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layout ontology_detail
id cl
label Cell Ontology
title Cell Ontology
homepage https://github.com/obophenotype/cell-ontology
jobs
build
checkout email_cc system method infallible
cl_edit@googlegroups.com
git
vcs
1
description The Cell Ontology is a structured controlled vocabulary for cell types in animals.
integration_server http://build.berkeleybop.org/job/build-cl/
contact
label email github
Alexander Diehl
addiehl@buffalo.edu
addiehl
license
url label
CC-BY
taxon
id label
NCBITaxon:33208
Metazoa
domain cells
tracker https://github.com/obophenotype/cell-ontology/issues
mailing_list https://lists.sourceforge.net/lists/listinfo/obo-cell-type
publications
id title
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
dependencies
id
uberon
id
go
id
ro
id
chebi
id
pato
canonical cl.owl
products
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
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
usages
user seeAlso type description reference
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 users Uberon to annotate samples
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
activity_status active

neuron lymphocyte epithelial

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

One of the main uses of the CL is to describe samples used in transcriptomic and functional genomics studies, such as FANTOM5, ENCODE and LINCS.

This is described in the following publications:

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), 22. doi:10.1186/s13059-014-0560-6

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)