Mla May 7


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  • Mla May 7

    1. 1. The Encyclopedia of Life, BioDiversity Heritage Library, Biodiversity Informatics MBLWHOI Library Cathy Norton Deputy Director, BHL Massachusetts Library Association May 7, 2008
    2. 2. <ul><li>“ The launch of the Encyclopedia of Life will have a profound and creative effect in science… this effort will lay out new directions for research in Every branch of biology: </li></ul><ul><ul><li>E.O. Wilson </li></ul></ul>
    3. 3. <ul><li>Collaborative Tree of Life distributed semantic Biodiversity Heritage Library ever evolving TED all information Synthesis Center Oh wow! SpeciesBase ClassificationBank Education and Outreach ANTS index MacArthur Foundation taxonomic intelligence modular software communal ownership user defined AvenueA | Razorfish OBIS MBL free visualization images WorkBench sounds phylogeny web 2.0 names-based infrastructure Atlas of Living Australia February 2008 Google Marine Biological Laboratory all species Smithsonian FISHBASE Harvard Field Museum Tree of Life E. O. Wilson aggregation / mashup EDIT ScratchPad widgets MOBOT NHM AMNH NYBotancial Sloan Foundation GBIF llison l NameBank videos National Geographic any classification TDWG/BIS </li></ul>
    4. 4. Encyclopedia of Life <ul><li>Major project to create a single Web page for every known species (1.8 million!) </li></ul><ul><li>Total funding will reach at least $50M </li></ul><ul><li>EOL needs the literature underpinning in the BHL project </li></ul><ul><li>BHL now key partner in EOL project </li></ul><ul><li>Launched on 9 th May, 2007 </li></ul><ul><ul><li>First 30,000 pages launched at TED Feb 27th, 2008 </li></ul></ul>
    5. 5. Serine Molecule Biodiversity Heritage Library Synthesis Center Field Museum Informatics Marine Biological Laboratory & MOBOT Education & Outreach Smithsonian/Harvard Secretariat Smithsonian
    6. 6. This library serves the all of the scientific institutions in Woods Hole and other scientific groups in the area. The Library is facing a new dynamic phase
    7. 9. <ul><ul><li>Digitize the core published literature on biodiversity and put on the Web </li></ul></ul><ul><ul><li>Agree on approaches with the global taxonomic community, rights holders and others </li></ul></ul>Mission: Provide Open Access to Biodiversity Literature Goals:
    8. 11. How big is the Biodiversity domain? <ul><li>Over 5.4 million books dating back to 1469 </li></ul><ul><li>800,000 monographs </li></ul><ul><li>40,000 journal titles ,(12,5000 current ) </li></ul><ul><li>50% pre1923 </li></ul>
    9. 12. Why now? <ul><li>Cost low – 10-19 cents a page </li></ul><ul><li>Other projects funded recently – BL/Microsoft /Google big ten </li></ul><ul><li>Tractable, well-defined scientific domain </li></ul><ul><li>Taxonomic information has exceptionally longevity </li></ul><ul><li>Supports GBIF and other international initiatives – including CBD, ABS, Darwin Declaration </li></ul>
    10. 13. <ul><li>Taxonomists and other scientists will have access to biodiversity literature - globally </li></ul><ul><li>Will provide the developing world with access to the historical literature </li></ul><ul><li>Scientists working in many biological domains – and other areas like meteorology, geology, ecology, genomics, etc – will get access </li></ul><ul><li>Advance objectives of the Convention on Biological Diversity </li></ul>Benefits
    11. 14. <ul><li>Less space needed for Library collections In Lillie – space freed for other uses </li></ul><ul><li>% material can be stored off-site in ‘dark storage. FTP </li></ul><ul><li>Our scientists will get access at their desk or in the field </li></ul><ul><li>Library focus will shift to informatics </li></ul><ul><li>Virtual web library will increase public access </li></ul><ul><li>Library staff will change – </li></ul>Benefits to the MBLWHOI Library
    12. 15. <ul><li>Key partner of Encyclopedia of Life </li></ul><ul><li>Working Groups have agreed technical plan , metadata standards and image standards </li></ul><ul><li>Internet Archive to be technical partner – scanning and hosting </li></ul><ul><li>‘ Scribe’ scanners now installed in NHM NYC and in Boston </li></ul><ul><li>4.1 million pages already available </li></ul>Where are we now?
    13. 16. <ul><li>Classes of texts </li></ul><ul><li>Public Domain – pre-1923 </li></ul><ul><li>Non-profit society journals </li></ul><ul><li>Post-1923 monographs </li></ul><ul><li>some with copyright renewals </li></ul><ul><li>some without copyright renewals </li></ul><ul><li>Commercial journals </li></ul>
    14. 17. <ul><li>BHL Seeks Permissions </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 learned society for reuse as they see fit. </li></ul><ul><li>Will index the issues using Taxonomic Intelligence increasing their usability. </li></ul>
    15. 18. <ul><li>Benefits </li></ul><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 so it’s contributors </li></ul><ul><li>Content will be integrated into EOL project through TI nomenclatural linking. </li></ul>
    16. 19. Levinus Vincent Elenchus tabularum, pinacothecarum, 1719 <ul><li>The cited half-life of publications in </li></ul><ul><li>Taxonomy is longer than in any other </li></ul><ul><li>Scientific discipline. </li></ul><ul><li>The decay rate is longer than in most </li></ul><ul><li>scientific disciplines. </li></ul><ul><li>Maco-economic case for open access </li></ul><ul><li>Tom Moritz </li></ul><ul><li>Current taxonomic literature often relies </li></ul><ul><li>on texts and specimens> 100 years old. </li></ul>
    17. 20. The Long NOW Strategy Georges Louis Leclerc, comte de Buffon Histoire naturelle : générale et particulière (Oiseaux) , 1799-1808 Convention on Biological Diversity: Article 17 <ul><li>Institutions that are creating the BHL exist to persist through time. </li></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><ul><ul><li>Interoperabilty is the key.. Repository islands will sink </li></ul></ul>
    18. 21. Biologia Centrali-American Physical Distribution… Now… you can Parse Date, harvest out data, Wealth of informaiton locked on the pages are now liberated!
    19. 22. Henry Walter Bates The Naturalist on the River Amazons , 1863 Most literature is in the developed world the Northern Hemisphere Most Biodiverstiy is in the developing world the Southern Hemisphere
    20. 23. Progne subis- Purple Martin Illustrations of the nest and eggs of birds of Ohio , 1879-1886 Library and Laboratory: the Marriage of Research, Data and Taxonomic Literature London, February 2005 Eighty participants from 22 countries gathered to discuss the status and future of access to the taxonomic literature and to propose an agenda for actions that would improve the research environment for taxonomy. The participants were taxonomists; librarians; publishers; representatives of learned and professional societies, private foundations and government agencies; and specialists in information and communications technology. Scalable Mass Scanning Contracts Firewalls Security Loading Docks Trucks 180 mile round trip!
    21. 24. Internet Archive Scribe: Boston
    22. 25. Ernest Ingersoll Hand-book to the National Museum … Smithsonian Institution , 1886 Mass Scanning Workflow Bid Lists Pick Lists Packing Lists Serials Management Monographic Management Stickers for Media and carts Rare Books-vaults
    23. 26. Jacob Christian Schäffer Elementa entomologica . . . 1766. BHL Portal Serve image and test files: create volume, Part, piece, metadata; ingest page level Metadata at scanning level; apply Globally Unique Identifiers (GUIDs) for linking to Other taxonomic services.
    24. 27. Biodiversity Heritage Library
    25. 28. Biodiverstiy Informatics
    26. 29. “ All accumulated information of a species is tied to a scientific name, a name that serves as a link between what has been learned in the past and what we today add to the body of knowledge.” ~ Grimaldi & Engel, 2005, Evolution of the Insects
    27. 30. Who knowth not the name, knoweth not the subject Linnaeus, 1737, Critica Botanica n 210 .
    28. 31. <ul><li>Information about named groups (taxa) of organisms (taxon-related information) </li></ul><ul><li>Extends back at least 1000 years </li></ul><ul><li>Books, journals, surveys </li></ul><ul><li>Museum specimens, herbaria </li></ul><ul><li>In many languages and is distributed </li></ul>From T.E. Glover, The Fishes of Southwestern Japan, c.1870
    29. 32. The challenge for contemporary DIGITAL libraries Goal: Use one name to find the content for all names related to “that” species.
    30. 33. Names – the only universal metadata for Biology Names offer a logical way to search for and index content <ul><li>Names annotate data objects </li></ul><ul><li>All names annotate all data objects </li></ul><ul><li>A compilation of all names ever used is the foundation of a universal index for biology or for a semantic web for biology </li></ul>
    31. 34. Who is affected by these problems? Libraries Publishers Museums Federal Agencies
    32. 35. Serious challenges in federated environments One organism 4 scientific names 4 maps We want one map
    33. 36. Reuse, don’t rebuild
    34. 38. <ul><li>All names & all Classifications ClassificationBank </li></ul><ul><li>Alternative names reconciled </li></ul><ul><li>Similar names disambiguated </li></ul><ul><li>Exploit hierarchies to browse and search, build a comprehensive classification </li></ul><ul><li>Improve performance with federated systems </li></ul><ul><li>Read documents, web sites, databases and taxonomically indexing the content </li></ul><ul><li>Create a unified portal to information about organisms on the internet </li></ul>Taxonomic intelligence is the inclusion of taxonomic practices, skills and knowledge within informatics services to manage information about organisms
    35. 39. <ul><li>data from various sources may be merged </li></ul><ul><li>red dots on the map link back to the website that provided the geographical </li></ul><ul><li>co-ordinates </li></ul>Specimen distribution data from remote sources
    36. 40. uBio Programmers BHL Taxonomic Intelligence Tool Georges Louis Leclerc, comte de Buffon Histoire naturelle : générale et particulière (Oiseaux) , 1799-1808
    37. 41. uBio <ul><li>10.7 Million+ Name Strings </li></ul><ul><li>Reconciliation Groups </li></ul><ul><li> </li></ul>
    38. 42. Training and Improving the Algorithm
    39. 43. uBioRSS Taxonomically Intelligent RSS Feed Aggregator
    40. 44. uBioRSS Taxonomically Intelligent RSS Feed Aggregator
    41. 45. MBL WHOI Library – Woods Hole authors’ publications
    42. 46. MBL WHOI Library – Woods Hole species publications
    43. 47. Taxonomic intelligence works miracles! <ul><li>It will benefit any initiative that uses distributed and heterogeneous information about biology </li></ul><ul><li>Distributed content on the same species can be drawn together because different names will be standardized through reconciliation </li></ul><ul><li>We can read documents, find names, catalog and taxonomically index documents </li></ul><ul><li>Produce a framework around which we can organize and assemble remote and local content </li></ul>
    44. 48. Taxonomically intelligent scientific text parsing
    45. 51. <ul><li>Search </li></ul><ul><li>Browse </li></ul>
    46. 52. <ul><li>“ It is exciting to anticipate the scientific chords we might hear once 1.8 million notes are brought together through this instrument. Potential EOL users are professional and citizen scientists, teachers, students, media, environmental managers, families and artists. The site will link the public and scientific community in a collaborative way that’s without precedent in scale.” </li></ul><ul><ul><ul><li>Jim Edwards, Executive Director, EOL </li></ul></ul></ul>
    47. 54. Acknowledgments Catherine Norton Patrick Leary David Remsen Diane Rielinger David Patterson Neil Sarkar A.W. Mellon Foundation Alfred P. Sloan Foundation John D. & Catherine T. MacArthur Foundation Internet Archive Christopher Freeland Tom Garnett M artin Kalfatovic Graham Higley BHL & EOL Teams
    48. 55.
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