Ensure that all TOP level HPO and MP terms have corresponding uPheno classes

obophenotype / upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.

https://obophenotype.github.io/upheno/

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Ensure that all TOP level HPO and MP terms have corresponding uPheno classes #948

Open matentzn opened 1 month ago

matentzn commented 1 month ago

Please review MP and HPO and figure out if they have corresponding uPheno classes.

HP top level classes:

MP top level classes:

Ideally create a table in Google sheets.

Ask @rays22 for advice if needed!

sbello commented 1 month ago

If it helps this is a mapping of the high level HPO terms to high level MP terms https://docs.google.com/spreadsheets/d/1BJfse2aSST0FFK__FweZREQC-jhrJ2fDwBiG_ieBsR8/edit?usp=sharing

matentzn commented 1 month ago

Very helpful, thanks @sbello

pnrobinson commented 1 month ago

It would be great to review the top level structure of upheno, which seems very heterogeneous, and it is often hard to find corresponding terms in the source ontologies where one would expect them. It would be great to schedule a workshop to review and discuss this!

sbello commented 1 month ago

Agree with @pnrobinson @matentzn if you would be interested we could put something together for the 2025 Biocuration meeting. The call for workshop proposals is going to go out soon

matentzn commented 1 month ago

It would be good if @ar-ibrahim and @rays22 you could meet with Sue and perhaps draft a concrete proposal for a workshop - Would be nice to run another one!

ar-ibrahim commented 2 weeks ago

Let me know if this is what you had in mind Nico >> upheno-HPO-MP_mapping spreadsheet

ar-ibrahim commented 2 weeks ago

Also @sbello and I have agreed to meet in mid-July to draft a workshop for Biocuration 2025.

matentzn commented 2 weeks ago

Very good, thank you! In the meantime, I will draft something based on the combination of the MP and HPO upper categories. Thanks for your help!!

matentzn commented 2 weeks ago

@sbello will share another experience with re-designing the upper level of VT

sbello commented 2 weeks ago

When we created the top level organization of VT we modified this from MP to expand the systems to cover all vertebrates. It could be helpful to look at the differences.

A few key things:

We created the top level sets of systems, subdivisions, and organism to deal with differences in groupings
In the systems
used alimentary to group gastrointestinal, liver/biliary and pancreas
connective tissue groups adipose bone cartilage and more
hemolymphoid groups hematopoietic and lymphatic systems
Organism subdivision has things like head and neck, thorax, rump
Organism has things like behavior, body temperature, growth, basically anything to do with the whole organism

It would also be helpful for the Alliance to consider the next level of organization under cellular phenotype as we need to be able to have a good slim set there as well.