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A Reappraisal of How to Build Modular, Reusable Models of Biological Systems

Figure 2

Two possible composite annotations that represent the concept “cytoplasmic glucose concentration of pancreatic beta cell.”

Although the annotations are semantically equivalent, an automated model-merging tool may not recognize them as such, as their component terms originate from different ontologies. Adhering to an agreed-upon set of orthogonal ontologies may help model annotators address this challenge. Abbreviations: OPB, Ontology of Physics for Biology; ChEBI, Chemical Entities of Biological Interest; SNOMED-CT, Systematized Nomenclature of Medicine—Clinical Terms; FMA, Foundational Model of Anatomy; GO, Gene Ontology [22]; NCIT, National Cancer Institute Thesaurus [23].

Figure 2