A Global Library of Life: The Biodiversity Heritage Library


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A Global Library of Life: The Biodiversity Heritage Library. Martin R. Kalfatovic. 2008 NFAIS Annual Conference. February 25, 2008. Philadelphia, PA

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  • A Global Library of Life: The Biodiversity Heritage Library

    1. 1. A Global Library for Life Martin R. Kalfatovic Smithsonian Institution Libraries 25 February 2008
    2. 2. The cultivation of natural science cannot be efficiently carried on without reference to an extensive library Charles Darwin, et al (1847)‏ Darwin, C. R. et al. 1847. Copy of Memorial to the First Lord of the Treasury [Lord John Russell], respecting the Management of the British Museum. Parliamentary Papers, Accounts and Papers 1847 , paper number (268), volume XXXIV.253 (13 April): 1-3. [Complete Works of Charles Darwin Online]
    3. 3. Taxonomic Literature <ul><li>Taxonomic descriptions must be published for the name to be valid </li></ul><ul><li>Publications must be available to the public through trusted sources </li></ul><ul><li>Libraries have been the traditional place </li></ul>
    4. 4. Taxonomic Literature The cited half-life of publications in taxonomy is longer than in any other scientific discipline * * * The decay rate is longer than in any scientific discipline ~ Macro-economic case for open access Tom Moritz
    5. 5. Taxonomic Literature <ul><li>Over 250 years of systematic description of life </li></ul><ul><li>Systema naturae (10 th ed. 1758) by Carl von Linné </li></ul>
    6. 6. BHL Timeline 2003. Telluride. Encyclopedia of Life meeting February 2005. London. Library and Laboratory: the Marriage of Research, Data and Taxonomic Literature May 2005. Washington. Ground work for the Biodiversity Heritage Library June 2006. Washington. Organizational and Technical meeting August 2006. New York Botanical Garden. BHL Director’s Meeting. October 2006. St. Louis/San Francisco. Technical meetings February 2007. Museum of Comparative Zoology. Organizational meeting May 2007. Encyclopedia of Life and BHL Portal Launch. Washington DC.
    7. 7. BHL Members American Museum of Natural History (New York) Field Museum (Chicago) Natural History Museum (London) Smithsonian Institution Libraries (Washington) Missouri Botanical Garden (St. Louis) New York Botanical Garden (New York)
    8. 8. <ul><li>Royal Botanic Garden, Kew </li></ul><ul><li>Botany Libraries, Harvard University </li></ul><ul><li>Ernst Mayr Library of the Museum of Comparative Zoology, Harvard University </li></ul><ul><li>Marine Biological Laboratory / Woods Hole Oceanographic Institution </li></ul>BHL Members
    9. 9. BHL Members <ul><li>University of Illinois, Urbana-Champaign (contributing member) </li></ul><ul><li>Scheme for addition of European and Asian partners underway </li></ul><ul><li>Additional categories of membership under consideration </li></ul>
    10. 10. BHL Focus: Literature
    11. 11. BHL Focus: Literature
    12. 12. <ul><li>Core literature pre-1923: 100 million pages (?) </li></ul><ul><li>All pre-1923: 120-150 million pages </li></ul><ul><li>All literature: 280-320 million pages </li></ul>BHL Focus: Literature
    13. 13. <ul><ul><li>1.3 million catalogue records </li></ul></ul><ul><ul><li>73% are monographs (remainder are serials at title-level) </li></ul></ul><ul><ul><li>63% is English language material </li></ul></ul><ul><ul><li>The next most popular language (9%) is German </li></ul></ul><ul><ul><li>About 30% of material was published before 1923 </li></ul></ul>BHL Collections
    14. 14. The Internet Archive <ul><li>501(c)(3) organization </li></ul><ul><li>Dedicated to “Universal Access to Human Knowledge” </li></ul><ul><li>Founder of the Open Content Alliance </li></ul><ul><li>Provides: </li></ul><ul><ul><li>Mass scanning </li></ul></ul><ul><ul><li>Archival storage of files </li></ul></ul><ul><ul><li>Image processing </li></ul></ul><ul><ul><li>Technology development </li></ul></ul>
    15. 15. Scribe Scanner <ul><li>Single Scribe Machine </li></ul><ul><ul><li>Custom built by the Internet Archive </li></ul></ul><ul><ul><li>Human operated </li></ul></ul><ul><ul><li>3,500 page per shift per day </li></ul></ul>
    16. 16. BHL Scanning Centers <ul><li>Northeast Regional Scanning Center </li></ul><ul><ul><li>10 Scribe machines </li></ul></ul><ul><ul><li>MBL/WHOI </li></ul></ul><ul><ul><li>Harvard </li></ul></ul><ul><li>New York Public Library </li></ul><ul><ul><li>10 Scribe machines </li></ul></ul><ul><ul><li>AMNH </li></ul></ul><ul><ul><li>NYBG </li></ul></ul>
    17. 17. BHL Scanning Centers <ul><li>University of Illinois </li></ul><ul><ul><li>2 Scribe machines </li></ul></ul><ul><li>Natural History Museum, London </li></ul><ul><ul><li>1 Scribe machine </li></ul></ul><ul><li>Missouri Botanical Garden </li></ul><ul><ul><li>Non-Scribe operation </li></ul></ul>
    18. 18. BHL Scanning Centers <ul><li>Washington, DC </li></ul><ul><ul><li>1 Scribe machine at Smithsonian Libraries </li></ul></ul><ul><ul><li>10 Scribe facility at Library of Congress with Fedlink (operational Spring 2008) </li></ul></ul>
    19. 19. Scanning Stats: Now <ul><li>5.5 million plus total pages scanned (and growing daily) </li></ul><ul><ul><li><90,000 Fieldiana (via UIUC) </li></ul></ul><ul><ul><li>>100,000 pages each Harvard, New York Botanical Garden, </li></ul></ul><ul><ul><li>225,000+ pages from the American Museum of Natural History </li></ul></ul><ul><ul><li>400,000+ from Smithsonian Libraries </li></ul></ul><ul><ul><li>500,000+ from the Natural History Museum, London </li></ul></ul><ul><ul><li>800,000 Missouri Botanical Garden Library </li></ul></ul><ul><ul><li>1,000,000+ from the MBL/WHOI library </li></ul></ul>
    20. 20. But what about ...
    21. 22. BHL Google (the difference between)‏ <ul><li>Bibliographic accuracy for all materials </li></ul><ul><li>Ability to re-purpose and reuse all data as needed </li></ul><ul><li>Congruence of original printed materials to digital versions </li></ul>
    22. 23. Persistent Identifiers <ul><li>Stable URL </li></ul><ul><li>Handle </li></ul><ul><li>DOI </li></ul><ul><li>BICI/SICI </li></ul><ul><li>ISSN </li></ul><ul><li>ISBN </li></ul><ul><li>LSIDs </li></ul>http://www.biodiversitylibrary.org
    23. 24. Structural Markup <ul><li><article> </li></ul><ul><li>  <title> A BRIEF CONSIDERATION OF CERTAIN POINTS IN THE MORPHOLOGY OFTHE FAMILY CHALCIDID^E.*. </title> </li></ul><ul><li>  <author> L. O. HOWARD. </author> </li></ul><ul><li>  <volume> 1 </volume> </li></ul><ul><li>  <issue> 2 </issue> </li></ul><ul><li>  <start_page> 65 </start_page> </li></ul><ul><li>  <end_page> 86 </end_page> </li></ul><ul><li>  <start_count_page> 85 </start_count_page> </li></ul><ul><li>  <end_count_page> 106 </end_count_page> </li></ul><ul><li>  <start_page_image_file> 3908800908001101smthrich_0085.djvu </start_page_image_file> </li></ul><ul><li>  <end_page_image_file> 3908800908001101smthrich_0106.djvu </end_page_image_file> </li></ul><ul><li>  </article> </li></ul>
    24. 25. Semantic Markup <ul><li>GoldenGATE The intention of the GoldenGATE editor is to build a bridge between NLP components and XML markup of natural language text according to arbitrary XML schemas. It allows the deployment of NLP components to marking up the bodies of literature they were designed for. In this way, it enables transforming the texts into XML content according to an XML schema that was designed to gain maximum benefit from the knowledge provided in them. </li></ul><ul><li>Integrated Open Taxonomic Access (INOTAXA) </li></ul>
    25. 26. <ul><li>10.7 million name strings in NameBank </li></ul><ul><li>Uses sophisticated algorithm (TaxonGrab) to locate likely name strings in OCR text </li></ul><ul><li>Iterative processing of BHL texts will both increase the number of name strings in NameBank and increase the accuracy of name string recognition </li></ul>Taxonomic Intelligence
    26. 27. BHL & Publishers
    27. 28. Permissions <ul><li>Seek permissions from copyright holders </li></ul><ul><li>Opt in Copyright Model: The BHL will actively work with professional societies and associations to integrate their publications into the BHL in a way that serves the societies’ missions and goals </li></ul><ul><li>BHL will digitize learned society backfiles and mount them through the BHL Portal at no cost. </li></ul><ul><li>Will provide a set of files to the publishers for reuse as they see fit </li></ul>
    28. 29. BHL Advantages <ul><li>Use of the articles will increase as evidenced by citation upsurge </li></ul><ul><li>Long-term management of the digital assets is provided by the BHL at no cost </li></ul><ul><li>Publishers’ content is embedded in the emerging knowledge ecology that is sweeping biology in this century </li></ul><ul><li>Structural markup of backfiles into conformance with NLM DTD (just starting) </li></ul>
    29. 30. Successes <ul><li>Entomological News </li></ul><ul><li>Journal of Hymenoptera Research </li></ul><ul><li>Herpetological Review </li></ul><ul><li>Publications of the San Diego Natural History Museum </li></ul><ul><li>California Academy of Sciences publications </li></ul><ul><li>And more ... </li></ul>
    30. 31. BHL Portal <ul><li>Library catalog-like interface to BHL literature </li></ul><ul><li>Enhanced structural analysis to provide volume/issue/article page access to the literature </li></ul><ul><li>Iterative development based on feedback from user community </li></ul><ul><li>Provide access to two key audiences: </li></ul><ul><ul><li>Humans </li></ul></ul><ul><ul><li>Machines </li></ul></ul>
    31. 32. Page Delivery
    32. 33. Taxonomic Intelligence
    33. 34. Web 2.0 Features <ul><li>Search </li></ul><ul><li>Browse </li></ul>
    34. 35. Discovered Bibliographies
    35. 36. Funding <ul><li>Initial grant from the MacArthur and Sloan Foundations (as part of the Encyclopedia of Life grant) </li></ul><ul><li>Additional support from parent institutions </li></ul><ul><li>Additional grants being actively pursued by BHL and individual members </li></ul>
    36. 38. Structure of the Encyclopedia of Life Serine Molecule
    37. 39. Serine Molecule Synthesis Center Field Museum Biodiversity Heritage Library Secretariat Smithsonian Education & Outreach Smithsonian/Harvard Informatics Marine Biological Laboratory & MOBOT
    38. 40. EOL Species Pages <ul><li>Built from a variety of new and existing sources </li></ul><ul><li>Views available for varying levels of expertise from novice to expert </li></ul><ul><li>Legacy literature a key component of the EOL species pages </li></ul>
    39. 43. Looking Forward <ul><li>Co-evolving bioinformatics resources produce a rich information ecology: </li></ul><ul><ul><li>Consortium for the Barcoding of Life (CBOL) with gene sequences deposited in GenBank. </li></ul></ul><ul><ul><li>GBIF’s Electronic Catalog of Taxonomic Names </li></ul></ul><ul><ul><li>Herbaria and museum specimen databases </li></ul></ul>
    40. 44. <ul><li>Quick ramp-up high early costs – development, mass scanning, etc. </li></ul><ul><li>Derive some long-term costs from the operating budgets of the member institutions (Examples under consideration: acquisitions budget, staff positions, etc.) </li></ul><ul><li>Integrate functions/tasks with wider efforts where appropriate, e.g. mass storage </li></ul>Looking Forward
    41. 45. The Long Now Strategy <ul><li>Institutions that are creating the BHL exist to persist through time. That’s an important part of their business </li></ul><ul><li>The future is uncertain, the technology landscape changes, people pass on. So create consortial structures that are low-overhead, flexible, and can respond quickly </li></ul>
    42. 46. A Global Library for Life In any well-appointed Natural History Library there should be found every book and every edition of every book dealing in the remotest way with the subjects concerned. Charles Davies Sherborn, Epilogue to Index Animalium , March 1922
    43. 49. Thank You ... for sticking around!
    44. 50. LINKS <ul><li>Biodiversity Heritage Library http://www.biodiversitylibrary.org/ </li></ul><ul><li>Biodiversity Heritage Library Blog http://biodiversitylibrary.blogspot.com </li></ul><ul><li>Encyclopedia of Life http://www.eol.org/ </li></ul><ul><li>Smithsonian Institution Libraries http:// www.sil.si.edu / </li></ul><ul><li>Universal Biological Indexer and Organizer http://www.ubio.org/ </li></ul><ul><li>Biologia Centrali-Americana http://www.sil.si.edu/digitalcollections/bca/ </li></ul>
    45. 51. CREDITS <ul><li>Thanks to: </li></ul><ul><ul><li>Chris Freeland, Missouri Botanical Garden </li></ul></ul><ul><ul><li>Tom Garnett, The Biodiversity Heritage Library </li></ul></ul><ul><ul><li>The staff at the Internet Archive </li></ul></ul><ul><li>Images from </li></ul><ul><ul><li>The Galaxy of Images, Smithsonian Libraries ( www.sil.si.edu/imagegalaxy ) </li></ul></ul><ul><ul><li>Martin R. Kalfatovic </li></ul></ul><ul><ul><li>Suzanne C. Pilsk </li></ul></ul><ul><ul><li>Bernard Scaife </li></ul></ul>