Кіріспе
Құстар геномының дерекқоры
Database of rat genomics
Құстар геномының дерекқоры (RGD) – құстар геномының, генетикасының, физиологиясының және функционалдық деректерінің, сондай-ақ құстар, адам және егеуқұйрық арасындағы салыстырмалы геномиканың дерекқоры. RGD құстар геномына биологиялық ақпаратты құрылымды сөздіктер немесе онтология, гендерге тағайындалған аннотациялар және сандық белгілер локустары (QTL) арқылы қосуға, сондай-ақ құстар штамдарының деректерін біріктіруге және оларды ғылыми қауымдастыққа қолжетімді етуге жауапты. Олар құстардың геномдық, физиологиялық және функционалдық деректерін, құстар, егеуқұйрық, адам және тағы бес түрдің салыстырмалы деректерін іздеу және талдау үшін құралдар жиынтығын да әзірлеп жатыр. RGD құстар генетикалық және геномдық зерттеулерімен айналысатын зерттеу институттарының бірлескен күш-жігерінің нәтижесінде құрылды. Оның мақсаты, Ұлттық денсаулық сақтау институтының гранттық өтінім сұранысында: HL 99 013 көрсетілгендей, ағымдағы құстар генетикалық және геномдық зерттеулерінен алынған деректерді жинау, біріктіру және интеграциялау үшін Құстар геномының дерекқорын құру және осы деректерді ғылыми қауымдастыққа кеңінен тарату. Екінші, бірақ маңызды мақсат – сандық белгілер локустары, белгілі мутациялар және басқа да фенотиптік деректер үшін карталанған орналасуларын сақтау. Құстар фармакология, токсикология, жалпы физиология, аурудың биологиясы мен патофизиологиясын зерттеу үшін зерттеушілер тарапынан үлгілік организм ретінде кеңінен қолданыла береді. Соңғы жылдары құстар генетикалық және геномдық деректерінің көлемі тез өсті. Бұған қоса, Құстар геномының дерекқоры зерттеулер үшін құстар туралы ақпараттың орталық нүктесіне айналды және қазір генетика мен геномика ғана емес, физиология және молекулалық биология туралы да ақпарат ұсынады. Осы салалардың барлығы үшін RGD қызметкерлері басқаратын құралдар мен деректер беттері қолжетімді.
The Rat Genome Database (RGD) is a database of 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. 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, human, and five other species. RGD began as a collaborative effort between research institutions involved in rat genetic and genomic research. Its goal, as stated in the National Institutes of Health’s Request for Grant Application: HL 99 013, is the establishment of a Rat Genome Database to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make this data widely available to the scientific community. A secondary, but critical goal is 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.
Деректер
RGD деректері RGD зерттеушілерінің қолмен түсіндірмелерінен, сондай-ақ әртүрлі көздерден импортталған түсіндірмелерден тұрады. RGD басқалармен бөлісу үшін өз түсіндірмелерін де экспорттайды. RGD деректер бетінде деректер базасында сақталған сегіз түрдегі деректердің тізімі келтірілген: гендер, QTL, маркерлер, карталар, штаммдар, онтологиялар, тізбектер және сілтемелер. Олардың алтауы белсенді түрде қолданылады және үнемі жаңартылып отырады. RGD карталарының дерек типі генетикалық және радиациялық гибридтік карталарды білдіреді. Бұл деректер көбінесе егеуқұйрықтың толық геномдық тізбегімен алмастырылған. Тізбектер дерек типі геномдық, транскрипциялық немесе белок тізбектерінің толық тізімі емес, көбінесе жай тізбек ұзындығы полиморфизмін (SSLP) және экспрессияланған тізбек белгісін (EST) анықтайтын ПТР праймер тізбектерін қамтиды. Мұндай тізбектер негізінен зерттеушілерге осы маркерлерді жануарлардың генотипін анықтау және бірдей атауы бар маркерлерді ажырату үшін пайдалы. RGD-дегі алты негізгі дерек типі мыналар:
RGD’s data consists of manual annotations from RGD researchers as well as imported annotations from a variety of different sources. RGD also exports their own annotations to share with others. 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 and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
Genes: Initial gene records are imported and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
Гендер: Бастапқы гендік жазбалар апта сайын Ұлттық биотехнологиялық ақпарат орталығының (NCBI) Гендік деректер базасынан импортталады және жаңартылады. Бұл процесте импортталатын деректерге Ген идентификаторы, Genbank/RefSeq нуклеотидтері мен белок тізбектерінің идентификаторлары, HomoloGene тобының идентификаторлары және Ensembl Ген, Транскрипт және Белок идентификаторлары кіреді. Белокқа қатысты қосымша деректер UniProtKB деректер базасынан импортталады. RGD кураторлары әдебиетті қарап шығып, Гендік онтологияны (GO), ауруларды, фенотиптерді және егеуқұйрық гендерінің жолдарын, тышқан гендерінің ауруларын және жолдарын, адам гендерінің ауруларын, фенотиптерін және жолдарын қолмен қадағалайды. Сонымен қатар, сайтта GO консорциумынан тышқан және адам гендері үшін GO түсіндірмелері, UniProt-тен тышқанның электрондық түсіндірмелері және Тышқан геномдық дерекқорынан/Тышқан геномдық ақпараттан (MGD/MGI) тышқанның фенотиптік түсіндірмелері импортталады.
RGD’s data consists of manual annotations from RGD researchers as well as imported annotations from a variety of different sources. RGD also exports their own annotations to share with others. 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 and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
Genes: Initial gene records are imported and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
QTL: RGD қызметкерлері тышқан және адам QTL-дері бойынша деректерді әдебиеттен немесе зерттеушілер тікелей ұсынған деректерден қолмен жинақтайды. Тышқанның QTL жазбалары, оның ішінде Сүтқоректілер фенотипі (MP) онтологиясы тапсырмалары тікелей MGI-ден импортталады. Тышқан және адам QTL-дері үшін курациялау MP, HP және ауру онтологиясы түсіндірмесін тағайындауды қамтиды. QTL позициялары пік және/немесе бүйірлік маркерлердің немесе бір нуклеотидтік полиморфизмдердің (SNP) геномдық позицияларына негізделген автоматты түрде тағайындалады. QTL жазбалары туысқан штаммдар, кандидат гендер, байланысты маркерлер және туысқан QTL туралы ақпаратқа сілтемелер береді.
RGD’s data consists of manual annotations from RGD researchers as well as imported annotations from a variety of different sources. RGD also exports their own annotations to share with others. 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 and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
Genes: Initial gene records are imported and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
Штамдар: QTL деректері сияқты RGD штамм деректері әдебиеттен қолмен жинақталады немесе зерттеушілер ұсынады. Штамның деректеріне штамның ресми символы, шығу тегі мен қолжетімділігі, байланысты фенотиптер, штамм адамның ауруының үлгісі болып табыла ма, жоқ па және асылдандыру, мінез-құлық, мал шаруашылығы және т.б. туралы кез келген ақпарат кіреді. Штам жазбалары туысқан гендер, аллельдер және QTL-дер, байланысты штаммдар (мысалы, ата-аналық штаммдар немесе субштаммдар) және, егер бар болса, штамға тән зиянды нуклеотидтік варианттар туралы ақпаратқа сілтемелер береді. Туған және мутантты штаммдар үшін геномдық позициялар интрогрессиялық аймаққа (туған штаммдар) немесе мутантты тізбектің орналасуына (мутантты штаммдар) тағайындалады.
RGD’s data consists of manual annotations from RGD researchers as well as imported annotations from a variety of different sources. RGD also exports their own annotations to share with others. 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 and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
Genes: Initial gene records are imported and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
Маркерлер: SSLP және EST сияқты генетикалық маркерлер QTL және штаммдар үшін қолданылғандықтан, RGD егеуқұйрық, адам және тышқанның маркерлік деректерін сақтайды. Маркерлік деректерде байланысты алдыңғы және артқы ПТР праймерлерінің тізбектері, геномдық позициялар және NCBI Probe деректер базасына сілтемелер бар. Маркерлік жазбалар байланысты QTL, штамм және гендік жазбаларға сілтеме жасайды.
RGD’s data consists of manual annotations from RGD researchers as well as imported annotations from a variety of different sources. RGD also exports their own annotations to share with others. 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 and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
Genes: Initial gene records are imported and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
Жасушалық желілер: RGD Cellosaurus импортқа негізделген жасушалық желілердің жазбаларын сақтайды. Олардың ең көп бөлігі адам мен тышқанның жасушалық желілері болса да, мысық, бонобо, ит, бөрік, шошқа, жасыл маймыл және жалаңаш түлкілер туралы деректер де бар.
RGD’s data consists of manual annotations from RGD researchers as well as imported annotations from a variety of different sources. RGD also exports their own annotations to share with others. 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 and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
Genes: Initial gene records are imported and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
Онтологиялар: RGD деректерін адам оқитын және есептеулік талдау мен алу үшін қолжетімді ету үшін RGD бірнеше онтологияларды пайдалануға негізделген. 2021 жылдың шілде айына қарай RGD-нің әртүрлі дерек түрлері үшін қолданылатын әртүрлі деректерді білдіру үшін 19 түрлі онтологияны қолданды. Онтология түсіндірмелері кураторлармен қолмен тағайындалады. Сыртқы көздерден импортталатын онтологиялар апта сайын жаңартылады.
RGD’s data consists of manual annotations from RGD researchers as well as imported annotations from a variety of different sources. RGD also exports their own annotations to share with others. 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 and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
Genes: Initial gene records are imported and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
Сілтемелер: RGD сілтемелері деректер базасына ақпаратты жинақтау үшін қолданылған ғылыми жарияланымдар және ресурстар, сондай-ақ QTL және штаммдар сияқты дерек нысандарының көздері болып табылады. NCBI PubMed арқылы қол жеткізілген сілтемелер үшін импортталатын деректерге атау, авторлар, сілтеме және PubMed идентификаторы, сондай-ақ RGD идентификаторы кіреді. Кейбір жағдайларда сілтемелер ішкі жазбалар ретінде жасалады, мысалы, автоматтандырылған құбырлардан жапсыру немесе дерек көздерімен жеке хабарласу. Бұл қосымша сілтемелер RGD пайдаланушыларына PubMed жазбалары қол жетімді емес нақты деректер мен дерек түрлерінің көзін анықтауға мүмкіндік береді. Сілтеме жазбаларының екі түрі де осы мақаладан немесе көзден жинақталған барлық деректерге, соның ішінде гендерге, QTL-дерге, штаммдарға, ауруларға және басқа онтология түсіндірмелеріне сілтемелер береді. Ақпарат үшін жинақталған ресурстар деректер базасынан сілтемелерді іздеу бетінен немесе нысан бетіндегі сілтемелер арқылы алынуы мүмкін. Қолданылмаған сілтемелер де қол жетімді, олар тиісті деректерді қамтиды деп белгілі, бірақ әлі қолмен қарастырылмаған. Оларды нысан есебінің (мысалы, ген есебі) «Сілтемелер – қолданылмаған» бөлімінде тізімделген PubMed сілтемелері ретінде табуға болады.
RGD’s data consists of manual annotations from RGD researchers as well as imported annotations from a variety of different sources. RGD also exports their own annotations to share with others. 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 and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
Genes: Initial gene records are imported and 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 Gene Ontology (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, HP, and disease ontology annotations. QTL positions are automatically assigned based on the genomic positions of peak and/or flanking markers or single nucleotide polymorphisms (SNPs). QTL records link to information about related strains, candidate genes, associated markers and related QTLs. Strains: Like QTL records, RGD strain records are either manually curated from the literature or submitted by researchers. Strain records include information about the official symbol of the strain, 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, alleles, and QTLs, associated strains (e. g. parental strains or substrains) and, where available, strain specific damaging 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). 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. Cell lines: RGD stores cell line records based on imports from Cellosaurus. Although the largest numbers of these are human and mouse cell lines, records are also available for rat, bonobo, dog, squirrel, pig, green monkey and naked mole rat. 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 2021, RGD used 19 different ontologies to express the various types of data applicable to RGD's diverse datatypes. Ontology annotations are assigned manually by curators Ontologies which are imported from outside sources are updated weekly. References: RGD references are scientific publications and resources that have been used for curation of information into the database, and 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, and an RGD ID is generated. In some cases, references are generated as internal records, such as bulk uploads from automated pipelines or personal communications with data sources. These additional references give RGD users an identification of the source of particular pieces and types of data for which PubMed records are not available. Both types of reference records provide links to all of the data curated from that article or source, including genes, QTLs, strains, disease and other ontology annotations. The resources curated for information can be retrieved from the database using the reference search page or links on an object page. Uncurated references are also available, which are known to contain relevant data but have not yet been manually reviewed. These are found as PubMed links listed in the ‘References – uncurated’ section of an object report (e. g. a gene report).
Геномдық құралдар
RGD-нің геномдық құралдары RGD-де жасалған бағдарламалық қамтамасы мен үшінші тараптан алынған құралдарды қамтиды.
RGD's Genome tools include both software tools developed at RGD and tools from third party sources.
RGD-де әзірленген геномдық құралдар
RGD дөңгелектер мен түрлер арасындағы талдаулар үшін RGD деректер базасында сақталған деректерді пайдалануға арналған веб-құралдарды әзірлейді. Оларға келесілер кіреді:
RGD develops web based tools designed to use the data stored in the RGD database for analyses in rat and across species. These include:
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
OntoMate: OntoMate – онтологияға негізделген, түсініктерге негізделген әдебиет іздеу жүйесі. RGD оны гендік курация жұмыс ағынындағы негізгі PubMed іздеу жүйесіне балама ретінде әзірледі. Ғылыми әдебиеттегі еркін мәтіннен деректерді іздеуге болатын құрылымдалған форматқа аудару – барлық модельдік организмдер деректер базасының маңызды міндеттерінің бірі. OntoMate RGD-де қолданылатын онтологиялар/сөздіктерден гендер атауларын, гендер мутацияларын, организмдер атауларын, ауруларды және басқа да терминдермен рефераттарды белгілейді. Рефератқа тегтелген барлық терминдер/объектілер іздеу нәтижелерінде рефератпен бірге тізімделеді. OntoMate сонымен қатар әдебиет іздеу үшін қажетті түрлер, дата және басқа параметрлер үшін пайдаланушы белсендірген сүзгілерді ұсынады, бұл PubMed-ті пайдаланумен салыстырғанда процесті жеңілдетті. RGD-нің ішкі курация процестерінде пайдалы болудан басқа, құрал RGD-нің барлық пайдаланушыларына қолжетімді.
RGD develops web based tools designed to use the data stored in the RGD database for analyses in rat and across species. These include:
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
Gene Annotator: Gene Annotator (GA) құралы гендік символдар тізімін, RGD ID-ді, GenBank қосылу нөмірлерін, Ensembl идентификаторларын немесе хромосомалық аймақты енгізу ретінде қабылдайды және RGD-дегі сәйкес гендер үшін гендік ортологтарды, сыртқы деректер қорының идентификаторларын және онтологиялық аннотацияларды алады. Деректерді Excel кестесіне жүктеуге немесе құрал арқылы талдау жасауға болады. Annotation Distribution функциясы жеті санаттың әрқайсысындағы терминдердің тізімін көрсетеді, онда әрбір терминге аннотациямен кіріс тізіміндегі гендердің пайызы көрсетіледі. Comparison Heat Map функциясы кіріс тізіміндегі гендерге арналған аннотацияларды екі онтологияда немесе бір онтологияның екі тармағында салыстыруға мүмкіндік береді.
RGD develops web based tools designed to use the data stored in the RGD database for analyses in rat and across species. These include:
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
Variant Visualizer: Variant Visualizer (VV) – тышқан штамдарына тән реттілік полиморфизмін көру және талдау құралы. VV ені ретінде гендік символдар тізімін немесе хромосома, бастау және аяқталу орындары немесе екі ген немесе маркерлік символдар арқылы анықталған гендік аймақты қабылдайды. Пайдаланушы сонымен қатар тұтас геномдық тізбектері бар штамдар тізімінен өздерінің қызығушылықтарын тудыратын штамдарды таңдауы керек және нәтиже жиынтығындағы нұсқалар үшін параметрлерді орната алады. Шығыс – варианттардың жылу картасы түріндегі көрсетілімі. Жеке варианттар бойынша қосымша ақпаратты егжей-тегжейлі панельде көруге болады.
RGD develops web based tools designed to use the data stored in the RGD database for analyses in rat and across species. These include:
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
Multi Ontology Enrichment Tool (MOET): MOET – веб-базалық онтологияны талдау құралы. RGD-нің гендік курация үшін қолданатын кез-келген немесе барлық онтологиялардағы (ауру, жол, фенотип, GO, ChEBI) терминдерді анықтау үшін қолданылады. Бұл терминдер гендерге жасалған аннотацияларда немесе басқа түрлердегі ортологтарда артық көрсетілген. Құрал жүктеуге болатын графикті және гипергеометриялық үлестіруді пайдалана отырып, пайдаланушының гендер тізіміндегі статистикалық жағынан артық көрсетілген терминдердің тізімін шығарады. MOET сондай-ақ нәтижелер бетінде сәйкес Бонферрони түзетуі мен қатынас коэффициентін көрсетеді.
RGD develops web based tools designed to use the data stored in the RGD database for analyses in rat and across species. These include:
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
Gene Ortholog Location Finder (GOLF): GOLF RGD түрлерінің немесе жиынтықтарының қызығушылық аймақтарындағы гендерді немесе позицияларды салыстыру үшін қолданылады. Нәтижелер екі түрдегі немесе екі жиынтықтағы сәйкес гендермен/орналасулармен қатар кесте түрінде көрсетіледі. GOLF-қа енгізілген және шығарылған деректерді талдау үшін басқа RGD құралдарына экспорттау немесе GOLF нәтижелер бетіндегі сілтемелерді пайдалану арқылы жүктеу мүмкін.
RGD develops web based tools designed to use the data stored in the RGD database for analyses in rat and across species. These include:
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
InterViewer: InterViewer – пайдаланушының кірісіне қатысты өзара әрекеттесу түрлері мен байланысты гендер туралы тиісті ақпаратты көрсететін белок-белок өзара әрекеттесуін көру құралы.
RGD develops web based tools designed to use the data stored in the RGD database for analyses in rat and across species. These include:
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
PhenoMiner: PhenoMiner әр түрлі тышқан штамдарының фенотиптік деректерін біріктіреді, сондықтан зерттеушілер іздеген сандық фенотиптік деректерді табу үшін сүзгілерді қолдана алады.
RGD develops web based tools designed to use the data stored in the RGD database for analyses in rat and across species. These include:
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
OLGA Object List Generator & Analyzer: OLGA – пайдаланушыларға бірнеше сұраныстарды орындауға, әр сұраныстан объектілер тізімін шығаруға және Бульдік ерекшеліктерді қолдана отырып, нәтижелерді икемді түрде біріктіруге мүмкіндік беретін іздеу жүйесі. OLGA ені ретінде объект символдарының тізімін немесе онтология аннотациясына немесе орнына негізделген іздеу параметрлерін қабылдайды. Гендердің, QTL-дардың немесе штаммдардың түпкілікті тізімін жүктеуге немесе GA құралына, Variant Visualizer-ға, Genome Viewer-ға немесе басқа RGD құралдарына тапсыруға болады.
RGD develops web based tools designed to use the data stored in the RGD database for analyses in rat and across species. These include:
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
Genome Viewer: Genome Viewer (GViewer) құралы пайдаланушыларға гендердің, QTL-дардың және функцияға, биологиялық процеске, жасушалық компонентке, фенотипке, ауруға, жолға немесе химиялық өзара әрекеттесуге аннотацияланған штаммдардың толық геномдық көрінісін ұсынады. GViewer бірнеше онтологияларда Бульдік іздеулерді жүргізуге мүмкіндік береді. Шығыс – тышқан геномының кариотипіне қарсы көрсетіледі.
RGD develops web based tools designed to use the data stored in the RGD database for analyses in rat and across species. These include:
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
Overgo Probe Designer: Overgo зондтары – қайталанудан тазартылған геномдық тізбектен алынған, жартылай жабысқан 22мер олигонуклеотидтерінің жұптары. Олар геномды картографиялау үшін жоғары белсенділікке ие зондтар ретінде қолданылады. Overgo Probe Designer құралы нуклеотидтік тізбекті енгізу ретінде қабылдайды және 3' ұштарында қажетті 8 нуклеотидтік жабысуға ие оптимизацияланған зонд тізімін шығарады.
RGD develops web based tools designed to use the data stored in the RGD database for analyses in rat and across species. These include:
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
ACP Haplotyper: ACP Haplotyper ACP жобасының аясында сипатталған 48 тышқан штамдарының кез келгені арасындағы сақталған және сақталмаған хромосомалық аймақтарды анықтауға арналған визуальды гаплотипті құрайды. Таңдалған хромосома үшін және таңдалған штаммдар арасында құрал таңдалған генетикалық немесе RH картасындағы микросателлиттік маркерлер үшін аллель өлшемдерін салыстырады.
RGD develops web based tools designed to use the data stored in the RGD database for analyses in rat and across species. These include:
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
OntoMate: OntoMate is an ontology driven, concept based literature search engine that has been developed by RGD as an alternative for the basic PubMed search engine in the gene curation workflow. Converting data from free text in the scientific literature to a structured searchable format is one of the main tasks of all model organism databases. OntoMate tags abstracts with gene names, gene mutations, organism names, disease, and other terms from the ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. OntoMate also provides user activated filters for species, date and other parameters relevant to the literature search, which has streamlined the process compared to using PubMed. Besides its usefulness for RGD internal curation processes, the tool is available to all RGD users. Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or analyzed in the tool. The Annotation Distribution function displays a list of terms in each of seven categories with the percentage of genes from the input list with annotations to each term. The Comparison Heat Map function allows comparisons of annotations for genes in the input list across two ontologies or across two branches of the same ontology. Variant Visualizer: Variant Visualizer (VV) is a viewing and analysis tool for rat strain specific sequence polymorphisms. VV takes as input a list of gene symbols or a genomic region as defined by chromosome, start and stop positions or by two gene or marker symbols. The user must also select their strains of interest from a list of strains for which whole genome sequences exist and can set parameters for the variants in the result set. Output is a heatmap type display of variants. Additional information for individual variants can be viewed in a detail pane display. Multi Ontology Enrichment Tool (MOET): MOET is a web based ontology analysis tool used to identify terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over represented in the annotations for those genes, or for orthologs in other species. It outputs a downloadable graph and a list of statistically overrepresented terms in the user’s list of genes using hypergeometric distribution. MOET also displays the corresponding Bonferroni correction and odds ratio on the results page. Gene Ortholog Location Finder (GOLF): GOLF is used to compare genes or positions within regions of interest across RGD species or assemblies. Results are displayed with the corresponding genes/positions in both species or on both assemblies in a side by side tabular view. Inputs and outputs to GOLF can be exported to other RGD tools for analysis or downloaded using the links on the GOLF results page. InterViewer: InterViewer is a protein protein interactive viewer that displays the appropriate information about types of interactions and links to associated genes pertaining to the user’s input. PhenoMiner: PhenoMiner combines phenotypic data from different rat strains, so researchers can use filters to find the quantitative phenotypic data they are looking for. OLGA Object List Generator & Analyzer: OLGA is a search engine designed to allow users to run multiple queries, generate a list of objects from each query and flexibly combine the results using Boolean specifications. OLGA takes as input either a list of object symbols or search parameters based on ontology annotations or position. The final list of genes, QTLs or strains can be downloaded or submitted to the GA Tool, the Variant Visualizer, the Genome Viewer or other RGD tools. Genome Viewer: The Genome Viewer (GViewer) tool provides users with complete genome views of genes, QTLs and mapped strains annotated to a function, biological process, cellular component, phenotype, disease, pathway, or chemical interaction. GViewer allows Boolean searches across multiple ontologies. Output is displayed against a karyotype of the rat genome. Overgo Probe Designer: Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool takes as input a nucleotide sequence and outputs a list of optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. ACP Haplotyper: The ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.
RGD деректерімен пайдалану үшін бейімделген үшінші тараптың геномдық құралдары
RGD деректер базасында сақталған деректерді пайдалана отырып, веб-сайтта қолдануға бейімделген бірнеше үшінші тарап бағдарламалық құралдарды ұсынады. Оларға мыналар жатады: JBrowse: JBrowse – тегін, өте ыңғайлы және деректер базасына арналған деректерді талдау құралы. Бұл бағдарламалық жасақтама Generic Model Organism Database жобасымен жасалған және қазіргі уақытта олар тарапынан қолдау көрсетілуде. Гендік және фенотиптік дерек түрлері, оның ішінде негізгі деректер жиынтығы және гендердің химиялық өзара әрекеттесу деректері, сондай-ақ геномдық тізбекке қатыстылығы JBrowse арқылы қолжетімді. RatMine: RatMine – InterMine бағдарламалық жасақтамасының егеуқырға бағытталған нұсқасы. Ол пайдаланушыларға RGD, NCBI, UniProtKB және Ensembl сияқты әртүрлі деректер базаларынан егеуқыр туралы деректерді бірыңғай форматта жинап, талдауға мүмкіндік береді. InterMine платформасы басқа деректер базаларындағы көптеген түрлерге бейімделген және пайдаланушылар RatMine интерфейсі арқылы түрлер бойынша сұраулар жіберу үшін инстанциялар арасында өзара байланыс жасай алатындай етіп жасалған.
RGD offers several third party software tools that have been adapted for use on the website utilizing data stored in the RGD database. These include:
JBrowse: JBrowse is a free, interactive, and database specific data analysis tool. The software was created and is currently maintained by the Generic Model Organism Database project, Genetic and phenotypic data types, including fundamental datasets and gene chemical interaction data, and their relationship to the genomic sequence can be accessed through JBrowse. RatMine: RatMine is a rat centric version of the InterMine software. It enables users to mine and analyze rat data from diverse databases including RGD, NCBI, UniProtKB and Ensembl in a single location using a consistent format. The InterMine platform has been adapted for multiple species in other databases and is designed to be interoperable between instances so that users can query across species from the RatMine interface.
JBrowse: JBrowse is a free, interactive, and database specific data analysis tool. The software was created and is currently maintained by the Generic Model Organism Database project, Genetic and phenotypic data types, including fundamental datasets and gene chemical interaction data, and their relationship to the genomic sequence can be accessed through JBrowse. RatMine: RatMine is a rat centric version of the InterMine software. It enables users to mine and analyze rat data from diverse databases including RGD, NCBI, UniProtKB and Ensembl in a single location using a consistent format. The InterMine platform has been adapted for multiple species in other databases and is designed to be interoperable between instances so that users can query across species from the RatMine interface.
Жолдар
RGD-нің Pathway ресурстарына Pathway терминдерінің Pathway Ontology (RGD-де әзірленген және қолдауға алынатын, метаболизмдік жолдарды ғана емес, сонымен қатар ауру, дәрі-дәрмек, реттеу және сигналдық жолдарды қамтитын) кіреді, сондай-ақ таңдалған жолдардың компоненттері мен өзара әрекеттесулерінің интерактивті диаграммалары бар. Диаграмма беттерінде сипаттама, жолдың гендік мүшелерінің тізімі және қосымша элементтер, жол мүшелерінің гендеріне жасалған ауру, жол және фенотиптік аннотациялардың кестелері, қатысты сілтемелер және онтологиялық жол диаграммасы ұсынылған. Pathway жиынтықтары мен желілік жиынтықтар, яғни глюкоза гомеостазы немесе гендік экспрессияны реттеу сияқты үлкен процеске үлес қосатын байланысты жолдардың топтамалары, сондай-ақ ағзалардың, тіндердің, жасушалардың және молекулалық жолдардың желілерін көрсететін физиологиялық жол диаграммалары ұсынылады.
RGD's Pathway resources include a Pathway Ontology of pathway terms (developed and maintained at RGD, encompassing not only metabolic pathways but also disease, drug, regulatory and signaling pathways), as well as interactive diagrams of the components and interactions of selected pathways. Included on the diagram pages are a description, lists of pathway gene members and additional elements, tables of disease, pathway and phenotype annotations made to pathway member genes, associated references and an ontology path diagram. Pathway Suites and Suite Networks, i. e. groupings of related pathways which all contribute to a larger process such as glucose homeostasis or gene expression regulation are presented, as well as Physiological Pathway diagrams which display networks of organs, tissues, cells and molecular pathways at the whole animal or systems level.
Нокаут
Соңғы уақытқа дейін егеуқұйрықтардың геномдарын тікелей, нақты өзгерту мүмкін болмады. Алайда, мырыш саусақты нуклеаза және CRISPR негізделген мутагенез техникалары сияқты технологиялардың дамуымен жағдай өзгерді. Егеуқұйрық гендерін жою және басқа да генетикалық өзгертілген егеуқұйрықтарды өндіретін топтардың қатарында MCW-дегі Адам және молекулалық генетика орталығы бар. RGD, осы зерттеулерде өндірілген егеуқұйрық штамдары туралы ақпаратқа PhysGen Knockout жобасы және MCW Gene Editing Rat Resource Center (GERRC) туралы беттер арқылы сілтеме жасайды, оларға RGD бетінің жоғарғы бөлімінен қол жеткізуге болады. PhysGenKO жобасы мен GERRC-ге Ұлттық жүрек, өкпе және қан институты (NHLBI) қаржы бөлді. Екі жобаның да мақсаты – NHLBI миссиясына қатысты бір немесе бірнеше нақты гендерде өзгерістері бар егеуқұйрықтарды жасау. Гендерді егеуқұйрық зерттеушілері ұсынды, ал ұсыныстарды Сыртқы кеңесшілер кеңесі қарап бекітті. PhysGenKO жобасы аясында топ өндірген көптеген егеуқұйрықтар стандартталған, жоғары өнімді фенотиптеу протоколы бойынша фенотиптелді, ал деректер RGD-нің PhenoMiner құралында қолжетімді.
Until recently, direct, specific genomic manipulations in the rat were not possible. However, with the rise of technologies such as Zinc finger nuclease and CRISPR based mutagenesis techniques, that is no longer the case. Groups producing rat gene knockouts and other types of genetically modified rats include the Human and Molecular Genetics Center at MCW. RGD links to information about the rat strains produced in these studies via pages about the PhysGen Knockout project and the MCW Gene Editing Rat Resource Center (GERRC), accessed from RGD page headers. Funding for both the PhysGenKO project and the GERRC came from the National Heart Lung and Blood Institute (NHLBI). The stated goal of both projects is to produce rats with alterations in one or more specific genes related to the mission of the NHLBI. Genes were nominated by rat researchers. Nominations were adjudicated by an External Advisory Board. In the case of the PhysGenKO project, many of the rats produced by the group were phenotyped using a standardized high throughput phenotyping protocol and the data is available in RGD's PhenoMiner tool.
Қоғамдық ауқымдылық және білім беру
RGD тышқан зерттеу қауымдастығымен электрондық пошта форумы, жаңалықтар беті, Facebook парақшасы, Twitter аккаунты және ғылыми жиналыстар мен конференцияларға тұрақты қатысу мен баяндамалар арқылы байланыс орнатады. Сонымен қатар, RGD құралдары мен деректерін пайдалану жолдарын түсіндіретін, сондай-ақ биомедициналық онтологиялар және биологиялық (яғни ген, QTL және штамм) номенклатурасы сияқты жалпы тақырыптарды қамтитын оқулық видеолар жасалады. Бұл видеоларды YouTube-ты қоса алғанда, бірнеше онлайн видеохостинг платформаларында қарауға болады.
RGD reaches out to the rat research community in a variety of ways including an email forum, a news page, a Facebook page, a Twitter account, and regular attendance and presentations at scientific meetings and conferences. Additional educational activities include the production of tutorial videos, both outlining how to use RGD tools and data, and on more general topics such as biomedical ontologies and biological (i. e. gene, QTL and strain) nomenclature. These videos can be viewed on several online video hosting sites including YouTube.
Қаржыландыру
RGD Ұлттық денсаулық сақтау институтының (NIH) атынан Ұлттық жүрек, өкпе және қан институтының (NHLBI) R01HL64541 грантымен қаржыландырылады. Гранттың жетекші зерттеушісі – философия докторы Энн Э. Квитек, ол 2020 жылдың наурыз айында Мэри Э. Шимоямадан бұл басшылық лауазымға тағайындалды. Мелинда Р. Дуинелл, философия докторы, қатысушы зерттеуші.
RGD is funded by grant R01HL64541 from the National Heart, Lung, and Blood Institute (NHLBI) on behalf of the National Institutes of Health (NIH). The principal investigator of the grant is Anne E. Kwitek, PhD, who was appointed to this leadership position from Mary E. Shimoyama, PhD in March of 2020. Melinda R Dwinell, PhD is Co Investigator.
Жаңа геном құрастыруы
Жаңа геномдық жиынтық, mRatBN7.2, Велком Сангер институтының «Дарвиннің өмір ағашы» жобасымен жасалды және Геномдық сілтеме консорциумына қабылданды. mRatBN7.2 бұрын секвенирленген әйел BN егесінің тікелей ұрпағы болған еркек BN/NHsdMcwi егесінен алынған. Жаңа BN егесінің эталондық геномы PacBio ұзақ оқулары, 10X байланысты оқулары, Bionano карталары және Arima Hi C сияқты әртүрлі технологияларды қолдану арқылы құрастырылды. Оның үздіксіздігі адам немесе тышқан эталондық жиынтықтарымен салыстырылады. Ол NCBI GenBank және RefSeq-те қолжетімді, ал жақын арада RGD-де басты жиынтық ретінде жарияланады.
The new genome rat assembly, mRatBN7.2, was generated by the Darwin Tree of Life Project at the Wellcome Sanger Institute and has been accepted into the Genome Reference Consortium. mRatBN7.2 was derived from a male BN/NHsdMcwi rat that is a direct descendant of the female BN rat previously sequenced. The new BN rat reference genome was created using a variety of technologies including PacBio long reads, 10X linked reads, Bionano maps and Arima Hi C. Its contiguity is similar to the human or mouse reference assemblies. It is available at NCBI’s GenBank and at RefSeq, and it will be made the primary assembly at RGD in the near future.