Hematopoietic cell types: prototype for a revised cell ontology

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.

Figure 1

Term placement for cell type term “macrophage” in the Cell Ontology. A. In the original Cell Ontology, showing its multiple inheritance structure. B. In the “CL1.5” incorporating the revisions to the hematopoietic cell types.

Figure 2

Examples of improvement in the representation of hematopoietic cells. A. OBO term stanza representative of CL1.5 term definitions for the term “induced T-regulatory cell.” B. OBO term stanza representative of CL2.0 showing logical definition of the same term as in A. C. Graphical view of the term relationships in B. (synonyms in A and B omitted for brevity)