DO NOT MERGE: New pattern abnDecEfficOfBiolProc June 28 2019

[chris-grove]

Created new pattern

abnormallyDecreasedEfficacyOfBiologicalProcess

All pattern schema checks have passed.

[matentzn]

Can you improve the description by adding an example and add a more detailed distinction of efficiacy from rate? (produces more output, was it?)

[matentzn]

Are deficiency and defectiveness really exact or rather broader synonyms of decreased efficiacy?

[chris-grove]

@matentzn
From PATO, 'decreased efficacy' (PATO:0015003)

def: A decrease in the ability of a process to produce its output.

Yes, I can add an example and more detail to the description. Efficacy refers to process output in general, rate specifically refers to process output per unit of time.

I would think that "deficiency" and "defectiveness" are exact synonyms, but perhaps "deficiency" is a narrow synonym specifically meaning decreased efficacy to the point that the output is insufficient to meet some criteria. "defectiveness" I think is exactly synonymous with "decreased efficacy". I am planning on using this pattern for all of our "defective process" terms.

[pnrobinson]

Please note that processes are not linear, and a defective process can produce not only less than required (e.g., slow heartbeat) but also otherwise abnormal results (e.g., irregular heartbeat). I am not sure that this definition will be very enlightening.

[chris-grove]

@pnrobinson
Thanks! To be clear, the definition says decreased efficacy (i.e. decreased ability) not decreased output. I am trying to distinguish "abnormal process" from "defective process" as we have many terms in the C. elegans phenotype ontology that are distinctly one or the other. I would take "defective process" to mean that some aspect(s) of the process is/are not working properly (i.e. reduced ability), as opposed to simply "abnormal process" which may include/subsume enhanced or increased processes or abilities.

[chris-grove]

Just to add: I had considered the PATO terms for "defective" but in one case it is simply a synonym of "abnormal" and in another it is a synonym of "non-functional", a physical object quality. I was looking for an appropriate PATO process quality term to capture the essence of "defective"

[matentzn]

@chris-grove can we somehow distinguish this pattern stronger from the decreased quality of process pattern?

[chris-grove]

Just to update, here is current proposed pattern:

pattern_name: abnormallyDecreasedEfficacyOfBiologicalProcess
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml
description: "An abnormally decreased efficacy (reduced ability to produce output) of a biological process compared to controls. For example, defective cytokinesis."

contributors:
  - https://orcid.org/0000-0001-9076-6015

classes:
  decreased efficacy: PATO:0015003
  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
  narrow_synonym: oio:hasNarrowSynonym

vars:
  biological_process: "'biological process'"

name:
  text: "decreased efficacy of %s"
  vars:
   - biological_process

annotations:
  - annotationProperty: narrow_synonym
    text: "Deficiency of %s"
    vars:
     - biological_process
  - annotationProperty: exact_synonym
    text: "Defective %s"
    vars:
     - biological_process

def:
  text: "Decreased efficacy of %s."
  vars:
    - biological_process

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

@matentzn
My understanding was that the "decreased quality of process" was intended to produce very generic grouping terms for terms referring to a decrease in any quality of a process. This pattern specifically refers to decreased efficacy, which I think is quite distinct as is.

@pnrobinson @matentzn
Is my intention clear and do you have any suggestions for different quality term(s) to use to achieve the desired effect? And/or suggestions for the description?

[matentzn]

@mah11 and @sbello can we get your input here, else I think this is good for the merge.

[mah11]

I find this pattern a little confusing, such that I'm not sure whether I'd use it for FYPO (and if so, for which phenotypes). In particular, I don't think I see where @matentzn's request for "a more detailed distinction of efficiacy from rate" has been addressed. Maybe the underlying problem is that I don't quite get how one detects or measures a process's ability to produce output other than by measuring level or rate of output production.

All that said, I don't have any reason to oppose adding this pattern, nor to its definition. I just won't use it until I actually get my head round it.

[chris-grove]

A common phenotype in C. elegans is "dauer defective", in which case larval worms that would otherwise form dauer larva (a stress-resistant, long-lived, alternative larval stage induced by low food and/or high population and in which the worm mouth and anus close off from the external environment) do not (i.e. are not able to) form dauers. The observation might be significantly reduced numbers of dauer larva compared to controls or possible a complete lack of any dauers when control plates have a substantial number of dauers.

We have lots of "chemotaxis defective" terms, many specifically pertaining to a particular chemical or odor, in which worms lose the ability to be attracted to or repulsed by a particular chemical/odor, as assessed by the number of animals localized near an odor or a control chemical on a plate after a certain period of time. These are usually reported using a "chemotaxis index" where +1 is complete attraction, -1 is complete repulsion, and 0 is no different from (an odorless) control.

"egg laying defective" is another common C. elegans phenotype, in which animals are unable to carry out the normal egg laying process. This can result in worms that end up with an abnormally large number of eggs inside the uterus of the worm.

An important point, I think, is that many times authors may report that some process is defective without explicitly providing the details as to how that was measured. Other times, the phenotypic assay may be quite particular such that creating a phenotype term for that specific assay would likely only cause confusion to end users and miss the point that the conclusion is that a well known biological process is not functioning properly or effectively.

[chris-grove]

OK after some discussion with @matentzn here is a new iteration of the pattern with "deficiency" narrow synonym removed and an expanded description:

pattern_name: abnormallyDecreasedEfficacyOfBiologicalProcess
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml
description: "An abnormally decreased efficacy (reduced ability to produce an output of normal amount and/or quality*) of a biological process compared to controls. *Here 'quality' refers specifically to the 'goodness', 'properness', or 'adequateness' of the output (as opposed to any characteristic in general) and 'output' can mean a particular physical entity (like metabolite as a product of a metabolic process) or state (or configuration) of a physical entity (like the fitness or health of a cell). This phenotype is usually inferred from more direct observations; for example, blood glucose levels may be measured by a colorimetric assay applied to a blood sample, which then is used to infer that blood glucose is high, low, or unstable, which can then itself be used to infer that blood glucose homeostasis is defective or has reduced efficacy."

contributors:
  - https://orcid.org/0000-0001-9076-6015

classes:
  decreased efficacy: PATO:0015003
  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: "decreased efficacy of %s"
  vars:
   - biological_process

annotations:
  - annotationProperty: exact_synonym
    text: "defective %s"
    vars:
     - biological_process

def:
  text: "Decreased efficacy of %s."
  vars:
    - biological_process

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

[chris-grove]

@matentzn @dosumis
Maybe we could revisit (and revive) this PR/proposal? I no longer remember what was/is holding this up. Are we still not happy with the text definition(s)? As per
#739
It sounds like we're OK with using the "efficacy"/"increased efficacy"/"decreased efficacy" PATO terms in patterns, but maybe the general application to process as proposed here is still not acceptable?

[dosumis]

I think we agreed on the call yesterday the efficacy was OK as long as it's clear that this refers to some effect on the output of the process. The only worry is that there may be many cases were we should probably go back and apply it.