title: Exploitation of ontological resources for scientific literature analysis: searching genes and related diseases.
abstract: Ontological resources such as controlled vocabularies, taxonomies and ontologies from the OBO foundry are used to represent biomedical domain knowledge. The development of such resources is a time consuming task. Once they are finished they contribute to standardization of information representation, interoperability of IT solutions, literature analysis and knowledge discovery. Text mining comprises IT solutions for information retrieval (IR) and information extraction (IE). IR technology exploits ontological resources to select documents that fit best to the processed query, for example, through indexing of the literature content with concept ids or through disambiguation of terms in the query. IE solutions make use of the ontological labels to identify concepts in the text. The text passages that denote conceptual entries are then used either to annotate named entities or to relate the named entities to each other. For knowledge discovery (KD) solutions the identified concepts in the scientific literature are used to relate entities to each other, e.g. to identify gene-disease relations based on shared molecular functions.
authors: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, U.K. yepes@ebi.ac.uk
authors: Antonio
authors: A
authors: Jimeno-Yepes
authors: Rafael
authors: R
authors: Berlanga-Llavori
authors: Dietrich
authors: D
authors: Rebholz-Schuhmann
mesh_terms: D001698:Biomedical Engineering; D019295:Computational Biology; D057225:Data Mining / Q000379:methods / Q000706:statistics & numerical data; D003628:Database Management Systems; D016208:Databases, Factual; D005796:Genes; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods* / Q000706:statistics & numerical data; D011642:Publications; D018875:Vocabulary, Controlled