
◊
When you first activate the User Password system in Biota, each of the
default users has a nonsense password assigned, for safety's sake. You will
Chapter 26 – Page 12
need to replace the password for any of the default user records you want to
use.
◊
Once you assign a password, it will appear as a string of "lock" symbols in
the "User" screen, as shown above. If you are not sure about an existing
password (the user may have changed it), delete the characters and reenter
the correct password.
Startup procedure. Biota has two alternative startup procedures, StartupEnglish
(no spaces) and StartupSpanish (no spaces).
◊
If you assign StartupEnglish (no spaces) to a particular user, Biota displays
the English language version of all dialogue screens (instructions, options,
warnings, errors, and result reports) for that user, regardless of the saved
Language setting in the Preferences screen (Special menu) (See "The
'Language' Tab" in Appendix B.)
◊
If you assign StartupSpanish (no spaces) to a particular user, Biota
displays a Spanish language version of all dialogue screens (instructions,
options, warnings, errors, and result reports) that are accessible to users with
Read Write Export, Read Export, or Read Only privileges, regardless of the
saved Language setting in the Preferences screen (Special menu). Dialogue
screens accessible only to users with Administration access privileges are
displayed in English for all users. (The justification for this policy is the
Administrator needs to be able to read this manual, which is not available in
Spanish.) All menus are in English for all users.
◊
If you leave the "Startup procedure" blank, Biota displays dialogue
screens in English or Spanish, depending on the saved Language setting in
the Preferences screen. If no user is likely to change the Language setting in
the Preferences screen, you can leave the Startup procedure setting blank for
all users.
"Last use" and "Number of uses." These areas display usage statistics for the
user. You can delete the displayed value to reset the counters. (Oddly, the
counters are also editable, if you can think of some legitimate reason to edit
them.)
"Default owner of objects created by this user." This panel has no function in
a compiled application such as Biota. Ignore it.
3.
When the user profile is complete, click the "OK" button in the User screen to
record it.
4.
To close the Password Editor and save any changes, click the close box of the
Password Editor window. (There is no Close or Save command in the menus.)
Adding a New User Record
You can add as many new user records as necessary to the User Password system.
However, once a user record is added, it can be edited but cannot be deleted. (This
puzzling limitation is built into 4th Dimension.) Although user records require very little
additional memory, you may wish to "recycle" the existing user records by editing them,
before adding any new ones.
1.
Open the Password Editor (see "Opening and Closing the Password Editor,"
earlier in this chapter).
Chapter 26 – Page 13
2.
From the Password menu, choose “New User.” The User screen appears with a
temporary name for the new user.
3.
Follow the guidelines in the previous section (“Editing a User’s Password and
Profile”) to complete the new user record and close the Password Editor.
Assigning Users to and Removing Users from Access Groups
Access Levels (see “Users, User Names, Passwords, and Access Levels” earlier in this
chapter) are determined for individual users in the Users list by assigning users to
Access Groups. Biota has five preset Access Groups, each named for the Access Level
assigned to the group. These Access Groups appear in the Groups list when you open
the Password Editor.
1.
Open the Password Editor (see “Opening and Closing the Password Editor”
earlier in this chapter).
2.
Select a User Name in the Users list by clicking it once. The “Belongs to” list
shows the Access Group (or groups) to which the user currently belongs.
Chapter 26 – Page 14
In the example above, the User Named Collaborator belongs to the Read Write
Export Access Group.
The “Belongs to” list will be blank if the selected user has not been assigned to any
Access Group.
3.
To remove a user from an Access Group, follow these steps:
a. In the Users list, select (single-click) the user to verify which group or groups
the user belongs to (see Step 2, above).
b. In the Groups list, select (single-click) the Access Group from which you
wish to remove the user. The user’s name should appear in the Members list in
the lower right panel.
Notice that Collaborator is included in the Members list for the Read Write Export
group along with Colaborador and Administration—the Administration group.
(Groups that are members of other groups are shown in italics with a “doublehead” icon; see “Pitfalls to Beware and Features to Ignore in the Password
Editor” later in this chapter.)
c. Using the mouse, select the name of the user in the Members list and drag
it anywhere outside the Members list panel. In the illustration below, the user
called Collaborator is being removed from the Read Write Export group.
Chapter 26 – Page 15
When you release the mouse button, the user’s name disappears from the
Members list, and the Access Group name disappears from the “Belongs to” list.
“ Belongs t o” list
4.
Members list
To add a user to an Access Group, follow these steps:
a. In the Users list, select (single-click) the user to verify to which Access Group
or groups the user currently belongs (see Step 2, above). If the user belongs to
the wrong group, remove the user from the group using the technique in Step 3,
above, before proceeding.
NOTE: In Biota, since access privileges are strictly hierarchical, there is no point
in a user belonging to more than one Access Group (although the Password
Editor permits it).
b. Drag the user’s name from the Users list over the name of the group (in the
Groups list) to which you want to assign the user. In the illustration below, the
user called Collaborator is being dragged over the “Administration” Group name
in the Groups list.
c. When the correct Access Group name is highlighted, release the mouse
button (“drag and drop”).
Chapter 26 – Page 16
As shown below, the user’s name now appears in the Members list, along with all
other members of the group. The name of the Access Group now appears in the
“Belongs to” list.
d. To close the Password Editor and save any changes, click the close box of
the Password Editor window. (There is no Close or Save command in the
menus.)
Pitfalls to Beware and Features to Ignore in the Password Editor
The Password Editor and its Password menu include a number of features that have no
application in Biota. This section of the chapter is intended to warn against certain
changes and satisfy the curious.
If you double-click the name of a group or select “Edit Group” from the
Password menu, an “Edit group” window appears, in which you can change the
name of the group. Do not change the name of Biota’s preset Access Groups, or
the access restrictions will not work. Biota looks for these particular group names in
order to limit access appropriately. There is absolutely nothing useful you can do
with the Edit Group tool.
Do not change the hierarchical (italicized) group memberships for higher
Access Groups (although the Password Editor permits it). Specifically, the Super
User group must remain a member of the Administration group, the Administration
group must remain a member of the Read Write Export group, and the Read Write
Export group must remain a member of the Read Export group for the hierarchical
privilege system to work.
If you accidentally change these settings, drag the appropriate group name in the
Groups list and drop it on the name of the group (also in the Groups list) of which it
should be a member, to recreate the hierarchy—or install a fresh copy of Biota from
the distribution CD or online source.
If you select the “New Group” command from the Password menu, a new
group icon will appear in the Groups list. The Password Editor does not allow you to
remove groups, once created.
Chapter 26 – Page 17
You can use this command to create your own groups, if you can think of a
reason to do so.
The “Save Groups,” “Load Groups,” and “External Package Access”
commands in the Password menu have no function in Biota.
Moving User Names, User Passwords and Access
Group Assignments to a New Copy of Biota
For security reasons, the User Password system is part of the Biota application itself, not
a component of Biota Data Files. If you have set up a custom list of User Names,
passwords, and Access Group assignments, and you need to install a fresh copy or a
new version of Biota, you will have to move the information to the new copy manually.
Here is a suggested strategy:
1.
Launch the old copy or old version of Biota (sign on as the Administrator).
2.
Open the Password Editor (see “Opening and Closing the Password Editor”
earlier in this chapter).
3.
Copy down the list of User Names (or, better, use the screen capture utility in
your operating system to copy it and paste it in a document). You can expand the
Password Editor window as large as your monitor screen permits.
4.
Select each user, one at a time, and record his or her group membership from
the “Belongs to” list.
5.
Double-click each user, one at a time, and record his or her Startup
procedure, if any.
6.
Quit the old copy or version of Biota and launch the new one.
7.
Recreate the password and access scheme in the new version, based on your
notes or screen captures.
Using the Data File Password Link
The User Password system protects your copy of the Biota application from
unauthorized use, as detailed in the previous sections of this chapter. By assigning
access privileges to each user, authorized users can be restricted to activities
appropriate to their training and responsibilities (see “Assigning Users to and Removing
Users from Access Groups” earlier in this chapter). The password and User Access
system, however, does not in itself protect Biota Data Files from unintended or
unauthorized access, which could occur by means of the unauthorized or accidental
installation of an unprotected copy of Biota.
You can create a secure link between a particular copy of Biota and a particular Data
File (or Files) using a Data File Password Link, as detailed below. You need not activate
the User Password system in order to activate the Data File Password Link, although it
usually makes sense to activate the User Password system if the Data File Password
Link is used. (The two systems are technically independent.)
Here’s how the Data File Password functions:
New Biota Data Files do not have the Data File Password Link activated.
Chapter 26 – Page 18
Any Biota Data File that has not had the Data File Password Link activated can
be opened by any copy of Biota. (If the User Password system has been activated,
however, the user must have a valid User Name and password to launch Biota.
Such a user is referred to, below, as an authorized user.)
Once you activate the Data File Password Link for a particular Data File (see
“Activating the Data File Password Link” later in this chapter), the copy of Biota that
you used to activate the Link opens that particular Data File without requiring
authorized users to enter the Data File Password.
If you use a fresh copy or a new version of Biota to open a protected Data File,
Biota will request the Data File Password at startup (see “Opening a PasswordProtected Data File with a New Copy or New Version of Biota” later in this chapter).
◊
If the correct Data File Password is entered, that copy of Biota will open the
file thereafter without requiring authorized users to enter the Data File Password.
◊
If the correct password is not entered (in up to three attempts), Biota quits
without opening the Data File.
If you assign the same Data File Password to more than one Data File, using
the same copy of Biota, all such files will open for any authorized user, without
requesting the Data File Password.
Activating the Data File Password Link
When you create an empty Biota Data File (see “Creating an Empty Biota Data File
While Launching Biota” in Chapter 3), the Data File Password in the Data File is blank (a
null string); the file can be opened with any copy of Biota. (If the User Password system
has been activated, you must have a valid User Name and password to launch Biota,
however.)
To activate the Data File Password Link, take these steps:
1.
Launch Biota.
If the User Password system has been activated, sign on as “Administrator”
(or with the alternative User Name you have given the user with Super User
privileges).
If the Password screen does not appear when you launch Biota, the User
Password system has not been activated. You are automatically signed on as
Administrator.
If you are already signed on as a different user, you need not quit Biota.
Choose “Change Password” from the Special menu and sign on as Administrator
without shutting down Biota. Be sure to reenter the Administrator’s password
correctly if you use this trick.
Chapter 26 – Page 19
NOTES:
2.
a.
“Administrator” is the User Name assigned to the database Administrator when
you first activate the User Password system. You can change the
Administrator’s User Name (see “Editing a User’s Password and Profile” earlier
in this chapter).
b.
You need not activate the User Password system in order to activate the Data
File Password Link. The two systems are functionally independent.
From the Special menu, choose “Edit Data File Password Link.”
If the Data File Password Link has not been activated, this message appears:
Continue with the next step in this section.
If the Data File Password Link has already been activated, this message
appears instead:
Go to the next section of this chapter, “Changing the Data File Password.”
3.
Click the “OK” button in the message window. A password request window
appears (illustrated in the next step).
Chapter 26 – Page 20
4.
Enter the new Data File Password (below) and click the “OK” button. The
password can consist of up to 15 characters, including letters, numbers, and
symbols.
You will need this password to open the Data File if you install a fresh copy or a
new version of Biota, or if you need to change the Data File Password—don’t forget
it!
Warning: Data File Passwords are case sensitive. If you create a Data File
Password that includes uppercase and/or lowercase letters, you must always
reproduce the case of each letter precisely.
Biota responds by requesting the new password a second time (illustrated in the
next step).
5.
Enter the same password again, carefully repeating the case of each letter. Click
the “OK” button.
If the two entries match, Biota confirms the new password and warns you not to
forget it.
Chapter 26 – Page 21
If the two entries do not match, Biota posts the message below. The Data File
Password Link remains inactivated. To activate it, begin again with Step 2, above
in this section.
6.
Click the “OK” button in the message window.
Changing the Data File Password
To change the password for the Data File Password Link, take these steps:
1.
Launch Biota. If the User Password system has been activated, sign on as
“Administrator” (or with the alternative User Name you have given the user with
Super User privileges). See Step 1 in the previous section “Activating the Data File
Password Link,” earlier in this chapter, for details.
2.
From the Special menu, choose “Edit Data File Password Link.”
If the Data File Password Link has been activated, this message appears:
Continue with the next step in this section.
If the Data File Password Link has not been activated, this message appears
instead:
Chapter 26 – Page 22
Go to the previous section of this chapter, “Activating the Data File Password
Link.”
3.
Click the “OK” button in the message window. A password window appears,
requesting the current Data File Password.
4.
Enter the current Data File Password and click the “OK” button.
WARNING: Data File Passwords are case sensitive. If the Data File Password
includes uppercase and/or lowercase letters, you must reproduce the case of each
letter precisely.
If you enter the correct password, Biota requests the new Data File Password.
See Step 4 in the section “Activating the Data File Password Link,” earlier in this
chapter, for instructions on completing the process of entering the new password.
If you do not enter the correct password, Biota posts this message:
Chapter 26 – Page 23
Deactivating the Data File Password Link
To deactivate the Data File Password Link, take these steps:
1.
Follow Steps 1 through 4 in the previous section, “Changing the Data File
Password.”
2.
When Biota requests the new Data File Password, enter nothing at all and
click the “OK” button.
Biota responds by requesting the new “password” a second time (illustrated in the
next step).
3.
Again, enter nothing at all and click the “OK” button.
If the two null entries match, Biota
confirms the deactivation of the Data
File Password Link.
If you made a mistake, Biota posts
the message to the right. The old
Data File Password is still in force
and the Data File Password Link is
still activated. To deactivate the link,
begin again with Step 1, above in
this section.
Chapter 26 – Page 24
Opening a Password-Protected Data File with a New Copy or
New Version of Biota
To open a password-protected Data File with a new copy or a new version of Biota, take
these steps.
1.
Launch the new copy or new version of Biota, finding and opening the existing
Data File as detailed in the section “Opening a Biota Data File When Launching
Biota” in Chapter 3.
If the Data File is protected by a Data File Password Link, the following request will
appear near the end of the startup process:
2.
Enter the Data File Password and click the “OK” button.
WARNING: Data File Passwords are case sensitive. If the Data File Password
includes uppercase and/or lowercase letters, you must reproduce the case of each
letter precisely.
You have three chances to enter the correct Data File Password.
If you enter the correct password,
Biota completes the startup process.
This copy of Biota is now authorized to
open this particular Data File in the
future, without requesting the Data File
Password.
If you do not enter the correct
password in three attempts, Biota
posts the message on the right and
shuts down.
Chapter 26 – Page 25
Using the Data File Password Link with Backup Files
One motivation for implementing a Data File Password Link is to guard against wellintended but mistaken use of the wrong Data File. Backup copies of Data Files are
particularly easy to confuse with the active copy of the same file.
Of course you should always make regular backups of any actively used Biota Data File,
using a clear naming convention for the backup files (see Appendix I, “Data File Backup,
Recovery, Compacting, and Segmenting”).
If you decide to use the Data File Password Link, consider changing the Data File
Password (see “Changing the Data File Password” earlier in this chapter) in each
backup, using the same naming convention for the Data File Password that you use for
the file name, so you can open the backups later if necessary. With this strategy, the
Data File Password for the active Data File remains constant and each backup has a
distinct Data File Password that you can remember easily, should it ever be needed.
If You Need High Security
The User Password system and Data File Password Link features of Biota are designed
to prevent accidental damage to your database through carelessness, ignorance, or
foolishness. A clever hacker can break into any file to which he or she has direct access,
including Biota Data Files. Of course, a hacker with direct access to the machine that
holds your database can find a way to copy any file in its entirety anyway.
If your database requires the highest level of security (if it includes collection or
incidence localities for endangered species of commercial value, for example), you
should not rely on software tools, alone, for security. Instead, run Biota4D under 4D
Server (Appendix E) in a physically secure room, and allow access to your database
only through 4D Client on remote machines, with the User Password system enabled. All
authentication of passwords is done by Biota4D on the Server, and the Data File itself
resides only on the Server. There is no data caching on Client machines between Biota
sessions. This is not an inexpensive solution, but good security is rarely cheap.
PART
7
Exporting and
Importing Data
Chapter 27
Exporting Data
Any database that cannot easily export any required set of fields and records in digital
form is likely to become a La Brea tarpit of extinct information. Biota has been designed
for maximum longevity for your data. There is nothing you can put into a Biota Data File
that you cannot later export to files that can be opened, read, and edited by text
processors, spreadsheet applications, database management applications, or image
processing applications.
General purpose export tools described in this chapter
◊
Biota’s Export Editor (see “Exporting Data by Tables and Fields” later in this
chapter) makes it easy to control the scope and format of any text data you need
to export from individual Biota tables to plain text flatfiles. (A flatfile is a row-bycolumn table of records and fields.)
◊
The Quick Report Editor (a 4th Dimension utility) offers an alternative way to
create your own, custom export format, by using fields from several tables at
once (see “Exporting Custom Flatfiles” later in this chapter). With the Quick
Report Editor, you can save the format, as well as exported text files, to disk.
Special purpose export tools described in this chapter
◊
Tools for exporting Notes. See “Exporting Notes” later in this chapter.
◊
A tool for exporting Taxonomic Flatfiles that show the taxonomic classification
for any selection of taxa. See “Exporting Taxonomic Flatfiles” later in this
chapter).
◊
A tool for exporting Specimen-based flatfiles, including virtually any field in
any Biota table. See “Exporting Specimen Flatfiles” later in this chapter.
◊
A tool for exporting formatted text for “Specimens Examined” (or
“Exsiccatae”) sections of taxonomic monographs. See “Exporting Specimens
Examined Lists for Publications” later in this chapter.
◊
A tool for exporting incidence or abundance matrices for input to ordination
and other statistical procedures. See “Exporting Place- by-Taxon Incidence or
Abundance Tables” later in this chapter.
Special purpose export tools described in other chapters
◊
Tools for exporting Images in individual or batch mode. See “Exporting and
Importing Images” in Chapter 19.
Chapter 27– Page 2
◊
Tools for exporting Auxiliary Fields. See “Exporting Auxiliary Field Values” in
Chapter 16.
◊
Tools for exporting References. See “Exporting References” in Chapter 20.
◊
,
A tool for exporting
NEXUS matrices (created. in Biota Auxiliary Fields) for
input to MacClade, PAUP, or other applications See “Exporting Auxiliary Fields in
the NEXUS Format” in Chapter 16.
◊
A tool for exporting hyperlinked static Web pages for any selection of records
and taxonomic scope, including Images and host-guest links. See Chapter 33,
“Exporting Static Web Pages.”
NOTE: Exporting data from a Biota Data File has no effect on the records in the file. A
copy of the data is exported to a text file, leaving the records themselves unaltered.
Exporting Data by Tables and Fields
Biota’s Export Editor (“Export by Tables and Fields,” from the Im/Export menu), can
export data to disk files from any Biota table, one table at a time (see Appendix A, “Biota
Tables, Fields, and Relational Links”). If you need to combine fields from several Biota
tables in an export file, use a different export tool (see the overview of export tools at the
beginning of this chapter).
The Export Editor creates free-format, delimited text (ASCII) files, such as the columnby-row, plain text files you can read and create with a spreadsheet application (e.g.,
Microsoft Excel), or import as text flatfiles to database management applications (e.g.,
SQL Server, Access, FileMaker, or 4th Dimension) or Geographic Information Systems
(GIS) applications.
Text files created by the Export Editor can be read in unaltered form by Biota’s Import
Editor (see Chapter 28, “Importing Data”), making it easy to move records from one
Biota Data File to another (see Appendix G, “Merging Two Biota Data Files”).
The Export Editor is designed to make exporting data flexible and easy. You choose a
Biota table to export from, and then choose which of its fields you want to export and
which records to export. You have complete control over the number and order of fields
in text files you create by exporting data, which need not match the number or order of
fields in the Biota source table. You can specify your choice of field and record delimiters
for the text file. If you wish, Biota can create column headings for the text file, based on
Biota field names.
NOTE: Although you may assign any character you wish as a record delimiter (see
“Exporting by Tables and Fields: Step by Step” later in this chapter), this section
assumes that you are exporting tab-delimited text files (using a line end character or
characters: ASCII Character 13 for Macintosh, ASCI 13 + 10 for Windows), so that Biota
records become table rows, and Biota fields become table columns in the exported text
file.
Chapter 27– Page 3
Key Fields
Most of the tables in Biota’s structure (see Appendix A, “Biota Tables, Fields, and
Relational Links”) have a Key field (Record Code, taxon name, etc.; see “Key Fields” in
Chapter 3) that contains a unique value for each record. The exceptions are the Notes
tables and the Determination History table, which do not require a unique Key (the
“Record Code” fields in these child tables are “foreign keys” that need not be unique),
and the Auxiliary Field Value and Reference Links tables, which have a two-field
(composite) Key.
Generally speaking, you will need to include the Key field, if there is one, among the
fields to be exported, so you can tell records apart in the text file that may be otherwise
identical. The Key field must be included (for any table that has one) if you intend later to
use the Import Editor to import text files into another Biota Data File (see Chapter 28,
“Importing Data”).
Field Types and Field Lengths
Appendix A (“Biota Tables, Fields, and Relational Links”) shows the field type and field
length (maximum number of characters) for each field in the Biota data structure. When
you export data from a Biota field, the exported data will reflect the type (and length) of
the Biota field it represents, as detailed below.
Alphanumeric fields. A value exported from an alphanumeric field may include any
ASCII characters. Biota exports only what it finds in an alphanumeric field without
adding trailing space characters. (In other words, Biota exports free-format fields,
not fixed-length fields.) For a particular alphanumeric field, the number of characters
exported will vary from none (if there was no entry in that field for a particular
record) to the maximum indicated for the field in Appendix A. If a field to be
exported is blank in a record, Biota nonetheless exports the field delimiter character,
so that columns in the exported file will be correctly aligned.
Date fields. Before exporting dates, please read or review the “Dates” in Chapter 9.
Whenever you select a Date field, using the Export Editor, Biota offers you a choice
of three standard date formats
for the export.
If you want exported dates in
some other format, you must
convert them after export.
Spreadsheet applications (e.g.,
Microsoft Excel) can easily
convert columns of dates from
the International or U.S. date
output formats to any other
format, by applying format
commands for date columns in
the spreadsheet.
Partial Dates: Date Flag fields. As explained in full in “Importing and Exporting
Partial Dates” in Chapter 9, for some date fields, Biota can display and print partial
dates: Month-Year dates and Year-only dates. These fields are [Collection] Date
Collected, [Collection] Date Coll End, [Specimen] Date Prepared, and [Specimen]
Date Determined. Each of these Date fields is paired with an integer Date Flag field
(Appendix A, “Biota Tables, Fields, and Relational Links”).
Chapter 27– Page 4
If you are exporting complete dates only, you need not export any values for Date
Flag fields, which have the value 0 (zero) for complete dates.
If you need to export partial dates, you should include the corresponding Date Flag
field along with the Date field in the list of fields to be exported. In the text file
produced by the Export Editor, you can then decode partial dates, as follows:
◊
Month-year dates. For a month-year date (e.g., May 1975), the Date field
itself will be exported as a complete date. The corresponding Date Flag field
will contain a “1,” the code for a month-year date. The value of the Day
element in the Date field of month-year dates is arbitrary. If the records were
created in Biota, however, Biota’s own convention will have been applied: the
first day of the month (e.g., May 1, 1975 for May 1975).
◊
Year-only dates. For year-only dates (e.g., 1975), the Date field itself will be
exported as a complete date. The corresponding Date Flag field will contain a
“2,” the code for a year-only date. The values of the Day and Month elements
in the Date field of year-only dates are arbitrary. If Biota created the records,
however, Biota’s own convention will have been applied: the last day of the
year (December 31, 1975 for 1975).
Latitude and Longitude fields. These two fields in the Locality table are of type
Real. Regardless of the coordinate display setting in the Preferences screen (see
“Setting the Display Format and Internal Resolution for Latitude and Longitude” in
Chapter 9), Latitude and Longitude are exported by the Export Editor in decimal
degrees, the standard for GIS, using the GIS conventions for hemispheres:
◊
North and East are positive values.
◊
South and West are negative values.
After export, you can convert decimal degrees to traditional Degree-Minute-Second
coordinates or to Degrees and Decimal Minutes (used by some GPS devices) by
the formulas detailed in the section “Conversion Formulas for Latitude and
Longitude Unit Systems” in Chapter 9.
Text fields. Biota uses text fields for the “Locality Name” field in the Locality table,
for the “Note” and “Heading” fields of the Project table, for several fields in the
Reference table, for the “Notes” field in the Personnel table, for the “Description”
field of the Loans table, and for the “Note Text” fields of Notes tables. A text field
may contain up to 32,000 characters.
Boolean fields. Boolean fields have one of two values: True or False. In an
exported text file, a Boolean field will have either a zero (for False) or a 1 (for True).
There are only 3 Boolean fields in Biota:
◊
The “Group” field in the Personnel table which, when True, identifies a
Personnel record as a Group Name record, rather than an Individual record.
The Group field has the value False for an individual (see “Entering
Personnel Data: The ‘Group’ Tab” in Chapter 11).
◊
The “Project” field in the Personnel table which, when True, identifies a
Personnel record as a Project-Linked record, rather than an Individual record.
(See “Personnel Input” in Chapter 11).
◊
The “Active” field in the Project table which, when True, identifies a
Project record as the Active Project record (there is only one Active Project at
any given time). See “Project Input” in Chapter 16.
Picture field. You cannot export the “Picture” (Image) field in the Image Archive
table using the Export Editor (although you can use it to export the alphanumeric
Chapter 27– Page 5
fields in the Image Archive table). Images can be exported to disk files using other
Biota tools. See “Exporting and Importing Images” in Chapter 19.
Exporting by Tables and Fields: Step by Step
Follow these steps to export records from a Biota Data File using the Export Editor. This
tool exports the fields and records you choose, for one Biota table at a time.
1.
Choose Export by Tables and Fields from the Im/Export menu. The Export Editor
appears.
2.
Select a table. From the “Table Name” popup list at the upper left, select the name
of the Biota table from which you want to export records (see Appendix A, “Biota
Tables, Fields, and Relational Links”).
Chapter 27– Page 6
3. Select the records for export. The three option buttons in the upper-right panel
define your options for selecting records for export. Once you choose a table from
the popup list, the words Table Name in the button text are replaced by the name of
the table you selected (“Collection” in this example).
Export the [Table Name] Record Set. This option is enabled if the table you
choose is a Core table (see “Core Tables” in Chapter 3) or the Determination
History table (see Chapter 22, “Determination Histories”), and you have
previously defined a current Record Set for the table (see “Record Sets” in
Chapter 3).
If you choose this option (when it is enabled), values for the fields you choose
(field choice is described in a later step in this section) will be exported for each
record in the current Record Set when you launch the export.
The button is disabled under two circumstances:
◊
If you select a Peripheral table other than Det History.
◊
If you select a Core table or the Determination History table, but the
current Record Set for the table is empty. In this case, Biota posts the
message illustrated below.
Export all [Table Name] records. This option is available for all tables. If you
click this button, values for the fields you choose (in a later step in this section)
will be exported for all records in the table when you launch the export.
Select [Table Name] records using the Query Editor. This option is available
for all tables except for the Lists table, from which all records must be exported
(see “Transferring Choice Lists to a Different Biota Data File” in Chapter 17). If
you choose this button, the “Launch Query Editor” button is activated.
Chapter 27– Page 7
When you click the “Launch Query Editor” button (above), the Query Editor
appears, set to search among all records for the table you selected. (See “The
Query Editor, a General-Purpose Tool for Finding Records Based on Content” in
Chapter 12, for help using the Query Editor.) If you use this method to select
records, Biota will inform you how many records it found, before you continue with
the rest of the Export procedure. When you launch the export, the fields you select
will be exported for the records you found using the Query Editor, as detailed below.
4.
Using the “Field Name/Alias” button. The
button below the “Biota Field Names or
Aliases” panel controls whether Biota lists
strictly Internal Field Names (as given in
Appendix A, “Biota Tables, Fields, and
Relational Links”) or substitutes a Field Alias
for the corresponding Internal Field Name for
each field you have given an Alias. (See
Chapter 18, “Re-naming Fields,” to learn about
Field Aliases.)
If no Aliases have been defined, the
button is disabled and reads: “Show Field
Aliases.” The caption to the right of the
button reads: “Internal Field Names appear
in the lists above. No Field Aliases have
been defined.”
If any Aliases have been defined, when
you first open the Export Editor the button is
enabled and reads: “Show Internal Names.”
The caption to the right of the button reads:
“Field Aliases you have defined are currently
included in the lists above in place of the corresponding Internal Field Names.”
If you click the “Show Internal Names” button, the button text changes to
“Show Field Aliases” and the caption reads: “Internal Field Names appear in the
lists above. Click the button to the left to include the Field Aliases you have
defined.”
Chapter 27– Page 8
5.
Choose the fields to
export. The Biota Field
Names or Aliases panel
is simply a source of
field names. The panel
labeled Text File Fields
(Table Columns), at the
right, is the list Biota will
consult in exporting data
from your Biota Data
File to a text file.
6.
Use the buttons
between the two lower panels in the Export Editor to create the list of fields in the
“Text File Fields” panel. The list of fields you create can include any or all of the field
names or aliases from the list available, in any order. You can even repeat fields if
you want.
“Append” button. Click a field in the “Biota Field Name” panel to
select it, then click the “Append” button. The field name is added
to the end of the list in the “Text File Fields” panel.
“Insert” button. Click a field already listed in the “Text File Fields”
panel to select it. Then click the field in the “Biota Field Name”
panel that you want to insert. When you click the “Insert” button,
the new field is inserted just above the selected field in the “Text
File Fields” panel.
“All” button. The “All” Button is a toggle. When the button text reads “All>>>,” it
means “Append All.” If you click the button, all fields in the “Biota Field Name”
panel are entered in the “Text File Fields” panel (in the order listed in the Field
Name Panel), replacing any fields already listed in the “Text File Fields” panel.
The button text then changes to read “<<<All,” meaning “Remove All.” If you click
the button again, the “Text File Fields” panel is cleared and the button text
changes back to “All>>>.”
“Remove” button. To remove a single field already entered in the “Text File
Fields” panel, select the field by clicking it in the list, then click the “Remove”
button.
7.
Set the Field and Record Delimiters. In the “Delimiters” panel of
the Export Editor, you specify the characters Biota will insert
between fields (columns) and at the end of records (rows) in the
exported text file. You may use any characters in the standard
ASCII set (Characters 33–126), but, of course, they must make
sense in the context of other applications you intend to use in
working with the text file. The “Delimiter Help” button presents a list
of common options.
Windows: The default delimiters are TAB (ASCII Character 9) for the field
delimiter and RETURN + LINE FEED (ASCII Characters 13 + 10), for the record
delimiter—the characters that Windows spreadsheet applications use for “TABseparated values” text files.
If you are exporting data to a Macintosh text file, using a Windows machine, click
the “DOS/Windows File” checkbox to uncheck it. The “End of Record” box will
then read “13.”
Chapter 27– Page 9
Macintosh: The default delimiters are TAB (ASCII Character 9) for the field
delimiter and RETURN (ASCII Character 13) for the record delimiter—the
characters that Macintosh spreadsheet applications use for “TAB-separated
values” text files.
If you are using a Mac OS machine to export data to a PC (DOS or Windows)
text file that uses the standard PC line termination (RETURN + LINE FEED, ASCII
Characters 13 + 10), click the “DOS/Windows File” checkbox to set the check
mark. The “End of Record” box will then read “1310.”
8.
Set the Options. There are two checkboxes in the
“Options” panel. Both are unchecked, by default.
“Export Field Names…” Checkbox. If you want the
first row (record) of the exported text file to consist of
column headings, you should check this option. Biota
will use the Internal Field Names to create column
headings. If you have included any Aliases in the list of
fields to be exported, however, Biota will instead create
headings from Aliases, where appropriate.
You can click the “First Record Help” button to review these instructions in
context.
“Save Export Setup” Checkbox. If you check this option, Biota will remember
the way you have set up the Export Editor, even if you Cancel without attempting
to export, for the duration of the current Biota session, or until you make changes
in the setup.
9.
Launch the export. When the list of “Text File Fields” and the settings are ready,
click the “Export” button to launch the export process.
Chapter 27– Page 10
The standard “Save File” window for your operating system appears.
10. Name the text file. Find the folder or directory where you want to create the text
file, name the file, and click the “OK” button (Windows) or the “Save” button
(Macintosh). The progress indicator appears.
When the export is complete, a message informs you.
11. To halt the export, click the “Cancel” button in the progress window. Biota posts a
warning that the text file may be incomplete.
NOTE: You can carry out other tasks with Biota or other applications while the export
is in progress.
Exporting Notes
For five Biota Core tables—Specimen, Species, Collection, Locality, and Loans—you
can create as many Notes as you want for each Core table record. Each Note is actually
a separate (child) record in a Notes table, linked to a parent record in the Core table (see
Appendix A, “Biota Tables, Fields, and Relational Links”).
Chapter 27– Page 11
Biota provides two tools for exporting Notes records, the Export Editor and the Export
Notes tool from the Im/Export menu. The Export Editor produces text files containing
fields you select from Notes tables only. In contrast, the Export Notes tool exports
certain fields from each parent record, along with full records for each selected Note.
Exporting Notes with the Export Editor
The Export Editor is discussed in detail earlier in this chapter (see “Exporting Data by
Tables and Fields”). Using the Export Editor, you can export any of the following:
All Notes records that are linked to any record in the current Record Set for the
parent table (see the next section of this chapter, “Exporting Notes Records Linked
to Records in the Current Parent-Table Record Set”).
All Notes records for a particular Notes table (see “Exporting All Notes Records for
a Notes Table” later in this chapter).
Notes records you find using the Query Editor (from the Export Editor itself), based
on content of the Notes records themselves, or on the content of parent records
(see “Exporting Notes Records Based on Their Own Content” or “Exporting Notes
Records Based on the Content of Parent Records” later in this chapter).
Exporting Notes Records Linked to Records in the Current Parent-Table
Record Set
To illustrate, suppose you want to export all Collection Notes for a particular group of
Collection records. Although Collection Notes will be used as an example, the technique
is the same for any Core table with Notes (Species, Specimen, Locality, and Loans, as
well as Collection).
1.
Display the group of Collection records for which you want to export Notes,
using any technique from the Find menu (see Chapter 12, “Finding and Updating
Records”).
2.
Designate these records as the current Collection Record Set (see “Record
Sets” in Chapter 3).
3.
From the Im/Export menu, select “Export by Tables and
Fields” to open the Export Editor.
4.
Select the “Collection Notes” table from the “Table Name”
popup list.