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Update cl.md to include CELLxGENE in applications #2644

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13 changes: 13 additions & 0 deletions ontology/cl.md
Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,15 @@ usages:
title: 'The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.'
type: annotation
user: https://hubmapconsortium.org/
- description: The single-cell transcriptomics platform CZ CELLxGENE uses CL to annotate all cell types. All datasets on CellXGene are annotated according to a standard schema that specifies the use of CL to record Cell Type.
examples:
- description: A CELLxGENE Cell Guide entry for 'luminal adaptive secretory precursor cell of mammary gland', which includes the CL ID (CL:4033057), CL definition and a visualizer of CL hierarchy
url: https://cellxgene.cziscience.com/cellguide/CL:4033057
publications:
- id: https://doi.org/10.1101/2021.04.05.438318
title: 'CELLxGENE: a performant, scalable exploration platform for high dimensional sparse matrices'
type: annotation
user: https://cellxgene.cziscience.com/
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- description: The Human Cell Atlas (HCA) is an international group of researchers using a combination of these new technologies to create cellular reference maps. The HCA use CL to annotate cells in their reference maps.
examples:
- description: HCA collection studies that are related B cell (CL:0000236) that is filtered through CL annotation
Expand Down Expand Up @@ -149,6 +158,10 @@ Uberon and various phenotype ontologies.

The following are some applications of the cell ontology along with their publications:

**CZ CELLxGENE**

CZI Single-Cell Biology Program, Shibla Abdulla, Brian Aevermann, Pedro Assis, Seve Badajoz, Sidney M. Bell, Emanuele Bezzi, et al. 2023. “CZ CELL×GENE Discover: A Single-Cell Data Platform for Scalable Exploration, Analysis and Modeling of Aggregated Data.” bioRxiv. [doi:10.1101/2023.10.30.563174](https://doi.org/10.1101/2023.10.30.563174).

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**HuBMAP**

HuBMAP Consortium (2019) The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature, 574, 187–192
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