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mgijax / mammalian-phenotype-ontology

Standard terms for annotating mammalian phenotypic data
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fixing incorrect labels #2997

Open sbello opened 5 years ago

sbello commented 5 years ago

fixing some term labels that don't follow the current MP standards that turned up in Nico's spreadsheets abnormal Bowman membrane abnormal cumulus oophorus abnormal intermediate mesoderm

sbello commented 5 years ago

also abnormal axial mesoderm

anna-anagnostop commented 5 years ago

Sue, I noticed that you also changed the term label for abnormal axial mesoderm MP:0001684 to ‘abnormal axial mesoderm morphology’ (see https://github.com/obophenotype/mammalian-phenotype-ontology/issues/2997)

Based on the textual definition “failure or abnormality in the formation of part of the middle of the three primary germ layers of the embryo which includes the prechordal mesoderm and the chordamesoderm and gives rise to the prechordal plate and to the notochord”, this refers to biological_process rather than abnormalMorphology so we should change the term label for MP:0001684 to ‘abnormal axial mesoderm formation’ which would still use the EQ statement 'has part' some (quality and ('inheres in' some 'axial mesoderm formation') and ('has modifier' some abnormal)), as is.

We would still need to create a new MP term for ‘abnormal axial mesoderm morphology’ which would be a parent term of ‘abnormal axial mesoderm formation’, correct?

Reply from Sue via e-mail Mon 6/3/2019 11:02 AM

Rather than formation I would change the label to development. We should also specify that the pattern should be development not morphology. Yes we would need to create a new term for morphology IF we actually need a morphology term. We’ll need to review the annotations to see if we need the morphology term.