cl.md

layout	id	title	canonical	contact	dependencies	depicted_by	description	domain	homepage	label	license	mailing_list	preferredPrefix	products	publications	repository	tags	taxon	tracker	twitter	usages	activity_status
ontology_detail	cl	Cell Ontology	cl.owl	email github label orcid [email protected] addiehl Alexander Diehl 0000-0001-9990-8331	id go id ncbitaxon id omo id pato id pr id ro id uberon	/images/CL-logo.jpg	The Cell Ontology is a structured controlled vocabulary for cell types in animals.	anatomy and development	https://obophenotype.github.io/cell-ontology/	Cell Ontology	label url CC BY 4.0 http://creativecommons.org/licenses/by/4.0/	https://groups.google.com/g/cl_edit	CL	id title description format is_canonical uses cl.owl Main CL OWL edition Complete ontology, plus inter-ontology axioms, and imports modules owl-rdf/xml true go ncbitaxon omo pato pr ro uberon id title derived_from description format cl.obo CL obo format edition cl.owl Complete ontology, plus inter-ontology axioms, and imports modules merged in obo id title derived_from description format cl.json CL OBOGraph-JSON format edition cl.owl Complete ontology, plus inter-ontology axioms, and imports modules merged in json id title description format cl/cl-basic.owl Basic CL Basic version, no inter-ontology axioms owl-rdf/xml id title description format cl/cl-basic.obo Basic CL (OBO version) Basic version, no inter-ontology axioms obo id title description format cl/cl-basic.json Basic CL (OBOGraph-JSON version) Basic version, no inter-ontology axioms json id title description format cl/cl-base.owl CL base module complete CL but with no imports or external axioms owl-rdf/xml id title description format cl/cl-base.obo CL base module (OBO version) complete CL but with no imports or external axioms obo id title description format cl/cl-base.json CL base module (OBOGraph-JSON version) complete CL but with no imports or external axioms json	id title https://www.ncbi.nlm.nih.gov/pubmed/27377652 The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.	https://github.com/obophenotype/cell-ontology	cells	id label NCBITaxon:33208 Metazoa	https://github.com/obophenotype/cell-ontology/issues	CellOntology	description examples publications type user 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. description url 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) https://knowledge.brain-map.org/celltypes/CCN202002013/CS202002013_193 description url PCL cell type used in cell type cards linked directly to CL cell types https://www.ebi.ac.uk/ols/ontologies/pcl/terms?iri=http://purl.obolibrary.org/obo/PCL_0011193 id title https://doi.org/10.1101/2021.10.10.463703 Brain Data Standards Ontology: A data-driven ontology of transcriptomically defined cell types in the primary motor cortex annotation https://biccn.org/ description examples publications type user 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. description url ASCT+B reporter showing CL being used to annotate cell types in the heart https://hubmapconsortium.github.io/ccf-asct-reporter/vis?selectedOrgans=heart-v1.1&playground=false id title https://www.ncbi.nlm.nih.gov/pubmed/31597973 The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. annotation https://hubmapconsortium.org/ description examples publications type user 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 url 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 https://cellxgene.cziscience.com/cellguide/CL:4033057 id title https://doi.org/10.1101/2021.04.05.438318 CELLxGENE: a performant, scalable exploration platform for high dimensional sparse matrices annotation https://cellxgene.cziscience.com/ description examples publications type user 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. description url HCA collection studies that are related B cell (CL:0000236) that is filtered through CL annotation https://singlecell.broadinstitute.org/single_cell?type=study&page=1&facets=cell_type%3ACL_0000236&scpbr=human-cell-atlas-main-collection id title https://www.ncbi.nlm.nih.gov/pubmed/29206104 The Human Cell Atlas annotation https://www.humancellatlas.org/ description examples publications type user 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. description url RNA-Seq CAGE (Cap Analysis of Gene Expression) analysis of mice cells in RIKEN FANTOM5 project annotated using cell types from CL https://www.ebi.ac.uk/gxa/experiments/E-MTAB-3578/Results id title https://www.ncbi.nlm.nih.gov/pubmed/31665515 Expression Atlas update: from tissues to single cells annotation https://www.ebi.ac.uk/gxa/home description publications seeAlso type user 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 id title https://www.ncbi.nlm.nih.gov/pubmed/25776021 Ontology application and use at the ENCODE DCC https://doi.org/10.25504/FAIRsharing.v0hbjs annotation https://www.encodeproject.org/ description examples type user FANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome analyses with cell-type and tissue-level specificity. description url FANTOM5 samples annotated to neuron http://fantom.gsc.riken.jp/5/sstar/CL:0000540 annotation http://fantom5-collaboration.gsc.riken.jp/	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 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 biological processes via the capable-of relationship type. CL also links to other ontologies such as chebi, pr and pato.

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.

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

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

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)