review: abnormallyDecreasedQualityOfBiologicalProcess

[chris-grove]

Pattern location as of May 7, 2019:

https://github.com/obophenotype/upheno/blob/master/src/patterns/dosdp-dev/abnormallyDecreasedQualityOfBiologicalProcess.yaml

Pattern as of May 7, 2019:

pattern_name: abnormallyDecreasedQualityOfBiologicalProcess
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedQualityOfBiologicalProcess.yaml
description: "Process that appears in some (unspecified) way impaired or decreased (less frequent, less strong)."

contributors:
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0001-5208-3432

classes:
  process quality: PATO:0001236
  abnormal: PATO:0000460
  biological process: GO:0008150

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym 

vars:
  biological_process: "'biological process'"
 
name:
  text: "decreased qualitatively %s"
  vars:
   - biological_process

def:
  text: "Decreased qualitatively %s."
  vars:
    - biological_process

equivalentTo:
  text: "'has_part' some ('process quality' and ('inheres_in' some %s) and ('qualifier' some 'abnormal'))"
  vars:
- biological_process

[chris-grove]

I think the "process quality" in the logical definition is intended to be "decreased process quality" or there should be another phrase like "and (has_modifier some 'decreased')" or something, otherwise it looks just like the "abnormalBiologicalProcess" pattern with the exception of 'qualifier' instead of 'has modifier'.

[chris-grove]

Also, I think the "decreased qualitatively %s" sounds a bit awkward. Adverbs don't usually follow the adjectives they modify, in English. Why not just "decreased quality of %s"?

I'm also in search of good patterns for "defective %s" whether %s is a process or an anatomical entity; I suppose this would be the appropriate one for process?

[pnrobinson]

Does "decreased quality" actually have any meaning in our context? What exactly is the use case of this pattern?

[chris-grove]

After discussing with @matentzn it sounds like this pattern was just intended to group all terms with a decreased quality of some kind. Then perhaps the description should reflect that or be made more general.