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

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

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