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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
MBL/WHOI Library
• Stewards of natural history information
• Provide services to our patrons
• Access to information
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
What information
• Local Data– Special Literature Collections– Specimen databases, herbaria,
sequence data• Remote data
– Journals– ILL– Serial Databases
• (ASFA, JSTOR, etc.)
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Information Delivery• Primary access interfaces
– Brute Force - Read it
– Search:
– Browse by hierarchical taxonomic category• Animalia
• Vertebrates• Birds
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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Problem: Multiple Names• Common names• Scientific Names• N:N• Persistent • Pervasive
– Pectinaria gouldii– Cistenides gouldii
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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Problem: Multiple categories
• No taxonomic opinion• Patron opinions are what counts• Multiple basis for derivation• Dynamic• Require any/all
ITISAnimaliaChordataOsteichthysActinopterygiiPerciformesPomatomidaePomatomussaltatrix
NCBIEukaryotaFungi/Metazoa groupMetazoaEumetazoaBilateriaCoelomataDeuterostomiaChordataCraniataVertebrataGnathostomataTeleostomiEuteleostomiActinopterygiiActinopteriNeopterygiiTeleosteiElopocephalaClupeocephalaEuteleosteiNeognathiNeoteleosteiEurypterygiiCtenosquamataAcanthomorphaEuacanthomorphaHolacanthopterygiiAcanthopterygiiEuacanthopterygiiPercomorphaPerciformesPercoideiPomatomidaePomatomussaltatrix
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Generalized Solution
• Ad-hoc Fix• Systematic Fix• Network thesaurus• “Plug” in applications• Any name• Any classification
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
What it should do
• Account for any “name” relevant to the defined “community”
• Provides taxonomic metadata to biological information providers– Libraries– Publishers
• Provides detailed accounting of usage of taxonomic metadata to contributors of knowledge
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
WHY do we want a solution
• Increase access to biological information assets• Too much information is inaccessible
• It should directly benefit contributors of knowledge
• Directly link usage to attribution
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Increase Access: How?
• Supplement name information that is available for searching and matching name strings – (Example)– Vernacular, homotypic, heterotypic
• Provide hierarchical structures for browsing large biological data collections– (Example)
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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
What we came up with:uBio• Database of taxonomic metadata (TNS)• Network Service (SOAP)• Workgroup management system
• Intent: – Demonstrate a need through pilot system– Add enough names to show that the system works at scale– Look for partners who can curate names
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
TNS
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
TNS: NameBank• Nomenclature -
– Scientific -> basionym– Vernacular -> scientific
• Objective Relationships– Vernacular mappings based on associations– Homotypic– Lexical variants– Management Classification
• No name left behind
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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
TNS: ClassificationBank
• Subjective• Hierarchies• Synonymies• Varying degrees of granularity
– Checklists (-Example)– Junior Synonyms (-Example)– Full bibliographic review (-Example) QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.
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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
TNS: Accounting• Multiple sources may be responsible for a single
data object• Any data change is linked to a source• Links all TNS data to a contributing Agent
– NameBank/ClassificationBank specific– Each interacts with it independently– (Example)
• Names belong to sourcesQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Network Service: Methods
• SOAP– http-based
• Four primary methods– nameBank_search (locate factual instance of name)– nameBank_object (objective metadata)– classificationBank_search (locate interpretations of name)– classificationBank__object (subjective metadata)– …more to come
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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Network Service :Attribution
• Every datum sent out via service is logged– nameBankID– datestamp– Client IP– Calling method– requestorIP
• <client optional>
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Log is Processed
• Network service <-> Contributing Agent– By date– By IP– By method– Full Accounting of usage
• Intent is to be a proxy for these data
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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Why
• Increase utility– Put data to work in multiple ways
• Increase value– When benefits are clear
• Increase support for it– We can garner support from these communities
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Workgroup Management System
PlatypusNetworkedMulti-platformMultiple UsersEase management burdenInput parser
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Collaborate
• Reduce duplication of effort• Maximize accountability to those that DO the work• Utilize funding resources for new work• New uses for existing work
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Multiple Initiatives
• Range of focus• Different priorities• Different scales• Multiple opinions
• Yet there is common data• Any name in list is useful to all
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Layered Systems Work
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Encapsulate: NameBank
• Nomenclature reference core
• Independent from any specific application/system
• Maintain full attribution to source and edits
• Makes our TNS portable
• Collaborative foundation
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Federate
• Layered architecture• Common Foundation• Multiple Directions• Interchange• Cooperation
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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Domain Layer
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Next
• Formalize the NameBank split from TNS• Empty it and start over
– uBio is only a prototype• Look for taxonomic partners• Focus on solutions for libraries• Bring library community to partnership
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