Universal Biological Indexer and Organizer
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Transcript of Universal Biological Indexer and Organizer
Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
The Tangled Tree of LifeInformatics 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 ProblemNames 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 QuickTime™ and a
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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•…
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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) PMID Date Unique
Notophthalmus viridescens 350 1965 349
Diemictylus viridescens 36 1959 36
Triturus viridescens 87 1949 86
Libraries Publishers Museums 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)
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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
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Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Organization (Chapin)
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Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Uses (Google)
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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 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
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 mouseZapus 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
<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>
TaxMLit 802 bytes
TaxonX169 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)
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Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Find Common Ground
Stovepipes
Frost ITIS NCBI GBIF Col2005Diemictylus viridescens x xDiemictylus viridescens viridescens x xDiemyctylus minatus viridescens x xNotophthalma viridescens xNotophthalmus viridescens x x x xNotophthalmus viridescens viridescens x x x xNotopthalmus viridescens xTriton viridescens xTriturus (Diemictylus) viridescens xTriturus (Triturus) viridescens xTriturus viridescens x x x xTriturus viridescens viridescens x
American Newt (English) xbroken-stripe newt (English) xBuchi-Imori (Japanese translit)central newt (English) xCommon Newt (English) xCommon Newt (English) xeastern newt (English) x x x xEft (English) xGrünliche Wassermolch (German)Green Triton (English) xpeninsula newt (English) xPunatäplävesilisko (Finnish)Red Eft (English) xRed Lizard (English) xRed-spotted Newt (English) x xSmall Red Lizard (English) xSpotted Evet (English) xSpotted Newt (English) xSpotted Triton (English) xtriton vert (French) x xtriton vert à points rouges (French)Water Lizard (English) xwater newt (English) xYellow Bellied Lizard (English) x
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 interpretationThe 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
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Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
A note on Service