Changes between Version 7 and Version 8 of PhenotypeAnnotationGuidelines
- Timestamp:
- Nov 8, 2016, 12:16:47 PM (4 years ago)
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PhenotypeAnnotationGuidelines
v7 v8 46 46 == Annotation extensions == 47 47 Phenotype annotations can have extensions to capture expressivity (severity), penetrance, and genes, transcripts or proteins used in an assay. Expressivity and penetrance can use qualitative values from the FYPO_EXT mini-ontology (in svn at pombe-embl/mini-ontologies/fypo_extension.obo), or penetrance can be specified quantitatively as a percent (I haven't run into any quantitative expressivity as of 2015-04-10 -mah). 48 * Expressivity is usually qualitative, e.g. has_expressivity(FYPO_EXT:0000003) (note: FYPO_EXT:0000003 = low). 49 * When specifying % values, then the percent reflects the amount changed compared to normal. E.g. decreased protien level + 10% expressivity = protein level was knoecked down by 10% (low expressivity). 48 * Expressivity is usually qualitative, e.g. has_expressivity(FYPO_EXT:0000003) (note: FYPO_EXT:0000003 = low). 50 49 * Penetrance 51 50 * Qualitative e.g. has_penetrance(FYPO_EXT:0000003)