• Biology databases: Ontologies, dictionaries, taxonomies, keywords.

    • Gene Ontology: Gene Ontology TM (GO) for standard terminologies in molecular biology.
    • MGED.org: website of the MGED project for the development of an ontology for microarray experiments.
    • SOFG: Standards and Ontologies for Functional Genomics web site.
    • Cancer ontology: National Cancer Institute Thesaurus - ontology.
    • OBO: Open Biomedical Ontologies collection of ontologies for the biological and biomedical domain.
    • KO: KO (KEGG Orthology), functional hierarchies of KEGG pathways, ortholog groups, and protein families
    • GENIA Ontology: Ontology for formal model of cell signaling reactions in human
    • UMLS: Unified Medical Language System
    • MeSH: Medical Subject Headings vocabulary and terms
    • NCBI Taxonomy: Organism taxonomy provided by NCBI
    • UniProtKB/Swiss-Prot keywords: Swiss-Prot keyword categories




    If you know of additional ontologies related to the biology and biomedical domains, especially those which are open access or downloadable, please be so kind and contact me: martink@cnb.uam.es. This way you help to improve completeness of this list of text mining resources for biology and biomedicine. So far the most important ontology in the molecular biology domain is Gene Ontology, which has been explored by a range of bioinformatics as well as text mining and information extraction tools. Nevertheless there is an growing interest in developing additional ontologies for this domain.







    HOME