PATO to COB connection

[cmungall]

Carried from #124

This is what we have in COB:

• [] COB:0000502 ! characteristic
  • [i] PATO:0002193 ! electric charge
  • [i] PATO:0000125 ! mass
  • [i] BFO:0000017 ! realizable entity
    • [i] OBI:0000260 ! plan
    • [i] BFO:0000023 ! role
    • [i] BFO:0000016 ! disposition
      • [i] BFO:0000034 ! function

I think there is no reason to import the specific PATO terms, so if we ignore these we have:

• [] COB:0000502 ! characteristic
  • [i] BFO:0000017 ! realizable entity
    • [i] OBI:0000260 ! plan
    • [i] BFO:0000023 ! role
    • [i] BFO:0000016 ! disposition
      • [i] BFO:0000034 ! function

In the old cob-to-external we had decided COB:0000502 was equivalent to PATO:0000001

COB:0000502     characteristic  owl:equivalentClass     PATO:0000001    quality https://github.com/OBOFoundry/COB/issues/124    semapv:ManualMappingCuration

(don't get distracted by the name, PATO:0000001 has always had a broader meaning than the BFO term, see #124).

The primary decision here is either

1. obsolete PATO:0000001 and replace by COB:0000502 (much preferable, would need some dedicated effort likely by @matentzn to announce and coordinate) OR
2. obsolete COB:0000502 and replace by PATO:0000001
   • 2a: with name as quality (requires no changes in PATO but is hugely confusing)
   • 2b: with name as characteristic (would entail a period of confusing double labels in import chains until PATO change propages)

[bpeters42]

A quick and strong vote for option 1. That is what the COB term was created for, namely to move on from the confusion between BFO:quality and PATO:quality which are labeled the same but mean different things. We want OBO ontology users and developers to use PATO without having to delve into those discussions.

[matentzn]

I made a more detailed issue here: pato-ontology/pato#594

Note that the churn of your preferred solution is immense. A compromise would be what I list as "Option 3" (subsume PATO:0000001 under COB:0000502.

Remember we will have to:

1. Update all ontologies referencing PATO:0000001
2. Update all database curation using PATO:0000001 (ZFIN etc)
3. Update all DOSDP patterns in all repos referencing PATO:0000001

Yes we have claude now but it will take me days to do this..