Controlled Vocabularies are standardized term lists, widely used in biological databases today. An understanding of the structure and usage of Controlled Vocabularies can improve researcher's database searches, and can assist biological programmers in standardizing many terms and analyses. Popular controlled vocabularies in biological science include Gene Ontology, MeSH, and the EC number system from the Enzyme Commission. The Open Biomedical Ontologies site provides access to many useful ontology collections for biologists and bioinformaticians, including species specific, anatomy and phenotype based ontologies.

You will learn:

  • the basic concepts of controlled vocabularies
  • to explore some of the most widely-used vocabularies
  • sites to examine additional vocabularies and resources employing them
  • how controlled vocabularies may improve your searching


This tutorial is a part of the tutorial group Text-related tools. You might find the other tutorials in the group interesting:

PubMatrix: PubMatrix, an on-line tool for multiplex literature mining of the PubMed database.

iHOP: Information Hyperlinked Over Proteins text mining resource

STRING: known and predicted protein-protein interactions

Textpresso: Text-mining the biological literature

Gene Ontology: Gene Ontology controlled vocabularies in biology

XplorMed: eXploring Medline abstracts

GoMiner: Ascribe biological significance to large lists of genes by annotating them with their corresponding GO categories

DAVID: A tool that analyzes large lists of genes to provide biological meaning

Entrez Overview: Overview of NCBI's Entrez Search Resource

PubMed: PubMed access to biomedical research literature


Literature and Text Mining : Tools which are related to scientific literature. Repositories, query tools, and mining resources are included.


More Big Data to Consider: Bioimage Informatics: I'm not sure any more when I signed up for complementary copies of Nature Methods, but just like clockwork my copy arrives each month. If you'd like to get it too, you can apply for a subscription here...

New and Updated Online Tutorials for Textpresso and Gene Ontology: Comprehensive tutorials on the Gene Ontology and Textpresso databases enable researchers to quickly and effectively use these invaluable resources. Seattle, WA (PRWEB) December 8, 2008 -- OpenHelix tod...


Recent BioMed Central research articles citing this resource

Özgür Arzucan et al., The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature. BioData Mining (2016) doi:10.1186/s13040-016-0118-0

Hicks Amanda et al., The ontology of medically related social entities: recent developments. Journal of Biomedical Semantics (2016) doi:10.1186/s13326-016-0087-8

Vita Randi et al., An ontology for major histocompatibility restriction. Journal of Biomedical Semantics (2016) doi:10.1186/s13326-016-0045-5

Fu Gang et al., PubChemRDF: towards the semantic annotation of PubChem compound and substance databases Graphical abstract:. Journal of Cheminformatics (2015) doi:10.1186/s13321-015-0084-4

Lapatas Vasileios et al., Data integration in biological research: an overview. Journal of Biological Research-Thessaloniki (2015) doi:10.1186/s40709-015-0032-5