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Published 20 hours ago • verified publisher icon OBOFoundry

Update cl.md

Open yongqunh opened this issue 1 year ago • 5 comments

Added another user case - Kidney Precision Medicine Project (KPMP).

yongqunh avatar Oct 17 '23 19:10 yongqunh

It would be good to also add in the usages.

For example: https://github.com/OBOFoundry/OBOFoundry.github.io/blob/bdaa350e75432cbefd93c11eb5104b580960058d/ontology/cl.md?plain=1#L66-L77

anitacaron avatar Oct 19 '23 08:10 anitacaron

Agreed!

matentzn avatar Oct 19 '23 11:10 matentzn

@yongqunh Could you add an example from KPMP in the 'usages' section as suggested by @anitacaron ?

deepakunni3 avatar Nov 07 '23 13:11 deepakunni3

@yongqunh Could you add an example from KPMP in the 'usages' section as suggested by @anitacaron ? This PR can be merged after the usages section is updated with the KPMP use case.

deepakunni3 avatar Dec 07 '23 09:12 deepakunni3

@anitacaron can you are one of the CL team maybe just do this? (add the usage)

matentzn avatar Dec 14 '23 13:12 matentzn

@deepakunni3 maybe we should just merge this.. This is open for a very long time..

matentzn avatar Apr 16 '24 16:04 matentzn

Sorry for the delay. Here is an example of KPMP using CL: https://ontobee.org/ontology/KTAO?iri=http://purl.obolibrary.org/obo/CL_1000497 Also, the paper for more information: https://www.nature.com/articles/s41581-020-00335-w

yongqunh avatar Apr 16 '24 22:04 yongqunh

@yongqunh Thank you for providing an example and a publication.

Would the following be appropriate and faithfully capture the KPMP usage:

- description: The Kidney Precision Medicine Project (KPMP) makes use of the Kidney Tissue Atlas Ontology (KTAO) which imports terms from CL for defining kidney-related terms and their relations.
  examples:
  - description: The Kidney Tissue Atlas Ontology (KTAO) imports terms from CL to define kidney-related cell types, cell states, gene markers, diseases and their relations
    url: https://ontobee.org/ontology/KTAO?iri=http://purl.obolibrary.org/obo/CL_1000497
  publications:
  - id: https://doi.org/10.1038/s41581-020-00335-w
    title: 'Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project'
  type: annotation
  user: https://www.kpmp.org/
activity_status: active

deepakunni3 avatar Apr 17 '24 09:04 deepakunni3

I am going to merge this as it is.

Will create a new PR to add a more structured representation of KPMP usage.

deepakunni3 avatar Apr 18 '24 13:04 deepakunni3