Update cl.md

[yongqunh]

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

[shawntanzk]

looks good to me :)

[anitacaron]

It would be good to also add in the usages.

For example:

OBOFoundry.github.io/ontology/cl.md

Lines 66 to 77 in bdaa350

	usages:
	- description: The BICCN created a high-resolution atlas of cell types in the primary motor based on single cell transcriptomics. These cell types are represented in the brain data standards ontology which anchors to cell types in the cell ontology.
	examples:
	- description: cell type card of a cell type linked to a PCL cell type (L2/3 IT primary motor cortex glutamatergic neuron) which is a subclass of cell types in CL (CL:4023041)
	url: https://knowledge.brain-map.org/celltypes/CCN202002013/CS202002013_193
	- description: PCL cell type used in cell type cards linked directly to CL cell types
	url: https://www.ebi.ac.uk/ols/ontologies/pcl/terms?iri=http://purl.obolibrary.org/obo/PCL_0011193
	publications:
	- id: https://doi.org/10.1101/2021.10.10.463703
	title: 'Brain Data Standards Ontology: A data-driven ontology of transcriptomically defined cell types in the primary motor cortex'
	type: annotation
	user: https://biccn.org/

[matentzn]

Agreed!

[deepakunni3]

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

[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.

[matentzn]

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

[matentzn]

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

[yongqunh]

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

[deepakunni3]

@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]

I am going to merge this as it is.

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