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Semantic Annotation of Scientific Articles
DC-2009 "Semantic Interoperability of Linked Data"
Sudeshna Das 1,2 & Tim Clark 1,2
[email protected], [email protected]
1MIND, Massachusetts General Hospital2Harvard Medical School
Alzforum:
The Pioneer in Biomedical Web Communities
Problem Statement
Shared terminology
Linked open data sources
Reus
able
sof
twar
eWeb 3.0
What is the SCF?
Science Collaboration Framework
• Replicate Alzforum like communities• Based on Drupal
– low barrier to entry
• Integrated Collaborative tools– Web 2.0
• Adapted to the Semantic Web– Leverages existing linked data – Uses shared ontologies/vocabularies– Interoperable with other SCF or Semantic Web communities
• Provides powerful “semantic search” capabilities
SCF Overview
StemBook
SCF Toolkit
PDOnlineAlzforum Pain
Semantic Annotation
• Tagging with a term or resource – belongs to a defined class – that has a URI (Uniform Resource Identifier)– controlled vocabularies or ontologies
• The tag has meaning!– Defined relationship between document and tag– Document “discusses” PhenomenonA– Document “majorTopic” Gene123– DocumentA “cites” DocumentB
• Provenance and status• Tag - annotation• http://swan.mindinformatics.org/ (ontology)
Search for beta-amyloid
Retrieve content with
“abeta”,
“amyloid-beta”,
“Aβ”, “Ab1-40”, “Ab1-42”, . . .
Semantic Search
Search for “BACE1”
Retrieve content with
“beta secretase”,
“beta-site APP cleaving enzyme”,
“membrane-associated aspartic protease”,
etc. . . .
Semantic Search
Search for “BACE1”
Associate database content
Enabling semantic annotation
• Semi-automatic text-mining– Use machines to “suggest terms”– Use editors to refine choice
• Currently mining for– Gene names– Gene Ontology terms– Tissue, Organs, Cell types
Powerful search across communities
SCFSoftware Engineer
Mark GoetzStéphane CorlosquetSam Brin
Project ManagementSudeshna DasTim Clark
Agaric DesignBen Melancon
HSCILisa GirardBrock Reeve
NeuroCommonsAlan RuttenbergJonathan Rees
AlzforumJune KinoshitaElizabeth Wu
Team
