First draft for trait to phenotype mappings

[matentzn]

In recent months we have migrated OBA to a modern infrastructure, so we should be able to create a draft mapping based on the following process:

• @rays22 Publish a VT-OBA mapping in SSSOM here and share with Elissa's team [oba_vt.sssom.tsv]
• Elissa's team will make sure that all relevant VT codes are present
• @rays22 Merge OBA, HP and MP (robot merge) and runs the reasoner. Run a ROBOT (SPARQL) query to determine all VT-MP/HP mappings (all of these are necessarily narrow from OBA to HP/MP!) [oba_upheno.sssom.tsv]
• @rays22 Send to share SSSOM mappings with Elissa's team
• @matentzn will share MONDO - OMIM mapping with Elissa's team
• Elissa's team will merge HPOA annotations (HP to OMIM p2d's) with [oba_upheno.sssom.tsv] and [oba_vt.sssom.tsv] to produce [vt_mondo.sssom.tsv, vt_hp.sssom.tsv, vt_mp.sssom.tsv] and provide feedback here
• If these "mappings" (not really mappings in the strict sense, but let's say vaguely mappings) are any good, then we are start thinking about adding other sources of p2d and streamlining this process for other trait to disease use cases like GWAS

[dosumis]

@matentzn - this all sounds reasonable. Would you be able to prepare some slides/figures detailing each step? It would be especially helpful to fill in the gaps between reasoning and SSSOM mapping files.

[matentzn]

Yeah, this is all a bit theoretical atm - we will create figures and slides for every step as it happens (I also need to wrap my head around the details) - the first one is a run of sssom-py that I will go through in our next Friday meeting.

[matentzn]

Also consider augmenting the MP-HP mappings with @sbello latest contribution:
#10

which maps COVID related phenotypes between MP and HP.

[matentzn]

While @obwalton is getting is a list of missing (unmapped) VT terms, here the world's first and entirely unreviewed set of phenotype-trait associations:

https://github.com/obophenotype/upheno-dev/blob/master/src/ontology/reports/phenotype_trait.sssom.tsv

@rays22

• Please review the first draft of phenotype-trait associations. 100% automated. Please let it be good! :D You can try to fit it all in a google sheet, but it is large.

[jamesamcl]

@matentzn Please could you explain the relationship between these two files:

https://github.com/obophenotype/upheno-dev/blob/master/src/ontology/reports/phenotype_trait.sssom.tsv mentioned above

https://raw.githubusercontent.com/obophenotype/upheno-dev/refs/heads/master/src/mappings/upheno-oba.sssom.tsv

[matentzn]

@matentzn Please could you explain the relationship between these two files:

This file

https://github.com/obophenotype/upheno-dev/blob/master/src/ontology/reports/phenotype_trait.sssom.tsv

is outdated and I now git rmed it. The other one is correct!