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Found 25 result(s)
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GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project.
The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-coding genes within the ENCODE regions (approx. 1% of Human genome). Given the initial success of the project, GENCODE now aims to build an “Encyclopedia of genes and genes variants” by identifying all gene features in the human and mouse genome using a combination of computational analysis, manual annotation, and experimental validation, and annotating all evidence-based gene features in the entire human genome at a high accuracy.
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Phytozome is the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute. Families of related genes representing the modern descendants of ancestral genes are constructed at key phylogenetic nodes. These families allow easy access to clade-specific orthology/paralogy relationships as well as insights into clade-specific novelties and expansions.
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BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.
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BioGRID ORCS is an open repository of CRISPR screens compiled through comprehensive curation efforts. The current index is version 1.0.3 and searches more than 49 publications and 58,161 genes to return more than 895 CRISPR screens from 3 major model organism species and 629 cell lines. All screen data are freely provided through our search index and available via download in a wide variety of standardized formats.
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Gramene is a platform for comparative genomic analysis of agriculturally important grasses, including maize, rice, sorghum, wheat and barley. Relationships between cereals are queried and displayed using controlled vocabularies (Gene, Plant, Trait, Environment, and Gramene Taxonomy) and web-based displays, including the Genes and Quantitative Trait Loci (QTL) modules.
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MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life.
MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.
MetaCyc applications include: Online encyclopedia of metabolism, Prediction of metabolic pathways in sequenced genomes, Support metabolic engineering via enzyme database, Metabolite database aids. metabolomics research.
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The mission of the GO Consortium is to develop a comprehensive, computational model of biological systems, ranging from the molecular to the organism level, across the multiplicity of species in the tree of life.
The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.
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HumanCyc provides an encyclopedic reference on human metabolic pathways. It provides a zoomable human metabolic map diagram, and it has been used to generate a steady-state quantitative model of human metabolism.
2016: Subscriptions are now required to access HumanCyc. For more information on obtaining a subscription, click here: http://www.phoenixbioinformatics.org/biocyc#product-biocyc-subscription
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DisGeNET is a discovery platform containing one of the largest publicly available collections of genes and variants associated to human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models and the scientific literature. DisGeNET data are homogeneously annotated with controlled vocabularies and community-driven ontologies. Additionally, several original metrics are provided to assist the prioritization of genotype–phenotype relationships.
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The iBeetle-Base stores gene related information for all genes of the official gene set (red box). Among others, RNA and protein sequences can be downloaded and links lead to the respective annotation in the genome browser. Further, the Drosophila orthologs are displayed including links to FlyBase. Wherever available, the phenotypic data gathered in the iBeetle screen is displayed below the gene information in separate sections for the pupal and larval screening parts (yellow box).
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Tthe Lipidomics Gateway - a free, comprehensive website for researchers interested in lipid biology, provided by the LIPID MAPS (Lipid Metabolites and Pathways Strategy) Consortium. The LIPID MAPS Lipidomics Gateway provides a rich collection of information and resources to help you stay abreast of the latest developments in this rapidly expanding field. LIPID Metabolites And Pathways Strategy (LIPID MAPS®) is a multi-institutional effort created in 2003 to identify and quantitate, using a systems biology approach and sophisticated mass spectrometers, all of the major — and many minor — lipid species in mammalian cells, as well as to quantitate the changes in these species in response to perturbation.
The ultimate goal of our research is to better understand lipid metabolism and the active role lipids play in diabetes, stroke, cancer, arthritis, Alzheimer's and other lipid-based diseases in order to facilitate development of more effective treatments.
Since our inception, we have made great strides toward defining the "lipidome" (an inventory of the thousands of individual lipid molecular species) in the mouse macrophage. We have also worked to make lipid analysis easier and more accessible for the broader scientific community and to advance a robust research infrastructure for the international research community. We share new lipidomics findings and methods, hold annual meetings open to all interested investigators, and are exploring joint efforts to extend the use of these powerful new methods to new applications
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BioModels is a repository of mathematical models of biological and biomedical systems. It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats. Our mission is to provide the systems modelling community with reproducible, high-quality, freely-accessible models published in the scientific literature.
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Established by the HLA Informatics Group of the Anthony Nolan Research Institute, IPD provides a centralized system for studying the immune system's polymorphism in genes. The IPD maintains databases concerning the sequences of human Killer-cell Immunoglobulin-like Receptors (KIR), sequences of the major histocompatibility complex in a number of species, human platelet antigens (HPA), and tumor cell lines. Each subject has related, credible news, current research and publications, and a searchable database for highly specific, research grade genetic information.
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The HUGO Gene Nomenclature Committee (HGNC) assigned unique gene symbols and names to over 35,000 human loci, of which around 19,000 are protein coding. This curated online repository of HGNC-approved gene nomenclature and associated resources includes links to genomic, proteomic and phenotypic information, as well as dedicated gene family pages.
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The BioCyc database collection of Pathway/Genome Databases (PGDBs) provides a reference on the genomes and metabolic pathways of thousands of sequenced organisms. BioCyc PGDBs are generated by software that predict the metabolic pathways of completely sequenced organisms, predict which genes code for missing enzymes in metabolic pathways, and predict operons. BioCyc also integrates information from other bioinformatics databases, such as protein feature and Gene Ontology information from UniProt. The BioCyc website provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions.
From 2016 on, access to the EcoCyc and MetaCyc databases will remain free. Subscriptions to the other 7,600 BioCyc databases will be available to institutions (e.g., libraries), and to individuals.
Access to licensed databases via: https://biocyc.org/Product-summary.shtml.
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TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but are only available to the authors, publication editors, or reviewers using a special access code.
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The Neuroscience Information Framework is a dynamic index of data, materials, and tools. Please note, we do not accept direct data deposits, but if you wish to make your data repository or database available through our search, please contact us. An initiative of the NIH Blueprint for Neuroscience Research, NIF advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment.
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EMAGE (e-Mouse Atlas of Gene Expression) is an online biological database of gene expression data in the developing mouse (Mus musculus) embryo. The data held in EMAGE is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. EMAGE is a freely available web-based resource funded by the Medical Research Council (UK) and based at the MRC Human Genetics Unit in the Institute of Genetics and Molecular Medicine, Edinburgh, UK.
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The NCI's Genomic Data Commons (GDC) provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine.
The GDC obtains validated datasets from NCI programs in which the strategies for tissue collection couples quantity with high quality.
Tools are provided to guide data submissions by researchers and institutions.
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EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.
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WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.
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This Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house all publicly available QTL and trait mapping data (i.e. trait and genome location association data; collectively called "QTL data" on this site) on livestock animal species for easily locating and making comparisons within and between species. New database tools are continuely added to align the QTL and association data to other types of genome information, such as annotated genes, RH / SNP markers, and human genome maps. Besides the QTL data from species listed below, the QTLdb is open to house QTL/association date from other animal species where feasible. Note that the JAS along with other journals, now require that new QTL/association data be entered into a QTL database as part of their publication requirements.
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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.
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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.
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KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies
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- EOSC FAIR-IMPACT
- re3data COREF
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- Cite this service: re3data.org - Registry of Research Data Repositories. https://doi.org/10.17616/R3D last accessed: 2024-04-25
