What does the Semantic Web have to do with Organ Transplant Rejection (or anything else?) Benjamin...
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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
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Transcript of What does the Semantic Web have to do with Organ Transplant Rejection (or anything else?) Benjamin...
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
An answer.
• A new kind of program for answering questions.
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
What is known about the top 100 candidate biomarker genes?
1.Discovery
2.Execution
3.Presentation
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
GO: Cellular Component
GO: Biological Process
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…
KEGG: analysis of gene set
Not just GO
Infinite possibilities: Good and Bad
Hugo: PDGFBHugo: PDGFc…
Input
Semantic web
Hugo: PDGFBHugo: PDGFc…
Input
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
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