Hematopoietic cell types: Prototype for a revised cell ontology

  • Authors:

  • Alexander D. Diehl;Alison Deckhut Augustine;Judith A. Blake;Lindsay G. Cowell;Elizabeth S. Gold;Timothy A. Gondré-Lewis;Anna Maria Masci;Terrence F. Meehan;Penelope A. Morel;Anastasia Nijnik;Bjoern Peters;Bali Pulendran;Richard H. Scheuermann;Q. Alison Yao;Martin S. Zand;Christopher J. Mungall

  • Affiliations:

  • The Jackson Laboratory, Bar Harbor, ME, USA;National Institute of Allergy and Infectious Disease, Bethesda, MD, USA;The Jackson Laboratory, Bar Harbor, ME, USA;Duke University Medical Center, Durham, NC, USA;Institute for Systems Biology, Seattle, WA, USA;National Institute of Allergy and Infectious Disease, Bethesda, MD, USA;Duke University Medical Center, Durham, NC, USA;The Jackson Laboratory, Bar Harbor, ME, USA;University of Pittsburgh, Pittsburgh, PA, USA;University of British Columbia, Vancouver, BC, USA;La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA;Emory University, Atlanta, GA, USA;University of Texas Southwestern Medical Center, Dallas, TX, USA;National Institute of Allergy and Infectious Disease, Bethesda, MD, USA;University of Rochester Medical Center, Rochester, NY, USA;Lawrence Berkeley Laboratory, Berkeley, CA, USA

  • Venue:
  • Journal of Biomedical Informatics
  • Year:
  • 2011

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Abstract

The Cell Ontology (CL) aims for the representation of in vivo and in vitro cell types from all of biology. The CL is a candidate reference ontology of the OBO Foundry and 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. We have now addressed the specific content of one area of the CL, the section of the ontology dealing with hematopoietic cells. This section has been extensively revised to improve its content and eliminate multiple inheritance in the asserted hierarchy, and the groundwork has been laid for structuring the hematopoietic cell type terms as cross-products incorporating logical definitions built from relationships to external ontologies, such as the Protein Ontology and the Gene Ontology. The methods and improvements to the CL in this area represent a paradigm for improvement of the entire ontology over time.