Obsolete PATO:0000001 (quality) in favor of COB:0000502 (characteristic)

[matentzn]

Summary

This issue proposes obsoleting PATO:0000001 (quality) and replacing it with COB:0000502 (characteristic) as part of aligning PATO with the Core Ontology for Biology and Biomedicine (COB).

Background

This change was discussed and (tentatively) agreed upon by major players in OBOFoundry/COB#315.

In the COB alignment work, it was determined that COB:0000502 (characteristic) is equivalent to PATO:0000001 (quality). The term "quality" in PATO has always had a broader meaning than the BFO term of the same name - it encompasses characteristics in general, not just the narrower BFO sense.

The COB issue presented two options:

1. Obsolete PATO:0000001 and replace with COB:0000502 (preferred)
2. Obsolete COB:0000502 and replace with PATO:0000001

Option 1 was selected as the preferred approach.

I would like to note that there was a third option, not discussed:

3. Subsume PATO:0000001 under COB:0000502

We ignore this here as it might be confusing that two classes that mean the exact same thing exact side by side, but it would safe a lot of churn for downstream uses of one of the most widely used ontology.

Proposed Changes

• Obsolete PATO:0000001
• Add replaced_by: COB:0000502
• Add explanatory comment
• Update direct children of PATO:0000001
  • PATO:0000068 (qualitative)
  • PATO:0001241 (physical object quality)
  • PATO:0001303 (variability)
  • PATO:0002326 (relational quality of process)
  • PATO:0070036 (dendrite quality)
  • PATO:0103000 (quantitative)
• Change IAO:0000700 (ontology root term) from PATO:0000001 to COB:0000502

Impact on Downstream Users

This is a breaking change for ontologies and applications that:

• Reference PATO:0000001 directly (ALL phenotype ontologies do this!)
• Use PATO:0000001 as a parent class
• Query for the root of the PATO hierarchy

Downstream users would have to:

1. Update references from PATO:0000001 to COB:0000502
2. Ensure they import COB (directly or transitively through PATO)
3. Update any hardcoded references to the PATO root term

Related Issues

• PATO to COB connection OBOFoundry/COB#315 - PATO to COB connection
• Where to place "phenotypic quality" (PATO) OBOFoundry/COB#124 - Original discussion on COB:0000502 equivalence

[matentzn]

As I note in OBOFoundry/COB#315, I am a little scared of the magnitude of the churn - I would go through with it, but it will be a huge effort in which I wont do other important things.