--- layout: ontology_detail id: cl title: Cell Ontology canonical: cl.owl contact: email: do12@sanger.ac.uk github: dosumis label: David Osumi-Sutherland orcid: 0000-0002-7073-9172 dependencies: - id: go - id: ncbitaxon - id: omo - id: pato - id: pr - id: ro - id: uberon depicted_by: /images/CL-logo.jpg description: The Cell Ontology is a structured controlled vocabulary for cell types in animals. domain: anatomy and development homepage: https://obophenotype.github.io/cell-ontology/ label: Cell Ontology license: label: CC BY 4.0 url: http://creativecommons.org/licenses/by/4.0/ mailing_list: https://groups.google.com/g/cl_edit preferredPrefix: CL products: - id: cl.owl title: Main CL OWL edition description: Complete ontology, plus inter-ontology axioms, and imports modules format: owl-rdf/xml is_canonical: true uses: - go - ncbitaxon - omo - pato - pr - ro - uberon - id: cl.obo title: CL obo format edition derived_from: cl.owl description: Complete ontology, plus inter-ontology axioms, and imports modules merged in format: obo - id: cl.json title: CL OBOGraph-JSON format edition derived_from: cl.owl description: Complete ontology, plus inter-ontology axioms, and imports modules merged in format: json - id: cl/cl-basic.owl title: Basic CL description: Basic version, no inter-ontology axioms format: owl-rdf/xml - id: cl/cl-basic.obo title: Basic CL (OBO version) description: Basic version, no inter-ontology axioms format: obo - id: cl/cl-basic.json title: Basic CL (OBOGraph-JSON version) description: Basic version, no inter-ontology axioms format: json - id: cl/cl-base.owl title: CL base module description: complete CL but with no imports or external axioms format: owl-rdf/xml - id: cl/cl-base.obo title: CL base module (OBO version) description: complete CL but with no imports or external axioms format: obo - id: cl/cl-base.json title: CL base module (OBOGraph-JSON version) description: complete CL but with no imports or external axioms format: json publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27377652 title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.' repository: https://github.com/obophenotype/cell-ontology tags: - cells taxon: id: NCBITaxon:33208 label: Metazoa tracker: https://github.com/obophenotype/cell-ontology/issues twitter: CellOntology 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/ - description: 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. examples: - description: ASCT+B reporter showing CL being used to annotate cell types in the heart url: https://hubmapconsortium.github.io/ccf-asct-reporter/vis?selectedOrgans=heart-v1.1&playground=false publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31597973 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/ - 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 url: https://singlecell.broadinstitute.org/single_cell?type=study&page=1&facets=cell_type%3ACL_0000236&scpbr=human-cell-atlas-main-collection publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/29206104 title: The Human Cell Atlas type: annotation user: https://www.humancellatlas.org/ - description: The 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. examples: - description: RNA-Seq CAGE (Cap Analysis of Gene Expression) analysis of mice cells in RIKEN FANTOM5 project annotated using cell types from CL url: https://www.ebi.ac.uk/gxa/experiments/E-MTAB-3578/Results publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31665515 title: 'Expression Atlas update: from tissues to single cells' type: annotation user: https://www.ebi.ac.uk/gxa/home - description: The 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 publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25776021 title: Ontology application and use at the ENCODE DCC seeAlso: https://doi.org/10.25504/FAIRsharing.v0hbjs type: annotation user: https://www.encodeproject.org/ - description: FANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome analyses with cell-type and tissue-level specificity. examples: - description: FANTOM5 samples annotated to neuron url: http://fantom.gsc.riken.jp/5/sstar/CL:0000540 type: annotation user: http://fantom5-collaboration.gsc.riken.jp/ activity_status: active --- Cell Ontology (CL) is an ontology designed to classify and describe cell types across different organisms. It serves as a resource for model organism and bioinformatics databases. The ontology covers a broad range of cell types in animal cells, with over 2700 cell type classes, and provides high-level cell type classes as mapping points for cell type classes in ontologies representing other species, such as the Plant Ontology or Drosophila Anatomy Ontology. Integration with other ontologies such as Uberon, GO, CHEBI, PR, and PATO enables linking cell types to anatomical structures, biological processes, and other relevant concepts. The Cell Ontology was created in 2004 and has been a core OBO Foundry ontology since the start of the Foundry. Since then, CL has been adopted by various efforts, including the HuBMAP project, Human Cell Atlas (HCA), cellxgene platform, Single Cell Expression Atlas, BRAIN Initiative Cell Census Network (BICCN), ArrayExpress, The Cell Image Library, ENCODE, and FANTOM5, for annotating cell types and facilitating cellular reference mapping, as documented through various publications and examples. ## Integration with other ontologies Cell types in CL are linked to [uberon](uberon.html) via part-of relationships. The cl.owl product imports a subset of the entire uberon ontology. To see all cell types in the context of all anatomical structures, use the uberon ext release. Cell types are linked to [GO](go.html) biological processes via the capable-of relationship type. CL also links to other ontologies such as [chebi](chebi.html), [pr](pr.html) and [pato](pato.html). In turn, CL is linked to from a variety of ontologies such as GO, Uberon and various phenotype ontologies. ## Applications 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). **HuBMAP** HuBMAP Consortium (2019) The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature, 574, 187–192 **Human Cell Atlas (HCA)** Regev,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. **Kidney Precision Medicine Project (KPMP)** Ong E, Wang LL, Schaub J, O'Toole JF, Steck B, Rosenberg AZ, Dowd F, Hansen J, Barisoni L, Jain S, de Boer IH, Valerius MT, Waikar SS, Park C, Crawford DC, Alexandrov T, Anderton CR, Stoeckert C, Weng C, Diehl AD, Mungall CJ, Haendel M, Robinson PN, Himmelfarb J, Iyengar R, Kretzler M, Mooney S, and He Y, Kidney Precision Medicine Project. Modeling Kidney Disease Using Ontology: insights from the Kidney Precision Medicine Project. Nature Review Nephrology. 2020 Nov;16(11):686-696. doi: 10.1038/s41581-020-00335-w. PMID: 32939051. PMCID: PMC8012202. **Single Cell Expression Atlas** Papatheodorou,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. **BRAIN Initiative Cell Census Network (BICCN)/Brain Data Standards Ontology** Tan,S.Z.K., Kir,H., Aevermann,B., Gillespie,T., Hawrylycz,M., Lein,E., Matentzoglu,N., Miller,J., Mollenkopf,T.S., Mungall,C.J., et al. (2021) Brain Data Standards Ontology: A data-driven ontology of transcriptomically defined cell types in the primary motor cortex. bioRxiv, 10.1101/2021.10.10.463703. **ENCODE** Malladi, V. S., Erickson, D. T., Podduturi, N. R., Rowe, L. D., Chan, E. T., Davidson, J. M., … Hong, E. L. (2015). Ontology application and use at the ENCODE DCC. Database : The Journal of Biological Databases and Curation, 2015, bav010–. [doi:10.1093/database/bav010](https://doi.org/doi:10.1093/database/bav010) **FANTOMS** Lizio, M., Harshbarger, J., Shimoji, H., Severin, J., Kasukawa, T., Sahin, S., … Kawaji, H. (2015). Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biology, 16(1), 22. [doi:10.1186/s13059-014-0560-6](https://doi.org/doi:10.1186/s13059-014-0560-6) **LINCS** [Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS)](http://jbx.sagepub.com/content/early/2014/02/11/1087057114522514.full)