The Compositional Structure of Gene Ontology Terms

Abstract

An analysis of the term names in the Gene Ontology reveals the prevalence of substring relations between terms: 65.3% of all GO terms contain another GO term as a proper substring. This substring relation often coincides with a derivational relationship between the terms. For example, the term regulation of cell proliferation (GO:0042127) is derived from the term cell proliferation (GO:0008283) by addition of the phrase regulation of. Further, we note that particular substrings which are not themselves GO terms (e.g. regulation of in the preceding example) recur frequently and in consistent subtrees of the ontology, and that these frequently occurring substrings often indicate interesting semantic relationships between the related terms. We describe the extent of these phenomena-substring relations between terms, and the recurrence of derivational phrases such as regulation of-and propose that these phenomena can be exploited in various ways to make the information in GO more computationally accessible, to construct a conceptually richer representation of the data encoded in the ontology, and to assist in the analysis of natural language texts.

On the Application of Formal Principles to Life Science Data: a Case Study in the Gene Ontology

“…As Ogren et al [25] have pointed out, almost two-thirds of all GO terms contain other GO terms as substrings, the including term being in many cases derived from the included term via operators such as 'regulation of ' or 'sensu'. Many of the latter recur consistently in certain kinds of subtrees of GO's three ontologies, and in ways which reflect ontologically significant relations between the corresponding classes.…”

Evaluation of Lexical Methods for Detecting Relationships Between Concepts From Multiple Ontologies

“…The identification of such relationships may also be valuable within an ontology, e.g. in order to improve compositionality [25,32,28,29] or in defining and populating novel relationships. The work reported here is relevant both to the mapping and to the alignment task.…”

“…Lexical analysis of an ontology is a powerful tool for suggesting relationships between concepts within the ontology [25,28,29,30,32] or among multiple ontologies [7,6]. However, there are many possible text types to match between (e.g.…”

Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language

“…However, we can add new axioms based in the label; we can add, for example, the axiom transports only (alanine or sodium) and exploit that axiom in querying and structural maintenance 4 . The large size and repetitive nature of much of this axiomatic enrichment (for example, many term names share a similar syntactic structure [2,3]) mandates the use of some form of transformation language that can be used to define reusable transformations.…”