RGD uses ontologies: hierarchical, controlled vocabularies to annotate genes, QTLs, strains and homologs: Gene Ontology, Mammalian Phenotype Ontology, Disease Ontology, Pathway Ontology and others.

The Ontology Browser allows you to retrieve all genes, QTLs, strains and homologs annotated to a particular term.

Search Ontology


Keyword:   

Sources for external ontologies:

GO: Molecular Function The Gene Ontology (GO) is downloaded weekly from the GO Consortium website (http://www.geneontology.org/GO.downloads.ontology.shtml). For more information, please see The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat. Genet.. May 2000;25(1):25-9.
MP: Mammalian Phenotype The Mouse Adult Gross Anatomy Ontology and Mammalian Phenotype Ontology are downloaded weekly from the Mouse Genome Informatics databases at Jackson Laboratories (ftp://ftp.informatics.jax.org/pub/reports/index.html). For more information about these ontologies, see the MGI Publications Page at http://www.informatics.jax.org/mgihome/other/publications.shtml.
RDO: RGD Disease Ontology RGD's Disease Ontology (RDO) is the MEDIC vocabulary developed and maintained by, and regularly downloaded from, the Comparative Toxicogenomics Database (CTD) at http://ctdbase.org/reports/CTD_diseases.obo.gz. Unique RDO IDs are assigned to each term during loading. For more information about MEDIC, see http://ctdbase.org/. Curated chemical–gene interactions are also downloaded weekly from the CTD database.

RGD Ontologies:

CMO
MMO
XCO
PW
RS
VT

The Clinical Measurement Ontology (CMO), Measurement Methods Ontology (MMO), and Experimental Condition Ontology (XCO) are currently being developed at the Rat Genome Database. For more information about these vocabularies please see Shimoyama et al. Three ontologies to define phenotype measurement data. Front Genet. 2012;3:87. Epub 2012 May 28 or contact us (http://rgd.mcw.edu/contact/index.shtml).

The Pathway Ontology (PW), is currently being developed at the Rat Genome Database. For more information about this vocabulary, please see Petri et al. The rat genome database pathway portal. Database (Oxford). 2011 Apr 8;2011:bar010. Print 2011 or contact us (http://rgd.mcw.edu/contact/index.shtml).

The Rat Strain Ontology (RS) is currently being developed at the Rat Genome Database. For more information about this vocabulary or to request additions or changes, please contact us (http://rgd.mcw.edu/contact/index.shtml).

The Vertebrate Trait Ontology (VT) is being developed as a collaborative effort between the Rat Genome Database at the Medical College of Wisconsin (RGD, http://rgd.mcw.edu), Mouse Genome Informatics at the Jackson Laboratory (http://www.informatics.jax.org/) and the Animal QTL database at Iowa State University (http://www.animalgenome.org/cgi-bin/QTLdb/index). For more information about this vocabulary, or to request additions or changes, please contact us (http://rgd.mcw.edu/contact/index.shtml).