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241 06 garnett

  1. 1. Biodiversity Heritage Library A Knowledge Domain Repository Community-Driven Open Access Tom Garnett Biodiversity Heritage Library SSP November Tom Garnett 112, 2007 Biodiversity Heritage
  2. 2. Biodiversity Heritage Library 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. Moreover for accurate work it is necessary for the student to verify every reference he may find; it is not enough to copy from a previous author; he must verify each reference itself from the original. Charles Davies Sherborn, Epilogue to Index Animalium, March 1922Charles Davies Sherborn (1861-1942) SSP November Tom Garnett 212, 2007 Biodiversity Heritage
  3. 3. Biodiversity Heritage Library 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.381Insecta. Diptera. Volume I (1886-1901) SSP November Tom Garnett 3 12, 2007 Biodiversity Heritage
  4. 4. Biodiversity Heritage Library The cited half-life of publications in taxonomy is longer than in any other scientific discipline -Macro-economic case for open access, Tom Moritz -Current taxonomic literature often relies on texts and specimens > 100 years old. Levinus Vincent Elenchus tabularum, pinacothecarum, 1719 SSP November Tom Garnett 412, 2007 Biodiversity Heritage
  5. 5. Biodiversity Heritage LibraryThe Taxonomic Impediment“The taxonomicimpediment is a termthat describes the gapsof knowledge in ourtaxonomic system” - Darwin Declaration, 1998Georges Louis Leclerc, comte de BuffonHistoire naturelle : générale et particulière (Oiseaux), 1799-1808 SSP November Tom Garnett 512, 2007 Biodiversity Heritage
  6. 6. Biodiversity Heritage Library The essential requirements for accessing and utilising this global information are: • that there is access to information held in national/regional/global collections • that electronic data is efficiently captured and provided in useable form • that existing information held in literature and by current experts is made available electronically • that stability of scientific names of organisms, used to access this Thylacine from Philip Lutley Sclater, information, is promoted Guide to the Gardens of the Zoological Society of London, - Darwin Declaration, 1998 1891 SSP November Tom Garnett 612, 2007 Biodiversity Heritage
  7. 7. Biodiversity Heritage LibraryConvention on BiologicalDiversity: Article 17… exchange of informationshall include exchange ofresults of technical, scientificand socio-economicresearch … It shall also,where feasible, includerepatriation of information. Henry Bates Insecta. Coleoptera, 1881-1884 SSP November Tom Garnett 7 12, 2007 Biodiversity Heritage
  8. 8. Biodiversity Heritage Library Biologia Centrali-Americana 8 Edited by Frederick Ducane 7 Godman and Osbert Salvin London : Pub. for the editors by R. 6 H. Porter, 1879-1915 5 Chart showing distribution in 4 public collections of the 3 complete 63 volume sets held 2 worldwide. 1 2 complete copies in Central 0 America held at the US & Canada Europe Mexico & C. America South America Smithsonian Tropical Research Institute Library SSP November Tom Garnett 812, 2007 Biodiversity Heritage
  9. 9. Biodiversity Heritage LibraryVishwas Chavan travels a lot. Aninformatician based at the NationalChemical Laboratory in Pune, India, hecollects data on what types of animal livewhere in India to enter into a biodiversitydatabase … Much of the informationChavan seeks is in old, out-of-printtomes … To find them, Chavan hasspent years trailing around libraries. Hedreams of the day when books such asthese are scanned and made availableas digital files on the Internet. “Science in the Web Age: The Real Death of Print” by Andreas von Bubnoff Nature 438, 550-552 1 December 2005 Henry Walter Bates The Naturalist on the River Amazons, 1863 SSP November Tom Garnett 9 12, 2007 Biodiversity Heritage
  10. 10. Biodiversity Heritage Library 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 biologists; librarians; conservation workers; publishers; representatives of learned and professional societies, private foundations and government agencies; and specialists in information Progne subis- Purple Martin technology. Illustrations of the nest and eggs of birds of Ohio, 1879-1886 SSP November Tom Garnett 1012, 2007 Biodiversity Heritage
  11. 11. Biodiversity Heritage LibraryBased on the clear priorities of the Londonconference, the libraries involved gathered inWashington to lay out the ground work for theBiodiversity Heritage Library, which is aresponse to a global community need.Representatives of a number of major naturalhistory and botanical libraries met at theSmithsonian National Museum of Natural Historyin Washington, D.C. to develop a strategy andoperational plan to digitize the publishedliterature of biodiversity held in their respectivecollections and to make that literature availablefor open access and responsible use as a part ofa global “biodiversity commons.” Ernest Ingersoll Hand-book to the National Museum … Smithsonian Institution, 1886 SSP November Tom Garnett 11 12, 2007 Biodiversity Heritage
  12. 12. Biodiversity Heritage Library• Museums – Natural History Museum (London) – Smithsonian Institution – American Museum of Natural History]• Botanical Gardens – Missouri Botanical Garden – New York Botanical Garden – Royal Botanic Gardens, Kew• University Libraries – Botany Libraries, Harvard University – Ernst Meyer Library of the Museum of Comparative Zoology, Harvard University• Research Institute Library – Marine Biological Laboratory / Woods Hole Oceanographic Institution Library (MBL/WHOI) SSP November Tom Garnett 1212, 2007 Biodiversity Heritage
  13. 13. Biodiversity Heritage Library Collaborators: Internet Archive International Commission on Zoological Nomenclature Open Content Alliance European Distributed Institute of Taxonomy Global Biodiversity Information Facility (GBIF) Many more under negotiation SSP November Tom Garnett 1312, 2007 Biodiversity Heritage
  14. 14. Biodiversity Heritage Library Internet Archive Set up scanning centers in London, New York, Washington, Boston, etc. High-quality, non- destructive Scanning. Image files and text derived from OCR. SSP November Tom Garnett 1412, 2007 Biodiversity Heritage
  15. 15. Biodiversity Heritage Library “Guano diggers among the albatrosses. Laysan Island” At this stage, we would have page pictures, “dirty OCR”, some metadata, but what good is it? Will researchers be left like these guano diggers in Hawaii?Lionel Walter RothschildThe avifauna of Laysan and the neighboring islands, 1893-1900 SSP November Tom Garnett 1512, 2007 Biodiversity Heritage
  16. 16. Biodiversity Heritage Library Mandates: Open Access: all content can be reused, repurposed, reformatted. Congruent: must fit in to and contribute to a healthy knowledge ecology. Reptilia and Batrachia. (1885-1902) by Albert C.L.G. Günther SSP November Tom Garnett 1612, 2007 Biodiversity Heritage
  17. 17. Biodiversity Heritage Library BHL Portal http://www.biodiversitylibrary.org Serve image and text files; create volume, part, piece metadata; ingest page level metadata at scanning level for the creation of page level Globally Unique Identifiers (GUIDs) for linking to otherJacob Christian Schäffer taxonomic servicesElementa entomologica . . . 1766. SSP November Tom Garnett 1712, 2007 Biodiversity Heritage
  18. 18. Biodiversity Heritage Library Classes of textsEach class presents a unique set of issues to resolve:Public Domain – pre-1923Post-1923 monographs some with copyright renewals some without copyright renewalsNon-profit learned society journals with permissionsCommercial journalsGray literatureArchival material SSP November Tom Garnett 1812, 2007 Biodiversity Heritage
  19. 19. Biodiversity Heritage Library BHL Seeks Permissions from Copyright HoldersOpt 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 goalsBHL 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.Will index the articles using Taxonomic Intelligence, thereby vastly increasing their usability. SSP November Tom Garnett 1912, 2007 Biodiversity Heritage
  20. 20. Biodiversity Heritage Library What Does the BHL Offer to Publishers?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 so it’s “SEP.”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 (working on it).Thirteen Permission Agreements to date. More under negotiation.Integration with gray literature in later phases of project. SSP November Tom Garnett 2012, 2007 Biodiversity Heritage
  21. 21. Biodiversity Heritage Library Embedding Content in the Knowledge EcologyThe BHL is primarily funded as a component of the Encyclopedia of Life, an international effort to create an authoritative website for every species of the earth’s biota. SSP November Tom Garnett 2112, 2007 Biodiversity Heritage
  22. 22. SSP November Tom Garnett 2212, 2007 Biodiversity Heritage
  23. 23. Biodiversity Heritage Library Embedding Content in the Knowledge EcologySpecies names, taxon concepts, and the classification of living organisms are the basis for linking multiple disciplines such as evolutionary biology, taxonomy, genomics, agriculture, conservation, etc.Taxonomic intelligence algorithms are being developed to mine the BHL content to link species names with other biological resources. SSP November Tom Garnett 2312, 2007 Biodiversity Heritage
  24. 24. Biodiversity Heritage Library SSP November Tom Garnett 2412, 2007 Biodiversity Heritage
  25. 25. Biodiversity Heritage Library SSP November Tom Garnett 2512, 2007 Biodiversity Heritage
  26. 26. Biodiversity Heritage Library SSP November Tom Garnett 2612, 2007 Biodiversity Heritage
  27. 27. Biodiversity Heritage Library SSP November Tom Garnett 2712, 2007 Biodiversity Heritage
  28. 28. Biodiversity Heritage Library SSP November Tom Garnett 2812, 2007 Biodiversity Heritage
  29. 29. Biodiversity Heritage Library 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 Hebaria and museum specimen databases Electronic Gazetteers and GPS. Additional services – you’re invited to help SSP November Tom Garnett 2912, 2007 Biodiversity Heritage
  30. 30. Biodiversity Heritage Library • Scientific and Scholarly Support Strategy – Make it too useful not to support. – Embed it current and developing workflows for the identification, tracking, documenting, and researching the biota. BHL is building on many documented use cases. – Network with many professional societies. – Automated structural markup of journal literature to bring the digitized ocr into conformance with the NLM DTD. SSP November Tom Garnett 3012, 2007 Biodiversity Heritage
  31. 31. Biodiversity Heritage Library • <article> •   <title>A BRIEF CONSIDERATION OF CERTAIN POINTS IN THE MORPHOLOGY OFTHE FAMILY  CHALCIDID^E.*.</title> •   <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> • - <article> •   <title>FURTHER NOTES ON PHENGODES AND ZARHIPIS.</title> •   <author>DR. C. V. RILEY.</author> •   <volume>1</volume> •   <issue>2</issue> •   <start_page>86</start_page> •   <end_page>96</end_page> •   <start_count_page>106</start_count_page> •   <end_count_page>116</end_count_page> •   <start_page_image_file>3908800908001101smthrich_0106.djvu</start_page_image_file> •   <end_page_image_file>3908800908001101smthrich_0116.djvu</end_page_image_file> •   </ SSP November Tom Garnett 3112, 2007 Biodiversity Heritage
  32. 32. Biodiversity Heritage Library • Legal Sustainability Strategy – Avoid legal conflicts. – Keep copyright infringement risk low. It is impossible to eliminate it altogether. – Obtain permissions where feasible . – Where it isn’t feasible, move on. SSP November Tom Garnett 3212, 2007 Biodiversity Heritage
  33. 33. Biodiversity Heritage Library • Financial Sustainability Strategy – Quick ramp-up high early costs – development, mass scanning, etc. Drive long-term costs down the asymptote toward zero. – 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. – Clear roles for staff who wear multiple hats. Two full- time grant funded positions currently but >15 staff who make substantive contributions. – Make the BHL absolutely essential. SSP November Tom Garnett 3312, 2007 Biodiversity Heritage
  34. 34. Biodiversity Heritage Library • The Long Now Strategy – Institutions that are creating the BHL exist to persist through time. That’s an important part of their business. Use them. – The future is uncertain, the technology landscape changes, people pass on. So create consortial structures that are low- overhead, flexible, and can respond quickly. F2F interaction is surprisingly necessary to create this. SSP November Tom Garnett 3412, 2007 Biodiversity Heritage
  35. 35. Biodiversity Heritage Library • The Long Now Strategy (cont.) – Take Risks. Why? – “We must, indeed, all hang together, or most assuredly we shall all hang separately.“ – Interoperability is the key. Repository islands will sink. – Interested in helping? Contact me. – garnettt@si.edu SSP November Tom Garnett 3512, 2007 Biodiversity Heritage
  36. 36. Biodiversity Heritage Library SSP November Tom Garnett 3612, 2007 Biodiversity Heritage