GBIF Jim Edwards uBio Presentation

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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 Organizer
Research 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 keywords
Finding 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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QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
Retention of lexical & nomenclatural variation
Loligo pealeii
Loligo pealii
Loligo 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 Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
Taxonomic Concept

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Libraries
Publishers
Museums
Federal 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 Synonyms
Nomenclatural Synoyms
Vernacular Names
Taxonomic Hierarchies
Taxonomic 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 Organizer
Research 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 Organizer
Research 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 Organizer
Research 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
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.

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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 Portal
Indexing 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 map
link back to the website that
provided the geographical
co-ordinates
Specimen distribution data from remote sources