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BAO Journal Club

BAO Journal Club. December 7th, 2009 Robin Smith. Pubchem assays by date. @Time of grant proposal: 1500 @Time of Robin start: 1885 @Yesterday: 1957. Bioassay Ontology: top down approach. How best to represent high throughput/content experiments using OWL?

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BAO Journal Club

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  1. BAO Journal Club December 7th, 2009 Robin Smith

  2. Pubchem assays by date @Time of grant proposal: 1500 @Time of Robin start: 1885 @Yesterday: 1957

  3. Bioassay Ontology: top down approach • How best to represent high throughput/content experiments using OWL? • Distinguish between simple concepts, such as: • How? How was the assay carried out. This includes the underlying technology. • What? What was measured by the experiment? A change in kinase activity or an increase in cell number? • Which? Which biological system was the assay carried out in? A reconstitued complex, a cell line

  4. Bioassay Ontology: key concepts • AssayBiologicalSystem • The environment in which the bioassay is being conducted, in addition to a specific target information. • AssayMeasure: • The physical process or activity that is being measured by the bioassay. • AssayTechnology • The underlying techniques used to obtain the results of the assay. • AssayDesign • General features of the assay, including the nature of the inputs and endpoints, as well as the assay’s status within a larger campaign.

  5. Is top-down ontology design best? • What’s the best way to build an ontology? Ph.D.

  6. Domain specific vocabulary extraction Domain Specific Vocabulary Ph.D. concentration Cell-based luciferase promoter Enzyme

  7. NCBO Bioportal Annotator • ~200 biomedical ontologies • ~1.5 million concepts • Can we extract domain specific vocabulary to aid in ontology construction? • Query web service using Pipeline Pilot

  8. The “SNOMED” (and NCI) problem 50,000 + annotations for each of name, description and protocol

  9. NCBO Recommender service

  10. Some ontologies may be useful

  11. Domain expert vocabulary extraction Domain Specific Vocabulary Ph.D. concentration Cell-based luciferase promoter Enzyme

  12. PubChem – Spotfire representation

  13. Simple AssayFormat Annotation

  14. Can use high level divisions to find smaller assay groups: has “luciferase”?

  15. Can use high level divisions to find smaller assay groups: has “enzyme”?

  16. Pubchem assays by screening stage • Screening assays and some “other” assays are difficult to annotate • Some “other” assays are in vivo screens • “Null” = on hold

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