The Cell Ontology • An ontology of cell types built by biologists for the needs of data annotation and analysis. • The main branch organizes and enumerates in vivo cell types. • The Cell Ontology covers cell types from all of biology. • The Cell Ontology is not – A list of specific cell lines, immortal or otherwise, although the Cell Ontology may be used to describe such cells if they correspond to an in vivo cell type. – A list of in vitro methods for preparing cell cultures, although the Cell Ontology may be used to describe the resulting cells if they correspond to an in vivo cell type.
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The Cell Ontology An ontology of cell types built by biologists for the needs of data annotation and analysis. The main branch organizes and enumerates.
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The Cell Ontology• An ontology of cell types built by biologists for the needs of data
annotation and analysis.
• The main branch organizes and enumerates in vivo cell types.
• The Cell Ontology covers cell types from all of biology.
• The Cell Ontology is not– A list of specific cell lines, immortal or otherwise, although the Cell
Ontology may be used to describe such cells if they correspond to an in vivo cell type.
– A list of in vitro methods for preparing cell cultures, although the Cell Ontology may be used to describe the resulting cells if they correspond to an in vivo cell type.
The Cell Ontology
• Initially developed in 2003 by Jonathan Bard, David States, Michael Ashburner, and Seung Rhee.
• First described in 2005, Genome Biology, 6:R21.
• Current version is available at http://obofoundry.org in the file cell.obo.
• Oliver Hoffman of SANBI is nominally “official” curator, although the position of editor for the ontology has been unfilled for 9 months.
• A Cell Ontology Working Group is currently considering ways to improve the ontology from an ontological perspective.
• Elimination of multiple is_a inheritance through instantiation of relationships to terms in outside ontologies, such as the GO cellular component, GO biological process, and the PATO phenotype ontologies.
• This a work in progress, and we can add terms to the existing ontology as necessary.