Clare72
commented
5 years ago Need a pattern for whole-organism phenotypes that are not behaviors e.g. sterile, uncoordinated, auxotrophic perhaps: "'has_part' some (%s and ('inheres_in' some 'organism') and ('has_modifier' some 'abnormal'))" where %s must be an 'organismal quality' couldn't find a suitable 'organism' term in UBERON that would apply to both multicellular and single-cell organisms - many other ontologies have 'organism'!
Need a pattern for abnormal 'positional polarity', which would be similar to the abnormal morphology pattern
Not sure what to do about 'cell lethal', as 'lethal (sensu genetics)' is supposed to inhere in a population, not a cell as we currently have it, perhaps we need to use 'population of cells'. Either way, I think this needs a new pattern - kind of related to https://github.com/obophenotype/upheno/issues/497, but I think this one means they all die, rather than just an increased amount of death.
I have started going through your tsv files; the next goal is to break out the individual phenotypes and assign them to the correct uPheno patterns.
https://github.com/FlyBase/drosophila-phenotype-ontology/blob/master/src/patterns/data/archive/dpoAbnormalAnatomicalEntityByQuality.tsv
For example:
Needs to be placed in a tsv corresponding to the increasedSizeOfAnatomicalEntity pattern.
After the tsv is created and the respective phenotypes are placed in there, you need to: 1) delete the rows from the dpoAbnormalAnatomicalEntityByQuality tsv (the ones you moved over) 2) delete the last two columns of the increasedSizeOfAnatomicalEntity.tsv (the quality and its label; these are now covered by the pattern).