Restrict the abnormalLevelOfChemicalEntity pattern to anatomical entities

[rays22]

Restrict the abnormalLevelOfChemicalEntity pattern to anatomical entities

• Update the EQ in src/patterns/dosdp-patterns/abnormalLevelOfChemicalEntity.yaml

so that the attribute is restricted chemicals in anatomical entities:

'has part' some 'amount'
        and (('characteristic of' some ('%'
            and ('part of' some 'anatomical entity')))
            and ('has modifier' some 'abnormal'))
% = chemical entity

This issue is to follow up obophenotype/bio-attribute-ontology#367 (review) .

[sbello]

What does this mean for abnormal level in exhaled gasses? See for example http://purl.obolibrary.org/obo/HP_0033036 while it is called nasal the thing being measured is the level of nitric oxide in the exhaled gas. It is only 'nasal' because that is where the probe is.

HPO also has
Positive hydrogen breath test
Positive lactose hydrogen breath test

Also we already have a pattern for chemical level in location https://raw.githubusercontent.com/obophenotype/upheno/master/src/patterns/dosdp-patterns/abnormalLevelOfChemicalEntityInLocation.yaml
This change would make the two patterns identical.

I'm inclined we just obsolete the pattern without location. The HPO terms do not have EQs now and Positive hydrogen breath test and Positive lactose hydrogen breath test both refer to elevated hydrogen in the exhaled breath with the only difference being what the person consumed before the test.

Before obsoleting we need to check with the single cell folks. Would they use the entity-less pattern for levels in the external media?

[matentzn]

I'm inclined we just obsolete the pattern without location.

This will make naming (what is the standard label etc) and the transition for this pattern much harder. the addiotion @rays22 suggests really does not create any work for any ontology using patterns (so, every ontology other than HPO and FYPO), while obsoleting this pattern will create a big amount of work for all patternised POs..

Your question about http://purl.obolibrary.org/obo/HP_0033036 is good though.. This is something @rays22 needs to think through :P

[sbello]

Agreed about the obsolete comment. This was written before you pointed out that the difference between this pattern and the inLocation pattern is that the location in this pattern is static not variable. I do think this needs a note at the top of the pattern to make it super clear.

And yes, what do we do about http://purl.obolibrary.org/obo/HP_0033036 or similar terms. Although, I do see that Uberon has a term for bodily gas http://purl.obolibrary.org/obo/UBERON_0034873 that covers all expelled gasses so we could ask for a term to cover exhaled gas. There is already one for excreted gas.

[rays22]

Your question about http://purl.obolibrary.org/obo/HP_0033036 is good though.. This is something @rays22 needs to think through :P

HP exhaled gas terms

None of HP:0033036 Decreased nasal nitric oxide, HP:6000259 Positive hydrogen breath test, HP:4000100 Positive lactose hydrogen breath test, HP:6001236 Elevated fraction exhaled nitric oxide are using this or any other uPheno pattern templates. In fact, they do not have any EQ definitions at all. Therefore, altering the abnormalLevelOfChemicalEntity pattern should not cause any extra work for HP.

Moreover, these exhaled gas terms should not be defined by the abnormalLevelOfChemicalEntity pattern (the subject of the current discussion), but rather by the abnormalLevelOfChemicalEntityInLocation pattern.

1. HP:0033036 Decreased nasal nitric oxide
   • This term lacks any EQ definition currently, so the change in this pattern should not cause any extra work for HP.
   • An EQ for this term based on the pattern abnormalLevelOfChemicalEntityInLocation can be created.
     • Entity: nitric oxide
     • Quality: decreased amount
     • Location: gas in respiratory system
   • The comment "... measurable in nasal air ..." and the term definition suggests that the anatomical location of the gas that is being characterised in this phenotypic trait is the respiratory system, that is exhaled from the lungs. For practical reasons, the gas is measured by a probe via the nasal cavity. (Please, note that UBERON:0001707 nasal cavity is a part of the UBERON:0001004 respiratory system)
2. Increased amount of hydrogen in the respiratory system. A new parent class for the following two HP terms could be logically defined using uPheno patterns. These two terms themselves somewhat obfuscate cause with effect. Thus, the differentiating factor is what causes or assumed to cause the phenotypic effect.
   • Entity: hydrogen
   • Quality: increased amount
   • Location: gas in respiratory system
   • 2.a. HP:6000259 Positive hydrogen breath test
     • This term lacks any EQ definition currently, so the change in this pattern should not cause any extra work for HP.
     • An EQ for its parent term based on the pattern abnormalLevelOfChemicalEntityInLocation can be created.
     • The comment "... The hydrogen-containing blood travels to the lungs where the hydrogen is released and exhaled in the breath where it can be measured..." suggests that that the anatomical location of the gas that is being characterised in this phenotypic trait is the respiratory system, that is exhaled from the lungs.
   • 2.b HP:4000100 Positive lactose hydrogen breath test
     • This term lacks any EQ definition currently, so the change in this pattern should not cause any extra work for HP.
     • An EQ for its parent term based on the pattern abnormalLevelOfChemicalEntityInLocation can be created.
     • "... Elevated hydrogen gas level in exhaled breath following oral administration of lactose ...". This could be also modelled as a process quality of "response to lactose".
3. HP:6001236 Elevated fraction exhaled nitric oxide
   • This term lacks any EQ definition currently, so the change in this pattern should not cause any extra work for HP.
   • An EQ for this term based on the pattern abnormalLevelOfChemicalEntityInLocation can be created.
     • Entity: nitric oxide
     • Quality: increased amount
     • Location: gas in respiratory system
   • "... The fractional exhaled nitric oxide ..."