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1. GBIF www gbif org 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 Description Date of release Author s 1 0 Proofed for evaluation version 8 April 2011 DR Cover juvenile manatee Trichechus manatus This document is also part of the GBIF Data Publishing Manual version 1 0 ISBN 87 92020 31 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 mega science initiative to address one of the great challenges of the 21 century harnessing knowledge of the Earth s biological diversity GBIF envisions a world in which biodiversity infor2. 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 public 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 DwC A 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 http data gbif org 3 http links gbif org ipt_user_manual 4 http links gbif org ipt_visibility April 2011 1 Publishing and Registering Data with GBIF Version 1 0 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 DwWC 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
3. 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 fe Apache2 1 5 x Fie Edit View Favorites Tools Help ay G peck P j search j Folders X 9 E Address C c Program Files Apache Group Apache2 E Go a bin im cgi bin me conf a a include onl ib Ga logs CJ manual E modules ra proxy pan ABOUT_APACHE ee CHANGES er INSTALL iy fi 9 LICENSE fe notice 2 README I 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 TapirLink BioCASe or DiGIR Please refer to the software guides for these tools to
4. publish your data 5 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 7 Distributed Generic Information Retrieval DiGIR See http digir sourceforge net April 2011 2 Publishing and Registering Data with GBIF Version 1 0 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 c
5. Mince date ae wad wae hace tala E ate wee ks 3 Using Spreadsheet Processor Make Your Own DwC A or other community tools 3 April 2011 Publishing and Registering Data with GBIF Version 1 0 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 Portal 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 DwWC 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 Follow the online user manual to get data uploaded and mapped
6. gistration is completed the registered dataset can be found on the GBIF Registry website 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 April 2011 4
7. mation 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 being 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 April 2011 iti Publishing and Registering Data with GBIF Table of Contents Version 1 0 ADOUT GBIFi i714 ci aest cue tied ack TR te ots valet Baty ad Tok abe dec abe in ee awed eateries iii Fable of Contents sriorireriri on eont i oeren Ea EEE EET eine asada ee wigs aie e aa aK iv Mtrod cti OM aa e aaee A EEA TEE penned REEE AE E EA EE a AEE we TERRE 1 Publishing data With GBIF sieg eese ree sehen wes E a s Seal Mies A N a eee R E ETE R 1 Using the Integrated Publishing Toolkit sssssssssssssssssssssessesssesssssssessesseees 1 Using Spreadsheet Processor or Make Your Own Darwin Core Archive DWC A 2 Using TapirLink BioCASe or DiGIR cece cece ee c eee e een nnennceeeeeeeeeeeeeeeeeees 2 Registering your dataset With GBIF 0 ccc cc cece cece cece eee eeeeee eee eeeeeeeeeeeneeee 3 USN IPM ETE EI E E tats Mile bunds cate tbc E
8. onfiguration 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 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 April 2011 3 Publishing and Registering Data with GBIF Version 1 0 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 re
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