ubio presentation to species 2000 may 2004
TRANSCRIPT
![Page 1: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/1.jpg)
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
![Page 2: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/2.jpg)
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
![Page 3: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/3.jpg)
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.)
![Page 4: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/4.jpg)
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
QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.
QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.
![Page 5: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/5.jpg)
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
QuickTime™ and aTIFF (LZW) decompressorare needed to see this picture.
QuickTime™ and aTIFF (LZW) decompressorare needed to see this picture.
![Page 6: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/6.jpg)
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
![Page 7: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/7.jpg)
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
![Page 8: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/8.jpg)
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
![Page 9: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/9.jpg)
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
![Page 10: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/10.jpg)
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)
QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.
QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.
![Page 11: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/11.jpg)
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
![Page 12: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/12.jpg)
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
TNS
![Page 13: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/13.jpg)
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
QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.
![Page 14: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/14.jpg)
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.
QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.
![Page 15: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/15.jpg)
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.
![Page 16: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/16.jpg)
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
QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.
![Page 17: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/17.jpg)
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>
![Page 18: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/18.jpg)
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
QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.
![Page 19: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/19.jpg)
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
![Page 20: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/20.jpg)
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Workgroup Management System
PlatypusNetworkedMulti-platformMultiple UsersEase management burdenInput parser
![Page 21: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/21.jpg)
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
![Page 22: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/22.jpg)
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
![Page 23: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/23.jpg)
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Layered Systems Work
![Page 24: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/24.jpg)
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
![Page 25: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/25.jpg)
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Federate
• Layered architecture• Common Foundation• Multiple Directions• Interchange• Cooperation
QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.
![Page 26: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/26.jpg)
Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Domain Layer
![Page 27: uBio presentation to Species 2000 May 2004](https://reader034.vdocument.in/reader034/viewer/2022042618/589b1b4b1a28abc1148b6427/html5/thumbnails/27.jpg)
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