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CL specifications


Unique identifier OMICS_14223
Name CL
Alternative name Cell Ontology
Restrictions to use None
Community driven Yes
Data access File download, Browse
User data submission Not allowed
Maintained Yes


  • person_outline Alexander Diehl

Publications for Cell Ontology


An ontology for cell types

2005 Genome Biol
PMCID: 551541
PMID: 15693950
DOI: 10.1186/gb-2005-6-2-r21

CL citations


ImmPort, toward repurposing of open access immunological assay data for translational and clinical research

Sci Data
PMCID: 5827693
PMID: 29485622
DOI: 10.1038/sdata.2018.15

[…] ImmPort data is annotated with terms from several ontologies including Cell Ontology, Disease Ontology (, Ontology for Biomedical Investigations (OBI;, Protein Ontology, and Vaccine Ontology. MedDRA ( is used for adve […]


Cells in experimental life sciences challenges and solution to the rapid evolution of knowledge

BMC Bioinformatics
PMCID: 5763506
PMID: 29322916
DOI: 10.1186/s12859-017-1976-2

[…] tablish the dialogue to move forward in finding the optimal solutions to these challenges. The workshop has laid out the communication channels between the Human Cell Atlas (HCA) ontologists with the Cell Ontology developers that connect back to the experimental biologists generating and analyzing single-cell data. The discussion has resulted in an agreement for the HCA ontologists to request modi […]


Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature

Front Immunol
PMCID: 5712582
PMID: 29238346
DOI: 10.3389/fimmu.2017.01656

[…] ell and cytokine entity was normalized to a reference database, we can associate relations described over many documents, even if the authors use various nomenclatures. Furthermore, since we used the Cell Ontology as the reference for cell names, its axioms can be explored to expand the graph.To obtain a knowledge graph for tolerogenic cell therapy, we first obtained a set of 3,264 documents about […]


Genomic and molecular control of cell type and cell type conversions

Cell Regen
PMCID: 5769489
PMID: 29348912
DOI: 10.1016/

[…] ation factors, has included modelling development onto patterns of gene expression, and approaches to discover ‘core’ TFs that are both cell type-specific and expressed at high levels. Mogrify used a cell ontology tree to map cell type-specific genes against their developmental pattern and so identify TFs specific to a developmental lineage. Mogrify also includes nearest neighbour protein–protein […]


The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY

Nucleic Acids Res
PMCID: 5753190
PMID: 29149325
DOI: 10.1093/nar/gkx1121

[…] s). This is a pragmatic consequence of immunopharmacology being a subset of pharmacology. The second is that we have made greater use of both the Gene Ontology (GO) (,) ( and the Cell Ontology (CO) () (http://obofoundry/ontology/cl.html) for classifying targets. The third is we have introduced new levels of disease linking, including associating ligands directly to diseases fo […]


Systematic tissue specific functional annotation of the human genome highlights immune related DNA elements for late onset Alzheimer’s disease

PLoS Genet
PMCID: 5546707
PMID: 28742084
DOI: 10.1371/journal.pgen.1006933

[…] Andersson et al. define their enhancer sets via bi-directional CAGE expression collected by the FANTOM consortium []. Cell facets were manually constructed using hierarchical FANTOM5 cell ontology term mappings to create mutually exclusive and broadly covered histological and functional annotations. Enhancers were considered differentially expressed in a facet using Kruskal-Wallis […]


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CL institution(s)
Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY, USA; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK; ZFIN, the Zebrafish Model Organism Database, University of Oregon, Eugene, OR, USA; Ontology Development Group, Library, Oregon Health and Science University, Portland, OR, USA; Department of Biology, University of South Dakota, Vermillion, SD, USA; National Evolutionary Synthesis Center, Durham, NC, USA; Southwestern Medical Center, University of Texas, Dallas, TX, USA; Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Oral Diagnostics Sciences, University at Buffalo School of Dental Medicine, Buffalo, NY, USA; The Jackson Laboratory, Bar Harbor, ME, USA; Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
CL funding source(s)
This work was supported by the NHGRI grants HG002273-09Z and HG002273; the U.S. Department of Energy under Contract No. DE-AC02-05CH11231; the NIGMS grant 2R01GM080646-06; the NIAID contract HHSN272201200028C; the NIH HG002659 and 1R01AI081062; the NIH Office of the Director 1R24OD011883; the NSF grants DBI-0641025, DBI-1062404, and DBI-1062542 and the National Evolutionary Synthesis Center under NSF EF-0423641 and NSF EF-0905606.

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