Abstract
AbstractThe Cell Ontology (CL) aims for the representation of in vivo and in vitro cell types from all of biology. Although the CL is a reference ontology of the OBO Foundry, it requires extensive revision to bring it up to current standards for biomedical ontologies, both in its structure and its coverage of various subfields of biology. A recent workshop sponsored by NIAID on hematopoietic cell types in the CL addressed both issues. The section of the ontology dealing with hematopoietic cells was extensively revised, and plans were set for structuring these cell type terms as cross-products with logical definitions built from relationships to external ontologies, such as the Protein Ontology and the Gene Ontology. The methods and improvement to the CL in this area represent a paradigm for improvement of the whole of the ontology over time.
Highlights
The Cell Ontology (CL) aims for the representation of in vivo and in vitro cell types from all of biology
The participants at the workshop agreed to focus on structural criteria where possible as the primary differentia, but to accept other types of differentia when necessary. This flexibility should make it possible to stick to the commonly accepted biological definitions of individual cell types and to organize the ontology according to sound ontological principles while still reflecting organization of hematopoietic cell types seen in the literature
Reflecting the above considerations, the participants at the NIAID workshop agreed upon a two-stage approach to further development of the hematopoietic cells in the Cell Ontology
Summary
The Cell Ontology (CL) aims for the representation of in vivo and in vitro cell types from all of biology. The first relationship is used to build an ontology of cellular subtypes; the latter relationship is used to indicate cell lineage relationships The ontology as it was initially developed relied upon a number of artificial high level terms to capture types of cellular qualities, such as “cell in vivo,” “cell by organism,” and “cell by class,” a term which itself has the is_a child terms “cell by function,” “cell by histology,” “cell by lineage,” “cell by ploidy,” etc. These subclasses of cells have further is_a children denoting more specific qualities of cells. This unwieldy ontological construct is not ideal for developing proper inference about cell types, nor does it always provide obvious placement of new cell type terms
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