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BIH-CEI / phenopacket_mapper

A package to map data from the RareLink format in REDCap to the GA4GH Phenopacket schema (v2).
MIT License
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CodySystems Names #101

Open aslgraefe opened 3 hours ago

aslgraefe commented 3 hours ago

We should have consistency in the name of all ontologies used.

e.g. ORDO should be:

ORDO = CodeSystem(
    name="Orphanet Rare Disease Ontology",
    namespace_prefix="ORPHA",
    url="http://www.orpha.net/"

we can take the official names and official namespace_prefixes from OLS: https://www.ebi.ac.uk/ols4/ontologies

aslgraefe commented 3 hours ago

also the RareLink test text_preprocess_redcap_code.py is importing the CodeSystems from Phenopacket_mapper. But in there are not the ones I added in my notebook. where do we gather the added RareLink ontologies to import for a test.

I will comment these out for now in my test - but we'll need to add them somewhere. let me know where you want to have those