1 / 9

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

Download Presentation

Ontology Team Meeting

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  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

More Related