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Ontology and Annotation
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

Examples: eye, SS BN Mcwi, kinase pathway ,

Sources for external ontologies:

GO: Molecular Function The Gene Ontology (GO) is downloaded weekly from the GO Consortium website (http://geneontology.org/docs/download-ontology/). 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 uses the Human Disease Ontology (DO, https://disease-ontology.org/) for disease curation across species. RGD automatically downloads each new release of the ontology on a monthly basis. Some additional terms which are required for RGD's curation purposes but are not currently covered in the official version of DO have been added. As corresponding terms are added to DO, these custom terms are retired and the DO terms substituted in existing annotations and subsequently used for curation.

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).