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

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

Search Ontology

Examples: eye, SS BN Mcwi, kinase pathway ,


About these ontologies

# Reference Title Reference Citation
1. The DO-KB Knowledgebase: a 20-year journey developing the disease open science ecosystem. Baron JA, etal., Nucleic Acids Res. 2024 Jan 5;52(D1):D1305-D1314. doi: 10.1093/nar/gkad1051.
2. The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. Diehl AD, etal., J Biomed Semantics. 2016 Jul 4;7(1):44. doi: 10.1186/s13326-016-0088-7.
3. The Human Phenotype Ontology in 2024: phenotypes around the world. Gargano MA, etal., Nucleic Acids Res. 2024 Jan 5;52(D1):D1333-D1346. doi: 10.1093/nar/gkad1005.
4. The Gene Ontology knowledgebase in 2023. Gene Ontology Consortium, etal., Genetics. 2023 May 4;224(1):iyad031. doi: 10.1093/genetics/iyad031.
5. The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes. Gkoutos GV, etal., Int Rev Neurobiol. 2012;103:69-87. doi: 10.1016/B978-0-12-388408-4.00004-6.
6. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. Haendel MA, etal., J Biomed Semantics. 2014 May 19;5:21. doi: 10.1186/2041-1480-5-21. eCollection 2014.
7. ChEBI in 2016: Improved services and an expanding collection of metabolites. Hastings J, etal., Nucleic Acids Res. 2016 Jan 4;44(D1):D1214-9. doi: 10.1093/nar/gkv1031. Epub 2015 Oct 13.
8. Modeling sample variables with an Experimental Factor Ontology. Malone J, etal., Bioinformatics. 2010 Apr 15;26(8):1112-8. doi: 10.1093/bioinformatics/btq099. Epub 2010 Mar 3.
9. Evolution of the Sequence Ontology terms and relationships. Mungall CJ, etal., J Biomed Inform. 2011 Feb;44(1):87-93. doi: 10.1016/j.jbi.2010.03.002. Epub 2010 Mar 10.
10. Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD. Nigam R, etal., J Biomed Semantics. 2013 Nov 22;4(1):36. doi: 10.1186/2041-1480-4-36.
11. The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species. Park CA, etal., J Biomed Semantics. 2013 Aug 9;4(1):13. doi: 10.1186/2041-1480-4-13.
12. The pathway ontology - updates and applications. Petri V, etal., J Biomed Semantics. 2014 Feb 5;5(1):7. doi: 10.1186/2041-1480-5-7.
13. Towards a unified open access dataset of molecular interactions. Porras P, etal., Nat Commun. 2020 Dec 1;11(1):6144. doi: 10.1038/s41467-020-19942-z.
14. Mouse Genome Informatics (MGI): latest news from MGD and GXD. Ringwald M, etal., Mamm Genome. 2022 Mar;33(1):4-18. doi: 10.1007/s00335-021-09921-0. Epub 2021 Oct 26.
15. The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications. Smith JR, etal., J Biomed Semantics. 2013 Oct 8;4(1):26. doi: 10.1186/2041-1480-4-26.
16. The Ontology of Biological Attributes (OBA)-computational traits for the life sciences. Stefancsik R, etal., Mamm Genome. 2023 Sep;34(3):364-378. doi: 10.1007/s00335-023-09992-1. Epub 2023 Apr 19.