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on page 1 showing 8 out of 8 results from 1 sources

    BioGRID

Cite this (BioGRID, RRID:SCR_007393)

URL: http://www.thebiogrid.org/

Resource Type: Resource, database, service resource, storage service resource, software resource, data repository, data or information resource

A curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts. The current version searches over 41,000 publications containing over 720,000 interactions (June 2014) and contributions are welcome. Complete coverage of the entire literature is maintained for budding yeast (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. It provides interaction data to several model organism databases, resources such as Entrez-Gene, SGD, TAIR, FlyBase and other interaction meta-databases. The entire BioGRID 3.0 data collection may be downloaded in multiple file formats, including IMEx compatible PSI MI XML. For developers, BioGRID interactions are also available via a REST based Web Service and Cytoscape plugin.

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Cite this (Caenorhabditis Genetics Center, RRID:SCR_007341)

URL: http://www.cgc.cbs.umn.edu

Resource Type: Resource, organism supplier, biomaterial supply resource, biospecimen repository, standard specification, narrative resource, service resource, storage service resource, cell repository, data or information resource, material resource, material storage repository

Acquires, maintains, and distributes genetic stocks and information about stocks of the small free-living nematode Caenorhabditis elegans for use by investigators initiating or continuing research on this genetic model organism. A searchable strain database, general information about C. elegans, and links to key Web sites of use to scientists, including WormBase, WormAtlas, and WormBook are available. Services Provided: * Animals: the CGC's collection of more than 11,273 strains includes one allele of each mapped gene, all available chromosome rearrangements, and selected multiple-mutant stocks for genetic mapping. Certain transgenic strains also are available, including strains that express various green fluorescent protein (GFP) reporter fusions. The CGC also has stocks of nematode species closely related to C. elegans and bacterial strains necessary for nematode growth and for performing RNA interference experiments. * Nomenclature Information: recommended guidelines and persons to contact for specific questions about C. elegans genetic nomenclature can be found at the website. Databases of gene names and laboratory strain designations with allele codes are also available at this site.

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    ClinVar

Cite this (ClinVar, RRID:SCR_006169)

URL: http://www.ncbi.nlm.nih.gov/clinvar/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Freely accessible, public archive of aggregated information about sequence variation and its relationship to human health that provides reports of the relationships among human variations and phenotypes along with supporting evidence. Submissions from clinical testing labs, research labs, locus-specific databases, expert panels and professional societies are welcome. The database has a flexible data model, so submissions may be minimal or very detailed. ClinVar collects reports of variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in the submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for individual users, laboratories that want to incorporate it in their daily workflow, and organizations that want to incorporate it into their own applications. They will work in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible. They emphasize reporting structured evidence supporting any genotype-phenotype relationship, in order to support computational (re)evaluation, both of genotypes and assertions, enabling the ongoing evolution and development of knowledge regarding variations and associated phenotypes. The ClinVar archive versions submissions, so when submitters update their records, the previous version is retained for review. The level of confidence in the accuracy of variation calls and assertions of clinical significance depends in large part on the supporting evidence, so this information, when available, is collected and visible to users. Since the availability of supporting evidence may vary, particularly in regard to retrospective data aggregated from published literature, the archive accepts submissions from multiple groups, and aggregates related information, to transparently reflect both consensus and conflicting assertions of clinical significance. A review status is also assigned to any assertion, to support communication about the trustworthiness of any assertion. Accessions, of the format SCV000000000.0, are assigned to each record. Reports about sets of assertions about the same variation/phenotype relationship can be aggregated and submitted as a reference accession of the format RCV000000000.0. Groups wishing to evaluate a set of ClinVar records thus can submit a review of a set of SCV or RCV records, with the result being the creation of a novel RCV record.

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Cite this (GeneReviews, RRID:SCR_006560)

URL: http://www.ncbi.nlm.nih.gov/books/NBK1116/

Resource Type: Resource, narrative resource, data or information resource, book, database

Searchable book of expert-authored, peer-reviewed disease descriptions (chapters) presented in a standardized format and focused on clinically relevant and medically actionable information on the diagnosis, management, and genetic counseling of patients and families with specific inherited conditions.

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Cite this (Human Phenotype Ontology Annotations, RRID:SCR_006219)

URL: http://www.human-phenotype-ontology.org/contao/index.php/downloads.html

Resource Type: Resource, data set, data or information resource

Downloadable dataset of Human Phenotype Ontology (HPO) annotations. HPO provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Terms in the HPO describe a phenotypic abnormality, such as atrial septal defect. The HPO was initially developed using information from Online Mendelian Inheritance in Man (OMIM), which is a hugely important data resource in the field of human genetics and beyond. The HPO is currently being developed using information from OMIM and the medical literature and contains approximately 10,000 terms. Over 50,000 annotations to hereditary diseases are available for download or can be browsed using the PhenExplorer. The HPO is now being developed in collaboration with members of the OBO Foundry (Open Biological and Biomedical Ontologies), and logical definitions for HPO terms are being developed using PATO and a number of other ontologies including the FMA, GO, ChEBI, and MPATH. The HPO can be used for clinical diagnostics in human genetics (Phenomizer), bioinformatics research on the relationships between human phenotypic abnormalities and cellular and biochemical networks, for mapping between human and model organism phenotypes, and for providing a standardized vocabulary for clinical databases, among many other things. There exists a webpage for every HPO-term. The HPO project encourages input from the medical and genetics community with regards to the ontology itself and to clinical annotations.

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    IMPC

Cite this (IMPC, RRID:SCR_006158)

URL: http://www.mousephenotype.org/

Resource Type: Resource, topical portal, organism supplier, production service resource, biomaterial supply resource, database, material service resource, service resource, portal, material resource, biomaterial manufacture, data or information resource

Produce knockout mice and carry out high-throughput phenotyping of each line in order to determine the function of every gene in the mouse genome. These mice will be preserved in repositories and made available to the scientific community representing a valuable resource for basic scientific research as well as generating new models for human diseases. The approaches that are being developed build on the efforts of a number of pilot programs around the world such as the EUMODIC programme and the MGP programme. The European EUMODIC consortium generated and phenotyped 500 mouse strains in a high-throughput fashion. This was completed early in 2012. From 2011/12 onwards the IMPC is continuing the task to generate knockout mice and phenotype the remainder of the 20,000 plus genes in a worldwide coordinated program. IMPC Goals: * Establish a world-wide consortium of mouse centers with capacity and expertise for large-scale primary phenotyping * Establish a world-wide consortium of mouse production centers to generate germ line transmission of targeted knockout mutations in embryonic stem cells for all known and predicted mouse genes * Test each mutant mouse line (4,000 mouse lines in the first 5 years, and ultimately up to 20,000) through a broad based primary phenotyping pipeline in all the major adult organ systems and most areas of major human disease * Through this activity and employing data annotation tools, systematically aim to discover and ascribe biological function to each gene, driving new ideas and underpinning future research into biological systems * Establish collaborative networks with specialist phenotyping consortia or laboratories, providing standardized secondary phenotyping that enriches the primary dataset, and end-user, project specific tertiary level phenotyping that adds value to the mammalian gene functional annotation and fosters hypothesis driven research * Provide a centralized data center and portal for free, unrestricted access to primary and secondary data by the scientific community, promoting sharing of data, genotype-phenotype annotation, and the development of open source data analysis tools

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Cite this (OMIA - Online Mendelian Inheritance in Animals, RRID:SCR_006436)

URL: http://omia.angis.org.au/

Resource Type: Resource, data or information resource, database

Database of genes, inherited disorders and traits in 196 animal species (other than human, mouse, and rats which have their own resources). The database contains textual information and references, as well as links to relevant records from OMIM, PubMed and Gene. It is authored by Professor Frank Nicholas of the University of Sydney, Australia, with help from many people over the years. Curators of the OMIA database can add to and update information in the database. If you would like to become a curator, contact Frank Nicholas to get a curator user name and password.

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    T3DB

Cite this (T3DB, RRID:SCR_002672)

URL: http://t3db.org/

Resource Type: Resource, data or information resource, database

Database that combines detailed toxin data with comprehensive toxin target information. The database currently houses 3,053 toxins described by 32,276 synonyms, including pollutants, pesticides, drugs, and food toxins, which are linked to 1,670 corresponding toxin target records. Altogether there are 37,084 toxin, toxin target associations. (March 2014) Each toxin record (ToxCard) contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information. This information has been extracted from over 5,454 sources sources, which include other databases, government documents, books, and scientific literature. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases. It is also fully searchable and supports extensive text, sequence, chemical structure, and relational query searches

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