ArticleJournal of biomedical semantics2013
Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.
Article in Journal of biomedical semantics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Rare disease research resources at the Rat Genome Database.Genetics · 2023Article
- A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data.Environmental health perspectives · 2023Article
- Integrated curation and data mining for disease and phenotype models at the Rat Genome Database.Database : the journal of biological databases and curation · 2019Article
- Quantitative phenotype analysis to identify, validate and compare rat disease models.Database : the journal of biological databases and curation · 2019Article
- Classification and analysis of a large collection of in vivo bioassay descriptions.PLoS computational biology · 2017Article
- Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database.Physiological genomics · 2016Article
- The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease.Nucleic acids research · 2015Article
- PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease.Database : the journal of biological databases and curation · 2015Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundThe Rat Genome Database (RGD) ( http://rgd.mcw.edu/) is the premier site for comprehensive data on the different strains of the laboratory rat (Rattus norvegicus). The strain data are collected from various publications, direct submissions from individual researchers, and rat providers worldwide. Rat strain, substrain designation and nomenclature follow the Guidelines for Nomenclature of Mouse and Rat Strains, instituted by the International Committee on Standardized Genetic Nomenclature for Mice. While symbols and names aid in identifying strains correctly, the flat nature of this information prohibits easy search and retrieval, as well as other data mining functions. In order to improve these functionalities, particularly in ontology-based tools, the Rat Strain Ontology (RS) was developed.
resultsThe Rat Strain Ontology (RS) reflects the breeding history, parental background, and genetic manipulation of rat strains. This controlled vocabulary organizes strains by type: inbred, outbred, chromosome altered, congenic, mutant and so on. In addition, under the chromosome altered category, strains are organized by chromosome, and further by type of manipulations, such as mutant or congenic. This allows users to easily retrieve strains of interest with modifications in specific genomic regions. The ontology was developed using the Open Biological and Biomedical Ontology (OBO) file format, and is organized on the Directed Acyclic Graph (DAG) structure. Rat Strain Ontology IDs are included as part of the strain report (RS: ######).
conclusionsAs rat researchers are often unaware of the number of substrains or altered strains within a breeding line, this vocabulary now provides an easy way to retrieve all substrains and accompanying information. Its usefulness is particularly evident in tools such as the PhenoMiner at RGD, where users can now easily retrieve phenotype measurement data for related strains, strains with similar backgrounds or those with similar introgressed regions. This controlled vocabulary also allows better retrieval and filtering for QTLs and in genomic tools such as the GViewer.The Rat Strain Ontology has been incorporated into the RGD Ontology Browser ( http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457#s) and is available through the National Center for Biomedical Ontology ( http://bioportal.bioontology.org/ontologies/1150) or the RGD ftp site ( ftp://rgd.mcw.edu/pub/ontology/rat_strain/).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.