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

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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

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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

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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

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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

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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

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The Concepts Problem (how do we integrate)

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Universal Biological Indexer and Organizer

Research Funded by the Andrew W. Mellon Foundation

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Who is addressing the problem

Universal Biological Indexer and Organizer

Research Funded by the Andrew W. Mellon Foundation

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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

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Search and Retrieval

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Universal Biological Indexer and Organizer

Research Funded by the Andrew W. Mellon Foundation

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Organization (Chapin)

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Universal Biological Indexer and Organizer

Research Funded by the Andrew W. Mellon Foundation

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Uses (Google)

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Universal Biological Indexer and Organizer

Research Funded by the Andrew W. Mellon Foundation

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Just another database

The response of the world…

Universal Biological Indexer and Organizer

Research Funded by the Andrew W. Mellon Foundation

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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

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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

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Lessons Learned Service works in both directions

Universal Biological Indexer and Organizer

Research Funded by the Andrew W. Mellon Foundation

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Give as we get (Attribution)

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Universal Biological Indexer and Organizer

Research Funded by the Andrew W. Mellon Foundation

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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

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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

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Separate fact from interpretationThe informatics value of facts

Universal Biological Indexer and Organizer

Research Funded by the Andrew W. Mellon Foundation

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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