bad logical definitions for intellectual impairment

[azankl]

I tried matching HP_0001249 Intellectual disability to MP. The best match I could find is MP_0014114 abnormal cognition, but interestingly the logical definitions don't quite match up:

MP_0014114 abnormal cognition

Equivalent to:
• has part some (
 quality and
    inheres in some cognitive behavior and
    has modifier some abnormal)

HP_0001249 Intellectual disability
Equivalent to:

• has part some (
    disrupted and
    inheres in some cognition and
    has modifier some abnormal)

the parent term of HP_0001249 Intellectual disability is HP_0100543 Cognitive Impairment and its logical definition is a bit closer to MP_0014114, but still not identical:

HP_0100543 Cognitive Impairment
Equivalent to:

• has part some (
    quality and
    inheres in part of some cognition and
    has modifier some abnormal)

I discussed this with @cmungall and he asked for it to be submitted here.

[matentzn]

@sbello @nicolevasilevsky @LCCarmody @drseb

I am liking http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedQualityOfBiologicalProcess.yaml for this (general unspecified abnormality of a process) and using 'cognition' instead of cognitive behaviour.. What do you think?

[matentzn]

@Clare72 @dosumis

[Clare72]

I agree that none of these three should be behaviors.

'intellectual disability' is another one defined by a particular number (IQ abnormally less than 70) and subclasses have different numerical ranges (including 70-85!!), so it would be difficult to logically distinguish its subclasses without using these numbers.

From its definition, the parent, 'cognitive impairment', sounds like it could be an increase or decrease, but the name suggests a decrease, if this is the case, this would also be difficult to differentiate 'intellectual disability' without using numbers.

'abnormal cognition' seems like it could be an increase or decrease in quality, so would need abnormalQualityOfBiologicalProcess (I don't think this exists yet?)

[dosumis]

May be better to use Mental functioning ontology - congnitive process? Sits outside behavior.

If we want to reference IQ ranges, we could potentially make PATO terms that bin ranges (e.g. 70-85) and define these bins using a data property.

[matentzn]

@Clare72

'abnormal cognition' seems like it could be an increase or decrease in quality, so would need abnormalQualityOfBiologicalProcess (I don't think this exists yet?)

https://raw.githubusercontent.com/obophenotype/upheno/master/src/patterns/dosdp-dev/abnormalBiologicalProcess.yaml

May be better to use Mental functioning ontology - congnitive process? Sits outside behavior.

@dosumis Interesting! What do other people think? Of course to avoid complexity, I would prefer GO, but since we will eventually hit the limit when talking about impaired mental functioning, MF might be a serious option!

[dosumis]

CC'ing @jannahastings for updates on status/work on MFO

[LCCarmody]

I am not sure what the advantage would be between GO cognition or MFO cognitive process, but I do vote for being able to bin IQ ranges. THis is the hierarchy of HPO's intellectual disability, and we would need to think about how to divide these: Neurodevelopmental abnormality -Intellectual disability --Intellectual disability, progressive --Intellectual disability, moderate --Intellectual disability, severe --Intellectual disability, mild --Intellectual disability, profound --Intellectual disability, borderline

[jannahastings]

@dosumis, at present the MFO does not have categories for different levels of intellectual disability. It includes just one general class imported from the Disease Ontology ('intellectual disability'). I could of course improve this if it is useful.

[azankl]

I think http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedQualityOfBiologicalProcess.yaml inhering in some cognition is a good definition for HP_0001249 Intellectual disability. I agree that abnormal cognition could apply to both an increase or decrease in cognition and in fact, MP_0014114 abnormal cognition has the child terms enhanced learning and impaired learning:

So maybe the equivalent of HP_0001249 Intellectual disability should be MP_0012315 impaired learning and MP_0012315 could have the logical definition abnormallyDecreasedQualityOfBiologicalProcess inhering in some cognition, like HP_0001249 Intellectual disability. I think differentiating between mild, moderate and severe intellectual disability in animals is very difficult and modelling this might therefore not be so important.