An ontology for cell types
Open accessAbstract
We describe an ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds. It includes over 680 cell types. These cell types are classified under several generic categories and are organized as a directed acyclic graph. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. The ontology is freely available at http://obo.sourceforge.net/ and can be viewed using standard ontology visualization tools such as OBO-Edit and COBrA.
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GO, CL, HPO and related projects provide widely used, manually curated ontologies that hierarchically factor entities such as biological processes, components and functions, cell types, and human phenotypes into progressively more specific subunits.
“The Gene Ontology (GO) (Ashburner et al., 2000), Cell Ontology (CL) (Bard et al., 2005; Diehl et al., 2016), Human Phenotype Ontology (HPO) (Robinson et al., 2008) and related projects provide a set of widely used, manually curated ontologies that attempt to hierarchically factor entities such as biological processes, components and functions (GO), cell types (CL), and human phenotypes (HPO) into”
From Mapping the multiscale structure of biological systems (2021) · cites this paper as Bard et al., 2005
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- Authors
- Bard, J., Rhee, S. Y., & Ashburner, M.
- Affiliations
- University of Edinburgh (GB)
- Carnegie Institution for Science (US)
- European Bioinformatics Institute (GB)
- Corresponding author
- Ashburner, Michael
- Venue
- Genome biology
- Published
- 2005-01-14
- Volume
- 6
- Issue
- 2
- Pages
- R21-R21
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC551541
- OpenAlex
- W1757909678
- Cited by
- 416
- References
- 9
- Citations by year
- 2026: 8 · 2025: 6 · 2024: 10 · 2023: 15 · 2022: 14 · 2021: 23 · 2020: 23 · 2019: 23 · 2018: 17 · 2017: 16 · 2016: 15 · 2015: 14 · 2014: 17 · 2013: 24 · 2012: 25
- FWCI
- 9.70
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Funders
- National Science Foundation (9978564, 0321666)
- National Institutes of Health
- Medical Research Council
- Biotechnology and Biological Sciences Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Physical Sciences › Computer Science › Artificial Intelligence › Semantic Web and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- cell types, ontology (information science), cell type classification, prokaryotic cells, fungal cells, animal cells, plant cells, directed acyclic graphs, biological databases
- MeSH terms
- Animals, Computer Graphics, Eukaryotic Cells, Humans, Prokaryotic Cells, Databases, Factual, Vocabulary, Controlled, Internet, Databases, Genetic, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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