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Building EOL species pages

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A talk presented January 20, 2013 in the Indo-US Joint Workshop on Biodiversity Informatics at the Ashoka Trust for Research in Ecology and the Environment in Bangalore, India.

A talk presented January 20, 2013 in the Indo-US Joint Workshop on Biodiversity Informatics at the Ashoka Trust for Research in Ecology and the Environment in Bangalore, India.

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  • Includes genetic information, geospatial information, descriptive information, evolutionary information, and published literature.Some of these are using ontologies and we are integrating with them in interesting ways.Box 3. Linking and sharing biodiversity dataA vast ecosystem of projects is already managing and, to somedegree, sharing information about living organisms. Figure Ishows an incompletely known network of biodiversity-relateddatabases. Two kinds of hub are apparent: hubs connectingdifferent kinds of data (e.g. EOL) and hubs that connect manypartners and subnetworks sharing the same kind of data (e.g. GBIF,BHL and Catalogue of Life). Most hubs have received majorfunding from research and charitable foundations and activelyfacilitate use of data-sharing standards, such as Darwin Core.Some non-hub projects have been leaders in connecting to manyhubs; these projects enjoy effective individual and/or institutionalsupport for data sharing. Such an analysis provides: (i) a baselineunderstanding of redundancy and resiliency for long-term dataaccess; (ii) characterization of the environment for distributedannotation and quality control; and (iii) identification of isolatedprojects and appropriate mechanisms for connecting them to thenetwork. A more complete analysis, including the volume of dataflow, could enable real-time assessment of network health. Theinformatics community assumes that this ‘eBiosphere’ [75] haspositive impacts on progress in evolutionary and biodiversityscience as well as societal challenges, but demonstrating theseimpacts remains a challenge.Figure I. An incompletely known network of biodiversity-related databases. Dots represent 1631 projects, clustered and color-coded by the Clauset-Newman-Moore algorithm[76] using NodeXL [77], with 1704 instances of data sharing (re-use of the same data), deep hyperlinking (e.g. a page for a taxon in one online database links to appropriateresources in another online database), or indexing. The size of dot reflects the degree (i.e. number of links); links between hubs (degree >15) are enlarged for emphasis.OBIS = Ocean Biogeographic Information System, WoRMS = World Register of Marine Species, AKN = Avian Knowledge Network. See main text and Box 1 for otheracronyms. Projects included Encyclopedia of Life (EOL), a leading online aggregator of descriptive information about all organisms, its partners and their partners, and 588projects registered in the Taxonomic Databases Working Group database. The cluster of unconnected dots indicates that no linkages are known among hundreds of projects.
  • Daphne Fautin’sHexacorallians of the world
  • Transcript

    • 1. Building and aggregating species pagesCynthia Parr, PhD @cydparrSpecies Pages Group @eolChief Scientist
    • 2. Goals1. To provide some practical information about tools for capturing and sharing species information2. To get feedback on EOL tools and processes for future improvement3. To discuss good ideas that can inspire each other as we work both together and separately
    • 3. Show of hands• Do you contribute to a website(s) already?• Do you run your own website?• Would you rather just publish scientific papers?
    • 4. Outline• EOL is part of a sharing network• Standards for sharing species descriptions• Tools for capturing content – Direct on EOL – Multimedia repositories – Wikis – Literature – Specialist web sites• Sharing content with EOL• Curating EOL content• Using content from EOL
    • 5. EOL is part of a rich data sharing ecosystem aboutliving organisms From Parr et al. 2012. Evolutionary informatics: unifying knowledge about the diversity of life. Trends in Ecology and Evolution 26: 94-103.
    • 6. The GBIF hub has subnetworks
    • 7. Key individuals seek out hubs TOLWeb
    • 8. EOL Schema Sources: Data standardsContent type Standards used• Taxa • Darwin Core Archive• Attribution & licensing • Dublin & Darwin Core• Text objects & links • Species Profile Model,• Multimedia Plinian Core, etc. • Dublin (+ Audubon Core)
    • 9. NCBITaxonomy is framework Not the goal ITIS and COL
    • 10. Use your own classification standardYou do NOT have to follow a designated classificationShare your taxonomic hierarchy with your EOL contentEOL does its best to match the content with pages wealready haveContribute to COL and ITIS (and their partners)Then all projects will have access
    • 11. Outline• EOL is part of a sharing network• Standards for sharing species descriptions• Tools for capturing content – Direct on EOL – Multimedia repositories – Wikis – Literature – Specialist web sites• Sharing content with EOL• Curating EOL content• Using content from EOL
    • 12. Contributing to EOL• Flexibility• Blank canvas• Consider curating http://eol.org/info/contribute
    • 13. Members can add text directly to EOL
    • 14. Choosing a subject determines whereon the EOL page the information isdisplayedAlso important for other applicationsthat want to use the content
    • 15. Be sure to add references
    • 16. If you have a lot of content• Work with a hub like India Biodiversity Portal• Spreadsheet upload to EOL• Find a specialist website that is already a partner with EOL
    • 17. http://eol.org/info/cp_getting_startedSpreadsheet method
    • 18. General images & video flickr.com/groups/encyclopediaoflife >3000 people, 163K images
    • 19. Professional research images morphbank.org
    • 20. Or add to online museum catalogue
    • 21. Or add to online museum catalogue
    • 22. Citizen science images inaturalist.org
    • 23. Other multimedia repositories Sound Video Soundcloud.com
    • 24. Wikipedia/WikimediaBUTOnly the English version, starts unreviewedHighly formatted, not always consistentNot always easy to reviewAbout 150K taxa, 122K imagesEasy to add new taxa
    • 25. Biodiversity Heritage Library biodiversitylibrary.org
    • 26. Pensoft.net• Pensoft has a process to generate EOL-compliant XML for new species• Also sends images to Morphbank, specimens to GBIF• They registered the URL at EOL• Our script checks for changes once a day• EOL Open Access Fund
    • 27. Plazi.org GoldenGATE markupPublished articles Zootaxa Smithsonian Contributions OthersPhoto credit: DIYLibrarian, Flickr CC-BY-SA
    • 28. If you need your own specialist websitePrepare to raise funds for a programmerSpend a lot of effort populating and keeping itrunningOR try
    • 29. .eu
    • 30. LifeDesks
    • 31. Outline• EOL is part of a sharing network• Standards for sharing species descriptions• Tools for capturing content – Direct on EOL – Multimedia repositories – Wikis – Literature – Specialist web sites• Sharing content with EOL• Curating EOL content• Using content from EOL
    • 32. Working with existing EOL partner? • Using their toolsAdd content Follow • May need to add special tags • May need to change licensesinstructions • May need to add to an EOL group • Your content will be updated That’s all! automatically whenever we harvest from that partner
    • 33. If you already have your own website (or spreadsheet) • Create EOL member account Register on EOL • Add content partner with contact infoPrepare resource • Spreadsheet OR Darwin Core Archive • EOL will work with you file • Provide file for one time uploadAdd resource file • Or provide URL and set harvest frequency • Notifications of traffic statisticsReceive feedback • Curation actions • Comments (Please respond!)
    • 34. http://eol.org/info/cp_getting_startedDarwin Core Archive
    • 35. Content partner registration http://eol.org/info/cp_getting_started
    • 36. Don’t forget the logo
    • 37. http://eol.org/info/cp_getting_started
    • 38. Outline• EOL is part of a sharing network for species• Standards for sharing species descriptions• Tools for capturing content – Direct on EOL – Multimedia repositories – Wikis – Literature – Specialist web sites• Sharing content with EOL• Curating EOL content• Using content from EOL
    • 39. EOL curation http://eol.org/info/curators• Trust, untrust, hide taxon associations• Add new taxon association • Leave a comment • Add a rating
    • 40. • Set preferred classifications• Add and set preferred common namesMore info at: http://eol.org/info/curators
    • 41. http://eol.org/info/curators• Register as a member at eol.org• Edit your profile and provide your credentials – For assistant curator, just your real name – For full curator need academic affiliation OR publication reference OR referral from another full curator• Curate only as much as you are able
    • 42. Outline• EOL is part of a sharing network• Standards for sharing species descriptions• Tools for capturing content – Direct on EOL – Multimedia repositories – Wikis – Literature – Specialist web sites• Sharing content with EOL• Curating EOL content• Using content from EOL
    • 43. Using content from EOLManually API No need to ask Docs at http://eol.org/api permission Follow license conditions Register for an API key Provide attribution Follow terms of use Set up either a dynamic query or refresh a cache of results
    • 44. Questions?• Contact our partners at the India Biodiversity Portal• Contact me at parrc@si.edu• Use the contact us form on EOLflickr.com/groups/encyclopediaoflifeinaturalist.org, morphbank.orgbiodiversitylibrary.orgpensoft.net, plazi.orgscratchpads.eueol.org/info/cp_getting_startedeol.org/info/curatorseol.org/api