title: Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation.
abstract: BACKGROUND
  Many bioinformatics data resources not only hold data in the form of sequences, but also as annotation. In the majority of cases, annotation is written as scientific natural language: this is suitable for humans, but not particularly useful for machine processing. Ontologies offer a mechanism by which knowledge can be represented in a form capable of such processing. In this paper we investigate the use of ontological annotation to measure the similarities in knowledge content or 'semantic similarity' between entries in a data resource. These allow a bioinformatician to perform a similarity measure over annotation in an analogous manner to those performed over sequences. A measure of semantic similarity for the knowledge component of bioinformatics resources should afford a biologist a new tool in their repertoire of analyses.
  
  
  RESULTS
  We present the results from experiments that investigate the validity of using semantic similarity by comparison with sequence similarity. We show a simple extension that enables a semantic search of the knowledge held within sequence databases.
  
  
  BACKGROUND
  Software available from http://www.russet.org.uk.
authors.affiliation: Department of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK. p.lord@russet.org.uk
authors.forename: P W
authors.initials: PW
authors.lastname: Lord
authors.forename: R D
authors.initials: RD
authors.lastname: Stevens
authors.forename: A
authors.initials: A
authors.lastname: Brass
authors.forename: C A
authors.initials: CA
authors.lastname: Goble
mesh_terms: D001185:Artificial Intelligence; D016208:Databases, Factual; D030541:Databases, Genetic; D004282:Documentation; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D009323:Natural Language Processing; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry* / Q000145:classification* / Q000235:genetics; D015203:Reproducibility of Results; D012660:Semantics; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods*; D013223:Statistics as Topic; D009626:Terminology as Topic
chemical_list: D011506:Proteins