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An International Cooperative Digital Library for Taxonomic Literature: The Biodiversity Heritage Library
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An International Cooperative Digital Library for Taxonomic Literature: The Biodiversity Heritage Library


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An International Cooperative Digital Library for Taxonomic Literature: The Biodiversity Heritage Library. Martin Kalfatovic. The Catholic University of America, School of Library and Information …

An International Cooperative Digital Library for Taxonomic Literature: The Biodiversity Heritage Library. Martin Kalfatovic. The Catholic University of America, School of Library and Information Science. LSC 715. 6 June 2008. Washington, DC.

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    • 1. An International Cooperative Digital Library for Taxonomic Literature Martin R. Kalfatovic Smithsonian Institution Libraries 6 June 2008
    • 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. Taxonomic Literature
      • Taxonomic descriptions must be published for the name to be valid
      • Publications must be available to the public through trusted sources
      • Libraries have been the traditional place
    • 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. Taxonomic Literature
      • Over 250 years of systematic description of life
      • Systema naturae (10 th ed. 1758) by Carl von Linné
    • 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. 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)‏ Royal Botanic Garden, Kew Botany Libraries, Harvard University Ernst Mayr Library of the Museum of Comparative Zoology, Harvard University Marine Biological Laboratory / Woods Hole Oceanographic Institution
    • 8. BHL Members
      • University of Illinois, Urbana-Champaign (contributing member)‏
      • Scheme for addition of European and Asian partners underway
      • Additional categories of membership under consideration
    • 9. BHL Focus: Literature
    • 10. BHL Focus: Literature
    • 11. The Internet Archive
      • 501(c)(3) organization
      • Dedicated to “Universal Access to Human Knowledge”
      • Founder of the Open Content Alliance
      • Provides:
        • Mass scanning
        • Archival storage of files
        • Image processing
        • Technology development
    • 12. Scribe Scanner
      • Single Scribe Machine
        • Custom built by the Internet Archive
        • Human operated
        • 3,500 page per shift per day
    • 13. BHL Scanning Centers
      • Northeast Regional Scanning Center
        • 10 Scribe machines
        • MBL/WHOI
        • Harvard
      • New York Public Library
        • 10 Scribe machines
        • AMNH
        • NYBG
    • 14. BHL Scanning Centers
      • University of Illinois
        • 2 Scribe machines
      • Natural History Museum, London
        • 1 Scribe machine
      • Missouri Botanical Garden
        • Non-Scribe operation
    • 15. BHL Scanning Centers
      • Washington, DC
        • 1 Scribe machine at Smithsonian Libraries
        • 10 Scribe facility at Library of Congress with Fedlink (operational Spring 2008)‏
    • 16. Scanning Stats: Now
      • 5.5 million plus total pages scanned (and growing daily)‏
        • <90,000 Fieldiana (via UIUC)‏
        • >100,000 pages each Harvard, New York Botanical Garden,
        • 225,000+ pages from the American Museum of Natural History
        • 400,000+ from Smithsonian Libraries
        • 500,000+ from the Natural History Museum, London
        • 800,000 Missouri Botanical Garden Library
        • 1,000,000+ from the MBL/WHOI library
    • 17. But what about ...
    • 18.  
    • 19. BHL Google (the difference between)‏
      • Bibliographic accuracy for all materials
      • Ability to re-purpose and reuse all data as needed
      • Congruence of original printed materials to digital versions
    • 20. Persistent Identifiers
      • Stable URL
      • Handle
      • DOI
      • BICI/SICI
      • ISSN
      • ISBN
      • LSIDs
    • 21. Structural Markup
      • <article>
      •   <author> L. O. HOWARD. </author>
      •   <volume> 1 </volume>
      •   <issue> 2 </issue>
      •   <start_page> 65 </start_page>
      •   <end_page> 86 </end_page>
      •   <start_count_page> 85 </start_count_page>
      •   <end_count_page> 106 </end_count_page>
      •   <start_page_image_file> 3908800908001101smthrich_0085.djvu </start_page_image_file>
      •   <end_page_image_file> 3908800908001101smthrich_0106.djvu </end_page_image_file>
      •   </article>
    • 22. Semantic Markup
      • 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.
      • Integrated Open Taxonomic Access (INOTAXA)
    • 23.
      • 10.7 million name strings in NameBank
      • Uses sophisticated algorithm (TaxonGrab) to locate likely name strings in OCR text
      • Iterative processing of BHL texts will both increase the number of name strings in NameBank and increase the accuracy of name string recognition
      Taxonomic Intelligence
    • 24. BHL & Publishers
    • 25. Permissions
      • Seek permissions from copyright holders
      • 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
      • BHL will digitize learned society backfiles and mount them through the BHL Portal at no cost.
      • Will provide a set of files to the publishers for reuse as they see fit
    • 26. BHL Advantages
      • Use of the articles will increase as evidenced by citation upsurge
      • Long-term management of the digital assets is provided by the BHL at no cost
      • Publishers’ content is embedded in the emerging knowledge ecology that is sweeping biology in this century
      • Structural markup of backfiles into conformance with NLM DTD (just starting)‏
    • 27. Successes
      • Entomological News
      • Journal of Hymenoptera Research
      • Herpetological Review
      • Publications of the San Diego Natural History Museum
      • California Academy of Sciences publications
      • And more ...
    • 28. BHL Portal
      • Library catalog-like interface to BHL literature
      • Enhanced structural analysis to provide volume/issue/article page access to the literature
      • Iterative development based on feedback from user community
      • Provide access to two key audiences:
        • Humans
        • Machines
    • 29. Funding
      • Initial grant from the MacArthur and Sloan Foundations (as part of the Encyclopedia of Life grant)‏
      • Additional support from parent institutions
      • Additional grants being actively pursued by BHL and individual members
    • 30.  
    • 31. Looking Forward
      • Co-evolving bioinformatics resources produce a rich information ecology:
        • Consortium for the Barcoding of Life (CBOL) with gene sequences deposited in GenBank.
        • GBIF’s Electronic Catalog of Taxonomic Names
        • Herbaria and museum specimen databases
    • 32.
      • Quick ramp-up high early costs – development, mass scanning, etc.
      • Derive some long-term costs from the operating budgets of the member institutions (Examples under consideration: acquisitions budget, staff positions, etc.)‏
      • Integrate functions/tasks with wider efforts where appropriate, e.g. mass storage
      Looking Forward
    • 33. The Long Now Strategy
      • Institutions that are creating the BHL exist to persist through time. That’s an important part of their business
      • The future is uncertain, the technology landscape changes, people pass on. So create consortial structures that are low-overhead, flexible, and can respond quickly
    • 34. 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
    • 35.  
    • 36.
      • Midrange estimate: 25% of 5 million species = 1.3 million species, or roughly 1 every 20 minutes
      • Low estimate: 15% of 4 million species = 0.6 million species, or roughly 1 every 44 minutes.
      • High estimate: 50% of 6 million species = 3 million species, or roughly 1 every 9 minutes
      • Conservation International
    • 37.  
    • 38.  
    • 39.  
    • 40.  
    • 41. Thank You ... for sticking around!
    • 42. LINKS
      • Biodiversity Heritage Library
      • Biodiversity Heritage Library Blog
      • Encyclopedia of Life
      • Smithsonian Institution Libraries http:// /
      • Universal Biological Indexer and Organizer
      • Biologia Centrali-Americana
    • 43. CREDITS
      • Thanks to:
        • Chris Freeland, Missouri Botanical Garden
        • Tom Garnett, The Biodiversity Heritage Library
        • The staff at the Internet Archive
      • Images from
        • The Galaxy of Images, Smithsonian Libraries ( )‏
        • Martin R. Kalfatovic
        • Suzanne C. Pilsk
        • Bernard Scaife