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monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Create module for turning loinc2hpo map to RDF #715

Open cmungall opened 5 years ago

cmungall commented 5 years ago

@diatomsRcool would find this useful for STAGE project, to go from d->p->loinc; checking with @pnrobinson if this is a good idea

the mappings are here:

https://github.com/TheJacksonLaboratory/loinc2hpoAnnotation/blob/master/Data/TSVSingleFile/annotations.tsv

Could be done in dipper, or we could work with @kingmanzahng could do this directly in https://github.com/monarch-initiative/loinc2hpo

@mbrush how would this be modeled? loinc codes as denoting OBI assays?

diatomsRcool commented 5 years ago

Related to this https://github.com/obophenotype/human-phenotype-ontology/issues/4580

diatomsRcool commented 5 years ago

The use case is that a STAGE user might like to search for "diabetes" and would want back data sets that contain measurements that are important for diabetes.

diatomsRcool commented 5 years ago

I do not see diabetes (HP:0005978) in the annotations.tsv file. Can this be added?

diatomsRcool commented 5 years ago

OK, I take that back. I found hyperglycemia HP:0003074 and it is linked to the proper loinc codes. So, the annotations file will work for this use case. What is the next step here? @TomConlin @mbrush ?

diatomsRcool commented 5 years ago

What is the chance that this can be accessible via the API in time for a June 4 demo to the NHLBI Council?

kingmanzhang commented 5 years ago

Sorry I did not notice this thread. Let me know if I can be of any help.