From b9a6d4028868aa9f1ba47cb6e275ce10c0be90ea Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Thu, 2 Nov 2023 14:23:34 +0000 Subject: [PATCH 1/3] Update README.md --- README.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/README.md b/README.md index a0871aeaf..d52bb7337 100644 --- a/README.md +++ b/README.md @@ -57,6 +57,14 @@ To trigger an automated human readable diff, add the following tag to a comment CL is used in a number of applications including: +**CellxGene** + +The Cell ontology is used to annotate cell types on the single cell transcriptomics platform CellxGene. All datasets on CellXGene are annotated according to a standard schema that specifies use of CL to record Cell Type. Uses in CellXgene tools: + - In the [Discover](https://cellxgene.cziscience.com/)) tool, the structure of CL is used to drive faceted searching for datasets and collections by Cell Type , + - In the [Gene Expression](https://cellxgene.cziscience.com/gene-expression), CL annotation is used to aggregate expression data + - In [CellGuide](https://cellxgene.cziscience.com/cellguide) CL term names and synonyms drive search, terms are used to structure the guide and ontology structure support a graphical browser + - The [Cell Census](https://chanzuckerberg.github.io/cellxgene-census/)) API allows cross-dataset matrices to be retrieved based on annotation with CL and other ontologies. + **HuBMAP** HuBMAP develops tools to create an open, global atlas of the human body at the cellular level. The Cell Ontology is used in annotating cell types in the tools developed. From 54fd70fd0497782c7b0fe98d84d8953e0cd5659c Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Fri, 3 Nov 2023 09:27:11 +0000 Subject: [PATCH 2/3] Update README.md --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index d52bb7337..ce471c3ba 100644 --- a/README.md +++ b/README.md @@ -59,11 +59,11 @@ CL is used in a number of applications including: **CellxGene** -The Cell ontology is used to annotate cell types on the single cell transcriptomics platform CellxGene. All datasets on CellXGene are annotated according to a standard schema that specifies use of CL to record Cell Type. Uses in CellXgene tools: - - In the [Discover](https://cellxgene.cziscience.com/)) tool, the structure of CL is used to drive faceted searching for datasets and collections by Cell Type , - - In the [Gene Expression](https://cellxgene.cziscience.com/gene-expression), CL annotation is used to aggregate expression data - - In [CellGuide](https://cellxgene.cziscience.com/cellguide) CL term names and synonyms drive search, terms are used to structure the guide and ontology structure support a graphical browser - - The [Cell Census](https://chanzuckerberg.github.io/cellxgene-census/)) API allows cross-dataset matrices to be retrieved based on annotation with CL and other ontologies. +The Cell ontology is used to annotate cell types on the single cell transcriptomics platform CellxGene. All datasets on CellXGene are annotated according to a standard schema that specifies the use of CL to record Cell Type. Uses in CellXgene tools: + - In the [Discover](https://cellxgene.cziscience.com/)) tool, the structure of CL is used to drive faceted searching for datasets and collections by Cell Type. + - In the [Gene Expression](https://cellxgene.cziscience.com/gene-expression), CL annotation is used to aggregate expression data. + - In [CellGuide](https://cellxgene.cziscience.com/cellguide) CL provides content and CL term names and synonyms drive search and graphical browsing. + - The [Cell Census](https://chanzuckerberg.github.io/cellxgene-census/) API supports retrieval of cross-dataset matrices containing transcriptmics data for cells annotated with specified terms from CL and other ontologies. **HuBMAP** From 83339f25a3f8d30db485c82de48c2c945e1927fa Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Fri, 3 Nov 2023 10:56:28 +0000 Subject: [PATCH 3/3] Update README.md Co-authored-by: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ce471c3ba..c9c3e9aad 100644 --- a/README.md +++ b/README.md @@ -60,7 +60,7 @@ CL is used in a number of applications including: **CellxGene** The Cell ontology is used to annotate cell types on the single cell transcriptomics platform CellxGene. All datasets on CellXGene are annotated according to a standard schema that specifies the use of CL to record Cell Type. Uses in CellXgene tools: - - In the [Discover](https://cellxgene.cziscience.com/)) tool, the structure of CL is used to drive faceted searching for datasets and collections by Cell Type. + - In the [Discover](https://cellxgene.cziscience.com/) tool, the structure of CL is used to drive faceted searching for datasets and collections by Cell Type. - In the [Gene Expression](https://cellxgene.cziscience.com/gene-expression), CL annotation is used to aggregate expression data. - In [CellGuide](https://cellxgene.cziscience.com/cellguide) CL provides content and CL term names and synonyms drive search and graphical browsing. - The [Cell Census](https://chanzuckerberg.github.io/cellxgene-census/) API supports retrieval of cross-dataset matrices containing transcriptmics data for cells annotated with specified terms from CL and other ontologies.