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 LemurHumanGorilla has Hair Thumbs BigMediumSmall has has_size

What is known about the top 100 candidate biomarker genes? 1.Discovery 2.Execution 3.Presentation

Resource Discovery Hugo: PDGFB Hugo: 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: PDGFB Hugo: PDGFc … HUGO_2_NCBI_GI HUGO_2_EC HUGO_2_SwissProt HUGO_2_OMIM NCBI_gi: NCBI_gi: … EC: EC: …

Chain through Hugo: PDGFB Hugo: PDGFc … HUGO_2_NCBI_GI HUGO_2_EC HUGO_2_SwissProt HUGO_2_OMIM NCBI_gi: NCBI_gi: … NCBI_GI_2_GO_ID NCBI_GO_Set_Analysis ???

Getting warmer.. Discover and execute again. NCBI_gi: NCBI_gi: … 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: PDGFB Hugo: PDGFc … HUGO_2_NCBI_GI HUGO_2_EC HUGO_2_SwissProt HUGO_2_OMIM EC: EC: …

Resource Execution Execute the services (SOAP method call using Moby API). EC_SET_2_KEGG EC: EC: …

KEGG: analysis of gene set Not just GO

Infinite possibilities: Good and Bad Hugo: PDGFB Hugo: PDGFc … Input

Semantic web Hugo: PDGFB Hugo: 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 Sponsors