Reflecting the above considerations, we have taken a two-stage approach to further development of the hematopoietic cells in the Cell Ontology. In the first stage, which is now complete, we revised current terms and added new terms so that all hematopoietic cell type terms now have textual definitions that contain all the necessary details to define the cells logically. These terms have been directly incorporated into the existing ontology. Fig. 2A shows a typical OBO term stanza for one of these new terms, “induced T-regulatory cell.”
We have also separated the hematopoietic terms from the complex hierarchy of the original CL as much as possible, so that the section of the ontology containing these terms represents a true is_a hierarchy. Fig. 1B shows the simplified hierarchy for the cell type “macrophage.” In restructuring the ontology for the hematopoietic cells, we have eliminated the multiple inheritance via the artifactual high-level terms such as “cell by histology.” “cell by nuclear number,” or “cell by function.” Instead, information about cellular qualities is captured in the textual definitions where it is relevant, and is being used to build logical definitions for the cell types in the second stage of the work, as described below.