Biodiversity Informatics <ul><li>Evolving in the Biological Sciences </li></ul>National Geographic News, 05/21/08  Tuatara...
encyclopedists <ul><li>Nomencaltor Animalia </li></ul><ul><li>“ Seahorse” </li></ul><ul><li>Conrad Gesner 1570 </li></ul>
encyclopedists <ul><li>Denis Diderot – 1751 </li></ul><ul><li>Encyclopedie </li></ul><ul><li>Precursor to Sematic Web Thin...
Serine Molecule Biodiversity Heritage  Library Synthesis Center Field Museum Informatics Marine Biological Laboratory & MO...
<ul><li>“ The launch of the Encyclopedia of Life will have a profound and creative effect in science… this effort will lay...
HOW to build this enterprise <ul><li>Recognition of the importance of all types of material in all formats </li></ul><ul><...
<ul><li>Collaborative   Tree of Life   distributed   semantic   Biodiversity Heritage Library   ever evolving   TED   all ...
Biodiversity Heritage Library Mission: Provide Open Access to Biodiversity Literature Goals: <ul><ul><li>Digitize the core...
 
 
BHL
Internet Archive Scribe: Boston
How big is the  Biodiversity domain? <ul><li>Over 5.4 million books dating back to 1469 </li></ul><ul><li>800,000 monograp...
Classes of Texts <ul><li>Public Domain – pre 1923 </li></ul><ul><li>Non-profit society journals </li></ul><ul><li>Post 192...
Where are we? <ul><li>5,000,000 scanned pages </li></ul><ul><li>13,000 volumes </li></ul><ul><li>BHL Portal </li></ul><ul>...
Carolus Linnaeus,  “father of modern taxonomy” <ul><li>“ Who Knowth not the name  </li></ul><ul><li>Knowth not the subject...
“ All accumulated information of a species is tied to a scientific name, a name that serves as a link between what has bee...
<ul><li>Information about named groups (taxa) of organisms (taxon-related information) </li></ul><ul><li>Extends back at l...
The challenge for contemporary DIGITAL libraries Goal: Use one name to find the content for all names
Names – the only universal metadata for Biology   Names offer a logical way to search for and index content <ul><li>Names ...
Who is affected by these problems? Libraries Publishers Museums Federal Agencies
Serious challenges in federated environments One organism 4 scientific names 4 maps We want one map
Reconciliation – linking alternative names for the same organism A query initiated with any name, can be expanded to all n...
 
<ul><li>All names  & all Classifications  ClassificationBank   </li></ul><ul><li>Alternative names reconciled </li></ul><u...
<ul><li>data from various sources  may be merged </li></ul><ul><li>red dots on the map link back to the website that provi...
Taxonomic Intelligence <ul><li>Lexicon of Scientific Names </li></ul><ul><li>Reconciliation and Disambiguation </li></ul><...
uBio <ul><li>10.7 Million+ Name Strings </li></ul><ul><li>Reconciliation Groups </li></ul><ul><li>http:// www.ubio.org </l...
uBioRSS Taxonomically Intelligent RSS Feed Aggregator
MBL WHOI Library – Woods Hole authors’ publications
MBL WHOI Library – Woods Hole species publications
Taxonomically intelligent scientific text parsing
 
 
<ul><li>Search </li></ul><ul><li>Browse </li></ul>
Taxonomic intelligence works miracles <ul><li>It will benefit any initiative that uses distributed and heterogeneous infor...
Acknowledgments Catherine Norton Patrick Leary David Remsen Diane Rielinger David Patterson Neil Sarkar Gerald Weissmann A...
 
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Special Libraries Associatin

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  • Living Dinosaur is the fastest-evolving animal…Tuatara – looks hasn’t changed much .. But DNA says differently.. They can adapt faster than bears, horses, and many other warm- blooded vertebrates 200 million years old… outside the same… inside is changing its DNA to adapt… and live through global warming, etc. Libraries look the same but they have evolved… !
  • Special Libraries Associatin

    1. 1. Biodiversity Informatics <ul><li>Evolving in the Biological Sciences </li></ul>National Geographic News, 05/21/08 Tuatara Libraries ?????
    2. 2. encyclopedists <ul><li>Nomencaltor Animalia </li></ul><ul><li>“ Seahorse” </li></ul><ul><li>Conrad Gesner 1570 </li></ul>
    3. 3. encyclopedists <ul><li>Denis Diderot – 1751 </li></ul><ul><li>Encyclopedie </li></ul><ul><li>Precursor to Sematic Web Thinking </li></ul><ul><li>“ So great is the power of linkage and order that even the mundane becomes important” DD </li></ul><ul><li>Encyclopedia… the word signifies unity of knowledge </li></ul>
    4. 4. Serine Molecule Biodiversity Heritage Library Synthesis Center Field Museum Informatics Marine Biological Laboratory & MOBOT Education & Outreach Smithsonian/Harvard Secretariat Smithsonian
    5. 5. <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>
    6. 6. HOW to build this enterprise <ul><li>Recognition of the importance of all types of material in all formats </li></ul><ul><li>Recognition that a single set of rules, a single mechanism, a single type of discovery tool cannot accomplish everything </li></ul><ul><li>Recognition that entities other than libraries can, want to, and will contribute to the information-finding construct </li></ul><ul><li>Recognition that all of us are part of the whole, and that it is an interdependent relationship, not the relationship of an all-powerful mother ship (LC) to a fleet of shuttle craft </li></ul><ul><li>Recognition that the way we have made decisions in the past may no longer serve us well </li></ul>
    7. 7. <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>
    8. 8. Biodiversity Heritage Library Mission: Provide Open Access to Biodiversity Literature Goals: <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>
    9. 11. BHL
    10. 12. Internet Archive Scribe: Boston
    11. 13. 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% pre-1923 </li></ul>
    12. 14. Classes of Texts <ul><li>Public Domain – pre 1923 </li></ul><ul><li>Non-profit society journals </li></ul><ul><li>Post 1923 monographs/journals </li></ul><ul><ul><li>Monographs without © renewals </li></ul></ul><ul><ul><li>Commercial journals with permission </li></ul></ul>
    13. 15. Where are we? <ul><li>5,000,000 scanned pages </li></ul><ul><li>13,000 volumes </li></ul><ul><li>BHL Portal </li></ul><ul><li>Sloan, MacArthur, Moore Foundation- funding </li></ul><ul><li>49 full run journals </li></ul>
    14. 16. Carolus Linnaeus, “father of modern taxonomy” <ul><li>“ Who Knowth not the name </li></ul><ul><li>Knowth not the subject” </li></ul><ul><li>Linnaeus, 1737, </li></ul><ul><li>Critica Botanica n 210. </li></ul>Royal Science Academy of Sweden, portrait
    15. 17. “ 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
    16. 18. <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>In books, journals, surveys, 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
    17. 19. The challenge for contemporary DIGITAL libraries Goal: Use one name to find the content for all names
    18. 20. 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>
    19. 21. Who is affected by these problems? Libraries Publishers Museums Federal Agencies
    20. 22. Serious challenges in federated environments One organism 4 scientific names 4 maps We want one map
    21. 23. Reconciliation – linking alternative names for the same organism A query initiated with any name, can be expanded to all names and will unify data associated with each
    22. 25. <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
    23. 26. <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
    24. 27. Taxonomic Intelligence <ul><li>Lexicon of Scientific Names </li></ul><ul><li>Reconciliation and Disambiguation </li></ul><ul><li>Hierarchical Inclusion </li></ul><ul><li>Integration into Information Retrieval </li></ul><ul><li>Linkage to Other Data Types (e.g., Molecular, Morphological, Phenotype) </li></ul>
    25. 28. uBio <ul><li>10.7 Million+ Name Strings </li></ul><ul><li>Reconciliation Groups </li></ul><ul><li>http:// www.ubio.org </li></ul><ul><li>FIND IT – scientific name recognition algorithm </li></ul><ul><li>Training and improving algorithm </li></ul>
    26. 29. uBioRSS Taxonomically Intelligent RSS Feed Aggregator
    27. 30. MBL WHOI Library – Woods Hole authors’ publications
    28. 31. MBL WHOI Library – Woods Hole species publications
    29. 32. Taxonomically intelligent scientific text parsing
    30. 35. <ul><li>Search </li></ul><ul><li>Browse </li></ul>
    31. 36. 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>
    32. 37. Acknowledgments Catherine Norton Patrick Leary David Remsen Diane Rielinger David Patterson Neil Sarkar Gerald Weissmann A.W. Mellon Foundation Alfred P. Sloan Foundation John D. & Catherine T. MacArthur Foundation Internet Archive Christopher Freeland Tom Garnett Martin Kalfatovic Graham Higley BHL & EOL Teams
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