Deprecate UPHENO:0001002, rename UPHENO:0001001 (#1009)#1026
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| defined_class defined_class_name bearer | ||
| http://purl.obolibrary.org/obo/UPHENO_0001001 phenotype owl:Thing | ||
| defined_class defined_class_name bearer defined_class_definition | ||
| http://purl.obolibrary.org/obo/UPHENO_0001001 phenotypic effect owl:Thing An observable characteristic of an organism expressed as a deviation, alteration, or qualified state relative to a reference condition, resulting from genetic, environmental, or gene-environment influences. |
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By defining 'phenotypic effect' this way and getting rid of phenotype the MP header terms (adipose tissue phenotype, behavior/neurological phenotype, etc) will no longer fall under this term. The MP header terms are all effect neutral and MGI uses annotations to them to capture normal phenotypes. The MP has these defined as 'the observable morphological and physiological characteristics of X that are manifested through development and lifespan' where manifested is doing the work of differentiating between the trait (the characteristic in potentia, e.g. eye color) and the phenotype (the characteristic we actually see, e.g. blue eyes).
Or is the intent that 'qualified state' covers the qualification 'normal'? I think we may need a note on this term to clarify what is meant. I do see further down the file the term 'normal meiosis phenotype' so possibly the intent is to cover normals?
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Discussed this with Nico, the intention is that qualified does cover any type of phenotype and is meant to do the work of distinguishing between the trait (e.g. eye color) and the phenotype (e.g. brown eyes). We should add a comment to this term to clarify the intent and scope. We'll draft a comment int he next editors' call.
sbello
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I need clarification on what 'qualified' state means. I do have a discussion of the scope of UPheno on the agenda for the next editors call.
| defined_class defined_class_name bearer | ||
| http://purl.obolibrary.org/obo/UPHENO_0001001 phenotype owl:Thing | ||
| defined_class defined_class_name bearer defined_class_definition | ||
| http://purl.obolibrary.org/obo/UPHENO_0001001 phenotypic effect owl:Thing An observable characteristic of an organism expressed as a deviation, alteration, or qualified state relative to a reference condition, resulting from genetic, environmental, or gene-environment influences. |
There was a problem hiding this comment.
By defining 'phenotypic effect' this way and getting rid of phenotype the MP header terms (adipose tissue phenotype, behavior/neurological phenotype, etc) will no longer fall under this term. The MP header terms are all effect neutral and MGI uses annotations to them to capture normal phenotypes. The MP has these defined as 'the observable morphological and physiological characteristics of X that are manifested through development and lifespan' where manifested is doing the work of differentiating between the trait (the characteristic in potentia, e.g. eye color) and the phenotype (the characteristic we actually see, e.g. blue eyes).
Or is the intent that 'qualified state' covers the qualification 'normal'? I think we may need a note on this term to clarify what is meant. I do see further down the file the term 'normal meiosis phenotype' so possibly the intent is to cover normals?
sbello
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sbello
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Approve with the qualification that we need to add a comment in the future to help users understand the scope of this term and UPheno in general.
| defined_class defined_class_name bearer | ||
| http://purl.obolibrary.org/obo/UPHENO_0001001 phenotype owl:Thing | ||
| defined_class defined_class_name bearer defined_class_definition | ||
| http://purl.obolibrary.org/obo/UPHENO_0001001 phenotypic effect owl:Thing An observable characteristic of an organism expressed as a deviation, alteration, or qualified state relative to a reference condition, resulting from genetic, environmental, or gene-environment influences. |
There was a problem hiding this comment.
Discussed this with Nico, the intention is that qualified does cover any type of phenotype and is meant to do the work of distinguishing between the trait (e.g. eye color) and the phenotype (e.g. brown eyes). We should add a comment to this term to clarify the intent and scope. We'll draft a comment int he next editors' call.
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Fixes #1009
Deprecate UPHENO:0001002 (phenotypic effect), rename UPHENO:0001001 to "phenotypic effect", update definition, repoint 202 grouping class parents.