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Universal Biological Indexer and Organizer

The Tangled Tree of Life Informatics and Biological Names. Universal Biological Indexer and Organizer. Research Funded by the Andrew W. Mellon Foundation. MBL / WHOI LIBRARY. Name-bearing data objects. If the names are lost the knowledge also disappears

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Universal Biological Indexer and Organizer

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  1. The Tangled Tree of Life Informatics and Biological Names Universal Biological Indexer and Organizer Research Funded by the Andrew W. Mellon Foundation MBL / WHOI LIBRARY

  2. Name-bearing data objects If the names are lost the knowledge also disappears -J.C. Fabricius, 1778, Philosophia Entomologica Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  3. The Names Problem Names are not stable Search: Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  4. Other Names Problems 5-10% scientific names become invalid per decade Scientific names aren’t unique Acalyptus Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  5. Newt: as concept • Triturus viridescens Rafinesque 1820 • Computers see string • String Properties • Nomenclatural concept • Single specimen viridis - to become green Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  6. Concepts:Nomenclatural • Triturus viridescens Rafinesque 1820 • Notopthalmus viridescens Baird 1850 • Notophthalmus viridescens Gray 1850 msp. • Notophthalma viridescens Gray 1858 msp. • Diemyctylus viridescens Hallowell 1856 • Triton viridescens Strauch, 1870 • Molge viridescens Boulanger, 1872 • Diemyctylus minatus viridescens Yarrow • … Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  7. Problems for locating information Libraries Publishers Museums Federal Agencies 476 unique Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  8. Concepts:Taxonomic Frost 2005 AMNH Dolbe 2004 • Notopthalmus viridescens Valid name • Triturus viridescens • Notopthalmus viridescens • Notophthalmus viridescens • Notophthalma viridescens • Diemyctylus viridescens • Triton viridescens • Molge viridescens • Diemyctylus minatus viridescens • Triturus viridescens dorsalis • Diemyctylus viridescens dorsalis • Notophthalmus viridescens dorsalis • … 24 others • Notopthalmus viridescensviridescens • Triturus viridescens • Notopthalmus viridescens • Notophthalmus viridescens • Notophthalma viridescens • Diemyctylus viridescens • Triton viridescens • Molge viridescens • Notophthalmus viridescens dorsalis • Triturus viridescens dorsalis • Diemyctylus viridescens dorsalis • Notophthalmus viridescens louisianensis Expert interpretation of the original specimens Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  9. Concepts:Taxonomic Frost 2005 AMNH NCBI 2005 • Amphibia • Urodela • Salamandridae • Notophthalmus • Notopthalmus viridescens • Amphibia • Batrachia • Caudata • Salamandroidea • Salamandridae • Notophthalmus • Notopthalmus viridescens Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  10. The Concepts Problem (how do we integrate) Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  11. Who is addressing the problem Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  12. uBio • Library origins • “System” must account for all names • Any classifications • Biological Name Server • 2 million nomenclatural concepts • 1.7 taxon concepts • (60 classifications) • SOAP web service • Tool for data organization/retrieval Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  13. NameBank Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  14. ClassificationBank (Concepts) Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  15. Search and Retrieval Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  16. Organization (Chapin) Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  17. Uses (Google) Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  18. The response of the world… Just another database Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  19. Lessons LearnedEveryone needs a job • Many systems • No consensus • Multiple standards • It’s not just technical • No one is solving my problem • There will always be multiple systems Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  20. Lessons LearnedToo much knowledge can be a dangerous thing It doesn’t exist Or it does Preble’s jumping meadow mouse Zapus hudsonius preblei Krutzsch, 1954 Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  21. Putting it all together Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  22. Account for how objects are actually recorded

  23. Lessons LearnedSo many standards so little time <OtherCitations> <OtherCitationAuthors> <OtherCitationAuthorString Explicit="true"> <OtherCitationAuthorText>Olivier</OtherCitationAuthorText> </OtherCitationAuthorString> <OtherCitationAuthorAtomised OrderOfAuthors="1" KindOfAuthor="Treatment"> <Author>Olivier</Author> </OtherCitationAuthorAtomised> </OtherCitationAuthors> <OtherCitation> <CitationPublicationDetails> <BookSeriesJournalTitle Explicit="true"> <BookJournalSeriesTitleText>Ent.</BookJournalSeriesTitleText> </BookSeriesJournalTitle> <Volume Explicit="true"> <VolumeIdentifier>v</VolumeIdentifier> </Volume> <Pagination Explicit="true"> <Pages>5</Pages> </Pagination> </CitationPublicationDetails> </OtherCitation> </OtherCitations> <tax:p> <tax:head> <tax:title> Ent. </tax:title> <tax:author> Olivier </tax:author> </tax:head> <tax:div type="introduction"><tax:p>v. p. 5 </tax:p> TaxonX 169 bytes TaxMLit 802 bytes Olivier, Ent., v., p. 5 Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  24. Lessons LearnedService works in both directions Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  25. Give as we get (Attribution) Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  26. Find Common Ground Stovepipes Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  27. Share and share alike “Furthermore, in contrast to normal synonyms, the relationships between basionyms and their combinations are purely nomenclatural and do not convey any information on classification. For this reason the relationship between a basionym and its combinations should be treated separately (on the NT side)…” Martin Pullan, The Prometheus Taxonomic Model: A Practical Approach to Representing Multiple Classifications

  28. Concepts:Summary Nomenclatural Concepts Taxonomic Concepts • Factual • Inter-relationships are objective • No new science required • (except to make new ones) • Stable • Expert scrutiny useful, not required • Compilation potentially FAST • uBio 1 million/year • share (no opinion attached) • Opinion • Interelationships are subjective • Derived from nomenclatural concepts • Expert scrutiny is required • Unstable • Compilation slow • CoL 50K / year • Diptera 200K/15 years • sharing concerns - opinions attached Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  29. Separate fact from interpretation The informatics value of facts Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  30. Federate • Layered architecture • Common Foundation • Diverse expression • Enhanced Interchange • Cooperation • Efficient Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

  31. A note on Service Universal Biological Indexer and Organizer MBL / WHOI LIBRARY Research Funded by the Andrew W. Mellon Foundation

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