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Ontology Team Meeting

Ontology Team Meeting. February 3 rd , 2010 Robin Smith. Breaking down a BioAssay. BioAssay. Perturbagen. Measure Group. Endpoint. e.g. Primary Measure e.g. CounterMeasure. MetaTarget. 3. 5. P. 1. 2. 4. Technology. e.g. ATPLuciferin. Format. e.g. PrimaryCells

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Ontology Team Meeting

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  1. Ontology Team Meeting February 3rd, 2010 Robin Smith

  2. Breaking down a BioAssay BioAssay Perturbagen Measure Group Endpoint e.g. Primary Measure e.g. CounterMeasure MetaTarget 3 5 P 1 2 4 Technology e.g. ATPLuciferin Format e.g. PrimaryCells e.g. PurifiedProtein

  3. Assay Components Each BioAssay has 6 components: • Perturbagen: Compounds, DNA, siRNAs, etc tested by the assay for the ability to produce a measurable change • Format: The assay system used: cell-based or cell free, treatments, media, etc. • MetaTarget: The presumed subject of the perturbagen. Could be a protein target, a process, a signaling pathway, etc. • Technology: The underlying method used to determine the activity of the perturbagen. • Endpoint: A metric used by the assay to quantitate or qualify activity. • Measure: Mainly for use by HCS assays, where multiple technologies and targets are used in the same assay. One measure comprises a technology, a set of targets, and a set of endpoints.

  4. Breaking down a BioAssay BioAssay Perturbagen Assay Specification • memberOf Campaign1234 • hasDescription “Assay X is a ….” Spec Measure Group Endpoint e.g. Primary Measure e.g. CounterMeasure MetaTarget 3 5 P 1 2 4 Spec Spec Technology e.g. ATPLuciferin Format e.g. PrimaryCells e.g. PurifiedProtein Spec Spec Spec

  5. Specifications • Descriptions that flesh out an assay or assay component. • Assay Specifications: Very generic assay details such as name, description, where it falls into a screening campaign, etc… • e.g. Assay342 hasScreeningStage SecondaryScreen • e.g. Assay 546 hasDescription “The HIV-1 nucleocapsid is a…” • Component Specifications: More specific details pertaining to each part of the assay • e.g. Fomat789 hasCellLine Hek293 • e.g. Endpoint283 hasEndpointUnit Micromolar • Specifications can be objects or data items, and are related through object and data properties.

  6. Example: AssayEndpoint EndpointComponent e.g. Assay 346, Column 5 is_a PubchemOutcome PubchemScore ResponseAtDefinedConcentration ResponseAtVariableConcentration TestedConcentration ConcentrationAtDefinedResponse EndpointSpecification hasEndpointAttribute EndpointAttribute e.g. DefinedResponse hasEndpointModeOfAction EndpointModeOfAction e.g. Stimulation hasEndpointUnit EndpointUnit hasEndpointAttributeUnit e.g. Log10Molar e.g. Percentage hasEndpointAttributeValue e.g. 50

  7. As RDF Triples: Assay Specifications

  8. More RDF Triples: Target Specifications rdf:type or rdfs:subClassOf?

  9. More RDF Triples: Measure Specifications

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