review: abnormallyPrematureBiologicalProcess

[jseager7]

This is a proposal for a pattern that is the inverse of 'abnormally delayed biological process'.

Note: The first draft of this pattern proposed a new quality 'expedited', but the quality that I was actually looking for was 'premature' (PATO:0000694).

Here's the current draft:

pattern_name: abnormallyPrematureBiologicalProcess
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyPrematureBiologicalProcess.yaml
description: "A biological process which starts earlier than the natural start time or the reference process."

contributors:
  - https://orcid.org/0000-0001-7487-610X

classes:
  premature: PATO:0000694
  abnormal: PATO:0000460
  biological process: GO:0008150

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  biological_process: "'biological process'"

name:
  text: "premature %s"
  vars:
   - biological_process

def:
  text: "Premature %s."
  vars:
    - biological_process

equivalentTo:
  text: "'has_part' some ('premature' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - biological_process

[matentzn]

@mah11 @dosumis @ybradford @sbello @chris-grove (and everyone else) for comments. :) Thanks!

[mah11]

tl;dr: @jseager7, could you see if PATO:0000694 will do?

As I suspected, dictionaries say that "expedite[d]" can mean either "happens sooner" OR "takes longer"; I'm not aware of any ontology-world usage that constrains "expedite" to the former meaning in a more specialized context.

In FYPO I have used PATO:0000694 'premature' in a de-facto pattern for processes that begin abnormally early. It's is_a PATO:0002325 'onset quality', and defined as "A quality of a process which starts earlier than the natural start time or the reference process. [PATO:LC]".

in principle I'm happy to upgrade the pattern globally to a new PATO class, but at the moment I don't understand what, if any, difference there is between PATO:00003694 and what @jseager7 is requesting here. Perhaps another synonym would suffice (and I'd think the scope should be RELATED because of the ambiguity in the vernacular meaning of "expedite").

[jseager7]

@mah11 PATO:0000694 sounds like exactly what we need, thanks. I must have missed the fact that 'premature' existed when making this issue, because the OLS was filtering the tree view to only show 'delayed'.

I agree that 'expedited' doesn't really capture the semantics properly due to the flaws you mentioned. I'll amend the issue to use 'premature' instead of 'expedited', and I'll recommend that we amend PHIPO's terminology to match (since I think PHIPO currently uses 'expedited' in its term labels).

[mah11]

@jseager7 Glad it works for you! I don't see any reason why PATO couldn't add the 'related' synonym anyway, to help with future searching.

[chris-grove]

+1 to 'premature' (PATO_0000694), which also has the synonyms 'precocious' and 'early'. We have many 'precocious' terms in the worm phenotype ontology that could use this pattern. Thanks!

[matentzn]

@jseager7 can you create a PR for this? Directly into dosdp-dev directory please!

THANKS :)

[jseager7]

@matentzn There's now a pull request open at #511.