universal biological indexer and organizer research funded by the andrew w. mellon foundation mbl /...

Universal Biological Indexer and Organizer

Research Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

The Tangled Tree of LifeInformatics and Biological Names



MBL / WHOI LIBRARY

Name-bearing data objects

If the names are lost the knowledge also disappears-J.C. Fabricius, 1778, Philosophia Entomologica



MBL / WHOI LIBRARY

The Names ProblemNames are not stable Search:



MBL / WHOI LIBRARY

Other Names Problems

5-10% scientific names become invalid per decade

Scientific names aren’t unique

Acalyptus



MBL / WHOI LIBRARY

Newt: as concept

• Triturus viridescens Rafinesque 1820• Computers see string• String Properties

• Nomenclatural concept• Single specimen QuickTime™ and a

TIFF (Uncompressed) decompressorare needed to see this picture.

viridis - to become green



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•…

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.



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



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



MBL / WHOI LIBRARY

Concepts:Taxonomic

• Amphibia• Urodela• Salamandridae• Notophthalmus• Notopthalmus viridescens

Frost 2005 AMNH

• Amphibia • Batrachia• Caudata • Salamandroidea• Salamandridae• Notophthalmus• Notopthalmus viridescens

NCBI 2005



MBL / WHOI LIBRARY

The Concepts Problem (how do we integrate)

QuickTime™ and aTIFF (LZW) decompressor




MBL / WHOI LIBRARY

Who is addressing the problem



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



MBL / WHOI LIBRARY

NameBank

http://uio.mbl.edu/SOAPbrowser/index.php?func=name_detail&ubioID=12294



MBL / WHOI LIBRARY

ClassificationBank (Concepts)



MBL / WHOI LIBRARY

Search and Retrieval



http://uio.mbl.edu/clients/jstor/index.php?func=name_search&restriction_flag=0&language_flag%5B%5D=0&qualify_flag=contains&target_name=bluefish



MBL / WHOI LIBRARY

Organization (Chapin)



http://uio.mbl.edu/amnh/browse.php?currID=209989



MBL / WHOI LIBRARY

Uses (Google)





MBL / WHOI LIBRARY

Just another database

The response of the world…



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



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



MBL / WHOI LIBRARY

Putting it all together

Account for how objects are actually recorded



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



MBL / WHOI LIBRARY

Lessons Learned Service works in both directions



MBL / WHOI LIBRARY

Give as we get (Attribution)



http://uio.mbl.edu/service/logs/reports.php?func=userDetails&userID=453



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



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



MBL / WHOI LIBRARY

Separate fact from interpretationThe informatics value of facts



MBL / WHOI LIBRARY

Federate• Layered architecture

• Common Foundation

• Diverse expression

• Enhanced Interchange

• Cooperation

• Efficient

QuickTime™ and aTIFF (Uncompressed) decompressor


http://www.oclc.org/americalatina/en/worldcat/grow.htm



MBL / WHOI LIBRARY

A note on Service

universal biological indexer and organizer research funded by the andrew w. mellon foundation mbl /...

Documents

dorsalis notophthalmus

dorsalis diemyctylus

dorsalis triturus

taxonomic notopthalmus

amnh notopthalmus

diemyctylus minatus

nomenclatural triturus

concept triturus