title: Logical development of the cell ontology.
abstract: BACKGROUND
  The Cell Ontology (CL) is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. By making the information in the ontology computable, we can use automated reasoners to detect errors and assist with classification. Here we report on the generation of computable definitions for the hematopoietic cell types in the CL.
  
  
  RESULTS
  Computable definitions for over 340 CL classes have been created using a genus-differentia approach. These define cell types according to multiple axes of classification such as the protein complexes found on the surface of a cell type, the biological processes participated in by a cell type, or the phenotypic characteristics associated with a cell type. We employed automated reasoners to verify the ontology and to reveal mistakes in manual curation. The implementation of this process exposed areas in the ontology where new cell type classes were needed to accommodate species-specific expression of cellular markers. Our use of reasoners also inferred new relationships within the CL, and between the CL and the contributing ontologies. This restructured ontology can be used to identify immune cells by flow cytometry, supports sophisticated biological queries involving cells, and helps generate new hypotheses about cell function based on similarities to other cell types.
  
  
  CONCLUSIONS
  Use of computable definitions enhances the development of the CL and supports the interoperability of OBO ontologies.
authors.affiliation: Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, USA. tmeehan@informatics.jax.org
authors.forename: Terrence F
authors.initials: TF
authors.lastname: Meehan
authors.forename: Anna Maria
authors.initials: AM
authors.lastname: Masci
authors.forename: Amina
authors.initials: A
authors.lastname: Abdulla
authors.forename: Lindsay G
authors.initials: LG
authors.lastname: Cowell
authors.forename: Judith A
authors.initials: JA
authors.lastname: Blake
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Mungall
authors.forename: Alexander D
authors.initials: AD
authors.lastname: Diehl
mesh_terms: D001773:Blood Cells / Q000145:classification*; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D016247:Information Storage and Retrieval / Q000379:methods; D018875:Vocabulary, Controlled