Assign dpoAbnormalAnatomicalEntityByQuality to uPheno patterns

[matentzn]

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:

http://purl.obolibrary.org/obo/FBcv_0000361	large body	http://purl.obolibrary.org/obo/FBbt_00000001	organism	http://purl.obolibrary.org/obo/PATO_0000586	increased size

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).

[Clare72]

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 obophenotype/upheno#497, but I think this one means they all die, rather than just an increased amount of death.

[Clare72]

'cell lethal' and 'abnormal cell polarity' todo:

https://github.com/FlyBase/drosophila-phenotype-ontology/blob/master/src/patterns/data/to_do/dpoAbnormalAnatomicalEntityByQuality.tsv