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Found 13 result(s)
MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. The projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, MouseMine Project, MouseCyc Project at MGI
The IMPC is a confederation of international mouse phenotyping projects working towards the agreed goals of the consortium: To undertake the phenotyping of 20,000 mouse mutants over a ten year period, providing the first functional annotation of a mammalian genome. Maintain and expand a world-wide consortium of institutions with capacity and expertise to produce germ line transmission of targeted knockout mutations in embryonic stem cells for 20,000 known and predicted mouse genes. Test each mutant mouse line 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; Maintain and expand collaborative “networks” with specialist phenotyping consortia or laboratories, providing standardized secondary level 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; and Provide a centralized data centre and portal for free, unrestricted access to primary and secondary data by the scientific community, promoting sharing of data, genotype-phenotype annotation, standard operating protocols, and the development of open source data analysis tools. Members of the IMPC may include research centers, funding organizations and corporations.
AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals’ transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated.
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iDog, an integrated resource for domestic dog (Canis lupus familiaris) and wild canids, provides the worldwide dog research community a variety of data services. This includes Genes, Genomes, SNPs, Breed/Disease Traits, Gene Expressions, Single Cell, Dog-Human Homolog Diseases and Literatures. In addition, iDog provides Online tools for performing genomic data visualization and analyses.
The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to: Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, Information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, Information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors, Tumor pathology reports and images, References, supporting MTB data and Links to other online resources for cancer.
The goals of the Drosophila Genome Center are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence. In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community.
Xenbase's mission is to provide the international research community with a comprehensive, integrated and easy to use web based resource that gives access the diverse and rich genomic, expression and functional data available from Xenopus research. Xenbase also provides a critical data sharing infrastructure for many other NIH-funded projects, and is a focal point for the Xenopus community. In addition to our primary goal of supporting Xenopus researchers, Xenbase enhances the availability and visibility of Xenopus data to the broader biomedical research community.
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SILVA is a comprehensive, quality-controlled web resource for up-to-date aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains alongside supplementary online services. In addition to data products, SILVA provides various online tools such as alignment and classification, phylogenetic tree calculation and viewer, probe/primer matching, and an amplicon analysis pipeline. With every full release a curated guide tree is provided that contains the latest taxonomy and nomenclature based on multiple references. SILVA is an ELIXIR Core Data Resource.
In early 2010 we updated the site to facilitate more rapid transfer of our data to the public database and focus our efforts on the core mission of providing expression pattern images to the research community. The original database https://www.fruitfly.org/index.html reproduced functions available on FlyBase, complicating our updates by the requirement to re-synchronize with FlyBase updates. Our expression reports on the new site still link to FlyBase gene reports, but we no longer reproduce FlyBase functions and therefore can update expression data on an ongoing basis instead of more infrequent major releases. All the functions relating to the expression patterns remain and we soon will add an option to search expression patterns by image similarity, in addition to annotation term searches. In a transitional phase we will leave both the old and the new sites up, but the newer data (post Release 2) will appear only on the new website. We welcome any feedback or requests for additional features. - The goals of the Drosophila Genome Center are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence. In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community.
The datacommons@psu was developed in 2005 to provide a resource for data sharing, discovery, and archiving for the Penn State research and teaching community. Access to information is vital to the research, teaching, and outreach conducted at Penn State. The datacommons@psu serves as a data discovery tool, a data archive for research data created by PSU for projects funded by agencies like the National Science Foundation, as well as a portal to data, applications, and resources throughout the university. The datacommons@psu facilitates interdisciplinary cooperation and collaboration by connecting people and resources and by: Acquiring, storing, documenting, and providing discovery tools for Penn State based research data, final reports, instruments, models and applications. Highlighting existing resources developed or housed by Penn State. Supporting access to project/program partners via collaborative map or web services. Providing metadata development citation information, Digital Object Identifiers (DOIs) and links to related publications and project websites. Members of the Penn State research community and their affiliates can easily share and house their data through the datacommons@psu. The datacommons@psu will also develop metadata for your data and provide information to support your NSF, NIH, or other agency data management plan.
PDBe is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - we work to collate, maintain and provide access to the global repository of macromolecular structure data. We develop tools, services and resources to make structure-related data more accessible to the biomedical community.
The Ensembl genome annotation system, developed jointly by the EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented by the creation of five new sites, for bacteria, protists, fungi, plants and invertebrate metazoa, enabling users to use a single collection of (interactive and programatic) interfaces for accessing and comparing genome-scale data from species of scientific interest from across the taxonomy. In each domain, we aim to bring the integrative power of Ensembl tools for comparative analysis, data mining and visualisation across genomes of scientific interest, working in collaboration with scientific communities to improve and deepen genome annotation and interpretation.
It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels.