ubio presentation to jim edwards 2006

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New Dimensions in Managing Biological Information @ the MBLWHOI LIBRARY

David Remsen

June 27, 2006

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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

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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

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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.

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The challenge of names as keywordsFinding this…

Type keyword…

With this…

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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

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• 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

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Many to One: Vernacular Concepts

• Equivalence implicit through co-occurrence

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Many to One: Lexical Synonyms

Many to One: Nomenclatural Synonyms

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Retention of lexical & nomenclatural variation

Loligo pealeiiLoligo pealiiLoligo pealei

Doryteuthis pealei

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Peranema – the fern

One to Many: Homonyms

Peranema – the euglenid

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

MBL / WHOI LIBRARY

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Taxonomic Concept

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LibrariesPublishers

MuseumsFederal Agencies

Name IR impediments in current systems: NLM, JSTOR

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Name IR impediments in current systems: OBIS

One organism

4 scientific names

4 maps

We want one map

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• 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

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Lexical SynonymsNomenclatural SynoymsVernacular Names

Taxonomic HierarchiesTaxonomic Synonyms

Primary Components of uBio

Indexes to content

Indexes to taxonomic views

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NameBank: An index of names and sources

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ClassificationBank

An index of taxon concepts

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

MBL / WHOI LIBRARY

Fitting In

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Fitting In: A datacentric perspective

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Network Service :Attribution

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

• <client optional>

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

MBL / WHOI LIBRARY

Tools and Applications: FindIT

• Is trainable

• Locates names & authorities

• Finds names it doesn’t know

• Finds names mangled by OCR

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

MBL / WHOI LIBRARY

Tools and Applications: LinkIT

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Applications

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Taxonomic intelligence applied to search

Synonymies expand the scope of queries

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uBioRSS: Embedding taxonomies into literature retrieval

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Embedding uBio into remote services: uBioRSS

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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

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uBio Portal: Building communities, enabling connections

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Elements of the PortalIndexing power from NameBank

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Alternative names

Vernacular names

Expert view

More or less specific

Suggestions & corrections

Indexing power from NameBank

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Results from an array of resources

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Additional information from specific projects

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content certified linkouts to authoritative resources

XML source

Additional information from specific projects

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Text source

Additional information from specific projects

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• 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