Digitizing Entomology: The Biodiversity Heritage Library @ the Smithsonian


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Digitizing Entomology: The Biodiversity Heritage Library @ the Smithsonian. Martin R. Kalfatovic. National Museum of Natural History, Department of Entomology Staff Meeting. Martin R. Kalfatovic. November 26, 2007. Washington, DC.

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  • Digitizing Entomology: The Biodiversity Heritage Library @ the Smithsonian

    1. 1. Digitizing Entomology The Biodiversity Heritage Library @ the Smithsonian Martin R. Kalfatovic Smithsonian Institution Libraries 26 November 2007 A Presentation for the Department of Entomology, National Museum of Natural History, Smithsonian Institution
    2. 2. Yet another physical difficulty is the task of assembling the library and indexes which will enable the student to work under proper conditions…. the beginner must now be prepared to spend liberally, or else must establish himself in an institution where a large library exists ; if he work by himself with only a few books, he will have to confine himself to a very narrow specialty indeed. 'The Limitations of Taxonomy' by J.M. Aldrich, Science , April 22, 1927, vol. LXV, no. 1686, p.381
    3. 3. BHL Timeline <ul><li>2003, Telluride. Encyclopedia of Life meeting </li></ul><ul><li>February 2005. London. Library and Laboratory: the Marriage of Research, Data and Taxonomic Literature </li></ul><ul><li>May 2005. Washington. Ground work for the Biodiversity Heritage Library </li></ul><ul><li>June 2006. Washington. Organizational and Technical meeting </li></ul><ul><li>August 2006. New York Botanical Garden. BHL Director’s Meeting. </li></ul><ul><li>October 2006. St. Louis/San Francisco. Technical meetings </li></ul><ul><li>February 2007. Museum of Comparative Zoology. Organizational meeting </li></ul><ul><li>May 2007. Encyclopedia of Life and BHL Portal Launch. Washington DC.. </li></ul>
    4. 4. BHL Members <ul><li>American Museum of Natural History (New York)‏ </li></ul><ul><li>Field Museum (Chicago)‏ </li></ul><ul><li>Natural History Museum (London)‏ </li></ul><ul><li>Smithsonian Institution (Washington) </li></ul><ul><li>Missouri Botanical Garden (St. Louis)‏ </li></ul><ul><li>New York Botanical Garden (New York)‏ </li></ul>
    5. 5. <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
    6. 6. BHL Members <ul><li>University of Illinois, Urbana-Champaign (contributing member)‏ </li></ul><ul><li>Scheme for addition of European and Asian partners under consideration </li></ul><ul><li>Additional categories of membership under consideration </li></ul>
    7. 8. Structure of the Encyclopedia of Life Serine Molecule
    8. 9. Serine Molecule Synthesis Center Field Museum Biodiversity Heritage Library Secretariat Smithsonian Education & Outreach Smithsonian/Harvard Informatics Marine Biological Laboratory & MOBOT
    9. 10. 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>
    10. 11. EOL Species Pages <ul><li>Legacy literature a key component of the EOL species pages </li></ul>
    11. 12. BHL Focus: Literature
    12. 13. BHL Focus: Literature
    13. 14. <ul><li>Core literature pre-1923: 400,000 (80 million pages)‏ </li></ul><ul><li>All pre-1923: 600-750,000 (120-150 million pages)‏ </li></ul><ul><li>All literature: 1.4-1.6 million (280-320 million pages)‏ </li></ul>Mass. Zoological and Botanical Survey Reports on the fishes, reptiles and birds of Massachusetts , 1839 BHL Focus: Literature
    14. 15. Selection Tools <ul><li>Combined Serial list for selection of title to scan to avoid duplication of effort </li></ul><ul><li>Mongraphic “de-duping” algorithm </li></ul><ul><li>OCLC Collection Analysis </li></ul>
    15. 16. <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
    16. 17. Selection <ul><li>Marine Biological Laboratory/WHOI </li></ul><ul><ul><li>Marine monographs </li></ul></ul><ul><ul><li>General Science </li></ul></ul><ul><li>Museum of Comparative Zoology </li></ul><ul><ul><li>MCZ publications </li></ul></ul><ul><ul><li>Herpetology monographs and serials </li></ul></ul><ul><ul><li>Ichthyology monographs and serials </li></ul></ul>
    17. 18. Selection <ul><li>University of Illinois </li></ul><ul><ul><li>Fieldiana </li></ul></ul><ul><ul><li>Natural history of Illinois </li></ul></ul><ul><li>American Museum of Natural History </li></ul><ul><ul><li>AMNH publications </li></ul></ul><ul><ul><li>Ornithology </li></ul></ul><ul><li>Natural History Museum </li></ul><ul><ul><li>NHM publications </li></ul></ul><ul><ul><li>Major natural history general serials </li></ul></ul>
    18. 19. Selection <ul><li>Botany Collections </li></ul><ul><ul><li>Missouri Botanical Garden, New York Botanical Garden, Harvard Botany Libraries, and Royal Botanic Garden, Kew will cooperatively develop a methodology for botanical publications </li></ul></ul>
    19. 20. Selection <ul><li>Smithsonian Institution Libraries </li></ul><ul><ul><li>Smithsonian publications </li></ul></ul><ul><ul><li>Marine mammals </li></ul></ul><ul><ul><li>Fishes </li></ul></ul><ul><ul><li>Selected special collections materials </li></ul></ul><ul><ul><li>Entomology collection </li></ul></ul>
    20. 21. 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>
    21. 22. 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 week </li></ul></ul>
    22. 23. BHL Scanning Centers <ul><li>Northeast Regional Scanning Center </li></ul><ul><ul><li>10 Scribe machines </li></ul></ul><ul><ul><li>MBL/WHO (scanning)‏ </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>
    23. 24. 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>
    24. 25. BHL Scanning Centers <ul><li>Washington, DC </li></ul><ul><ul><li>1 Scribe machine at Smithsonian Libraries </li></ul></ul><ul><ul><li>Planned 10 Scribe facility in the Washington area (Spring 2008)‏ </li></ul></ul>
    25. 26. Scanning Stats <ul><li>2 million plus total pages scanned </li></ul><ul><li>250,000 plus from the Natural History Museum, London </li></ul><ul><li>150,000 from the MBL/WHOI library </li></ul><ul><li>Fieldiana, 15,000 plus pages </li></ul>
    26. 27. Scanning Stats <ul><li>Smithsonian Libraries </li></ul><ul><ul><li>250,000 pages (non-Scribe scanned, 1996-2007)‏ </li></ul></ul><ul><ul><li>50,000 Scribe scanned pages (since August 2007)‏ </li></ul></ul><ul><li>Other libraries (non-Scribe)‏ </li></ul><ul><ul><li>MOBOT: 780,000 </li></ul></ul><ul><ul><li>AMNH: 150,000 </li></ul></ul>
    27. 28. But what about ...
    28. 30. <ul><li>Difficult (impossible?) to re-purpose much of the material </li></ul><ul><li>Quality of images often questionable </li></ul><ul><li>“ Frankenbooks” </li></ul><ul><li>Sketchy / inaccurate bibliographic data </li></ul>But what about
    29. 31. 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>http://www.biodiversitylibrary.org
    30. 32. 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>
    31. 33. 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>
    32. 34. <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
    33. 35. BHL & Publishers
    34. 36. 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>
    35. 37. 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>
    36. 38. 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>University of Kansas natural history publications </li></ul><ul><li>And more ... </li></ul>
    37. 39. 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>
    38. 40. Page Delivery
    39. 41. Taxonomic Intelligence
    40. 42. Web 2.0 Features <ul><li>Search </li></ul><ul><li>Browse </li></ul>
    41. 43. Discovered Bibliographies
    42. 44. Funding & the Future <ul><li>Initial grant from the MacArthur and Sloan Foundations (as part of the Encylopedia 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>
    43. 45. Funding & the Future <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>Hebaria and museum specimen databases </li></ul></ul>
    44. 46. <ul><li>Financial Sustainability Strategy </li></ul><ul><li>Quick ramp-up high early costs – development, mass scanning, etc. Drive long-term costs down the asymptote toward zero. </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><ul><li>Clear roles for staff who wear multiple hats. Two full-time grant funded positions currently but >15 staff who make substantive contributions. </li></ul>Funding & the Future
    45. 47. <ul><li>The Long Now Strategy </li></ul><ul><ul><li>Institutions that are creating the BHL exist to persist through time. That’s an important part of their business. Use them! </li></ul></ul><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></ul>Funding & the Future
    46. 48. 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. One never knows wherein one edition differs from or supplements the other and unless these are on the same table at the same time it is not possible to collate them properly. Charles Davies Sherborn, Epilogue to Index Animalium , March 1922
    47. 49. Thank You
    48. 50. 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 Project </li></ul></ul><ul><ul><li>Suzanne C. Pilsk, Smithsonian Institution Libraries </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>Keri Thompson </li></ul></ul><ul><ul><li>Bernard Scaife </li></ul></ul>