"user manual"
Publishing and Registering Data with GBIF
Version 1.0
April 2011
Publishing and Registering Data with GBIF
1.0
Suggested citation:
GBIF (2011). Getting Started, Overview of Data Publishing in the GBIF Network,
(contributed by Braak, K., Remsen, D., Hahn, A., Ko, B., Chavan, V., Raymond, M.,
Copenhagen: Global Biodiversity Information Facility, 16 pp. Accessible at
http://links.gbif.org/dwc-a_publishing_guide_en_v1
ISBN: 87-92020-29-1
Persistent URI: http://links.gbif.org/dwc-a_publishing_guide_en_v1
Language: English
Copyright © Global Biodiversity Information Facility, 2011
License:
This document is licensed under a Creative Commons Attribution 3.0 Unported License
Document Control:
Version
1.0
Description
Proofed for evaluation version
Date of release
8 April 2011
Author(s)
DR
Cover: juvenile manatee, Trichechus manatus
This document is also part of the 'GBIF Data Publishing Manual version 1.0, ISBN 87-9202031-3, available at http://links.gbif.org/data_publishing_manual
April 2011
Publishing and Registering Data with GBIF
Version 1.0
About GBIF
The Global Biodiversity Information Facility (GBIF) was established as a global megascience initiative to address one of the great challenges of the 21st century – harnessing
knowledge of the Earth’s biological diversity. GBIF envisions ‘a world in which biodiversity
information is freely and universally available for science, society, and a sustainable
future’. GBIF’s mission is to be the foremost global resource for biodiversity information,
and engender smart solutions for environmental and human well-being1. To achieve this
mission, GBIF encourages a wide variety of data publishers across the globe to discover
and publish data through its network.
.
1
GBIF (2011). GBIF Strategic Plan 2012-16: Seizing the future. Copenhagen: Global Biodiversity Information
Facility. 7pp. ISBN: 87-92020-18-6. Accessible at http://links.gbif.org/sp2012_2016.pdf
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Publishing and Registering Data with GBIF
Version 1.0
Table of Contents
About GBIF .............................................................................................. iii Table of Contents ..................................................................................... iv Introduction ............................................................................................. 1 Publishing data with GBIF ............................................................................. 1 Using the Integrated Publishing Toolkit ........................................................ 1 Using Spreadsheet Processor or Make-Your-Own Darwin Core Archive (DwC-A) ......... 2 Using TapirLink, BioCASe or DiGIR ............................................................... 2 Registering your dataset with GBIF .................................................................. 3 Using IPT............................................................................................. 3 Using Spreadsheet Processor, Make-Your-Own DwC-A, or other community tools....... 3 April 2011
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Publishing and Registering Data with GBIF
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Introduction
The purpose of this “Publishing and Registering Data with GBIF” guide is to instruct users
to go through the publishing and registering steps after they have used tools to map their
data or have produced a Darwin Core Archive file. A Frequently Asked Questions section is
provided at the end to give users an estimate about the time required before their data
are available on the GBIF Data Portal2 and what will happen afterwards.
Publishing data with GBIF
After completing the previous steps, whether using the Integrated Publishing Toolkit (IPT),
Spreadsheet Processor, Making your own DwC-A or a community option like TapirLink, the
next step is to publish the dataset and its metadata, then register them with GBIF so the
data are shared within the GBIF network.
To “publish” data means to make the data publicly available on the web. If the IPT,
TapirLink, BioCASe Provider Software or DiGIR is used, the publishing functionality is built
in. If the Spreadsheet Processor is used or a DwC-A file is generated manually, the user
will need put the resulting files on a web server for download so they are “published”.
Using the Integrated Publishing Toolkit
1. Follow the online user manual to get data uploaded and mapped3.
2. In the “Managing Resources” page of your resource, there is a “Visibility”
section with a “Public” button. Click the button and then your resource
overview can be viewed from the home page of the IPT. At this stage, your
resource is open to the public4.
3. In the same “Managing Resources” page of your resource, there is a “Published
Release” section with a “Publish” button. By clicking the “publish” button, IPT
will generate a new release of your resource and make download links to a DwCA file and an EML.xml, which contains the metadata. At this stage, your data is
publicly available for download. Go to http://links.gbif.org/ipt_publish for
more details.
2
3
4
http://data.gbif.org/
http://links.gbif.org/ipt_user_manual
http://links.gbif.org/ipt_visibility
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Publishing and Registering Data with GBIF
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You must complete both step 2 and 3 to make your data ready to be registered.
Using Spreadsheet Processor or Make-Your-Own Darwin Core Archive (DwC-A)
If you selected to use Spreadsheet Processor or you have made your own DwC-A, you
should have had a zip file as the product of the preparing procedure.
Now, to publish it, all you need to do is to put it in a web server that constantly
connected to the Internet and serving contents to the public. For operations on a web
server, it is strongly suggested to contact your web administrator to assist in making the
file available online.
See Figure 1 for the file location on a typical web server running on Windows XP. Once
you put the file within the “htdocs” folder, the file is then downloadable to the public.
For example, if your web server is configured to have its domain name as
“some.insitution.org,” and the DwC-A file is named as “Specimen_NHM.zip,”, once this zip
file is put into the “htdocs” folder, people can download it by pointing their browsers to
http://some.institution.org/Specimen_NHM.zip. You should keep this URL for registering
with GBIF in the next step.
Please note that the IP address or the Domain Name of the web server should be stable, so
the resource is constantly available online. Please also note that the URL is case sensitive
Figure 1. Web directory of Apache2 Web Server on
Windows XP. Usually “htdocs,” indicated by a red
square, is the document root of the web server.
by default, and the access permission of the file should be properly set.
Using TapirLink5, BioCASe6 or DiGIR7
Please refer to the software guides for these tools to publish your data.
5
6
7
TapirLink. http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirLinkManual
BioCASe is a protocol designed by Biological Collection Access Services. See http://www.biocase.org/
Distributed Generic Information Retrieval (DiGIR). See http://digir.sourceforge.net/
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Publishing and Registering Data with GBIF
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Once you have the metadata and dataset published using these tools, you should have
both the metadata URL and dataset URL ready. Keep these URLs for the next step.
Registering your dataset with GBIF
Using IPT
The IPT supports automatic registration in the GBIF network. In the “Managing Resources”
page of your resource, there is a “Visibility” section. If the status is public, then there
should be a “Register” button and a drop-down list for institutions. Choose the institution
with which the resource or dataset is associated, and click the “Register” button. Now
your dataset and metadata are registered with the GBIFS. See the online manual for the
IPT.
Using Spreadsheet Processor, Make-Your-Own DwC-A, or other community
tools
There is no automatic registration for these options. Therefore, you need to use the data
registration form at http://tools.gbif.org/dwca-register/ and provide the following
information:
1. Dataset title
2. Dataset description
3. Technical contact (the person to be contacted in matters regarding technical
availability or resource configuration issues on the side of the dataset or data
publisher)
4. Administrative contact (the person to be contacted in all matters regarding
scientific data content and usage of a specific dataset or data publisher)
5. Institution name
6. Your relation to this Institution
7. The name of the GBIF Participant Node that can endorse the publishing
institution
8. The dataset URL: either the access point URL (if you are publishing using one of
the provider softwares), or the DwC-Archive URL (if you are publishing via a
zipped DwC-Archive)
9. The metadata document URL
Please ensure you have all of the information before you send the email. After sending the
email, some questions are frequently asked:
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Publishing and Registering Data with GBIF
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How Long Until My Dataset Gets Registered?
Upon receiving your email, the GBIF Helpdesk will try to attend to your registration
request as quickly as possible. The Helpdesk will first contact the GBIF Node selected
with the registration, and ask them whether they want to endorse the new data provider
installation in their domain. Each new registration needs to get formal endorsement from
a GBIF Participant Node manager (who best knows the institutions and databases in their
country/organisation) before it is allowed into the GBIF Registry. This is a simple quality
control step required by the GBIF Participant Node Managers Committee.
Once endorsement has been received and the registration is completed, the registered
dataset can be found on the GBIF Registry website8. Try searching by institution name or
dataset title.
How Long Until My Dataset Gets Indexed By GBIF?
Following registration, the GBIF Helpdesk will queue the newly registered dataset for
indexing. Depending on the size of the dataset, indexing can take anywhere from minutes
to weeks. If problems are encountered during indexing, the GBIF Helpdesk will try to work
with you to resolve them as quickly as possible.
When indexing is successful, the new dataset will become publicly available in the GBIF
Data Portal (http://data.gbif.org) in the next “rollover” from the non-public indexing
database with the public web portal database.
At present, GBIF attempts to update each registered dataset at least once every three
months. The accumulated updates become public with each following "rollover", about
every six weeks.
What Happens When My Dataset Is Indexed?
During indexing, a set of core data elements is retrieved from your dataset and is stored in
the GBIF index, so that the dataset will become accessible for searches.
8
http://gbrds.gbif.org
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