BHL @ #TDWG09 - with discussion

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BHL @ #TDWG09 - with discussion

  1. 1. LINKED LITERATURE BHL DEVELOPMENTS CITEBANK Chris Freeland Technical Director, BHL
  2. 2. BHL Members
  3. 3. BHL Members: US/UK <ul><li>Academy of Natural Science (Philadelphia, PA) </li></ul><ul><li>American Museum of Natural History (New York, NY) </li></ul><ul><li>California Academy of Science (San Francisco, CA) </li></ul><ul><li>The Field Museum (Chicago, IL) </li></ul><ul><li>Harvard University Botany Libraries (Cambridge, MA) </li></ul><ul><li>Harvard University, Ernst Mayr Library of the Museum of Comparative Zoology (Cambridge, MA) </li></ul><ul><li>Marine Biological Laboratory / Woods Hole Oceanographic Institution (Woods Hole, MA) </li></ul><ul><li>Missouri Botanical Garden (St. Louis, MO) </li></ul><ul><li>Natural History Museum (London, UK) </li></ul><ul><li>The New York Botanical Garden (New York, NY) </li></ul><ul><li>Royal Botanic Gardens, Kew (Richmond, UK) </li></ul><ul><li>Smithsonian Institution Libraries (Washington, DC) </li></ul>
  4. 4. BHL Members: BHL-Europe <ul><li>Museum für Naturkunde - Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin </li></ul><ul><li>Natural History Museum, UK </li></ul><ul><li>Narodni muzeum NMP CZ </li></ul><ul><li>Angewandte Informationstechnik Forschungsgesellschaft mbH </li></ul><ul><li>Freie Universität Berlin FUBBGBM </li></ul><ul><li>Georg-August-Universität Göttingen Stiftung Öffentlichen Rechts </li></ul><ul><li>Naturhistorisches Museum Wien </li></ul><ul><li>Hungarian Natural History Museum </li></ul><ul><li>Museum and Institute of Zoology, Polish Academy of Sciences </li></ul><ul><li>University of Copenhagen </li></ul><ul><li>Stichting Nationaal Natuurhistorisch Museum, Naturalis </li></ul><ul><li>National Botanic Garden of Belgium </li></ul><ul><li>Royal Museum for Central Africa, </li></ul><ul><li>Royal Belgian Institute of Natural Sciences </li></ul><ul><li>Bibliothèque nationale de France </li></ul><ul><li>Museum national d’histoire naturelle </li></ul><ul><li>Consejo Superior de Investigaciones Cientificas </li></ul><ul><li>Università degli Studi di Firenze </li></ul><ul><li>Royal Botanic Garden, Edinburgh </li></ul><ul><li>Species 2000 </li></ul><ul><li>John Wiley & Sons limited </li></ul><ul><li>Helsingin yliopisto UH-Viikki </li></ul>
  5. 5. Stats: Now Online <ul><li>15,000 titles </li></ul><ul><li>40,000 volumes </li></ul><ul><li>16.4mil pages </li></ul><ul><li>Soon: </li></ul><ul><ul><li>34,000 titles </li></ul></ul><ul><ul><li>65,000 volumes </li></ul></ul><ul><ul><li>24mil pages </li></ul></ul>Oldest book: Schöffer’s Herbarius , 1484.
  6. 6. Stats: Usage <ul><li>Jan – Sep 2009 </li></ul><ul><ul><li>266,000 visitors </li></ul></ul><ul><ul><li>436,000 visits </li></ul></ul><ul><ul><li>2.1million pageviews </li></ul></ul><ul><li>Daily average </li></ul><ul><ul><li>970 visitors </li></ul></ul><ul><ul><li>1,600 visits / day </li></ul></ul><ul><ul><li>7,700 pageviews / day </li></ul></ul>Jan – Sep 2009 Launch to 30 Sep 2009
  7. 7. Cloud storage & computing
  8. 8. Global, coordinated development <ul><li>New functionality from BHL-Europe </li></ul><ul><ul><li>Improved deduplication tools </li></ul></ul><ul><ul><li>Semantic interface </li></ul></ul><ul><ul><li>OAIS-compliant preservation infrastructure </li></ul></ul><ul><li>Building a community of developers </li></ul><ul><ul><li>Funded & volunteer </li></ul></ul><ul><ul><li>RubyBHL: http://github.com/mjy/rubyBHL </li></ul></ul><ul><ul><li>PyBHL: http://linux.softpedia.com/get/Programming/Libraries/pybhl-51612.shtml </li></ul></ul><ul><li>New partners, new content </li></ul>
  9. 9. Open Source Pageturning UI http://github.com/openlibrary/bookreader
  10. 10. Open Software & Development <ul><li>BHL Bits: </li></ul><ul><ul><li>Portal code, utilities, services </li></ul></ul><ul><ul><li>http://code.google.com/p/bhl-bits/ </li></ul></ul><ul><li>Taxonomic Literature Group </li></ul><ul><ul><li>Google Group for discussion of “taxonomic literature & the services required to make literature interoperable within biodiversity research and biodiversity informatics.” </li></ul></ul><ul><ul><li>http://groups.google.com/group/taxonlit </li></ul></ul>
  11. 11. Open Data <ul><li>Downloads </li></ul><ul><ul><li>Simple tab-delimited exports of core data </li></ul></ul><ul><ul><li> http://www.biodiversitylibrary.org/data/BHLExportSchema.pdf </li></ul></ul><ul><li>Data model </li></ul><ul><ul><li>DB schema as ERD </li></ul></ul><ul><ul><li> http://bhl-bits.googlecode.com/files/20090930_BHLDataModel.pdf </li></ul></ul>
  12. 12. Services <ul><li>Names Service </li></ul><ul><ul><li>Return all occurrences of a name throughout BHL digitized corpus </li></ul></ul><ul><ul><ul><li>Documentation: http://bit.ly/2e6sg9 </li></ul></ul></ul><ul><ul><li>Access to 51million name strings using TaxonFinder </li></ul></ul><ul><ul><ul><ul><li>1.4million unique names </li></ul></ul></ul></ul><ul><ul><li>Working out a strategy for obscure species </li></ul></ul><ul><ul><li>Algorithm improvements to detect nomenclatural & taxonomic acts </li></ul></ul><ul><li>OpenURL </li></ul><ul><ul><li>Facilitate links to citations: protologues, articles, references </li></ul></ul><ul><ul><ul><li>Documentation: http://www.biodiversitylibrary.org/openurlhelp.aspx </li></ul></ul></ul><ul><ul><li>Useful to Nomenclators, Reference Systems </li></ul></ul><ul><ul><ul><li>IPNI </li></ul></ul></ul><ul><ul><ul><li>Tropicos </li></ul></ul></ul>
  13. 13. Services: OpenURL http://www.biodiversitylibrary.org/openurl? pid=title:3934&volume=14&issue=&spage=301&date=1879 http://www.tropicos.org/Name/1200408
  14. 14. Services: OpenURL Disambiguation <ul><li>Looking for: </li></ul><ul><li>BHL returns: </li></ul>
  15. 15. Services: OpenURL Results
  16. 16. How? <ul><li>Tropicos maintains internal authority list of publications: </li></ul><ul><li>Each protologue/reference tied to authority: </li></ul><ul><li>Matched Tropicos TitleIDs to BHL TitleIDs: </li></ul><ul><li>Throw citations at resolver at regular intervals & cache data in Tropicos </li></ul>http://www.tropicos.org/Publication/775 http://www.biodiversitylibrary.org/title/3934 http://www.tropicos.org/Publication/775 = http://www.biodiversitylibrary.org/openurl? pid=title:3934&volume=14&issue=&spage=301&date=1879
  17. 17. Encyclopedia of Life <ul><li>522,000 species pages linked to BHL </li></ul><ul><li>#1 referring site </li></ul>
  18. 18. Other Consumers <ul><li>EarthCape Labs </li></ul><ul><ul><li>Sort/Search capabilities with harvested names </li></ul></ul><ul><ul><li>YouTube demo: http://www.youtube.com/watch?v=qw7qw87JTOs </li></ul></ul><ul><li>BioGUID / iPhylo </li></ul><ul><ul><li>BHL Name Timeline & Comparison </li></ul></ul><ul><ul><ul><li>http://bioguid.info/bhl/ </li></ul></ul></ul><ul><ul><ul><li>http://bioguid.info/bhl/compare.php </li></ul></ul></ul><ul><ul><li>New Viewer </li></ul></ul><ul><ul><li>Tagging </li></ul></ul><ul><ul><li>So much cool stuff we can’t keep up! </li></ul></ul><ul><ul><ul><li>http://iphylo.blogspot.com/search/label/BHL </li></ul></ul></ul>@rdmpage
  19. 19. http://bioguid.info/bhl/compare.php?name1=Physeter+catodon&name2=Physeter+macrocephalus
  20. 20. Crowdsourced Articles <ul><li>http://www.biodiversitylibrary.org/pdfgen/17298 </li></ul>Demo: http://youtube.com/watch?v=oidf3b26jVs
  21. 21. Crowdsourced Articles <ul><li>12,000 PDFs generated through September 2009 </li></ul><ul><ul><li>4,900 submitted with article metadata </li></ul></ul><ul><ul><li>Analysis: http://bit.ly/4Jqu9 </li></ul></ul>
  22. 22. Great, but how to… <ul><li>display / manage? </li></ul><ul><li>meet community demands for bibliography / citation management? </li></ul><ul><li>build from more open source tools? </li></ul>
  23. 23. Development goals re: citations <ul><li>Create a repository for community-vetted taxonomic bibliographies. </li></ul><ul><li>Ability to ingest, display, download, and index articles so that the BHL can operate as an article repository. </li></ul><ul><li>Build from existing community of work around Drupal / Biblio. </li></ul><ul><ul><li>In use by collaborators </li></ul></ul>
  24. 24. <ul><li>“ something like GenBank or NameBank for citations…” </li></ul><ul><li>So, CitationBank…or CiteBank (saves chars) </li></ul>Need…
  25. 25. http://citebank.biodiversitylibrary.org/
  26. 26. Crowdsourced Articles <ul><li>PDFs from BHL pushed into Drupal/Biblio: </li></ul>
  27. 27. http://citebank.biodiversitylibrary.org/ search
  28. 28. http://citebank.biodiversitylibrary.org/node/47423
  29. 29. PDF http://www.biodiversitylibrary.org/pdf1/000295100017298.pdf
  30. 31. CiteBank boundaries Book Citation Pageturning UI PDF OCR eBook/Kindle Stored *somewhere* & retrievable via HTTP URI Citation Citation Citation Bibliography CiteBank
  31. 32. BHL Data Flow – Sep 2009 CiteBank
  32. 33. Copyright <ul><li>Bold statements that need some good legal counsel: </li></ul><ul><ul><li>Citations don’t have copyright </li></ul></ul><ul><ul><ul><li>Unless you get them from OCLC, other services </li></ul></ul></ul><ul><ul><li>Bibliographies have copyright </li></ul></ul><ul><ul><ul><li>They’re a scholarly work </li></ul></ul></ul><ul><ul><li>Underlying content has copyright </li></ul></ul><ul><ul><ul><li>Except when it doesn’t </li></ul></ul></ul>
  33. 34. Up for discussion…
  34. 35. Who can upload & edit? <ul><li>Trusted repositories? </li></ul><ul><li>Approved specialists? </li></ul><ul><li>BHL Librarians? </li></ul><ul><li>People in this session? </li></ul><ul><li>Citizen scientists? </li></ul><ul><li>6 th graders? </li></ul><ul><li>Rod Page? </li></ul>Discussion: Session participants thought it important that BHL get as many citations as possible, then find ways of implementing trust mechanisms for users such as iSpot (Drupal module), ratings systems, ways of tagging inappropriate materials.
  35. 36. What about duplicates? <ul><li>3 Bibliographies had Syst. Nat. </li></ul><ul><ul><li>All 3 in different reference manager formats </li></ul></ul><ul><ul><li>All 3 had variant forms of title: </li></ul></ul><ul><li>Syst. Nat. </li></ul><ul><li>Systema Naturae </li></ul><ul><li>Systema naturae per regna tria naturae </li></ul><ul><ul><li>Library catalogues: </li></ul></ul><ul><ul><li>Caroli Linnaei...Systema naturae per regna tria naturae :secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. </li></ul></ul>Discussion: Important to have all the ways in which materials have been referred to over time, then have algorithms & people aggregate titles/articles (translations) into reconciliation groups, resulting in a master index.
  36. 37. Accuracy <ul><li>How clean is clean? </li></ul><ul><li>How dirty is dirty? </li></ul><ul><li>What’s good enough? </li></ul><ul><ul><li>How to Rank </li></ul></ul><ul><ul><ul><li>Gold/Platinum? </li></ul></ul></ul><ul><li>Dirty Bucket/Clean Bucket? </li></ul>Discussion: Let users decide which is the “right” form for use; may differ from project to project. BHL should take it all in, then refine using our libraries’ collected knowledge + involvement from domain specialists.
  37. 38. Right technologies? <ul><li>“ But Drupal’s awful…just ask ___ for their bad experience.” </li></ul><ul><li>“ Drupal’s great!” </li></ul><ul><li>“ MySQL won’t scale” </li></ul><ul><li>“ MySQL’s great!” </li></ul>Discussion: Drupal has limitations, but a large community of developers & implementers. There may be a “Montpellier Declaration” to centralize efforts within biodiversity informatics around the framework. Drupal/Biblio is a good starting point for CiteBank, needs further evaluation after more data are loaded & site is used.
  38. 39. Next steps <ul><li>Bring hardware online at MBL </li></ul><ul><ul><li>Have one point of redundancy </li></ul></ul><ul><ul><li>By Q1 2010 </li></ul></ul><ul><li>Bring BHL-Europe & other nodes online </li></ul><ul><ul><li>In conjunction with DuraCloud & other solutions </li></ul></ul><ul><li>Release CiteBank for beta & sandbox testing </li></ul><ul><ul><li>Beta at http://citebank.biodiversitylibrary.org </li></ul></ul><ul><ul><li>Sandbox at http://sandcite.biodiversitylibrary.org </li></ul></ul><ul><ul><li>Production release by Q2 2010 </li></ul></ul><ul><li>Integration of BHL-Europe tools & content </li></ul>
  39. 40. Coming soon <ul><li>Darwin’s Library </li></ul><ul><ul><li>AMNH, NHM, CUL, BHL (MOBOT) </li></ul></ul><ul><ul><li>Funded by NEH/JISC </li></ul></ul><ul><ul><li>Digitization of Darwin’s personal library, with annotations </li></ul></ul><ul><ul><ul><li>New interfaces for recording, indexing, displaying annotations </li></ul></ul></ul><ul><li>Inhouse scanning from partners/contributors </li></ul>
  40. 41. Fun: BHL In Your Pocket! <ul><li>Content now available in EPUB format </li></ul><ul><ul><li>Used by Stanza, transferable to Kindle </li></ul></ul><ul><li>Blog post by John Mignault (NYBG): </li></ul><ul><ul><li>http://john.mignault.net/blog/2009/10/28/first-bhl-e-book-experiments/ </li></ul></ul>
  41. 43. Links & such Biodiversity Heritage Library http://biodiversitylibrary.org CiteBank beta http://citebank.biodiversitylibrary.org CiteBank sandbox http://sandcite.biodiversitylibrary.org Go play! http://twitter.com/BioDivLibrary Follow BHL on
  42. 44. Thanks! <ul><li>Chris Freeland </li></ul><ul><li>Technical Director, BHL </li></ul><ul><li>Director, Center for Biodiversity Informatics, Missouri Botanical Garden </li></ul><ul><ul><li>[email_address] </li></ul></ul><ul><ul><li>http://twitter.com/chrisfreeland </li></ul></ul><ul><li>Presentation online through TDWG & at http://www.chrisfreeland.com </li></ul>

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