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I have ...

  • A database with patient phenotypes in, stored as HPO terms
  • Genetic data in whatever format I need

I want ...

  • To store drug names in a way that won't make my life difficult
  • If it's feasible, to make them so that you could draw links between HPO terms, medications, genetic changes, and outcomes. Note that I'm not actively trying to do that, but I don't want to exclude the possibility of it in the future

Ideally, I'd like those drug names in some kind of ontology, and even more ideally an ontology that's available on http://bioportal.bioontology.org

So - what's the best drug ontology to use in this case?

Update

What relationships would this drug ontology describe? Structural similarity of the compounds? Affected pathways? How would they be linked? Do you want all drugs that can cause the same side effect linked, for instance? Or all drugs that can be used for the same disease? Drugs by disease would be the most useful. The information that would be most useful would be something like

  • Atenolol
    • Atenolol 25mg
    • Atenolol 50mg
    • Atenolol 100mg
  • Propanolol
    • Propanolol 10mg
    • Propanolol 40mg
    • Propanolol 80mg
    • ...

In short, being able to get a list of dosages for a given drug. It'd be extra-useful if I could also retrieve a set of drugs for a given condition, so in the above example to retrieve a list of beta blockers (Atenolol, Metoprolol, Nebivolol, ...)

Have you looked at any of the various drug ontologies listed in bioportal.bioontology.org? Which ones have you discarded so we don't suggest the same ones? What were they missing that you need?

  • MDDB doesn't seem to be structured as above
  • Likewise The Drug Ontology
  • RxNorm seems to be the best available that I've seen
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    $\begingroup$ What relationships would this drug ontology describe? Structural similarity of the compounds? Affected pathways? How would they be linked? Do you want all drugs that can cause the same side effect linked, for instance? Or all drugs that can be used for the same disease? Have you looked at any of the various drug ontologies listed in bioportal.bioontology.org? Which ones have you discarded so we don't suggest the same ones? What were they missing that you need? $\endgroup$ – terdon Nov 17 '17 at 11:47
  • $\begingroup$ @terdon - added some more information to the question, hopefully that answers your questions. Apologies for the slight vagueness in some of my answers, the reason is purely because I don't know - for me it's almost just a popularity contest as to which is the best for me! $\endgroup$ – Algy Taylor Nov 17 '17 at 12:15
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    $\begingroup$ The thing is, we don't really do such broad questions on the Stack Exchange network. There's even a specific close reason for them ("too broad") so this is not the right place to ask for a general discussion of the pros and cons. We might be able to help you with a specific case, but not on "what's best" which is just a question of preference and will depend on what you want to do. What's best for you might not be best for me. So please make it as specific as you can. $\endgroup$ – terdon Nov 17 '17 at 12:26
  • $\begingroup$ @terdon - changed the wording, is that better? :) $\endgroup$ – Algy Taylor Nov 20 '17 at 15:57
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Since this question's been asked there's been a (what looks like a first useful?) release of Drug Ontology DRON. Perhaps worth checking again?

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