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IHCC-cohorts / GECKO

Genomics Cohorts Knowledge Ontology
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sync issue #54

Open mcourtot opened 3 years ago

mcourtot commented 3 years ago

The same GECKO ID points to 2 different terms

on the registry:

https://registry.ihccglobal.app/ontologies/gecko/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGECKO_0000019&viewMode=All&siblings=false

Screenshot 2021-01-20 at 14 57 17

On the OLS:

https://www.ebi.ac.uk/ols/ontologies/gecko/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGECKO_0000019

Screenshot 2021-01-20 at 14 57 46

jamesaoverton commented 3 years ago

We have two versions of GECKO:

  1. the OBO version is more ontological, with labels that follow OBO conventions
  2. the IHCC version is closer to the CINECA model, with labels that follow CINECA patterns, and with different groupings to match CINECA
mcourtot commented 3 years ago

but "fasting or non fasting" does not match "blood that is collected from an organism that has been fasting for a given amount of time"?

beckyjackson commented 3 years ago

@mcourtot I agree that this doesn't make sense here.

I'd like to propose actually removing this "fasting or non-fasting" term entirely. It isn't displayed in the Atlas, and we use it in the mappings maybe once. What are your thoughts?