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monarch-initiative / mondo

Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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Representation of responses to drugs #860

Closed maglott closed 4 years ago

maglott commented 5 years ago

Should a category be created for pharmacologic responses?

If these are in scope for MONDO, seems the category could be more specific than MONDO_0003847, inherited genetic disease

Thanks, Donna

nicolevasilevsky commented 5 years ago

@pnrobinson and @cmungall what are your thoughts?

pnrobinson commented 5 years ago

This definitely should not be represented as "MONDO_0003847, inherited genetic disease". I would think that it is probably best to integrate the MONDO data with something like https://www.pharmgkb.org/

cmungall commented 5 years ago

Yes, obsolete these. I think the best home is OBA, since these are traits

On Tue, Oct 1, 2019 at 8:28 AM Peter Robinson notifications@github.com wrote:

This definitely should not be represented as "MONDO_0003847, inherited genetic disease". I would think that it is probably best to integrate the MONDO data with something like https://www.pharmgkb.org/

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nicolevasilevsky commented 5 years ago

Ontology of Biological Attributes: http://www.obofoundry.org/ontology/oba.html

nicolevasilevsky commented 5 years ago

@maglott are there other terms besides MONDO_0014330 'eculizumab, poor response to' that should be obsoleted and added to OBA instead?

Do you want to make a ticket in OBA for the terms you need? https://github.com/obophenotype/bio-attribute-ontology

Thanks!

cmungall commented 5 years ago

I think we can make a first pass at these ourselves

On Wed, Oct 2, 2019 at 2:48 PM Nicole Vasilevsky notifications@github.com wrote:

@maglott https://github.com/maglott are there other terms besides MONDO_0014330 'eculizumab, poor response to' that should be obsoleted and added to OBA instead?

Do you want to make a ticket in OBA for the terms you need? https://github.com/obophenotype/bio-attribute-ontology

Thanks!

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cmungall commented 5 years ago

but any help welcome of course!

On Wed, Oct 2, 2019 at 2:50 PM Chris Mungall cjmungall@lbl.gov wrote:

I think we can make a first pass at these ourselves

On Wed, Oct 2, 2019 at 2:48 PM Nicole Vasilevsky notifications@github.com wrote:

@maglott https://github.com/maglott are there other terms besides MONDO_0014330 'eculizumab, poor response to' that should be obsoleted and added to OBA instead?

Do you want to make a ticket in OBA for the terms you need? https://github.com/obophenotype/bio-attribute-ontology

Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/monarch-initiative/mondo/issues/860?email_source=notifications&email_token=AAAMMOLYSRO5UCGIJYNMBVDQMUJLVA5CNFSM4I4KV6N2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAGJPUA#issuecomment-537696208, or mute the thread https://github.com/notifications/unsubscribe-auth/AAAMMOOEFOHOUDWBEH5WG4LQMUJLVANCNFSM4I4KV6NQ .

nicolevasilevsky commented 5 years ago

@cmungall there are 98 responses listed on this webpage: https://www.ncbi.nlm.nih.gov/gtr/tests/558523/indication/

Should all of these be added to OBA? If yes, I can make a ticket. I am not sure if I have ever edited OBA though. It is all pattern based, right?

cmungall commented 5 years ago

do these denote abnormal response, or the general response trait? If former, also belong in HPO? How is this coordinated with loinc2hpo? cc @pnrobinson

pnrobinson commented 5 years ago

We have a request to add a general abnormal response to medication X, still considering this. I am not sure where best to put these terms & worried about combinatorial explosions (even more :-0). This would not be directly connected to LOINC2HPO, which does not include the genetic infos.

maglott commented 5 years ago

For consideration: When ClinVar receives submissions from PharmGKB, there is a parent (unqualified) response to medication X, and then depending on the drug and the metabolic effect, e.g. simvastatin response - Toxicity/ADR simvastatin response - Efficacy https://www.ncbi.nlm.nih.gov/medgen/?term=simvastatin

Compare to the terms that Orphanet made obsolete: https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=240985 https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=240913

maglott commented 5 years ago

Sorry, I did not read from the top of the thread. Here are more concepts from UMLS and OMIM that we have categorized in part as pharmacologic responses: C1861502|Colchicine resistance|120080| C0750384|Warfarin response|122700| C1860214|Acetophenetidin sensitivity|200300| C1859352|Carbimazole sensitivity|212060| C0878587|Slow acetylator due to N-acetyltransferase enzyme variant|243400| C1838854|Aminoglycoside-induced deafness|580000| C1827409|Disorder due cytochrome p450 CYP2D6 variant|608902| C1836023|CYP2C19-related poor drug metabolism|609535| C3281153|Efavirenz response|614546|

And of course , there are the LOINC codes for function and metabolizer status

nicolevasilevsky commented 5 years ago

Thanks @maglott

@cmungall This is a list of terms that are candidates to be obsoleted from Mondo, and I will create a ticket to request these in OBA:

MONDO_0007348 Colchicine resistance MONDO_0008697 'acetophenetidin sensitivity' MONDO_0008906 Carbimazole sensitivity MONDO_0012294 CYP2C19-related poor drug metabolism MONDO_0012148 'drug metabolism, poor, CYP2D6-related' MONDO_0014330 'eculizumab, poor response to'

cmungall commented 5 years ago

Note that anything with 'poor' in the label is out of scope for OBA, as it should be the value-neutral trait. However, you can still make terms for the agnostic form.

Anything with 'poor' is a candidate for HPO, pending Peter's decision on this

On Thu, Oct 3, 2019 at 3:53 AM maglott notifications@github.com wrote:

For consideration: When ClinVar receives submissions from PharmGKB, there is a parent (unqualified) response to medication X, and then depending on the drug and the metabolic effect, e.g. simvastatin response - Toxicity/ADR simvastatin response - Efficacy

Compare to the terms that Orphanet made obsolete: https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=240985 https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=240913

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