From 67595189069f6f7b190cc4ad259d756544d1f5d2 Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Thu, 17 Oct 2024 16:19:54 +0100 Subject: [PATCH 1/6] Update cl.md to include CELLxGENE in applications --- ontology/cl.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/ontology/cl.md b/ontology/cl.md index 070362d6c..f2c3daf95 100644 --- a/ontology/cl.md +++ b/ontology/cl.md @@ -149,6 +149,10 @@ Uberon and various phenotype ontologies. The following are some applications of the cell ontology along with their publications: +**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). + **HuBMAP** HuBMAP Consortium (2019) The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature, 574, 187–192 From 1e2865ed2b802c75f27e5c21232ff8c06e46d7f3 Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Thu, 17 Oct 2024 16:34:10 +0100 Subject: [PATCH 2/6] Update CZ CELLxGENE name --- ontology/cl.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontology/cl.md b/ontology/cl.md index f2c3daf95..35c104786 100644 --- a/ontology/cl.md +++ b/ontology/cl.md @@ -149,7 +149,7 @@ Uberon and various phenotype ontologies. The following are some applications of the cell ontology along with their publications: -**CellxGene** +**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). From e3db69caec3334642d0c8a82f329249fa34aea02 Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 22 Oct 2024 13:44:33 +0100 Subject: [PATCH 3/6] Add CELLxGEN as a user in CL --- ontology/cl.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/ontology/cl.md b/ontology/cl.md index 35c104786..a713d86b3 100644 --- a/ontology/cl.md +++ b/ontology/cl.md @@ -84,6 +84,12 @@ 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: + 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/ - 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 From 3b0ffb448c587832610e792eaaa7a617a12c62a3 Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 22 Oct 2024 13:50:19 +0100 Subject: [PATCH 4/6] Fix bugs Colon wrongly placed and missing apostrophes --- ontology/cl.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ontology/cl.md b/ontology/cl.md index a713d86b3..3f6b7e3e9 100644 --- a/ontology/cl.md +++ b/ontology/cl.md @@ -84,10 +84,10 @@ 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: +- 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. publications: - id: https://doi.org/10.1101/2021.04.05.438318 - title: CELLxGENE: a performant, scalable exploration platform for high dimensional sparse matrices + title: 'CELLxGENE: a performant, scalable exploration platform for high dimensional sparse matrices' type: annotation user: https://cellxgene.cziscience.com/ - 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. From adbeba90962b8fd345b18494889c372014738a7f Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 22 Oct 2024 14:02:30 +0100 Subject: [PATCH 5/6] Remove trailing spaces --- ontology/cl.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontology/cl.md b/ontology/cl.md index 3f6b7e3e9..bba2a35a5 100644 --- a/ontology/cl.md +++ b/ontology/cl.md @@ -84,7 +84,7 @@ 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. +- 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. publications: - id: https://doi.org/10.1101/2021.04.05.438318 title: 'CELLxGENE: a performant, scalable exploration platform for high dimensional sparse matrices' From b513fa5d403970fbd45203257e59ffa48c44cabd Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 29 Oct 2024 10:31:33 +0000 Subject: [PATCH 6/6] Include example An example to a Cell Guide entry has been added, which provides information of all CL terms used by CELLxGENE and connects them. --- ontology/cl.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/ontology/cl.md b/ontology/cl.md index bba2a35a5..007eeb8cb 100644 --- a/ontology/cl.md +++ b/ontology/cl.md @@ -85,6 +85,9 @@ usages: 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'