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ontology_detail
cl
Cell Ontology
Cell Ontology
checkout email_cc system method infallible
cl_edit@googlegroups.com
git
vcs
1
The Cell Ontology is a structured controlled vocabulary for cell types in animals.
label email github orcid
Alexander Diehl
addiehl@buffalo.edu
addiehl
0000-0001-9990-8331
id label
NCBITaxon:33208
Metazoa
anatomy and development
cells
id title
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
id
uberon
id
go
id
ro
id
chebi
id
pato
id
pr
id
ncbitaxon
cl.owl
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 description format derived_from
cl.obo
CL obo format edition
Complete ontology, plus inter-ontology axioms, and imports modules merged in
obo
cl.owl
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
user type description examples publications
annotation
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.
url 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 description
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
user type description examples publications
annotation
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.
url description
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.
user type description examples publications
annotation
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.
url description
HCA collection studies that are related B cell (CL:0000236) that is filtered through CL annotation
id title
The Human Cell Atlas
user type description examples publications
annotation
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.
url description
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
user seeAlso type description publications
annotation
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
user type description examples
annotation
FANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome analyses with cell-type and tissue-level specificity.
url description
FANTOM5 samples annotated to neuron
active
CL

logo

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), 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)