Transcript Semantic Web for Life Sciences - W3C Public Mailing List Archives

Semantic Web for Life Sciences
W3C
BOF 2005 ISMB
Agenda
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What is SW?
Current Activities
Use Case Scenarios
Resources
What do we need to focus on next?
What is SW?
• RDF - Web-transportable descriptive model
of all information
• OWL - Web Ontology Language; 3 levels of
complexity/expressivity
• Focus on Semantic rather than Syntax
• Open world Graph model of all information
on the Web
• Rules - SWRL
RDF-XML
DTD
Semantic Web for Life Sciences
• An Open Scientific Forum for
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Defining Cross-Disciplinary Life Science needs
Show-Casing Working Examples
Initiating SW Work Groups
Capturing Best Practices
• Charter being completed
• Promote LSID awareness and use
• Sandbox for BioDASH demo and semantic
lenses
• Identify Semantic Issues for CT and HC
• Recent members include Merck, caBIG/NCI,
TeraNode
W3C Semantic Web for Life
Sciences
• Mission Statement
The Semantic Web for Life Sciences (SWLS) Interest Group is chartered to
facilitate use of Semantic Web in life sciences, drug discovery, and healthcare
through the development of core vocabularies, implementation of unique
identifiers, and discussion of implementations among users.
The SWLS Working Group will also work with the other Semantic Web
working groups and the Semantic Web Interest Group to gather suggestions
for further SWLS development work and liaison with other Working Groups
within the W3C and other organizations to promote the use of Semantic Web
technologies and foster the growth of machine-readable, policy-aware data
and databases in the life sciences.This work falls within the Technology and
Society Domain.
Potential SW Applications
• Data Integration and Aggregation
• Semantic Interoperability for Services
• Manage Terminology and Semantics of
Communities
• Semantically Linking Scientific Literature
• Organization and Business Flow Modeling
• Manage Knowledge Assets: R&D insights, IP
Ref: “A Life Science Semantic Web: Are We There
Yet?” Science-STKE issue 283, pp. pe22, 10 May 2005
6 Proposed Objectives for SW in
Life Sciences
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Database Conversions and Transforms: query in SPARQL
and retrieve in RDF
Unique identifiers that are supported by the SW URI
model
Tools Conversant in RDF-OWL (Web-Services)
Coordination and management of terminologies and
ontologies: SW collaborative communities
Knowledge-encoding practices: Named-Graphs for
theories, hypotheses, models
Semantics accounts and channels: store and share semantic
annotations (based on RDF)
SWLS Current and Proposed Activities
• Enabling (wrapping) Databases in RDF
– MolBio (NCBI, Uniprot), Pathways (BioPAX),
– RDB-Access, XML-RDAL, SPARQL
• Development and demonstration of the public
tools
– Haystack, Simile, JENA, ?
• Need to define “Context”: Use cases?
– Types: Biological, Axiomatic, Experimental
– Named Graphs: http://www.wiwiss.fu-
berlin.de/suhl/bizer/pub/Carroll_etall-TrustWorkshop-ISWC2004.pdf
• Public Semantic spaces (shareable annotations)
Haystack Semantic Web Browser – MIT/IBM
http://haystack.lcs.mit.edu
BioDASH Topic View
Tools
• RDB-RDF-Access – http://www.w3.org/2004/04/30-RDF-RDB-access/
– http://www.w3.org/2004/10/04-pharmaFederate/
• XML-->RDF - http://www.w3.org/2005/02/13-KEGG/
• Protégé - http://protege.stanford.edu/
• SESAME - http://www.openrdf.org/
• JENA - http://www.hpl.hp.com/semweb/jena2.htm
• SWOOP - http://www.mindswap.org/2004/SWOOP/
Demos/POCs
• BioDash/Haystack – http://www.w3.org/2005/04/swls/BioDash/Demo/
• Simile/Longwell/Welkin – http://www.w3.org/2005/04/swls/simile/
– myGRID-Taverna • http://taverna.sourceforge.net/
• Connotea (NPG) • http://www.connotea.org/
Pathway Polymorphisms
•Identify targets with
lowest chance of
variance
•Predict parts of
pathways with
highest functional
variability
•Map genetic
influence to potential
pathway elements
•Select mechanisms
of action that are
minimally impacted
by polymorphisms
Pathway Semantic Lens example
add { :predicateSet
rdf:type
graph:CollectionPredicateSet ;
rdf:type
graph:PredicateSet ;
dc:title
"BioPAX pathway arrows" ;
hs:member biopax:NEXT-STEP ;
hs:member :pointingTo ;
hs:member ${
rdf:type
vowl:RDFQueryLens ;
vowl:sourceExistential ?s ;
vowl:targetExistential ?t ;
rdfs:label
"" ;
vowl:existentials
@( ?s ?t ?type ) ;
vowl:statement ${
vowl:subject
?type ;
vowl:predicate
biopax:LEFT ;
vowl:object
?s
} ;
vowl:statement ${
vowl:subject
?type ;
vowl:predicate
biopax:RIGHT ;
vowl:object
?t
}
}
}
Multiple Ontologies Used Together
Disease
OMIM
UMLS
Group
FOAF
Disease
Polymorphisms
SNP
Drug target
ontology
UniProt
Protein
BioPAX
Person
PubChem
Patent
ontology
Extant ontologies
Chemical
entity
Under development
Bridge concept
Scales of Ontologies
• Large Vertical Models (UMLS, GO) – common
semantics
• Small Locally-defined models – local definitions
specific to organizations
• Bridging Ontologies – small semantics used to
adjoin elements of other ontologies
• Ad hoc forms by individuals that are explorative
and evolving
Power of Semantic Lenses in
Research
• Separates information collection and presentation
from information processing: not all require coding!
• Database federation can be achieved using lenses
• Allows users to create powerful context-specific
views of combined information, that can be annotated
and shared
• Lenses do not require programming, can be extended,
and can be shared/traded
• Less development time, more definition be
scientists More can be achieved in less time and for
less cost!
SIMILE-MIT
• Annotation Accounts
• Piggy-Bank plug-in for FireFox
• Welkin SW Graph viewer
New Regulatory Issues Confronting
Pharmaceutics
Tox/Efficacy
ADME Optim
from Innovation or Stagnation, FDA Report March 2004
 Support All Stakeholders
Relate information from different platforms and
different projects
What should we do next?
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caBIG coordination
Clarify LSID <=> RDF id relations
Handling Ontology versioning
Citation and references in LSIDs
How to become active?
• Mailing list - [email protected]
• Coordinate your projects with us
• Become a W3C member Semantic Web for
Life Sciences
• www.w3.org/2005/04/swls