Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD

作者: Rajni Nigam , Diane H Munzenmaier , Elizabeth A Worthey , Melinda R Dwinell , Mary Shimoyama

DOI: 10.1186/2041-1480-4-36

关键词: Strain (biology)Computational biologyOntology (information science)Data miningRat Genome DatabaseControlled vocabularyCongenicChromosome (genetic algorithm)BiologyRat strain

摘要: The Rat Genome Database (RGD) ( http://rgd.mcw.edu/ ) is the premier site for comprehensive data on different strains of laboratory rat (Rattus norvegicus). strain are collected from various publications, direct submissions individual researchers, and providers worldwide. strain, substrain designation nomenclature follow Guidelines Nomenclature Mouse Strains, instituted by International Committee Standardized Genetic Mice. While symbols names aid in identifying correctly, flat nature this information prohibits easy search retrieval, as well other mining functions. In order to improve these functionalities, particularly ontology-based tools, Strain Ontology (RS) was developed. reflects breeding history, parental background, genetic manipulation strains. This controlled vocabulary organizes type: inbred, outbred, chromosome altered, congenic, mutant so on. addition, under altered category, organized chromosome, further type manipulations, such or congenic. allows users easily retrieve interest with modifications specific genomic regions. ontology developed using Open Biological Biomedical (OBO) file format, Directed Acyclic Graph (DAG) structure. IDs included part report (RS: ######). As researchers often unaware number substrains within a line, now provides an way all accompanying information. Its usefulness evident tools PhenoMiner at RGD, where can phenotype measurement related strains, similar backgrounds those introgressed also better retrieval filtering QTLs GViewer. has been incorporated into RGD Browser http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457#s available through National Center http://bioportal.bioontology.org/ontologies/1150 ftp ftp://rgd.mcw.edu/pub/ontology/rat_strain/ ).

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