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What does the Semantic Web have to do with Organ Transplant Rejection
(or anything else?)
Benjamin Good
CIHR/MSFHR
Bioinformatics Training program
Wilkinson Laboratory
iCAPTURE Centre,
St. Paul’s Hospital
March 10, 2005
Outline
• Define “Semantic Web”
• “What is known about a set of 100 genes that are candidate biomarkers of transplant rejection?”
The Semantic Web
“The Semantic Web is not a separate Web but an extension of the current one, in which information is given well-defined meaning, better enabling computers and people to work in cooperation.”
Tim Berners-Lee
“Meaning” through “Ontology”
Animal
Mammal
Primate
Lemur HumanGorilla
<rdf xmlns:primate=‘http://PrimateOntology#’> <primate:Gorilla>
</primate:Gorilla></rdf>
has
Hair
Thumbs
Big MediumSmall
has
has_size
Resource Discovery
Hugo: PDGFBHugo: PDGFc…
HUGO_2_NCBI_GI
HUGO_2_EC
HUGO_2_SwissProt
HUGO_2_OMIM
BioMOBY
Resource Execution
• Execute the services (SOAP method call using Moby API).
Hugo: PDGFBHugo: PDGFc…
HUGO_2_NCBI_GI
HUGO_2_EC
HUGO_2_SwissProt
HUGO_2_OMIM
NCBI_gi: 191827NCBI_gi: 100230…
EC: 1.2.1.26EC: 1.2.2.29…
Chain through
Hugo: PDGFBHugo: PDGFc…
HUGO_2_NCBI_GI
HUGO_2_EC
HUGO_2_SwissProt
HUGO_2_OMIM
NCBI_gi: 191827NCBI_gi: 100230…
NCBI_GI_2_GO_ID
NCBI_GO_Set_Analysis
???
Getting warmer..
• Discover and execute again.
NCBI_gi: 191827NCBI_gi: 100230…
NCBI_GI_2_GO_ID
GO:cell proliferation
GO:response to wounding
GO:platelet derived growth factor receptor binding
NCBI_GO_Set_Analysis
Another Path
Hugo: PDGFBHugo: PDGFc…
HUGO_2_NCBI_GI
HUGO_2_EC
HUGO_2_SwissProt
HUGO_2_OMIM
EC: 1.2.1.26EC: 1.2.2.29…
Resource Execution
• Execute the services (SOAP method call using Moby API).
EC_SET_2_KEGGEC: 1.2.1.26EC: 1.2.2.29…
Summary
• We want to:– Answer questions about the biomarkers of transplant
rejection– This will require the use of Internet resources– Build a generic tool that will allow for the automatic
creation and execution of pipelines of Internet-accessible resources.
• Metadata for resources in the form of ontologies– Will help computers and humans navigate the
exponential pipeline space.
Conclusion
• The Semantic Web– Facilitates the organization of Internet resources
– Biology is an Internet-resource intensive domain
• Bioinformatics can benefit from a semantic web approach.
Conclusion - Biologist
• Your software will do what you do with Google and Excel automatically.
• Discover• Execute• Integrate• Present• So that you spend more time with the information
that you need.
Thanks
• Wilkinson Lab– Mark– Nina– Eddie– Samuel– Morgan– Clarence– Andrea
[email protected]://bioinfo.icapture.ubc.ca/bgood
Sponsors