Review: abnormallyIncreasedRateOfBehavior.yaml

[Clare72]

increasedRateOfBehavior.yaml

I'm not comfortable with defining this as an improvement as it will often mean that the organism is performing worse than controls. For example, increased wandering behavior in larvae usually means that they are eating less of a perfectly good food source (which may not be measured directly to be captured as a 'decreased food intake' phenotype). It is also possible that quality decreases as rate increases, e.g. a male fly may sing his courtship song more quickly, but the female may be less impressed by it!

[matentzn]

Yeah, my thoughts exactly; thats why I renamed the pattern from enhancedBehavior to increasedRateOfBehavior, and took the PATO definition for increased rate to describe the pattern. Where do you still see that it is defined as an improvement?

[Clare72]

In the text definition

[matentzn]

Ah I can see it. Synonym, description and label :P Never look at those. +1 (100%) on the suggestion!

[Clare72]

Similar thing for decreased rate being described as 'impaired'

[nicolevasilevsky]

pattern_name: increasedRateOfBehavior pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/increasedRateOfBehavior.yaml description: "Behavior occurs with a higher frequency (more often) than usual (per unit of time)"

classes: increased rate: PATO:0000912 abnormal: PATO:0000460 behavior process: NBO:0000313

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

annotationProperties: exact_synonym: oio:hasExactSynonym

vars: behavior_process: "'behavior process'"

name: text: "Enhanced %s" vars:

• behavior_process

def: text: "Enhanced or improved %s." vars: - behavior_process

equivalentTo: text: "'has_part' some ('increased rate' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))" vars: - behavior_process

@obophenotype/phenotype-editors could you all review this pattern above and sign off on it in the spreadsheet. Nico hopes to have these all reviewed by mid-March, in time for the workshop at Biocuration2019.

[chris-grove]

I agree completely with @Clare72 and @matentzn Can we just make the name "Abnormally increased rate of %s" instead of "Enhanced %s"? Also, make the definition "Abnormally increased rate of %s" instead of "Enhanced or improved %s."? Or are we deliberately trying to make the name and definition non-identical? Otherwise, I'm fine with the pattern.

[chris-grove]

Updating ticket: Updating title to "abnormallyIncreasedRateOfBehavior"

Pattern GitHub location as of May 9, 2019: https://github.com/obophenotype/upheno/blob/master/src/patterns/dosdp-dev/abnormallyIncreasedRateOfBehavior.yaml

Pattern IRI as of May 9, 2019: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedRateOfBehavior.yaml

Pattern as of May 9, 2019:

pattern_name: abnormallyIncreasedRateOfBehavior
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedRateOfBehavior.yaml
description: "Behavior occurs with a higher frequency (more often) than usual (per unit of time)"

contributors: 
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432

classes:
  increased rate: PATO:0000912
  abnormal: PATO:0000460
  behavior process: NBO:0000313

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym 

vars:
  behavior_process: "'behavior process'"
 
name:
  text: "Enhanced %s"
  vars:
   - behavior_process

def:
  text: "Enhanced or improved %s."
  vars:
    - behavior_process

equivalentTo:
  text: "'has_part' some ('increased rate' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
- behavior_process

[Clare72]

There is also this proposed change to PATO that came out of the POTATO workshop: https://github.com/pato-ontology/pato/pull/228/files This splits rate into rate of occurrence and rate of continuous process.

We probably want to cover both of these in the increased / decreased rate of behavior patterns (and continue using 'increased rate'), e.g. 'increased rate of feeding behavior' ('feeding behavior' = GO:0007631) may or may not mean more meals. The pattern description sounds like it is referring to rate of occurrence and should be clarified to something like: "Behavior occurs more quickly and/or more often than usual."

Also, GO behaviors should also be able to be used by this pattern, as discussed here: https://github.com/obophenotype/upheno/issues/331