Введение
База данных геномики крыс
Database of rat genomics
База данных генома крыс (RGD) – это база данных геномики, генетики, физиологии и функциональных данных крыс, а также данных для сравнительной геномики крысы, человека и мыши. RGD отвечает за прикрепление биологической информации к геному крысы посредством структурированной терминологии, или онтологии, аннотаций, присвоенных генам и количественным локусам признаков (QTL), а также за консолидацию данных о штаммах крыс и предоставление их научному сообществу. Они также разрабатывают набор инструментов для извлечения и анализа геномных, физиологических и функциональных данных крысы, а также сравнительных данных для крысы, мыши, человека и пяти других видов. RGD возникла как совместная работа между исследовательскими институтами, участвующими в генетических и геномных исследованиях крыс. Её цель, как указано в запросе Национального института здоровья на получение гранта: HL 99 013, заключается в создании базы данных генома крысы для сбора, консолидации и интеграции данных, полученных в ходе продолжающихся генетических и геномных исследований крысы, и предоставления этих данных широкому научному сообществу. Вторичная, но важная цель – обеспечить курацию отображенных позиций для количественных локусов признаков, известных мутаций и других фенотипических данных. Крыса продолжает широко использоваться исследователями в качестве модельного организма для изучения фармакологии, токсикологии, общей физиологии, биологии и патофизиологии заболеваний. В последние годы наблюдается быстрый рост генетических и геномных данных о крысах. Кроме того, база данных генома крысы стала центральным источником информации о крысах для исследований и теперь содержит информацию не только о генетике и геномике, но и о физиологии и молекулярной биологии. Для всех этих областей доступны инструменты и страницы данных, которые курируются сотрудниками RGD.
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.
Данные
Данные RGD состоят из ручных аннотаций исследователей RGD, а также импортированных аннотаций из различных источников. RGD также экспортирует собственные аннотации для обмена с другими. На странице данных RGD перечислены восемь типов данных, хранящихся в базе данных: гены, QTL, маркеры, карты, штаммы, онтологии, последовательности и ссылки. Из них шесть активно используются и регулярно обновляются. Тип данных RGD Maps относится к устаревшим генетическим и радиационным гибридным картам. Эти данные в значительной степени заменены последовательностью всего генома крысы. Тип данных Sequences не представляет собой полный список геномных, транскриптных или белковых последовательностей, а содержит в основном последовательности ПЦР-праймеров, определяющие простой полиморфизм длины последовательности (SSLP) и маркеры экспрессированных последовательностей (EST). Такие последовательности полезны прежде всего для исследователей, которые все еще используют эти маркеры для генотипирования своих животных и для различения маркеров с одинаковым названием. Шесть основных типов данных в RGD следующие:
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).
Гены: начальные записи генов импортируются и обновляются из базы данных генов Национального центра биотехнологической информации (NCBI) еженедельно. Данные, импортируемые в ходе этого процесса, включают идентификатор гена, идентификаторы нуклеотидных и белковых последовательностей Genbank/RefSeq, идентификаторы групп HomoloGene и идентификаторы генов, транскриптов и белков Ensembl. Дополнительные данные, связанные с белками, импортируются из базы данных UniProtKB. Кураторы RGD просматривают литературу и вручную курируют генную онтологию (GO), заболевания, фенотипы и пути для генов крыс, заболевания и пути для генов мыши, а также заболевания, фенотипы и пути для генов человека. Кроме того, сайт импортирует аннотации GO для генов мыши и человека из консорциума GO, электронные аннотации для крыс из UniProt и аннотации фенотипов мыши из базы данных генома мыши/информатики генома мыши (MGD/MGI).
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: сотрудники RGD вручную курируют данные для QTL крыс и человека из литературы, где такие публикации существуют, или из записей, непосредственно представленных исследователями. Записи QTL мыши, включая назначения онтологии фенотипа млекопитающих (MP), импортируются непосредственно из MGI. Для QTL крыс и человека курирование включает назначение MP, HP и аннотаций онтологии заболеваний. Позиции QTL автоматически присваиваются на основе геномных позиций пиковых и/или фланкирующих маркеров или однонуклеотидных полиморфизмов (SNP). Записи QTL связаны с информацией о родственных штаммах, кандидатных генах, ассоциированных маркерах и родственных QTL.
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).
Штаммы: как и записи QTL, записи штаммов RGD либо вручную курируются из литературы, либо представляются исследователями. Записи штаммов включают информацию об официальном символе штамма, происхождении и доступности штамма, связанных с ним фенотипах, является ли штамм моделью для заболевания человека, а также любую доступную информацию о разведении, поведении, содержании и т. д. Записи штаммов связаны с информацией о родственных генах, аллелях и QTL, ассоциированных штаммах (например, родительских штаммах или подштаммах) и, при наличии, специфичных для штамма вариантах нуклеотидов, вызывающих повреждения. Для конгенных и мутантных штаммов геномные позиции присваиваются интрогрессирующей области (конгенные штаммы) или местоположению мутировавшей последовательности (мутантные штаммы).
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).
Маркеры: поскольку генетические маркеры, такие как SSLP и EST, использовались и продолжают использоваться для QTL и штаммов, RGD хранит данные маркеров для крыс, людей и мышей. Данные маркеров включают последовательности соответствующих прямых и обратных ПЦР-праймеров, геномные позиции и ссылки на базу данных Probe NCBI. Записи маркеров связаны с ассоциированными записями QTL, штаммов и генов.
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).
Клеточные линии: RGD хранит записи клеточных линий на основе импорта из Cellosaurus. Хотя наибольшее количество из них составляют клеточные линии человека и мыши, доступны также записи для крыс, бонобо, собак, белок, свиней, зеленых обезьян и голых землекопов.
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).
Онтологии: чтобы сделать данные RGD читаемыми для человека и доступными для вычислительного анализа и извлечения, RGD полагается на использование нескольких онтологий. По состоянию на июль 2021 года RGD использовал 19 различных онтологий для выражения различных типов данных, применимых к разнообразным типам данных RGD. Аннотации онтологий присваиваются вручную кураторами. Онтологии, импортируемые из внешних источников, обновляются еженедельно.
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).
Ссылки: ссылки RGD — это научные публикации и ресурсы, которые использовались для курирования информации в базу данных и являются источниками объектов данных, таких как QTL и штаммы. Для ссылок, доступных через NCBI PubMed, импортируемые данные включают название, авторов, цитирование и идентификатор PubMed, а также генерируется идентификатор RGD. В некоторых случаях ссылки генерируются как внутренние записи, такие как массовая загрузка из автоматизированных конвейеров или личное общение с источниками данных. Эти дополнительные ссылки предоставляют пользователям RGD идентификацию источника определенных фрагментов и типов данных, для которых записи PubMed недоступны. Оба типа записей ссылок предоставляют ссылки на все данные, курированные из этой статьи или источника, включая гены, QTL, штаммы, заболевания и другие аннотации онтологий. Ресурсы, курируемые для информации, можно получить из базы данных с помощью страницы поиска ссылок или ссылок на странице объекта. Также доступны некурируемые ссылки, которые, как известно, содержат соответствующие данные, но еще не были проверены вручную. Они находятся в виде ссылок PubMed, перечисленных в разделе «Ссылки — некурируемые» отчета об объекте (например, отчета о гене).
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).
Инструменты генома
Инструменты генома RGD включают в себя как программное обеспечение, разработанное в RGD, так и инструменты из внешних источников.
RGD's Genome tools include both software tools developed at RGD and tools from third party sources.
Инструменты генома, разработанные в RGD
RGD разрабатывает веб-инструменты, предназначенные для использования данных, хранящихся в базе данных RGD, для анализа у крыс и между видами. Они включают в себя:
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 – это поисковая система по научной литературе, основанная на онтологиях и концепциях, разработанная RGD как альтернатива стандартному поиску в PubMed в процессе курирования генов. Преобразование данных из свободного текста в научной литературе в структурированный формат, пригодный для поиска, является одной из основных задач всех баз данных модельных организмов. OntoMate помечает аннотации названиями генов, мутациями генов, названиями организмов, заболеваниями и другими терминами из онтологий и словарей, используемых в RGD. Все термины/сущности, связанные с аннотацией, отображаются вместе с аннотацией в результатах поиска. OntoMate также предоставляет пользователям фильтры по виду, дате и другим параметрам, релевантным для поиска литературы, что упрощает процесс по сравнению с использованием PubMed. Помимо использования в процессах внутренней курирования RGD, инструмент доступен всем пользователям RGD.
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: Инструмент Gene Annotator (GA) принимает на вход список символов генов, идентификаторов RGD, номеров доступа GenBank, идентификаторов Ensembl или хромосомный регион и извлекает ортологи генов, идентификаторы внешних баз данных и аннотации онтологий для соответствующих генов в RGD. Данные можно загрузить в электронную таблицу Excel или проанализировать непосредственно в инструменте. Функция «Распределение аннотаций» отображает список терминов в каждой из семи категорий с указанием процента генов из входного списка, имеющих аннотации к каждому термину. Функция «Тепловая карта сравнения» позволяет сравнивать аннотации генов из входного списка в двух онтологиях или в двух ветвях одной и той же онтологии.
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) – это инструмент для просмотра и анализа полиморфизмов последовательности, специфичных для линий крыс. VV принимает на вход список символов генов или геномный регион, определяемый хромосомой, начальной и конечной позициями, или двумя символами генов или маркеров. Пользователь также должен выбрать интересующие его линии крыс из списка линий, для которых существуют полные геномные последовательности, и задать параметры для вариантов в результирующем наборе. Результатом является отображение вариантов в виде тепловой карты. Дополнительная информация об отдельных вариантах может быть просмотрена в панели подробностей.
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 – это инструмент для анализа онтологий, используемый для выявления терминов из любой или всех онтологий, используемых RGD для курирования генов (Заболевание, Путь, Фенотип, GO, ChEBI), которые представлены в аннотациях для этих генов или для ортологов у других видов. Он выдает загружаемый график и список статистически значимых терминов в списке генов пользователя, рассчитанных с использованием гипергеометрического распределения. MOET также отображает соответствующую поправку Бонферрони и отношение шансов на странице результатов.
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 используется для сравнения генов или позиций в интересующих регионах у различных видов или сборок RGD. Результаты отображаются в виде таблицы, содержащей соответствующие гены/позиции для обоих видов или обеих сборок. Входные и выходные данные GOLF могут быть экспортированы в другие инструменты RGD для анализа или загружены по ссылкам на странице результатов GOLF.
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 – это интерактивный просмотрщик белок-белковых взаимодействий, отображающий соответствующую информацию о типах взаимодействий и ссылках на связанные гены, относящиеся к введенным пользователем данным.
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 объединяет фенотипические данные из разных линий крыс, позволяя исследователям использовать фильтры для поиска количественных фенотипических данных.
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 – это поисковая система, позволяющая пользователям выполнять несколько запросов, генерировать список объектов из каждого запроса и гибко объединять результаты с использованием булевых спецификаций. OLGA принимает на вход либо список символов объектов, либо параметры поиска, основанные на аннотациях онтологии или позиции. Окончательный список генов, QTL или линий можно загрузить или отправить в инструмент GA, Variant Visualizer, Genome Viewer или другие инструменты RGD.
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: Инструмент Genome Viewer (GViewer) предоставляет пользователям полные геномные представления генов, QTL и картированных линий, аннотированных функцией, биологическим процессом, клеточным компонентом, фенотипом, заболеванием, путем или химическим взаимодействием. GViewer позволяет выполнять булевы поиски по нескольким онтологиям. Результаты отображаются на фоне кариотипа генома крысы.
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-зонды – это пары частично перекрывающихся олигонуклеотидов длиной 22 основания, полученных из геномной последовательности с маскировкой повторов, и используемых в качестве высокоспецифичных зондов для картирования генома. Инструмент Overgo Probe Designer принимает на вход последовательность нуклеотидов и выдает список оптимизированных последовательностей зондов, содержащих необходимый перехлест в 8 нуклеотидов на 3'-концах.
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 создает визуальный гаплотип, который можно использовать для идентификации консервативных и некосервативных хромосомных регионов между любой из 48 линий крыс, охарактеризованных в рамках проекта ACP. Для выбранной хромосомы и между выбранными линиями инструмент сравнивает данные о размере аллелей для микросателлитных маркеров на выбранной генетической или RH-карте.
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.
Третьи лица адаптировали инструменты геномной обработки для использования с данными RGD
RGD предлагает несколько сторонних программных инструментов, адаптированных для использования на веб-сайте с использованием данных, хранящихся в базе данных RGD. К ним относятся:
JBrowse: JBrowse – это бесплатный, интерактивный инструмент для анализа данных, специфичный для баз данных. Программное обеспечение было разработано и в настоящее время поддерживается проектом базы данных модельных организмов. Через JBrowse можно получить доступ к генетическим и фенотипическим типам данных, включая основные наборы данных и данные о химическом взаимодействии генов, а также к их связи с геномной последовательностью. RatMine: RatMine – это версия программного обеспечения InterMine, ориентированная на крыс. Она позволяет пользователям извлекать и анализировать данные о крысах из различных баз данных, включая RGD, NCBI, UniProtKB и Ensembl, в одном месте, используя единый формат. Платформа InterMine была адаптирована для нескольких видов в других базах данных и разработана для обеспечения совместимости между экземплярами, чтобы пользователи могли выполнять запросы по разным видам непосредственно из интерфейса RatMine.
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.
Пути
Ресурсы Pathway RGD включают в себя онтологию терминов Pathway (разработанную и поддерживаемую в RGD, охватывающую не только метаболические пути, но и пути, связанные с заболеваниями, лекарственными средствами, регуляцией и передачей сигналов), а также интерактивные диаграммы, отображающие компоненты и взаимодействия выбранных путей. На страницах диаграмм представлены описание, списки генов-участников пути и дополнительные элементы, таблицы аннотаций заболеваний, путей и фенотипов, сделанных для генов-участников пути, соответствующие ссылки и диаграмма онтологического пути. Также представлены наборы и сети путей, то есть объединения связанных путей, которые вносят вклад в более крупный процесс, такой как гомеостаз глюкозы или регуляция экспрессии генов, а также диаграммы физиологических путей, отображающие сети органов, тканей, клеток и молекулярных путей на уровне целого организма или системы.
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.
Нокауты
До недавнего времени прямые, специфические геномные манипуляции на крысах были невозможны. Однако с развитием таких технологий, как нуклеазы цинковых пальцев и методов мутагенеза на основе CRISPR, ситуация изменилась. К группам, создающим нокаутные модели генов крыс и другие типы генетически модифицированных крыс, относится Центр человеческой и молекулярной генетики при MCW. RGD предоставляет доступ к информации о штаммах крыс, полученных в ходе этих исследований, через страницы, посвященные проекту PhysGen Knockout и Центру геномного редактирования крыс MCW (GERRC), ссылки на которые находятся в заголовках страниц RGD. Финансирование проектов PhysGenKO и GERRC осуществлялось Национальным институтом сердца, легких и крови (NHLBI). Основной целью обоих проектов являлось создание крыс с изменениями в одном или нескольких конкретных генах, связанных с задачами NHLBI. Гены предлагались исследователями, работающими с крысами. Предложения рассматривались внешним консультативным советом. В рамках проекта PhysGenKO многие из созданных крыс были фенотипированы с использованием стандартизированного протокола высокопроизводительного фенотипирования, а данные доступны в инструменте PhenoMiner, разработанном RGD.
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.
Общественная пропаганда и образование
RGD взаимодействует с исследовательским сообществом, изучающим крыс, различными способами, включая email-форум, страницу новостей, страницу в Facebook, аккаунт в Twitter, а также регулярное участие и выступления на научных встречах и конференциях. Дополнительные образовательные мероприятия включают создание обучающих видеороликов, демонстрирующих как использование инструментов и данных RGD, так и более общие темы, такие как биомедицинские онтологии и биологическая (т.е. генная, QTL и штаммовая) номенклатура. Эти видеоролики доступны для просмотра на нескольких онлайн-видеохостингах, включая YouTube.
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.
Финансирование
RGD финансируется грантом R01HL64541 от Национального института сердца, легких и крови (NHLBI) от имени Национальных институтов здоровья (NIH). Главным исследователем по гранту является Энн Э. Квитек, доктор философии, которая сменила Мэри Э. Шимояму, доктор философии, на этой руководящей должности в марте 2020 года. Мелинда Р. Дуинелл, доктор философии, является соисследователем.
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.
Сборка нового генома
Новая сборка генома крысы, mRatBN7.2, была получена в рамках проекта «Древо жизни Дарвина» в Институте Велкома Сэнгера и принята Консорциумом геномных ссылок. mRatBN7.2 получена из самца крысы BN/NHsdMcwi, являющегося прямым потомком ранее секвенированной самки крысы BN. Новый эталонный геном крысы BN был создан с использованием различных технологий, включая длинные прочтения PacBio, прочтения 10X Genomics с линковкой, карты Bionano и Arima Hi-C. Его контигуозность сопоставима с эталонными сборками геномов человека и мыши. Он доступен в GenBank NCBI и RefSeq и в ближайшем будущем станет основной сборкой в RGD.
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.