The Experts below are selected from a list of 120 Experts worldwide ranked by ideXlab platform
Mary Shimoyama - One of the best experts on this subject based on the ideXlab platform.
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Disease Ontology: improving and unifying disease annotations across species
The Company of Biologists, 2018Co-Authors: Susan M. Bello, Stanley J. F. Laulederkind, Elvira Mitraka, Mary Shimoyama, Cynthia L. Smith, Janan T. Eppig, Lynn M SchrimlAbstract:Model organisms are vital to uncovering the mechanisms of human disease and developing new therapeutic tools. Researchers collecting and integRating relevant model organism and/or human data often apply dispaRate terminologies (vocabularies and ontologies), making comparisons and inferences difficult. A unified disease ontology is required that connects data annotated using diverse disease terminologies, and in which the terminology relationships are continuously maintained. The Mouse Genome Database (MGD, http://www.informatics.jax.org), Rat Genome Database (RGD, http://rgd.mcw.edu) and Disease Ontology (DO, http://www.disease-ontology.org) projects are collaboRating to augment DO, aligning and incorpoRating disease terms used by MGD and RGD, and improving DO as a tool for unifying disease annotations across species. Coordinated assessment of MGD's and RGD's disease term annotations identified new terms that enhance DO's representation of human diseases. Expansion of DO term content and cross-references to clinical vocabularies (e.g. OMIM, ORDO, MeSH) has enriched the DO's domain coverage and utility for annotating many types of data geneRated from experimental and clinical investigations. The extension of anatomy-based DO classification structure of disease improves accessibility of terms and facilitates application of DO for computational research. A consistent representation of disease associations across data types from cellular to whole organism, geneRated from clinical and model organism studies, will promote the integRation, mining and compaRative analysis of these data. The coordinated enrichment of the DO and adoption of DO by MGD and RGD demonstRates DO's usability across human data, MGD, RGD and the rest of the model organism Database community
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novel unsupervised named entity recognition used in text annotation tool ontomate at Rat Genome Database
International Conference on Bioinformatics, 2017Co-Authors: Omid Ghiasvand, Mary ShimoyamaAbstract:In model organism Databases, one of the important tasks is to convert free text in biomedical liteRature to a structured data format. CuRators in the Rat Genome Database (RGD), the primary source of Rat genomic, genetic, and physiological data, spend considerable time and effort cuRating functional information for genes, QTLs, and strains from the liteRature. To increase cuRation efficiency and prioritize liteRature for data extraction OntoMate was developed at RGD. This tool tags Pubmed abstracts with genes, gene names, gene mutations, organism name and terms from 16 ontologies/vocabularies, including synonyms and aliases, used to represent functional information. In this project, we have used an unsupervised tagging method to reduce human effort for creating training data. In this approach, a machine learning tool based on decision tree classification techniques has been developed. Mentions that are uniquely belong to a semantic type play positive sample roles, and those with semantic types other than desired group are assumed to be negative samples. An interface allows the user to create a complex query incorpoRating terms from any of the ontologies, gene symbols, organisms, dates and other parameters. The results return abstracts along with all tagged parameters indicated in the query, along with children of the ontology terms chosen. Results can be further filtered by the user through a panel that lists organisms, genes and diseases with number of paper returned. Abstracts and papers are provided in rank order by relevance to the query. The tool is fully integRated into cuRation software so citations and abstracts can be automatically entered into the RGD Database and given ID and genes and ontology terms in the tags can be checked to create annotations linked to the paper. The system was built with a scalable and open architecture, and liteRature is updated daily. This tool uses Solr indexing technology and categorizes papers based on a relevance score. It indexes and tags more than 27 million abstracts. With the use of bioNLP tools, RGD has added more automation to its cuRation workflow.
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introducing a text annotation tool ontomate assisting cuRation at Rat Genome Database
International Conference on Bioinformatics, 2016Co-Authors: Omid Ghiasvand, Mary ShimoyamaAbstract:In model organism Databases, one of the important tasks is to convert free text in biomedical liteRature to a structured data format. CuRators in the Rat Genome Database (RGD), the primary source of Rat genomic, genetic, and physiological data, spend considerable time and effort cuRating functional information for genes, QTLs, and strains from the liteRature. To increase cuRation efficiency and prioritize liteRature for data extraction OntoMate was developed at RGD. This tool tags Pubmed abstracts and full papers in PubMed Central with genes, gene names, gene mutations, organism name and terms from 16 ontologies/vocabularies, including synonyms and aliases, used to represent functional information. The tagging process is currently a dictionary based method that is going to be improved by machine learning techniques such as CRF and/or SVM to handle ambiguous terms. An interface allows the user to create a complex query incorpoRating terms from any of the ontologies, gene symbols, organisms, dates and other parameter. The results return abstracts along with all tagged parameters indicated in the query, along with children of the ontology terms chosen. Results can be further filtered by the user through a panel that lists organisms, genes and diseases with number of paper returned. Abstracts and papers are provided in rank order by relevance to the query. The tool is fully integRated into cuRation software so citations and abstracts can be automatically entered into the RGD Database and given ID and genes and ontology terms in the tags can be checked to create annotations linked to the paper. The system was built with a scalable and open architecture, and liteRature is updated daily. This tool uses Solr indexing technology and categorizes papers based on a relevance score. It indexes and tags more than two million Pubmed Central papers and more than 23 million abstracts. With the use of bioNLP tools, RGD has added more automation to its cuRation workflow.
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exploring human disease using the Rat Genome Database
Disease Models & Mechanisms, 2016Co-Authors: Mary Shimoyama, Rajni Nigam, Thomas G Hayman, Shurjen Wang, Victoria Petri, Jeff De Pons, Marek Tutaj, Stanley J. F. Laulederkind, Jennifer R. Smith, Omid GhiasvandAbstract:ABSTRACT Rattus norvegicus, the laboRatory Rat, has been a crucial model for studies of the environmental and genetic factors associated with human diseases for over 150 years. It is the primary model organism for toxicology and pharmacology studies, and has features that make it the model of choice in many complex-disease studies. Since 1999, the Rat Genome Database (RGD; http://rgd.mcw.edu) has been the premier resource for genomic, genetic, phenotype and strain data for the laboRatory Rat. The primary role of RGD is to cuRate Rat data and validate orthologous relationships with human and mouse genes, and make these data available for incorpoRation into other major Databases such as NCBI, Ensembl and UniProt. RGD also provides official nomenclature for Rat genes, quantitative trait loci, strains and genetic markers, as well as unique identifiers. The RGD team adds enormous value to these basic data elements through functional and disease annotations, the analysis and visual presentation of pathways, and the integRation of phenotype measurement data for strains used as disease models. Because much of the Rat research community focuses on understanding human diseases, RGD provides a number of datasets and software tools that allow users to easily explore and make disease-related connections among these datasets. RGD also provides comprehensive human and mouse data for compaRative purposes, illustRating the value of the Rat in translational research. This article introduces RGD and its suite of tools and datasets to researchers – within and beyond the Rat community – who are particularly interested in leveraging Rat-based insights to understand human diseases.
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comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database
Physiological Genomics, 2016Co-Authors: Shurjen Wang, Rajni Nigam, Thomas G Hayman, Victoria Petri, Marek Tutaj, Stanley J. F. Laulederkind, Jennifer R. Smith, Melinda R. Dwinell, Mary ShimoyamaAbstract:Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where Genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuRation at RGD, including disease, genetic, and pathway data. The RGD cuRation team uses controlled vocabularies/ontologies to organize data cuRated from the published liteRature or imported from disease and pathway Databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to Genome objects. Screen shots from the web pages are used to demonstRate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually cuRated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other Databases enriches the collection of disease genes not only in quantity but also in quality.
Jennifer R. Smith - One of the best experts on this subject based on the ideXlab platform.
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the year of the Rat the Rat Genome Database at 20 a multi species knowledgebase and analysis platform
Nucleic Acids Research, 2019Co-Authors: Jennifer R. Smith, Thomas G Hayman, Shurjen Wang, Marek Tutaj, Stanley J. F. Laulederkind, Jyothi Thota, Matthew J Hoffman, Mary L Kaldunski, Harika S Nalabolu, Santoshi L R EllankiAbstract:Formed in late 1999, the Rat Genome Database (RGD, https://rgd.mcw.edu) will be 20 in 2020, the Year of the Rat. Because the laboRatory Rat, Rattus norvegicus, has been used as a model for complex human diseases such as cardiovascular disease, diabetes, cancer, neurological disorders and arthritis, among others, for >150 years, RGD has always been disease-focused and committed to providing data and tools for researchers doing compaRative genomics and translational studies. At its inception, before the sequencing of the Rat Genome, RGD started with only a few data types localized on genetic and radiation hybrid (RH) maps and offered only a few tools for querying and consolidating that data. Since that time, RGD has expanded to include a wealth of structured and standardized genetic, genomic, phenotypic, and disease-related data for eight species, and a suite of innovative tools for querying, analyzing and visualizing this data. This article provides an overview of recent substantial additions and improvements to RGD's data and tools that can assist researchers in finding and utilizing the data they need, whether their goal is to develop new precision models of disease or to more fully explore emerging details within a system or across multiple systems.
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integRated cuRation and data mining for disease and phenotype models at the Rat Genome Database
Database, 2019Co-Authors: Shurjen Wang, Thomas G Hayman, Marek Tutaj, Stanley J. F. Laulederkind, Jennifer R. Smith, Matthew Hoffman, Yiqing Zhao, Jyothi Thota, Elizabeth R BoltonAbstract:Rats have been used as research models in biomedical research for over 150 years. These disease models arise from naturally occurring mutations, selective breeding and, more recently, Genome manipulation. Through the innovation of Genome-editing technologies, Genome-modified Rats provide precision models of disease by disrupting or complementing targeted genes. To facilitate the use of these data produced from Rat disease models, the Rat Genome Database (RGD) organizes Rat strains and annotates these strains with disease and qualitative phenotype terms as well as quantitative phenotype measurements. From the cuRated quantitative data, the expected phenotype profile ranges were established through a meta-analysis pipeline using inbred Rat strains in control conditions. The disease and qualitative phenotype annotations are propagated to their associated genes and alleles if applicable. Currently, RGD has cuRated nearly 1300 Rat strains with disease/phenotype annotations and about 11% of them have known allele associations. All of the annotations (disease and phenotype) are integRated and displayed on the strain, gene and allele report pages. Finding disease and phenotype models at RGD can be done by searching for terms in the ontology browser, browsing the disease or phenotype ontology branches or entering keywords in the general search. Use cases are provided to show different targeted searches of Rat strains at RGD.
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a primer for the Rat Genome Database rgd
Methods of Molecular Biology, 2018Co-Authors: Stanley J. F. Laulederkind, Thomas G Hayman, Shurjen Wang, Victoria Petri, Jeff De Pons, Marek Tutaj, Jennifer R. Smith, Omid Ghiasvand, Matthew HoffmanAbstract:The laboRatory Rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the Rat have relevance to human physiology and disease. The Rat Genome Database (RGD, http://rgd.mcw.edu ) is a model organism Database that provides access to a wide variety of cuRated Rat data including disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components for genes, quantitative trait loci, and strains. We present an overview of the Database followed by specific examples that can be used to gain experience in employing RGD to explore the wealth of functional data available for the Rat.
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exploring human disease using the Rat Genome Database
Disease Models & Mechanisms, 2016Co-Authors: Mary Shimoyama, Rajni Nigam, Thomas G Hayman, Shurjen Wang, Victoria Petri, Jeff De Pons, Marek Tutaj, Stanley J. F. Laulederkind, Jennifer R. Smith, Omid GhiasvandAbstract:ABSTRACT Rattus norvegicus, the laboRatory Rat, has been a crucial model for studies of the environmental and genetic factors associated with human diseases for over 150 years. It is the primary model organism for toxicology and pharmacology studies, and has features that make it the model of choice in many complex-disease studies. Since 1999, the Rat Genome Database (RGD; http://rgd.mcw.edu) has been the premier resource for genomic, genetic, phenotype and strain data for the laboRatory Rat. The primary role of RGD is to cuRate Rat data and validate orthologous relationships with human and mouse genes, and make these data available for incorpoRation into other major Databases such as NCBI, Ensembl and UniProt. RGD also provides official nomenclature for Rat genes, quantitative trait loci, strains and genetic markers, as well as unique identifiers. The RGD team adds enormous value to these basic data elements through functional and disease annotations, the analysis and visual presentation of pathways, and the integRation of phenotype measurement data for strains used as disease models. Because much of the Rat research community focuses on understanding human diseases, RGD provides a number of datasets and software tools that allow users to easily explore and make disease-related connections among these datasets. RGD also provides comprehensive human and mouse data for compaRative purposes, illustRating the value of the Rat in translational research. This article introduces RGD and its suite of tools and datasets to researchers – within and beyond the Rat community – who are particularly interested in leveraging Rat-based insights to understand human diseases.
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comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database
Physiological Genomics, 2016Co-Authors: Shurjen Wang, Rajni Nigam, Thomas G Hayman, Victoria Petri, Marek Tutaj, Stanley J. F. Laulederkind, Jennifer R. Smith, Melinda R. Dwinell, Mary ShimoyamaAbstract:Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where Genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuRation at RGD, including disease, genetic, and pathway data. The RGD cuRation team uses controlled vocabularies/ontologies to organize data cuRated from the published liteRature or imported from disease and pathway Databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to Genome objects. Screen shots from the web pages are used to demonstRate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually cuRated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other Databases enriches the collection of disease genes not only in quantity but also in quality.
Victoria Petri - One of the best experts on this subject based on the ideXlab platform.
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a primer for the Rat Genome Database rgd
Methods of Molecular Biology, 2018Co-Authors: Stanley J. F. Laulederkind, Thomas G Hayman, Shurjen Wang, Victoria Petri, Jeff De Pons, Marek Tutaj, Jennifer R. Smith, Omid Ghiasvand, Matthew HoffmanAbstract:The laboRatory Rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the Rat have relevance to human physiology and disease. The Rat Genome Database (RGD, http://rgd.mcw.edu ) is a model organism Database that provides access to a wide variety of cuRated Rat data including disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components for genes, quantitative trait loci, and strains. We present an overview of the Database followed by specific examples that can be used to gain experience in employing RGD to explore the wealth of functional data available for the Rat.
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exploring human disease using the Rat Genome Database
Disease Models & Mechanisms, 2016Co-Authors: Mary Shimoyama, Rajni Nigam, Thomas G Hayman, Shurjen Wang, Victoria Petri, Jeff De Pons, Marek Tutaj, Stanley J. F. Laulederkind, Jennifer R. Smith, Omid GhiasvandAbstract:ABSTRACT Rattus norvegicus, the laboRatory Rat, has been a crucial model for studies of the environmental and genetic factors associated with human diseases for over 150 years. It is the primary model organism for toxicology and pharmacology studies, and has features that make it the model of choice in many complex-disease studies. Since 1999, the Rat Genome Database (RGD; http://rgd.mcw.edu) has been the premier resource for genomic, genetic, phenotype and strain data for the laboRatory Rat. The primary role of RGD is to cuRate Rat data and validate orthologous relationships with human and mouse genes, and make these data available for incorpoRation into other major Databases such as NCBI, Ensembl and UniProt. RGD also provides official nomenclature for Rat genes, quantitative trait loci, strains and genetic markers, as well as unique identifiers. The RGD team adds enormous value to these basic data elements through functional and disease annotations, the analysis and visual presentation of pathways, and the integRation of phenotype measurement data for strains used as disease models. Because much of the Rat research community focuses on understanding human diseases, RGD provides a number of datasets and software tools that allow users to easily explore and make disease-related connections among these datasets. RGD also provides comprehensive human and mouse data for compaRative purposes, illustRating the value of the Rat in translational research. This article introduces RGD and its suite of tools and datasets to researchers – within and beyond the Rat community – who are particularly interested in leveraging Rat-based insights to understand human diseases.
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comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database
Physiological Genomics, 2016Co-Authors: Shurjen Wang, Rajni Nigam, Thomas G Hayman, Victoria Petri, Marek Tutaj, Stanley J. F. Laulederkind, Jennifer R. Smith, Melinda R. Dwinell, Mary ShimoyamaAbstract:Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where Genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuRation at RGD, including disease, genetic, and pathway data. The RGD cuRation team uses controlled vocabularies/ontologies to organize data cuRated from the published liteRature or imported from disease and pathway Databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to Genome objects. Screen shots from the web pages are used to demonstRate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually cuRated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other Databases enriches the collection of disease genes not only in quantity but also in quality.
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the disease portals disease gene annotation and the rgd disease ontology at the Rat Genome Database
Database, 2016Co-Authors: Thomas G Hayman, Rajni Nigam, Shurjen Wang, Victoria Petri, Jeff De Pons, Marek Tutaj, Stanley J. F. Laulederkind, Jennifer R. Smith, Melinda R. Dwinell, Mary ShimoyamaAbstract:The Rat Genome Database (RGD;http://rgd.mcw.edu/) provides critical datasets and software tools to a diverse community of Rat and non-Rat researchers worldwide. To meet the needs of the many users whose research is disease oriented, RGD has created a series of Disease Portals and has prioritized its cuRation efforts on the datasets important to understanding the mechanisms of various diseases. Gene-disease relationships for three species, Rat, human and mouse, are annotated to capture biomarkers, genetic associations, molecular mechanisms and therapeutic targets. To geneRate gene-disease annotations more effectively and in greater detail, RGD initially adopted the MEDIC disease vocabulary from the CompaRative Toxicogenomics Database and adapted it for use by expanding this framework with the addition of over 1000 terms to create the RGD Disease Ontology (RDO). The RDO provides the foundation for, at present, 10 comprehensive disease area-related dataset and analysis platforms at RGD, the Disease Portals. Two major disease areas are the focus of data acquisition and cuRation efforts each year, leading to the release of the related Disease Portals. CollaboRative efforts to realize a more robust disease ontology are underway. Database URL:http://rgd.mcw.edu.
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the Rat Genome Database 2015 genomic phenotypic and environmental variations and disease
Nucleic Acids Research, 2015Co-Authors: Mary Shimoyama, Weisong Liu, Rajni Nigam, Thomas G Hayman, Victoria Petri, Jeff De Pons, Marek Tutaj, Stanley J. F. Laulederkind, Jennifer R. Smith, Shurjen WangAbstract:The Rat Genome Database (RGD, http://rgd.mcw.edu) provides the most comprehensive data repository and informatics platform related to the laboRatory Rat, one of the most important model organisms for disease studies. RGD maintains and updates datasets for genomic elements such as genes, transcripts and increasingly in recent years, sequence variations, as well as map positions for multiple assemblies and sequence information. Functional annotations for genomic elements are cuRated from published liteRature, submitted by researchers and integRated from other public resources. Complementing the genomic data catalogs are those associated with phenotypes and disease, including strains, QTL and experimental phenotype measurements across hundreds of strains. Data are submitted by researchers, acquired through bulk data pipelines or cuRated from published liteRature. Innovative software tools provide users with an integRated platform to query, mine, display and analyze valuable genomic and phenomic datasets for discovery and enhancement of their own research. This update highlights recent developments that reflect an increasing focus on: (i) genomic variation, (ii) phenotypes and diseases, (iii) data related to the environment and experimental conditions and (iv) datasets and software tools that allow the user to explore and analyze the interactions among these and their impact on disease.
Shurjen Wang - One of the best experts on this subject based on the ideXlab platform.
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the year of the Rat the Rat Genome Database at 20 a multi species knowledgebase and analysis platform
Nucleic Acids Research, 2019Co-Authors: Jennifer R. Smith, Thomas G Hayman, Shurjen Wang, Marek Tutaj, Stanley J. F. Laulederkind, Jyothi Thota, Matthew J Hoffman, Mary L Kaldunski, Harika S Nalabolu, Santoshi L R EllankiAbstract:Formed in late 1999, the Rat Genome Database (RGD, https://rgd.mcw.edu) will be 20 in 2020, the Year of the Rat. Because the laboRatory Rat, Rattus norvegicus, has been used as a model for complex human diseases such as cardiovascular disease, diabetes, cancer, neurological disorders and arthritis, among others, for >150 years, RGD has always been disease-focused and committed to providing data and tools for researchers doing compaRative genomics and translational studies. At its inception, before the sequencing of the Rat Genome, RGD started with only a few data types localized on genetic and radiation hybrid (RH) maps and offered only a few tools for querying and consolidating that data. Since that time, RGD has expanded to include a wealth of structured and standardized genetic, genomic, phenotypic, and disease-related data for eight species, and a suite of innovative tools for querying, analyzing and visualizing this data. This article provides an overview of recent substantial additions and improvements to RGD's data and tools that can assist researchers in finding and utilizing the data they need, whether their goal is to develop new precision models of disease or to more fully explore emerging details within a system or across multiple systems.
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integRated cuRation and data mining for disease and phenotype models at the Rat Genome Database
Database, 2019Co-Authors: Shurjen Wang, Thomas G Hayman, Marek Tutaj, Stanley J. F. Laulederkind, Jennifer R. Smith, Matthew Hoffman, Yiqing Zhao, Jyothi Thota, Elizabeth R BoltonAbstract:Rats have been used as research models in biomedical research for over 150 years. These disease models arise from naturally occurring mutations, selective breeding and, more recently, Genome manipulation. Through the innovation of Genome-editing technologies, Genome-modified Rats provide precision models of disease by disrupting or complementing targeted genes. To facilitate the use of these data produced from Rat disease models, the Rat Genome Database (RGD) organizes Rat strains and annotates these strains with disease and qualitative phenotype terms as well as quantitative phenotype measurements. From the cuRated quantitative data, the expected phenotype profile ranges were established through a meta-analysis pipeline using inbred Rat strains in control conditions. The disease and qualitative phenotype annotations are propagated to their associated genes and alleles if applicable. Currently, RGD has cuRated nearly 1300 Rat strains with disease/phenotype annotations and about 11% of them have known allele associations. All of the annotations (disease and phenotype) are integRated and displayed on the strain, gene and allele report pages. Finding disease and phenotype models at RGD can be done by searching for terms in the ontology browser, browsing the disease or phenotype ontology branches or entering keywords in the general search. Use cases are provided to show different targeted searches of Rat strains at RGD.
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a primer for the Rat Genome Database rgd
Methods of Molecular Biology, 2018Co-Authors: Stanley J. F. Laulederkind, Thomas G Hayman, Shurjen Wang, Victoria Petri, Jeff De Pons, Marek Tutaj, Jennifer R. Smith, Omid Ghiasvand, Matthew HoffmanAbstract:The laboRatory Rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the Rat have relevance to human physiology and disease. The Rat Genome Database (RGD, http://rgd.mcw.edu ) is a model organism Database that provides access to a wide variety of cuRated Rat data including disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components for genes, quantitative trait loci, and strains. We present an overview of the Database followed by specific examples that can be used to gain experience in employing RGD to explore the wealth of functional data available for the Rat.
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exploring human disease using the Rat Genome Database
Disease Models & Mechanisms, 2016Co-Authors: Mary Shimoyama, Rajni Nigam, Thomas G Hayman, Shurjen Wang, Victoria Petri, Jeff De Pons, Marek Tutaj, Stanley J. F. Laulederkind, Jennifer R. Smith, Omid GhiasvandAbstract:ABSTRACT Rattus norvegicus, the laboRatory Rat, has been a crucial model for studies of the environmental and genetic factors associated with human diseases for over 150 years. It is the primary model organism for toxicology and pharmacology studies, and has features that make it the model of choice in many complex-disease studies. Since 1999, the Rat Genome Database (RGD; http://rgd.mcw.edu) has been the premier resource for genomic, genetic, phenotype and strain data for the laboRatory Rat. The primary role of RGD is to cuRate Rat data and validate orthologous relationships with human and mouse genes, and make these data available for incorpoRation into other major Databases such as NCBI, Ensembl and UniProt. RGD also provides official nomenclature for Rat genes, quantitative trait loci, strains and genetic markers, as well as unique identifiers. The RGD team adds enormous value to these basic data elements through functional and disease annotations, the analysis and visual presentation of pathways, and the integRation of phenotype measurement data for strains used as disease models. Because much of the Rat research community focuses on understanding human diseases, RGD provides a number of datasets and software tools that allow users to easily explore and make disease-related connections among these datasets. RGD also provides comprehensive human and mouse data for compaRative purposes, illustRating the value of the Rat in translational research. This article introduces RGD and its suite of tools and datasets to researchers – within and beyond the Rat community – who are particularly interested in leveraging Rat-based insights to understand human diseases.
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comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database
Physiological Genomics, 2016Co-Authors: Shurjen Wang, Rajni Nigam, Thomas G Hayman, Victoria Petri, Marek Tutaj, Stanley J. F. Laulederkind, Jennifer R. Smith, Melinda R. Dwinell, Mary ShimoyamaAbstract:Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where Genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuRation at RGD, including disease, genetic, and pathway data. The RGD cuRation team uses controlled vocabularies/ontologies to organize data cuRated from the published liteRature or imported from disease and pathway Databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to Genome objects. Screen shots from the web pages are used to demonstRate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually cuRated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other Databases enriches the collection of disease genes not only in quantity but also in quality.
Stanley J. F. Laulederkind - One of the best experts on this subject based on the ideXlab platform.
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the year of the Rat the Rat Genome Database at 20 a multi species knowledgebase and analysis platform
Nucleic Acids Research, 2019Co-Authors: Jennifer R. Smith, Thomas G Hayman, Shurjen Wang, Marek Tutaj, Stanley J. F. Laulederkind, Jyothi Thota, Matthew J Hoffman, Mary L Kaldunski, Harika S Nalabolu, Santoshi L R EllankiAbstract:Formed in late 1999, the Rat Genome Database (RGD, https://rgd.mcw.edu) will be 20 in 2020, the Year of the Rat. Because the laboRatory Rat, Rattus norvegicus, has been used as a model for complex human diseases such as cardiovascular disease, diabetes, cancer, neurological disorders and arthritis, among others, for >150 years, RGD has always been disease-focused and committed to providing data and tools for researchers doing compaRative genomics and translational studies. At its inception, before the sequencing of the Rat Genome, RGD started with only a few data types localized on genetic and radiation hybrid (RH) maps and offered only a few tools for querying and consolidating that data. Since that time, RGD has expanded to include a wealth of structured and standardized genetic, genomic, phenotypic, and disease-related data for eight species, and a suite of innovative tools for querying, analyzing and visualizing this data. This article provides an overview of recent substantial additions and improvements to RGD's data and tools that can assist researchers in finding and utilizing the data they need, whether their goal is to develop new precision models of disease or to more fully explore emerging details within a system or across multiple systems.
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integRated cuRation and data mining for disease and phenotype models at the Rat Genome Database
Database, 2019Co-Authors: Shurjen Wang, Thomas G Hayman, Marek Tutaj, Stanley J. F. Laulederkind, Jennifer R. Smith, Matthew Hoffman, Yiqing Zhao, Jyothi Thota, Elizabeth R BoltonAbstract:Rats have been used as research models in biomedical research for over 150 years. These disease models arise from naturally occurring mutations, selective breeding and, more recently, Genome manipulation. Through the innovation of Genome-editing technologies, Genome-modified Rats provide precision models of disease by disrupting or complementing targeted genes. To facilitate the use of these data produced from Rat disease models, the Rat Genome Database (RGD) organizes Rat strains and annotates these strains with disease and qualitative phenotype terms as well as quantitative phenotype measurements. From the cuRated quantitative data, the expected phenotype profile ranges were established through a meta-analysis pipeline using inbred Rat strains in control conditions. The disease and qualitative phenotype annotations are propagated to their associated genes and alleles if applicable. Currently, RGD has cuRated nearly 1300 Rat strains with disease/phenotype annotations and about 11% of them have known allele associations. All of the annotations (disease and phenotype) are integRated and displayed on the strain, gene and allele report pages. Finding disease and phenotype models at RGD can be done by searching for terms in the ontology browser, browsing the disease or phenotype ontology branches or entering keywords in the general search. Use cases are provided to show different targeted searches of Rat strains at RGD.
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Disease Ontology: improving and unifying disease annotations across species
The Company of Biologists, 2018Co-Authors: Susan M. Bello, Stanley J. F. Laulederkind, Elvira Mitraka, Mary Shimoyama, Cynthia L. Smith, Janan T. Eppig, Lynn M SchrimlAbstract:Model organisms are vital to uncovering the mechanisms of human disease and developing new therapeutic tools. Researchers collecting and integRating relevant model organism and/or human data often apply dispaRate terminologies (vocabularies and ontologies), making comparisons and inferences difficult. A unified disease ontology is required that connects data annotated using diverse disease terminologies, and in which the terminology relationships are continuously maintained. The Mouse Genome Database (MGD, http://www.informatics.jax.org), Rat Genome Database (RGD, http://rgd.mcw.edu) and Disease Ontology (DO, http://www.disease-ontology.org) projects are collaboRating to augment DO, aligning and incorpoRating disease terms used by MGD and RGD, and improving DO as a tool for unifying disease annotations across species. Coordinated assessment of MGD's and RGD's disease term annotations identified new terms that enhance DO's representation of human diseases. Expansion of DO term content and cross-references to clinical vocabularies (e.g. OMIM, ORDO, MeSH) has enriched the DO's domain coverage and utility for annotating many types of data geneRated from experimental and clinical investigations. The extension of anatomy-based DO classification structure of disease improves accessibility of terms and facilitates application of DO for computational research. A consistent representation of disease associations across data types from cellular to whole organism, geneRated from clinical and model organism studies, will promote the integRation, mining and compaRative analysis of these data. The coordinated enrichment of the DO and adoption of DO by MGD and RGD demonstRates DO's usability across human data, MGD, RGD and the rest of the model organism Database community
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a primer for the Rat Genome Database rgd
Methods of Molecular Biology, 2018Co-Authors: Stanley J. F. Laulederkind, Thomas G Hayman, Shurjen Wang, Victoria Petri, Jeff De Pons, Marek Tutaj, Jennifer R. Smith, Omid Ghiasvand, Matthew HoffmanAbstract:The laboRatory Rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the Rat have relevance to human physiology and disease. The Rat Genome Database (RGD, http://rgd.mcw.edu ) is a model organism Database that provides access to a wide variety of cuRated Rat data including disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components for genes, quantitative trait loci, and strains. We present an overview of the Database followed by specific examples that can be used to gain experience in employing RGD to explore the wealth of functional data available for the Rat.
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exploring human disease using the Rat Genome Database
Disease Models & Mechanisms, 2016Co-Authors: Mary Shimoyama, Rajni Nigam, Thomas G Hayman, Shurjen Wang, Victoria Petri, Jeff De Pons, Marek Tutaj, Stanley J. F. Laulederkind, Jennifer R. Smith, Omid GhiasvandAbstract:ABSTRACT Rattus norvegicus, the laboRatory Rat, has been a crucial model for studies of the environmental and genetic factors associated with human diseases for over 150 years. It is the primary model organism for toxicology and pharmacology studies, and has features that make it the model of choice in many complex-disease studies. Since 1999, the Rat Genome Database (RGD; http://rgd.mcw.edu) has been the premier resource for genomic, genetic, phenotype and strain data for the laboRatory Rat. The primary role of RGD is to cuRate Rat data and validate orthologous relationships with human and mouse genes, and make these data available for incorpoRation into other major Databases such as NCBI, Ensembl and UniProt. RGD also provides official nomenclature for Rat genes, quantitative trait loci, strains and genetic markers, as well as unique identifiers. The RGD team adds enormous value to these basic data elements through functional and disease annotations, the analysis and visual presentation of pathways, and the integRation of phenotype measurement data for strains used as disease models. Because much of the Rat research community focuses on understanding human diseases, RGD provides a number of datasets and software tools that allow users to easily explore and make disease-related connections among these datasets. RGD also provides comprehensive human and mouse data for compaRative purposes, illustRating the value of the Rat in translational research. This article introduces RGD and its suite of tools and datasets to researchers – within and beyond the Rat community – who are particularly interested in leveraging Rat-based insights to understand human diseases.
