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The Rat Genome Database (RGD) is the premiere location for rat genomics, genetics, physiology and functional data, as well as data for comparative genomics between rat, human and mouse. RGD is responsible for attaching biological information to the rat genome via structured vocabulary, or ontology, annotations assigned to genes and quantitative trait loci (QTL), and for consolidating rat strain data and making it available to the research community. RGD is working with groups such as the Programs for Genomic Applications at MCW and the National BioResource Project for the Rat (NBPR-Rat) in Japan to collect and make available comprehensive physiologic data for a variety of rat strains. They are also developing a suite of tools for mining and analyzing genomic, physiologic and functional data for the rat, and comparative data for rat, mouse and human. RGD began as a collaborative effort between leading research institutions involved in rat genetic and genomic research. Its goal, as stated in RFA: HL-99-013, was the establishment of a Rat Genome Database to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. A secondary, but critical goal was to provide curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data. The rat continues to be extensively used by researchers as a model organism for investigating pharmacology, toxicology, general physiology and the biology and pathophysiology of disease. In recent years, there has been a rapid increase in rat genetic and genomic data. In addition to this, the Rat Genome Database has become a central point for information on the rat for research and now features information on not just genetics and genomics, but physiology and molecular biology as well. There are tools and data pages available for all of these fields that are curated by RGD staff. ==Data== RGD's Data page lists eight types of data stored in the database: Genes, QTLs, Markers, Maps, Strains, Ontologies, Sequences and References. Of these, six are actively used and regularly updated. The RGD "Maps" datatype refers to legacy genetic and radiation hybrid maps. This data has been largely supplanted by the rat whole genome sequence. The "Sequences" data type is not a full list of either genomic, transcript or protein sequences, but rather mostly contains PCR primer sequences which define simple sequence length polymorphism (SSLP) and expressed sequence tag (EST) Markers. Such sequences are useful primarily for researchers still using these markers for genotyping their animals and for distinguishing between markers of the same name. The six major data types in RGD are as follows: *Genes: Initial gene records are imported/updated from the National Center for Biotechnology Information's (NCBI's) Gene database on a weekly basis. Data imported during this process includes the Gene ID, Genbank/RefSeq nucleotide and protein sequence identifiers, HomoloGene group IDs and Ensembl Gene, Transcript and Protein IDs. Additional protein-related data is imported from the UniProtKB database. RGD curators review the literature and manually curate GO, diseases, phenotypes and pathways for rat genes, diseases and pathways for mouse genes, and diseases, phenotypes and pathways for human genes. In addition, the site imports GO annotations for mouse and human genes from the GO Consortium, rat electronic annotations from UniProt and mouse phenotype annotations from the Mouse Genome Database/Mouse Genome Informatics (MGD/MGI). *QTLs: RGD's staff manually curates data for rat and human QTLs from the literature where such publications exist or from records directly submitted by researchers. Mouse QTL records, including Mammalian Phenotype (MP) ontology assignments, are imported directly from MGI. For rat and human QTLs, curation includes assigning MP and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleeotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. *Strains: As for QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the origin and availability of the strain, associated phenotypes, whether the strain is a model for a human disease, and any information that is available about breeding, behavior, husbandry, etc. Strain records link to information about related genes and QTLs, associated strains (e.g. parental strains or substrains) and, where available, strain-specific nucleotide variants. For congenic and mutant strains, genomic positions are assigned for the introgressed region (congenic strains) or the location of the mutated sequence (mutant strains). RGD does not import data for mouse strains. *Markers: Because genetic markers such as SSLPs and ESTs have been, and continue to be, used for QTLs and strains, RGD stores marker data for rat, human and mouse. Marker data includes the sequences of the associated forward and reverse PCR primers, genomic positions and links to NCBI's Probe database. Marker records link to associated QTL, strain and gene records. *Ontologies: In order to make RGD's data both human readable and available for computational analysis and retrieval, RGD relies on the use of multiple ontologies. As of July 2015, RGD used 16 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators〔〔 or are imported from external sources through the use of automated pipelines. Six of the ontologies in use at RGD were created or co-created at RGD and seven are under development by RGD staff members and/or collaborators, these being ontologies for Pathway (PW), Rat Strains (RS), Vertebrate Traits (VT), Disease (RDO), Clinical Measurements (CMO), Measurement Methods (MMO) and Experimental Conditions (XCO). Ontologies which are imported from outside sources are updated weekly. *References: RGD references are scientific publications that have been used for curation or are sources for data objects such as QTLs and strains. For references accessed via NCBI's PubMed, imported data includes the title, authors, citation and PubMed ID. In some cases, a reference is an internal record for processes such as automated pipelines or a personal communication, giving users of the database an indication of the source of a particular piece of data. PubMed records are not available for these. Each reference record links to all of the data curated from that article, including genes, QTLs, strains and ontology annotations. 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「Rat Genome Database」の詳細全文を読む スポンサード リンク
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