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Biodiversity Heritage Library Project “Underway” Taxonomic Intelligence for LARGE Scale Digitization Projects
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Biodiversity Heritage Library Project “Underway” Taxonomic Intelligence for LARGE Scale Digitization Projects


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Biodiversity Heritage Library Project “Underway” Taxonomic Intelligence for LARGE Scale Digitization Projects by Cathy Norton, Marine Biological Laboratory / Woods Hole Oceanographic Institution …

Biodiversity Heritage Library Project “Underway” Taxonomic Intelligence for LARGE Scale Digitization Projects by Cathy Norton, Marine Biological Laboratory / Woods Hole Oceanographic Institution Library. 33rd IAMSLIC: Changes on the Horizon.
October 7-11, 2007. Sarasota. FL

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    • 1. Biodiversity Heritage Library Project “Underway” Taxonomic Intelligence for LARGE Scale Digitization Projects 33 rd IAMSLIC Conference Sarasota, FL Cathy Norton MBLWHOI Library Director Oct. 7-11, 2007
    • 2. This library serves the MBL, WHOI, USGS, NMFS, SEA, WHRC, and other scientific groups in the area. Facing a new dynamic phase NMFS - 1871 MBL - 1888 WHOI - 1930 USGS - 1960 SEA - 1971 WHRC - 1985 Woods Hole Scientific Community
    • 3.
      • Biodiversity Heritage Libraries
      • Open Content Alliance, Principles
      • Internet Archive Partner
      • Northeast Regional Digitizing Center @Boston Public Library
      • Taxonomic Intelligence- modernizing the literature
    • 4.  
    • 5. Vision Build a Digital Open Access Library for Biodiversity Literature
    • 6. Meetings in Colorado,2005 London, 2005 laboratories and libraries Washington BHL 2006 Simultaneous Meetings in Woods Hole for BHL& EOL 2006
    • 7. Members
      • American Museum of Natural History
      • Botany Library- Harvard
      • British Natural History Museum, UK
      • Field Museum
      • MBLWHOI Library
      • Missouri Botanical Gardens
      • Museum of Comparative Zoology-Harvard
      • New York Botanical Gardens
      • Royal Botanical Gardens @ Kew ,UK
      • Smithsonian Museum of Natural History
        • University of Illinois, contributing member
    • 8.
      • Legacy Taxonomic Literature available in museums has limited access
      • Much of it is rare
      • Systematic literature depends on the historic literature
      • The cited half-life of natural history is longer than that of any other scientific domain
      • 90% of Biodiversity Information is in these libraries
      • 90% of Biodiversity is in 3rd world countries like Africa and South America
      Why BHL now ?
    • 9. The Open Content Alliance (OCA) represents the collaborative efforts of a group of cultural, technology, nonprofit, and governmental organizations from around the world that will help build a permanent archive of multilingual digitized text and multimedia content.
    • 10. Principles of OCA
      • The OCA will encourage the greatest possible degree of access to and reuse of collections in the archive, while respecting the rights of content owners and contributors.
      • Contributors will determine the terms and conditions under which their collections are distributed and how attribution should be made.
      • IA need not be obligated to accept all content that is offered to it and may give preference to that which can be made widely accessible.
      • IA will offer collection and item-level metadata of its hosted collections in a variety of formats.
      • IA welcomes efforts to create and offer tools (including finding aids, catalogs, and indexes) that will enhance the usability of the materials in the archive.
      • Copies of IA collections will reside in multiple archives internationally to ensure their long-term preservation and accessibility to all.
    • 11. Name: BioDiversity Heritage Library Wiki- for all involved Web Presence! Where to begin?
    • 12.  
    • 13.  
    • 14.  
    • 15.  
    • 16.  
    • 17.  
    • 18.  
    • 19.  
    • 20.  
    • 21.  
    • 22.  
    • 23. In the end… simplicity…
    • 24.
      • BHL invited to be a part of the EOL project.
      • EOL - build one web page for each known species… 1.8 million!
      • Alfred P. Sloan and Macarthur Foundations
    • 25.  
    • 26.  
    • 27. Northeast Digitization Center
      • Boston Public Library
        • Space infrastructure
      • 10 Scanning Stations
      • .10 ¢ per page
      • 50 Books per day
      • Journals- metadata,foldouts
      • Transportation
        • ILL delivery
        • moving company
        • 15 rolling carts per trip
      Photo by lesveilleus 9/20/07 Cathy Norton, Bernie Margolis, Brewster Kale
    • 28. Economies of Scale
      • North East Regional Digitization Center
      • Agreements made with the Boston Public Library to Include the Boston Library Consortium and NE BHL members.
      • Smithsonian and Library of Congress
      • Field Museum of Ill
      • BNH UK and Kew UK*
      Bernie Margolis- Boston Public Library Judy Warnement - Harvard Botany Library, Brewster Kale-Internet Archive Cathy Norton-MBLWHOI Library Doran Weber- Alfred P. Sloan Foundation
    • 29.  
    • 30. 10 scribes BPL
    • 31. Biology Digitization Projects Problems, Dilemmas,Puzzles,Difficulties
      • Copyright - Pre 1923, 1923-1964 , orphan works, out-of-print
        • Stanford University Copyright Renewal Database
      • Permissions
      • Collaboration with publisher, societies, institutions, etc.
      • Duplicates, journals 85,000 - 14,000 BID LIST
      • Monographs, collection analysis-- Ref Works
    • 32. Name Changes over Time Taxonomic Intelligence
    • 33. “ 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
    • 34. The challenge for contemporary DIGITAL libraries Goal: Use one name to find the content for all names
    • 35. Names are even misspelled, such as Loligo pealei Loligo pealeii Loligo pealii Loligo pealei
    • 36. One name can refer to more than one organism Peranema – the fern Peranema – the euglenid Yet, despite this, taxonomists have used names and hierarchies to manage information about organisms very effectively for 250 years
    • 37. Who is affected by these problems? Libraries Publishers Museums Federal Agencies
    • 38. Serious challenges in federated environments One organism 4 scientific names 4 maps We want one map
    • 39. 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
    • 40.
      • All names & all Classifications ClassificationBank
      • Alternative names reconciled
      • Similar names disambiguated
      • Exploit hierarchies to browse and search, build a comprehensive classification
      • Improve performance with federated systems
      • Read documents, web sites, databases and taxonomically indexing the content
      • Create a unified portal to information about organisms on the internet
      Taxonomic intelligence is the inclusion of taxonomic practices, skills and knowledge within informatics services to manage information about organisms
    • 41. Taxonomically intelligent aggregation technology builds portals to distribute information about organisms
      • There are many resources out there, but no single comprehensive resource for species information
      • Rather than building another big database, we can create a new way to link existing information using an aggregation portal
      • This places little or no burden on data providers
      • Protecting ownership and diversity of initiatives
    • 42. Alternative names Expert view Indexing power from NameBank Vernacular names More or less specific Suggestions & corrections
    • 43. Results from an array of resources
    • 44.
      • data from various sources may be merged
      • red dots on the map link back to the website that provided the geographical
      • co-ordinates
      Specimen distribution data from remote sources
    • 45. FindIT - uBio’s Scientific Name Recognition Algorithm
    • 46. Training and Improving the Algorithm
    • 47. uBioRSS Taxonomically Intelligent RSS Feed Aggregator
    • 48. uBioRSS Taxonomically Intelligent RSS Feed Aggregator
    • 49. MBL WHOI Library – Woods Hole authors’ publications
    • 50. MBL WHOI Library – Woods Hole species publications
    • 51. Taxonomically intelligent scientific text parsing
    • 52. Taxonomic intelligence works miracles
      • It will benefit any initiative that uses distributed and heterogeneous information about biology
      • Distributed content on the same species can be drawn together because different names will be standardized through reconciliation
      • We can read documents, find names, catalog and taxonomically index documents
      • Produce a framework around which we can organize and assemble remote and local content
    • 53. “ Taxonomic intelligence” enhances search
    • 54.
      • Documents go to Internet Archive for OCR and storage
      • The documents are added to the BHL collection
      • uBio checks the BHL collection for new documents
      • The documents are scanned for names
      • TaxonFinder adds new strings to Namebank
      • Document markup with anchors
      • TaxonFinder adds all namebankIDs to Taxonomic Index
      • This index is called upon by various applications...
    • 55. Biological Data Revolution Biomedical Knowledge Biodiversity Knowledge
    • 56. Scientific Names Escherichia coli No Complete List of Scientific Names Published Variants 112,133 741,872  49,382 Objective Synonyms Bacterium coli Bacillus coli Mis-spellings Escheria coli * *Scientific Names ≠ Species
    • 57. Taxonomic Knowledge
    • 58. BHLVision Information coming from Everywhere
    • 59. What role will libraries play once the scanning is done?
      • Will you be negotiators like you are now with serials?
      • Public domain publications restricted FOREVER by contract…. or open?
    • 60. Road map
      • US libraries -- 12 billion per year ( OCLC)
      • Acquisitions--- 3-4 billion per year
      • 1% - could scan 1 million BKS/vols per year
      • Librarians will create informatics tools that will enhance indexing and organizing for not only their users but world wide
    • 61. Acknowledgments A.W. Mellon Foundation Alfred P Sloan Foundation Macarthur Foundation Martin Kalfatovic Tom Garnet Graham Higley Connie Rinaldo Neil Sarkar David Remsen David Patterson Diane Rielinger
    • 62. URLS The Public Domain: How to Find & Use Copyright-Free Writingsk Music, Art & More by Attorney Stephen Fishman
    • 63. BHL Bid List for Serials http://obsidian. nhm .ac. uk/test/library/bhlseriallist/ Taxa Toy