Hematopoietic cell types: Prototype for a revised cell ontology

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

Research output: Contribution to journalArticle

24 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)75-79
Number of pages5
JournalJournal of Biomedical Informatics
Volume44
Issue number1
DOIs
StatePublished - Feb 2011

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Ontology
Biological Ontologies
Gene Ontology
Cell Biology
Foundries
Genes
Proteins

Keywords

  • Hematopoietic cells
  • Immunology
  • Ontology

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics

Cite this

Diehl, A. D., Augustine, A. D., Blake, J. A., Cowell, L. G., Gold, E. S., Gondré-Lewis, T. A., ... Mungall, C. J. (2011). Hematopoietic cell types: Prototype for a revised cell ontology. Journal of Biomedical Informatics, 44(1), 75-79. https://doi.org/10.1016/j.jbi.2010.01.006

Hematopoietic cell types : Prototype for a revised cell ontology. / Diehl, Alexander D.; Augustine, Alison Deckhut; Blake, Judith A.; Cowell, Lindsay G.; Gold, Elizabeth S.; Gondré-Lewis, Timothy A.; Masci, Anna Maria; Meehan, Terrence F.; Morel, Penelope A.; Nijnik, Anastasia; Peters, Bjoern; Pulendran, Bali; Scheuermann, Richard H.; Yao, Q. Alison; Zand, Martin S.; Mungall, Christopher J.

In: Journal of Biomedical Informatics, Vol. 44, No. 1, 02.2011, p. 75-79.

Research output: Contribution to journalArticle

Diehl, AD, Augustine, AD, Blake, JA, Cowell, LG, Gold, ES, Gondré-Lewis, TA, Masci, AM, Meehan, TF, Morel, PA, Nijnik, A, Peters, B, Pulendran, B, Scheuermann, RH, Yao, QA, Zand, MS & Mungall, CJ 2011, 'Hematopoietic cell types: Prototype for a revised cell ontology', Journal of Biomedical Informatics, vol. 44, no. 1, pp. 75-79. https://doi.org/10.1016/j.jbi.2010.01.006
Diehl, Alexander D. ; Augustine, Alison Deckhut ; Blake, Judith A. ; Cowell, Lindsay G. ; Gold, Elizabeth S. ; Gondré-Lewis, Timothy A. ; Masci, Anna Maria ; Meehan, Terrence F. ; Morel, Penelope A. ; Nijnik, Anastasia ; Peters, Bjoern ; Pulendran, Bali ; Scheuermann, Richard H. ; Yao, Q. Alison ; Zand, Martin S. ; Mungall, Christopher J. / Hematopoietic cell types : Prototype for a revised cell ontology. In: Journal of Biomedical Informatics. 2011 ; Vol. 44, No. 1. pp. 75-79.
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