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by the ROBOT](https://img.shields.io/static/v1?label=Powered%20by\u0026message=ROBOT\u0026color=green\u0026style=flat)](http://robot.obolibrary.org/)\n\u003ca href=\"http://dashboard.obofoundry.org/dashboard/cl/dashboard.html\"\u003e\u003cimg src=\"https://img.shields.io/endpoint?url=https%3A%2F%2Fraw.githubusercontent.com%2FOBOFoundry%2Fobo-dash.github.io%2Fgh-pages%2Fdashboard%2Fcl%2Fdashboard-qc-badge.json\" /\u003e\u003c/a\u003e\n\u003ca href=\"http://dashboard.obofoundry.org/dashboard/cl/dashboard.html\"\u003e\u003cimg src=\"https://img.shields.io/endpoint?url=https%3A%2F%2Fraw.githubusercontent.com%2FOBOFoundry%2Fobo-dash.github.io%2Fgh-pages%2Fdashboard%2Fcl%2Fdashboard-score-badge.json\" /\u003e\u003c/a\u003e\n\u003c!--\u003ca href=\"https://cthoyt.com/obo-community-health/\"\u003e\u003cimg src=\"https://bioregistry.io/health/cl\"/\u003e\u003c/a\u003e--\u003e\n\n\u003cimg src=\"https://user-images.githubusercontent.com/112839/107354015-9375bb00-6ac5-11eb-9394-7318df343ec2.png\" width=30% height=30%\u003e\n\n\n# Cell Ontology \n\nThis repository contains the source for the Cell Ontology. Most users do not need to edit content in this repo directly.  However we are happy to train new editors.\n\n\u003cb\u003eRequest changes to the ontology\u003c/b\u003e\u003cbr\u003e\n\nWe welcome edit requests from anyone - especially if you plan to use the Cell Ontology for annotation.  To request a new term, please use our [new term request template](https://github.com/obophenotype/cell-ontology/issues/new?assignees=\u0026labels=new+term+request\u0026projects=\u0026template=a_adding_term.md\u0026title=%5BNTR%5D). For any other requests please choose one of our [other templates](https://github.com/obophenotype/cell-ontology/issues/new/choose)), or open a blank ticket.  If you wish to request a set of related terms, you may link a [MIRACL sheet](https://docs.google.com/spreadsheets/d/1FBbarq3aCM3CUGd9oIOuYY5Sljzt2Pegl-sdx8OwbfI/edit#gid=0) ([Lubiana _et al_., 2022](https://arxiv.org/abs/2204.09673)) to a ticket containing a general description of the requested set of terms. \n\n\u003cb\u003eBrowse the ontology using OLS\u003c/b\u003e\u003cbr\u003e\nhttps://www.ebi.ac.uk/ols4/ontologies/cl\n\n\u003cb\u003eLatest CL release files\u003c/b\u003e\u003cbr\u003e\nhttps://github.com/obophenotype/cell-ontology/releases/latest\n\n\u003cb\u003eDescription of release files\u003c/b\u003e\u003cbr\u003e\nhttps://oboacademy.github.io/obook/reference/release-artefacts/\n\n\nFor more details on CL see:\n- [CL Website](https://cell-ontology.github.io/)\n- [CL on the OBO Foundry](http://obofoundry.org/ontology/cl.html)\n\n\nEditors documentation: \n* [CL Editor doc](https://obophenotype.github.io/cell-ontology/)\n* [Generic ODK workflows](src/ontology/README-editors.md)\n* [OBO Academy oBook](https://oboacademy.github.io/obook/getting-started/) - General ontology editor and developer documentation and tutorials.\n\nTraining materials from the 2020 CL Training Workshop are available at https://github.com/obophenotype/cell-ontology-training.\n\n\n## Twice monthly calls\n  \nThird Wednesday of the month, 8am PT/11am ET (CL)  \nThird Monday of the month, 8am PT/11am ET (Uberon)  \n[Agenda here.](https://docs.google.com/document/d/1XvMbNvr0FEsdqGhg79BYCYEHSqUxRHMcvhbGizEAht8/edit)  \n\n## Cite\n\nDiehl,A.D., Meehan,T.F., Bradford,Y.M., Brush,M.H., Dahdul,W.M., Dougall,D.S., He,Y., Osumi-Sutherland,D., Ruttenberg,A., Sarntivijai,S., et al. (2016) The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J. Biomed. Semantics, 7, 44.\n\n## GitHub Actions Triggers\n\nTo trigger an automated human readable diff, add the following tag to a comment in your pull request: #gogoeditdiff\n\n## Applications\n\nCL is used in a number of applications including: \n\n**CellxGene**\n\nThe 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:\n - 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.\n - In the [Gene Expression](https://cellxgene.cziscience.com/gene-expression), CL annotation is used to aggregate expression data.\n - In [CellGuide](https://cellxgene.cziscience.com/cellguide) CL provides content and CL term names and synonyms drive search and graphical browsing.\n - The [Cell Census](https://chanzuckerberg.github.io/cellxgene-census/) API supports retrieval of cross-dataset matrices containing transcriptomics data for cells annotated with specified terms from CL and other ontologies.\n\n**HuBMAP**\n\nHuBMAP 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.\n\nHuBMAP Consortium (2019) The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature, 574, 187–192\n\n**Human Cell Atlas (HCA)**\n\nThe 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 annotated cells in their reference maps.\n\nRegev,A., Teichmann,S.A., Lander,E.S., Amit,I., Benoist,C., Birney,E., Bodenmiller,B., Campbell,P., Carninci,P., Clatworthy,M., et al. (2017) The Human Cell Atlas. Elife, 6.\n\n**Single Cell Expression Atlas**\n\nThe EBI single cell expression atlas is an extension to EBI expression atlas that displays gene expression in single cells. Cell types in the single cell expression atlas linked with terms from the Cell Ontology.\n\nPapatheodorou,I., Moreno,P., Manning,J., Fuentes,A.M.-P., George,N., Fexova,S., Fonseca,N.A., Füllgrabe,A., Green,M., Huang,N., et al. (2020) Expression Atlas update: from tissues to single cells. Nucleic Acids Res., 48, D77–D83.\n\n**BRAIN Initiative Cell Census Network (BICCN)/Brain Data Standards Ontology**\n\nThe 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.\n\nTan, S.Z.K., Kir, H., Aevermann, B.D. et al. Brain Data Standards - A method for building data-driven cell-type ontologies. Sci Data 10, 50 (2023). https://doi.org/10.1038/s41597-022-01886-2\n\n**ENCODE**\n\nThe National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The ENCODE DCC uses Uberon to annotate samples\n\nMalladi, V. S., Erickson, D. T., Podduturi, N. R., Rowe, L. D., Chan,\nE. T., Davidson, J. M., … Hong, E. L. (2015). Ontology application and\nuse at the ENCODE DCC. Database : The Journal of Biological Databases\nand Curation, 2015, bav010–. [doi:10.1093/database/bav010](https://doi.org/doi:10.1093/database/bav010)\n\n**FANTOMS**\n\nFANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome analyses with cell-type and tissue-level specificity.\n\nLizio, M., Harshbarger, J., Shimoji, H., Severin, J., Kasukawa, T.,\nSahin, S., … Kawaji, H. (2015). Gateways to the FANTOM5 promoter level\nmammalian expression atlas. Genome Biology, 16(1),\n22. [doi:10.1186/s13059-014-0560-6](https://doi.org/doi:10.1186/s13059-014-0560-6)\n\n**LINCS**\n\nMetadata Standard and Data Exchange Specifications\nto Describe, Model, and Integrate Complex and Diverse High-Throughput\nScreening Data from the Library of Integrated Network-based Cellular\nSignatures\n(LINCS) http://jbx.sagepub.com/content/early/2014/02/11/1087057114522514.full\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fobophenotype%2Fcell-ontology","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fobophenotype%2Fcell-ontology","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fobophenotype%2Fcell-ontology/lists"}