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.
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.
In turn, CL is linked to from a variety of ontologies such as GO, Uberon and various phenotype ontologies.
The following are some applications of the cell ontology along with their publications:
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.
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
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),
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)
|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|