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

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

bgood@mrl.ubc.cahttp://bioinfo.icapture.ubc.ca/bgood

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