Add ratio related patterns and examples

[rays22]

1. The purpose of pattern template compound_attributes is to extend PATO with compound qualities, i.e. qualities that are defined by using primitive (I mean existing PATO) qualities.
   The two-component quality is then used in the entity_attribute pattern to define a new term, e.g. digit length ratio.
2. When there is a ratio-type quality between two other unrelated qualities, like the proportionality of mass and length in BMI, then I propose the use of proportion_of_attributes template to define such OBA attributes.
   Fix Create new 'ratio' DOS-DP pattern template #272 .

[rays22]

Suggested change

	text: "('proportionality_to'
	text: "'proportionality_to'

[rays22]

Suggested change

	and ('has_part' some %s))
	and ('has_part' some %s)

[rays22]

I have found two TO examples of ratio-type traits that also have logical definitions:

• TO:0000278 root to shoot ratio
• TO:0000525 sodium to potassium content ratio

The two classes above appear to defined by the following EQ pattern:

(proportionality to
    and (TO_has_dividend_quality some TRAIT-1)
    and (TO_has_divisor_quality some TRAIT-2)

, where proportionality to, TRAIT-1 and TRAIT-2 are qualities.

The two relationships used in the above TO pattern are defined outside of the OBO Relations Ontology:

1. TO:has_dividend_quality
2. TO:has_divisor_quality

I am proposing the pattern

'proportionality_to'
    and ('has_part' some TRAIT-1)
    and ('has_part' some TRAIT-2)
    and ('characteristic_of_part_of' some ENTITY)

or more tersely:

'proportionality_to'
    and ('has_part' some (TRAIT-1 and TRAIT-2)
    and ('characteristic_of_part_of' some ENTITY)

In my suggested pattern I am using the standard RO has part relationship in place of TO:has_dividend_quality and TO:has_divisor_quality.
Please note, that in my model the ratio quality is indifferent about the direction the calculation of a mathematical ratio. For example, the 'sodium to potassium' or 'potassium to sodium' ratios would be part of the same category.

[cmungall]

This is definitely wrong:

'proportionality_to'
    and ('has_part' some (TRAIT-1 and TRAIT-2)
    and ('characteristic_of_part_of' some ENTITY)

if this doesn't show up as unsatisfiable we are doing something wrong

This has cryptic incoherencies:

'proportionality_to'
    and ('has_part' some TRAIT-1)
    and ('has_part' some TRAIT-2)
    and ('characteristic_of_part_of' some ENTITY)

It loses directionality so {increased, decreased} x {A:B, B:A} become indistinguishable

[rays22]

This is definitely wrong:

'proportionality_to'
    and ('has_part' some (TRAIT-1 and TRAIT-2)
    and ('characteristic_of_part_of' some ENTITY)

if this doesn't show up as unsatisfiable we are doing something wrong

This has cryptic incoherencies:

'proportionality_to'
    and ('has_part' some TRAIT-1)
    and ('has_part' some TRAIT-2)
    and ('characteristic_of_part_of' some ENTITY)

It loses directionality so {increased, decreased} x {A:B, B:A} become indistinguishable

@cmungall, thanks for your feedback.
I gather from your comment that we need directionality in the trait ratio pattern to be interoperable with uPheno phenotypes.
I am wondering if I should request new RO terms equivalent to

1. TO:has_dividend_quality
2. TO:has_divisor_quality
   and use an EQ based on the TO pattern above or do you have something else in mind that would work better?

[cmungall]

It’s less about interoperability and more about coherency. It’s really important the logical definition matches the label and the text definition. If my argument doesn’t make sense we should explore further, and it’s possible I’m wrong! As to my preferred solution, yes I think we need to distinguish the roles of the different sub quantities and specific relations seem easiest

…

On Fri, Jan 26, 2024 at 5:35 AM Ray Stefancsik ***@***.***> wrote: This is definitely wrong: 'proportionality_to' and ('has_part' some (TRAIT-1 and TRAIT-2) and ('characteristic_of_part_of' some ENTITY) if this doesn't show up as unsatisfiable we are doing something wrong This has cryptic incoherencies: 'proportionality_to' and ('has_part' some TRAIT-1) and ('has_part' some TRAIT-2) and ('characteristic_of_part_of' some ENTITY) It loses directionality so {increased, decreased} x {A:B, B:A} become indistinguishable @cmungall <https://github.com/cmungall>, thanks for your feedback. I gather from your comment that we need directionality in the trait ratio pattern to be interoperable with uPheno phenotypes. I am wondering if I should request new RO terms equivalent to 1. TO:has_dividend_quality <https://www.ebi.ac.uk/ols4/ontologies/to/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FTO_has_dividend_quality?lang=en> 2. TO:has_divisor_quality <https://www.ebi.ac.uk/ols4/ontologies/to/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FTO_has_divisor_quality?lang=en> and use an EQ based on the TO pattern above or do you have something else in mind that would work better? — Reply to this email directly, view it on GitHub <#312 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOLP3HKUN6HKXP6FYSTYQOWLBAVCNFSM6AAAAABCCFIGB6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJSGA3TSOBZGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[rays22]

There are two term requests in RO that look relevant to the modelling of qualities emerging from two qualities that are in a ratio/proportion relationship:

• Adding the now deprecated relation "has divisor entity" from PATO #774
• Adding the now deprecated relation "has dividend entity" from PATO #775

[rays22]

The resolution of this PR depends on oborel/obo-relations#792 .

[matentzn]

We need this pattern now for another project, is there anything left to finalise it @rays22 ?

[rays22]

We need this pattern now for another project, is there anything left to finalise it @rays22 ?

@matentzn ,
The resolution of this issue depends on a new RO release.

[matentzn]

@anitacaron can you make one soon?

[anitacaron]

yes, I just need to finish reviewing some PRs, and I'll make one.

[matentzn]

@rays22 can you bring the PR to conclusion soon? We need it for a major project coming up in OBA in the next weeks

[anitacaron]

I'm still waiting for another person to approve the RO release.

[cmungall]

approved

…

On Wed, May 1, 2024 at 5:44 AM Anita Caron ***@***.***> wrote: I'm still waiting for another person to approve the RO release. — Reply to this email directly, view it on GitHub <#312 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOKTNMEOOIJV5POEL7DZADPRVAVCNFSM6AAAAABCCFIGB6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBYGQYTGMJVGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[cmungall]

not totally sure why this clause is here but I'm sure it's OK

[matentzn]

Also would like a reminder!

[rays22]

The purpose is to limit to the classes to systems that are relevant to OBA (and make them subclasses of OBA:0000001). I want to avoid grouping urinary sodium to potassium ratio together with some sea water sodium to potassium ratio measurement class, for example in Ubergraph. Also, without the ('characteristic_of_part_of' some 'anatomical_entity') part, I am getting some new ratio terms (see the examples in attributes_ratio.tsv) that are not subclasses of OBA:0000001 and are flagged up as biological attribute child violation error by the QC pipeline.

[matentzn]

Smart, its so unfortunate that this is necessary in OWL (its because of the tree model property which makes it impossible to constrain how references entities within an expression are related).

The same logic should be considered for abnormal chemical (without "in location") patterns.