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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
addiehl
Alexander Diehl
0000-0001-9990-8331
id
chebi
id
go
id
ncbitaxon
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
Cell Ontology
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
uberon
chebi
go
pr
pato
ncbitaxon
ro
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 description format
cl/cl-basic.obo
Basic CL
Basic version, no inter-ontology axioms
obo
id title description
cl/cl-base.owl
CL base module
complete CL but with no imports or external axioms
id title
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
cells
id label
NCBITaxon:33208
Metazoa
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)
description url
PCL cell type used in cell type cards linked directly to CL cell types
id title
Brain Data Standards Ontology: A data-driven ontology of transcriptomically defined cell types in the primary motor cortex
annotation
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
id title
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.
annotation
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
id title
CELLxGENE: a performant, scalable exploration platform for high dimensional sparse matrices
annotation
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
id title
The Human Cell Atlas
annotation
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
id title
Expression Atlas update: from tissues to single cells
annotation
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
Ontology application and use at the ENCODE DCC
annotation
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
annotation
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)