logo Cell Ontology

The Cell Ontology is a structured controlled vocabulary for cell types in animals.

The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types. This ontology is not organism specific. It covers cell types from prokaryotes to mammals. However, it excludes plant cell types, which are covered by PO.

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:

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.

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),

  1. 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)

Products

cl.owl Main CL OWL edition Complete ontology, plus inter-ontology axioms, and imports modules
cl.obo CL obo format edition Complete ontology, plus inter-ontology axioms, and imports modules merged in
cl/cl-basic.obo Basic CL Basic version, no inter-ontology axioms
cl/cl-base.owl CL base module complete CL but with no imports or external axioms

Usages

User
https://biccn.org/
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.
Type
annotation
Examples
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)
PCL cell type used in cell type cards linked directly to CL cell types
Publications
User
https://hubmapconsortium.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.
Type
annotation
Examples
ASCT+B reporter showing CL being used to annotate cell types in the heart
Publications
User
https://www.humancellatlas.org/
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.
Type
annotation
Examples
HCA collection studies that are related B cell (CL:0000236) that is filtered through CL annotation
Publications
User
https://www.ebi.ac.uk/gxa/home
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.
Type
annotation
Examples
RNA-Seq CAGE (Cap Analysis of Gene Expression) analysis of mice cells in RIKEN FANTOM5 project annotated using cell types from CL
Publications
User
https://www.encodeproject.org/
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
Type
annotation
See also
https://www.biosharing.org/biodbcore-000034
Publications
User
http://fantom5-collaboration.gsc.riken.jp/
Description
FANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome analyses with cell-type and tissue-level specificity.
Type
annotation
Examples
FANTOM5 samples annotated to neuron