EQ for Abnormal circulating cholesterol concentration HP:0003107

[anna-anagnostop]

Please consider reviewing EQ for Abnormal circulating cholesterol concentration HP:0003107 and its synonyms.

EQ currently uses:

has part some (quality and (inheres in part of some cholesterol metabolic process) and (has modifier some abnormal))

which does not appear to match the textual definition.

Note that, currently, there is no pattern available for abnormalLevelOfChemicalEntityInLocation although patterns do exist for abnormallyIncreasedLevelOfChemicalEntityInLocation and abnormallyDecreasedLevelOfChemicalEntityInLocation (using PATO terms for increased amount PATO:0000470 and decreased amount PATO:0001997, respectively).

Also, there is a pattern available for abnormalConcentrationOfChemicalEntityInLocation but no patterns for the abnormallyIncreased/Decreased counterparts.

Any feedback on whether it is more appropriate to use ‘amount’ or ‘concentration’ in the EQ would be greatly appreciated.

Comments from @LCCarmody are most welcome.

Thanks so much,

Anna

[pnrobinson]

@matentzn @LCCarmody I think this (cholesterol metabolic process) is a left over from our very first efforts to make EQ definitions. Probably this should just be Abb. concentration etc etc etc ?

[matentzn]

I assigned @rays22 (@rays22 is our new EQ expert and can be tagged on all EQ related tickets) to respond and help @LCCarmody to determine a solution.

[LCCarmody]

This should be relatively easy to fix with new pattern.

[pnrobinson]

@rays22 @LCCarmody can we implement this?

[LCCarmody]

Sorry, I should have followed through with this.

This isn't as straight forward as I thought. However, the majority of terms in HP follow the abnormallyIncreasedLevelOfChemicalEntityInLocation and abnormallyDecreasedLevelOfChemicalEntityInLocation patterns, but not all. As far as I can tell, only one logical definition is using concentration.

Abnormal circulating cholesterol concentration HP:0003107 children also uses increased/decreased amount. Therefore, I propose this logical definition be changed to:

`equivalentTo: text: "'has_part' some ('amount' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))" vars:

• chemical_entity`

Also will need to open a uPheno ticket addressing this and systematically going through HP terms to make them consistent. @pnrobinson @rays22 @matentzn Does this make sense?

[matentzn]

It does make sense!

[pnrobinson]

@LCCarmody it does make sense - can we implement this?

[LCCarmody]

I'll start today

[LCCarmody]

Fixing several EQs. I have added a couple that were not present. I would add more, but there were several that did not have CHEBI terms imported. I thought I knew how to do add terms, but it isn't working for me. @matentzn Do you know how to do this?

[matentzn]

@LCCarmody can you try:

sh run.sh make refresh-merged

If the terms are either in src/ontology/imports/chebi_terms.txt or used inside an EQ, it will work I hope!.

[LCCarmody]

@matentzn I can't make this work. I will make a new ticket with the CHEBI terms needed to import.

[pnrobinson]

@LCCarmody @matentzn @rays22 can we move forward with this?

[LCCarmody]

This is part of the Chem phenotype patternization. It will be fixed with the entire batch.