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monarch-initiative / MAxO

Medical action ontology
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Help with the pharmacotherapy hierarchy #12

Closed LCCarmody closed 5 years ago

LCCarmody commented 5 years ago

I have been implementing drug class by therapeutic areas. I am using the FDA recommended guidelines to do this.

They have 3 levels to describe classes: Therapeutic Category | Pharmacologic Class | Formulary Key Drug Types

For the most part it is straight forward, but there are antidepressant and Anxiolytics therapeutic classes. However, there is an 'antidepressants' Pharmacologic class under antixiolytics. I added this therapeutic class as 'antidepressant Anxiolytics' for now, but would love input.

LCCarmody commented 5 years ago

Forgot the FDA link: https://www.fda.gov/RegulatoryInformation/LawsEnforcedbyFDA/SignificantAmendmentstotheFDCAct/FoodandDrugAdministrationAmendmentsActof2007/FDAAAImplementationChart/ucm232402.htm

cmungall commented 5 years ago

Are you doing all of this manually? The dipper team may have code that can make an OWL file from some standard drug classifications if that helps.

Somewhat related, ongoing project to map the CHEBI role hierarchy to what they do mechanistically: https://github.com/cmungall/chiro

LCCarmody commented 5 years ago

Currently, I am doing it manually--to get the framework going. I am interested in leveraging other ontologies--and using ROBOT patternization--for this ontology. Particularly of interest is using UBERON to develop the hierarchy of some of the procedure/imaging terms. I.e., Biopsy of the liver, CT scan of abdomen. I intentionally didn't use this for the drug branch because @pnrobinson said to not make a very deep drug hierarchy, and we didn't really want to bring in significant portions of other ontologies. The idea was only to have drug classes and not the drugs themselves. Your input is definitely welcome and helpful. The link you sent is already very helpful for how to do the logical terms.

cmungall commented 5 years ago

OK, sounds good, we can have a chat about this sometime after next week

On Wed, Jan 23, 2019 at 5:58 AM Leigh Carmody notifications@github.com wrote:

Currently, I am doing it manually--to get the framework going. I am interested in leveraging other ontologies--and using ROBOT patternization--for this ontology. Particularly of interest is using UBERON to develop the hierarchy of some of the procedure/imaging terms. I.e., Biopsy of the liver, CT scan of abdomen. I intentionally didn't use this for the drug branch because @pnrobinson https://github.com/pnrobinson said to not make a very deep drug hierarchy, and we didn't really want to bring in significant portions of other ontologies. The idea was only to have drug classes and not the drugs themselves. Your input is definitely welcome and helpful. The link you sent is already very helpful for how to do the logical terms.

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LCCarmody commented 5 years ago

This has been implemented. Closing.