Changes between Version 6 and Version 7 of PhenotypeAnnotationGuidelines


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Timestamp:
Nov 8, 2016, 11:43:44 AM (4 years ago)
Author:
al637
Comment:

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  • PhenotypeAnnotationGuidelines

    v6 v7  
    4646== Annotation extensions ==
    4747Phenotype 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)
     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).
    4950 * Penetrance
    5051  * Qualitative e.g. has_penetrance(FYPO_EXT:0000003)