ubio presentation to jim edwards 2006

universal Biological indexer and organizer 1

New Dimensions in Managing Biological Information @ the MBLWHOI LIBRARY

David Remsen

June 27, 2006


All accumulated information of a species is tied to a scientific name, a name that serves as a link between what has been learned in the past and what we today add to the body of knowledge.

- Grimaldi & Engel, 2005, Evolution of the Insects


a name that serves as a link between what has been learned in the past

From T.E. Glover, The Fishes of Southwestern Japan, c.1870


Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

…and what we today add to the body of knowledge.


The challenge of names as keywordsFinding this…

Type keyword…

With this…


Names – the only universal metadata for Biology

Names offer a logical way to search for and index content

• Names annotate data objects• All names annotate all data objects• A compilation of all names ever used is the foundation of a universal index for biology• or for a semantic web for biology


• Many names refer to one concept• Vernacular concept• Lexical or Nominal synonym• Nomenclatural synonym• Taxonomic Synonym

• Single name refers to many concepts• Homonyms• Taxonomic concepts• Vernacular concepts• Taxonomic Groups/Classifications

The Taxonomic Names Problem in Biology


Many to One: Vernacular Concepts

• Equivalence implicit through co-occurrence


Many to One: Lexical Synonyms

Many to One: Nomenclatural Synonyms


QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.

Retention of lexical & nomenclatural variation

Loligo pealeiiLoligo pealiiLoligo pealei

Doryteuthis pealei


Peranema – the fern

One to Many: Homonyms

Peranema – the euglenid



MBL / WHOI LIBRARY



Taxonomic Concept

http://names.ubio.org/rss/


LibrariesPublishers

MuseumsFederal Agencies

Name IR impediments in current systems: NLM, JSTOR


Name IR impediments in current systems: OBIS

One organism

4 scientific names

4 maps

We want one map


• Basis for Relationships: Facts• Vernacular concept• Lexical or Nominal synonym• Nomenclatural synonym• Homonyms

• Basis for Relationship: Opinion• Taxonomic Synonym• Vernacular concepts• Taxonomic Groups/Classifications

Division of Concepts


Lexical SynonymsNomenclatural SynoymsVernacular Names

Taxonomic HierarchiesTaxonomic Synonyms

Primary Components of uBio

Indexes to content

Indexes to taxonomic views


NameBank: An index of names and sources


ClassificationBank

An index of taxon concepts



MBL / WHOI LIBRARY

Fitting In


Fitting In: A datacentric perspective


Network Service :Attribution

• Every datum sent out via service is logged– nameBankID– datestamp– Client IP– Calling method– requestorIP

• <client optional>

http://www.ubio.org/service/logs/reports.php



MBL / WHOI LIBRARY

Tools and Applications: FindIT

• Is trainable

• Locates names & authorities

• Finds names it doesn’t know

• Finds names mangled by OCR



MBL / WHOI LIBRARY

Tools and Applications: LinkIT


Applications

http://namebank.ubio.org/bulletin/process.php


Taxonomic intelligence applied to search

Synonymies expand the scope of queries




uBioRSS: Embedding taxonomies into literature retrieval



Embedding uBio into remote services: uBioRSS



Taxonomic hierarchies enhance data browsing

• Birds of the Belgian Congo

• 4500 pages• One page has a

species of dipteran• How would someone

interested find it?• 50,000+ Diptera

species to choose from

Both enhancements apply to all name-annotated content


uBio Portal: Building communities, enabling connections

http://portal.ubio.org/


Elements of the PortalIndexing power from NameBank


Alternative names

Vernacular names

Expert view

More or less specific

Suggestions & corrections

Indexing power from NameBank


Results from an array of resources


Additional information from specific projects


content certified linkouts to authoritative resources

XML source



Text source


http://portal.ubio.org/old/index.php?tnsnav=lists&tnsclient=Yahoo&search=Araneus+gemmoides


• data from various sources may be merged

• red dots on the maplink back to the website thatprovided the geographical co-ordinates

Specimen distribution data from remote sources

http://portal.ubio.org/old/index.php?tnsnav=lists&tnsclient=Yahoo&map=mapexplorer&search=Loligo+pealeii

ubio presentation to jim edwards 2006

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