Review DPO EQ defs and assign to uPheno patterns

[matentzn]

For this or the next VFB ontology call, it would be good to do the following:

1. Review all the tsv files in the original pipeline -> @dosumis suggests to do this carefully together with dpo paper, phenotype by phenotype. If you want, you can put the four tables into a google sheets for easier collaboration; thats how we did it with the other MODs
2. Assign all phenotypes in these spreadsheets to appropriate uPheno patterns; maybe best to suggest an appropriate pattern and then review with @dosumis
3. The outcome should be that all or most of the phenotypes are in tsv files that are named after there corresponding uPheno pattern, for example abnormalAnatomicalEntity.tsv
4. Once @dosumis gives me the go, I will switch the patterns to the standard pipeline

[matentzn]

@dosumis raised a special concern about the use of inheres_in_part_of in the abnormalBehaviour pattern; this discussion should be had on the uPheno level ideally, so that all groups can input (especially since behavioural phenotypes might be one of the next big things :P)

You can find the current (undocumented, i.e. no metadata) patterns in the src/patterns/dosdp-patterns directory for reference.

[matentzn]

(this does NOT have to happen before this weeks release!)

[Clare72]

Would it be easy to populate the _label columns? This would make review easier.

[matentzn]

This is akaik unfortunately not currently possible (dosdp-tools limitation). But I made a ticket to make this possible in the future.

[matentzn]

Note to self: Example pattern support dxrefs can be found here.

Not sure whether the dosdp tools matching mechanism copes with that kind of granularity, but we will see after the pattern review is completed.

[dosumis]

Not sure whether the dosdp tools matching mechanism copes with that kind of granularity, but we will see after the pattern review is completed.

Pretty sure it doesn't - but we can relatively easily extract annotations from the JSON version, given IDs/IRIs for the terms.

[Clare72]

Finished moving phenotypes to abnormalAnatomicalEntity, abnormalBiologicalProcess and abnormalBehavior.

By the way our 'thermotaxis behavior defective' is not a 'behavior defective' as GO:'thermotaxis' is not a behavior, so I will make a ticket to rename this to 'thermotaxis defective'.

[matentzn]

@Clare72 Can you just copy paste the ones here in the ticket that still need doing (apart from lethal)?

[Clare72]

Todo list:
#24
#22
#14