Ontology Search Help

What Is an "Ontology"?

An ontology is a controlled vocabulary of well-defined terms with specified relationships between them capable of interpretation by both humans and computers. This systematized knowledge facilitates data sharing between experiments and data sources thus encouraging cooperative usage of data produced in this new information age.

To learn more about what biomedical ontologies are and how they are used, view RGD's Introduction to Biomedical Ontologies Video series.

You can also explore a number of ontologies and learn more about their use in the biomedical sciences at the National Center for Biomedical Ontologies.


RGD Ontologies

RGD has used ontologies to standardize curated data and provide that data to  users in an organized manner. Over time the ontologies used at RGD have grown in number to provide more comprehensive data. The first implemented ontology at RGD is the gene ontology. It uses  controlled vocabularies in three aspects-biological process, cellular component and molecular, to describe genes and gene products.   A recent change in disease ontology has combined MeSH terms  (“C” branch and terms from supplementary concept data) and OMIM terms (Online Mendelian Inheritance in Man). This new disease  ontology  developed at the Comparative Toxicogenomics Database increases the granularity of disease vocabularies so more specific information can be curated. Another change in ontology vocabulary was conversion from Mesh-based behavior vocabulary to the NeuroBehavior Ontology developed at the University of Cambridge.  RGD has created  the Pathway ontology for gene and disease curation,  and four ontologies, Clinical Measurement Ontology, Measurement Method Ontology, Experimental Condition Ontology, Rat Strain Ontology, to curate and display quantitative phenotype data in a standardized manner.


The search keyword can be a single word, or portions of phrases. This tool searches all available ontologies for terms, synonyms, or accesion numbers (database IDs).



Using angiogenesis as an example, the ontology search first returns a list of ontologies in which “angiogenesis” appears, along with a count of terms found in each ontology. Click one of the ontologies, GO:Biological Process,  will bring up  a term results table listing all terms associated with  angiogenesis under GO:Biological Process.

The  term results table lists  all terms associated with  angiogenesis under GO;Biological Process. The accession number  and annotation count for each term and its children are listed next to the term in the table.  The results table provides links to both the ontology report page and the ontology browser.
This branch icon, brings users to ontology browser page. Click on annotation terms will bring up ontology report page  to view all objects associated with the term.