opensafely-core / opensafely-core/opencodelists
Medicines Definition Builder: Snomed hierachy link to dm+d
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- Python
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Description
In #176 I have recorded some notes. Although NHS dm+d exists as a standalone comprehensive reference source it actually is the local UK extension of SnoMed. We can utilise the hierarchies of snomed to support categorisation and building codelists. As we know Snomed is quite extensive and complex, some of the categories don't actually make sense to me however using the East Kent browser and the Australian Shrimp browser it looks like it will be very useful.
Using Atorvastatin 20mg chewable tabs and taking the ancestors displayed on EK browser here are some examples and uses of the SnoMed hierarchy.
| Snomed CT ancestor | Brian’s expectation |
|---|---|
| Enzyme inhibitor-containing product | Unexpected but useful. Enzyme inhibition is not a black and white issue - this classification is more suited to decision support type content as opposed to blac&white ontology. |
| Nitrogen and nitrogen compound-containing product | I had no clue atorvastatin has nitrogen in it and not a clue of relevance clinically. It is accurate! There will be chemists, different flavours of nerd pharmacists and pharmacologists who might make use of searching or studies where the principle chemical components are of interest as opposed to mechanism of action/clinical use. |
| HMG-CoA reductase inhibitor-containing product | Expected - this is technical term for statins, named after mechanism of action. |
| Azole-containing product | Similar to N but in this case I can’t see an azole in the chemical structure. (note to check accuracy when have time but I imagine it is fine) |
| Atorvastatin | Expected |
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing issue #176 and the East Kent and Australian SNOMED browsers referenced here to understand the proposed hierarchy use cases. The issue names no repository file, test, or entry point; done would require an agreed implementation scope for linking SNOMED hierarchies to dm+d categorisation and codelist building.
Written by the indexing model from the issue text.
Assessment
- Domain
- data, search
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100