Ontology Search - Rat Genome Database

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Keyword

ONTOLOGY GENERAL SEARCH

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 with similar annotations.

To search, you can specify a single word or multiple, space separated words. You can also use wildcard character '*'.

List of searchable ontologies:

Click ontology name to browse term tree.

CHEBI: Chebi Ontology +

CL: Cell Ontology +

CMO: Clinical Measurement +

GO: Biological Process +

GO: Cellular Component +

GO: Molecular Function +

MA: Mouse Anatomy +

MMO: Measurement Methods +

MP: Mammalian Phenotype +

NBO: Neuro Behavioral Ontology +

PW: Pathway Ontology +

RDO: RGD Disease Ontology +

RS: Rat Strains +

SO: Sequence Ontology +

VT: Vertebrate Trait Ontology +

XCO: Experimental Condition +

Sources for external ontologies:

	The Chemical Entities of Biological Interest (ChEBI) ontology is downloaded weekly from EMBL-EBI at http://www.ebi.ac.uk/chebi/. The data is made available under the Creative Commons License (CC BY 3.0, http://creativecommons.org/licenses/by/3.0/). For more information see: Degtyarenko et al. (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344–D350.
	The Cell Ontology (CL) is downloaded weekly from the SourceForge CVS repository at http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/anatomy/cell_type/. For more information about this ontology, see the NCBO Bioportal page for the Cell type ontology at http://bioportal.bioontology.org/ontologies/1006, or Bard et al, An ontology for cell types. Genome Biol. 2005;6(2):R21.
	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.
	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.
	The Neuro Behavior Ontology (NBO) is downloaded weekly from the Google code repository. For more information, view the project home page for the NBO at http://code.google.com/p/behavior-ontology/ or the NBO page at NCBO's BioPortal at http://bioportal.bioontology.org/ontologies/1621.
	The RGD/CTD Disease ontology (RDO) is developed and maintained by, and is regularly downloaded from, the Comparative Toxicogenomics Database (CTD), Mount Desert Island Biological Laboratory, Salisbury Cove, Maine. World Wide Web (URL: http://ctdbase.org/). Curated chemical–gene interactions are also downloaded weekly from the CTD database.
	The Sequence Types and Features Ontology (SO) is downloaded weekly from the SourceForge CVS repository at http://song.cvs.sourceforge.net/viewvc/song/ontology/. For more information about this ontology, see the Sequence Ontology Home Page at http://www.sequenceontology.org/.

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).