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

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Presentation transcript:

Universal Biological Indexer and Organizer Research Funded by the Andrew W. Mellon Foundation MBL / WHOI LIBRARY 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 -J.C. Fabricius, 1778, Philosophia Entomologica

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

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

Universal Biological Indexer and Organizer Research Funded by the Andrew W. Mellon Foundation MBL / WHOI LIBRARY 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 Research Funded by the Andrew W. Mellon Foundation MBL / WHOI LIBRARY 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 Research Funded by the Andrew W. Mellon Foundation MBL / WHOI LIBRARY Problems for locating information 476 unique Name (Nomenclatural Synonyms)PMIDDateUnique Notophthalmus viridescens Diemictylus viridescens Triturus viridescens LibrariesPublishersMuseums Federal Agencies

Universal Biological Indexer and Organizer Research Funded by the Andrew W. Mellon Foundation MBL / WHOI LIBRARY Concepts:Taxonomic 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 Frost 2005 AMNH Notopthalmus viridescens viridescens 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 Dolbe 2004 Expert interpretation of the original specimens

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

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

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

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

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

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

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

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

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

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

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

Account for how objects are actually recorded

Universal Biological Indexer and Organizer Research Funded by the Andrew W. Mellon Foundation MBL / WHOI LIBRARY Lessons Learned So many standards so little time Olivier Olivier Ent. v 5 Ent. Olivier v. p. 5 TaxMLit 802 bytes TaxonX 169 bytes Olivier, Ent., v., p. 5

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

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

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

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

Universal Biological Indexer and Organizer Research Funded by the Andrew W. Mellon Foundation MBL / WHOI LIBRARY Concepts:Summary 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) Nomenclatural Concepts 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 Taxonomic Concepts

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

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

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