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obophenotype / human-phenotype-ontology

Ontology for the description of human clinical features
http://obophenotype.github.io/human-phenotype-ontology/
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NTR: Increased blood lead level #4364

Closed callahantiff closed 5 years ago

callahantiff commented 5 years ago

NTR: Increased blood lead level

Parent: HP_0410172 Blood xenobiotic

For LOINC code: 10368-9 Lead [Mass/volume] in Capillary blood

Biocurator ID for loinc2hpo: UCDenver:tjcallahan

pnrobinson commented 5 years ago

This is not really a xenobiotic -- lead is not a "biotic". How should we categorise this? @cmungall @nicolevasilevsky @LCCarmody

nicolevasilevsky commented 5 years ago

The definition of xenobiotic from Chebi is: A xenobiotic (Greek, xenos "foreign"; bios "life") is a compound that is foreign to a living organism. Principal xenobiotics include: drugs, carcinogens and various compounds that have been introduced into the environment by artificial means.

So seems like lead would fit under this def?

pnrobinson commented 5 years ago

Thanks, Nicole, I agree! I do not think I previously appreciated the full definition of xenobiotic, but I think this is 100% correct.

nicolevasilevsky commented 5 years ago

Cool - I can add this term :)

cmungall commented 5 years ago

Be careful using the role hierarchy in chebi - first, chebi don't model these as physical entities so this will cause issues where we use them in patterns where a physical entity is expected

also the role hierarchy is a bit odd and many structure-role associations are contextual rather than all-some