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Table 1 Pharmspresso ontology examples.

From: Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text

Biological entity Example words/phrases
Cell or cell group germ line cells, intenstines, sensory neurons
Cellular component* axons, integrins, mitochondrial membrane
Disease stroke, chronic leukemia, tuberculoma
Drug acebutolol, mechlorethamine, tartaric acid
Gene ABCB1, CYP2C9, coagulation factor V
Organism mice, rat, xenopus laevis
Polymorphism T168N, 1039G-A, 236Arg->Lys
Relationships between entities Example words/phrases
Action assists, acomplishes, recognizes
Association associates, binds, interacts
Biological Process* acetylated, matures, reactivations
Characterization has, contains, displays, includes, lacks
Comparison correlates, differs, equally, matches
Effect accumulates, aggregates, causes
  1. Examples of Textpresso biological entities and relationships, along with additions for Pharmspresso (in bold). The ontology includes 35 categories of two types: (1) biological entities and (2) relationships between entities. Category names and examples of these categories are shown. * marks categories imported from Gene Ontology (GO).