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Found 53 result(s)

MolTable

Molecule table

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<<<<!! The database is archived: https://web.archive.org/web/20071012173502/http://moltable.ncl.res.in/index.htm !!>>>> MolTable: An Open Access (Molecule Table) Portal for "Advanced Chemoinformatics Research, Training and Services"

KRISHI - Knowledge based Resources Information Systems Hub for Innovations in Agriculture

ICAR Research Data Repository for Knowledge Management

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KRISHI Portal is an initiative of Indian Council of Agricultural Research (ICAR) to bring its knowledge resources to all stakeholders at one place. The portal is being developed as a centralized data repository system of ICAR consisting of Technology, Data generated through Experiments/ Surveys/ Observational studies, Geo-spatial data, Publications, Learning Resources etc. For implementation of research data management electronically in ICAR Institutes and digitization of agricultural research, KRISHI (Knowledge based Resources Information Systems Hub for Innovations in Agriculture) Portal has been developed as ICAR Research Data Repository for knowledge management. Data Inventory Repository aims at creating Meta Data Inventory through information related to data availability at Institute level. The portal consists of six repositories viz. technology, publication, experimental data, observational data survey data and geo-portal. The portal can be accessed at http://krishi.icar.gov.in. During the period of 2016-17, input data on latitude and longitude of all KVKs under this Zone was submitted to the concerned authority to put them in geo-portal. One brainstorming session was organized at this institute for all scientists on its use and uploading information in portal. As per guidelines of the council, various kinds of publications pertaining to this institute were also uploaded in this portal.

HUGO Gene Nomenclature Committee

HGNC

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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.

ToxoDB

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ToxoDB is a genome database for the genus Toxoplasma, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including toxoplasmosis.

Animal QTLdb

Animal Quantitative Trait Loci

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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.

Organelle Genome Megasequencing Program

OGMP

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The Organelle Genome Megasequencing Program (OGMP) provides mitochondrial, chloroplast, and mitochondrial plasmid genome data. OGMP tools allow direct comparison of OGMP and NCBI validated records. Includes GOBASE, a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts.

UniSave

UniProtKB Sequence/Annotation Version Archive

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The UniProtKB Sequence/Annotation Version Archive (UniSave) has the mission of providing freely to the scientific community a repository containing every version of every Swiss-Prot/TrEMBL entry in the UniProt Knowledge Base (UniProtKB). This is achieved by archiving, every release, the entry versions within the current release. The primary usage of this service is to provide open access to all entry versions of all entries. In addition to viewing their content, one can also filter, download and compare versions.

FlyReactome

a curated knowledgebase of drosophila melanogaster pathways

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<<<!!!<<< This repository is no longer available. This record is out dated >>>!!!>>>- eir fields, maintained by the FlyReactome staff.

EMBL-EBI

European Molecular Biology Laboratory - European Bioinformatics Institute

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The European Bioinformatics Institute (EBI) has a long-standing mission to collect, organise and make available databases for biomolecular science. It makes available a collection of databases along with tools to search, download and analyse their content. These databases include DNA and protein sequences and structures, genome annotation, gene expression information, molecular interactions and pathways. Connected to these are linking and descriptive data resources such as protein motifs, ontologies and many others. In many of these efforts, the EBI is a European node in global data-sharing agreements involving, for example, the USA and Japan.

NCBI Protein Clusters

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The Entrez Protein Clusters database contains annotation information, publications, structures and analysis tools for related protein sequences encoded by complete genomes. The data available in the Protein Clusters Database is generated from prokaryotic genomic studies and is intended to assist researchers studying micro-organism evolution as well as other biological sciences. Available genomes include plants and viruses as well as organelles and microbial genomes.

MGnify

formerly: EBI Metagenomics

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MGnify (formerly: EBI Metagenomics) offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.

Ensembl Metazoa

e!EnsemblMetazoa

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Ensembl Metazoa is a genome-centric portal for metazoan species of scientific interest.

Human Proteinpedia

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Human Proteinpedia is a community portal for sharing and integration of human protein data. This is a joint project between Pandey at Johns Hopkins University, and Institute of Bioinformatics, Bangalore. This portal allows research laboratories around the world to contribute and maintain protein annotations. Human Protein Reference Database (HPRD) integrates data, that is deposited in Human Proteinpedia along with the existing literature curated information in the context of an individual protein. All the public data contributed to Human Proteinpedia can be queried, viewed and downloaded. Data pertaining to post-translational modifications, protein interactions, tissue expression, expression in cell lines, subcellular localization and enzyme substrate relationships may be deposited.

Cancer GenomeAtlas Data Portal

Cancer Genome Atlas Data Portal

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The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The Data Coordinating Center (DCC) is the central provider of TCGA data. The DCC standardizes data formats and validates submitted data.

Ensembl Plants

e!EnsemblPlants

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EnsemblPlants is a genome-centric portal for plant species. Ensembl Plants is developed in coordination with other plant genomics and bioinformatics groups via the EBI's role in the transPLANT consortium.

Deutsches BioBanken-Register

German Biobank Registry

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<<<!!!<<< This product is in the archive and is no longer current. >>>!!!>>> Biobanks are a key prerequisite for modern medical research. By linking samples and clinical data they make it possible to clarify the causes and the course of diseases. The German Biobank Registry pools the medically relevant biobanks in Germany. The German Biobank Registry provides an overview of the medical biobanks in Germany; increases the international visibility of German biobanks; facilitates the networking of biobanks; promotes an exchange of information and samples between research teams; supports the use of existing resources; provides information for investments in biobanks and promotes transparency and trust in research where human samples are used. Searching for samples in all biobanks is possible at the project portal (P2B2) https://p2b2.fraunhofer.de/ after registration.

bii

BioInvestigationIndex

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BioInvestigation Index database enables storing and querying functionalities of experimental biological and biomedical metadata of Leibniz Institute of Plant Biochemistry

Bacterial and Viral Bioinformatics Resource Center

BV-BRC

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The Bacterial and Viral Bioinformatics Resource Center (BV-BRC) is an information system designed to support research on bacterial and viral infectious diseases. BV-BRC combines two long-running BRCs: PATRIC, the bacterial system, and IRD/ViPR, the viral systems.

DrugBank

Open Data Drug & Drug Target Database

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The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The latest release of DrugBank (version 5.1.1, released 2018-07-03) contains 11,881 drug entries including 2,526 approved small molecule drugs, 1,184 approved biotech (protein/peptide) drugs, 129 nutraceuticals and over 5,751 experimental drugs. Additionally, 5,132 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries. Each DrugCard entry contains more than 200 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data.

GeneCards

The Human Gene Database

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GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.

ErythronDB

Erythron Database

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<<<!!!<<< The original ErythronDB site is now retired! Code for generating the web site is available here https://github.com/ErythronDB/erythrondb-docker. >>>!!!>>>

MG-RAST

Metagenomics analysis server

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The MG-RAST server is an open source system for annotation and comparative analysis of metagenomes. Users can upload raw sequence data in fasta format; the sequences will be normalized and processed and summaries automatically generated. The server provides several methods to access the different data types, including phylogenetic and metabolic reconstructions, and the ability to compare the metabolism and annotations of one or more metagenomes and genomes. In addition, the server offers a comprehensive search capability. Access to the data is password protected, and all data generated by the automated pipeline is available for download in a variety of common formats. MG-RAST has become an unofficial repository for metagenomic data, providing a means to make your data public so that it is available for download and viewing of the analysis without registration, as well as a static link that you can use in publications. It also requires that you include experimental metadata about your sample when it is made public to increase the usefulness to the community.

NCBI Genome

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<<<!!!<<< Effective May 2024, NCBI's Genome resource will no longer be available. NCBI Genome data can now be found on the NCBI Datasets taxonomy pages. https://www.re3data.org/repository/r3d100014298 >>>!!!>>> The Genome database contains annotations and analysis of eukaryotic and prokaryotic genomes, as well as tools that allow users to compare genomes and gene sequences from humans, microbes, plants, viruses and organelles. Users can browse by organism, and view genome maps and protein clusters.

EcoCyc Database

EcoCyc E. coli Database

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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.

Cancer Genomics Hub

CGHub

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>>>>!!!!<<<< The Cancer Genomics Hub mission is now completed. The Cancer Genomics Hub was established in August 2011 to provide a repository to The Cancer Genome Atlas, the childhood cancer initiative Therapeutically Applicable Research to Generate Effective Treatments and the Cancer Genome Characterization Initiative. CGHub rapidly grew to be the largest database of cancer genomes in the world, storing more than 2.5 petabytes of data and serving downloads of nearly 3 petabytes per month. As the central repository for the foundational genome files, CGHub streamlined team science efforts as data became as easy to obtain as downloading from a hard drive. The convenient access to Big Data, and the collaborations that CGHub made possible, are now essential to cancer research. That work continues at the NCI's Genomic Data Commons. All files previously stored at CGHub can be found there. The Website for the Genomic Data Commons is here: https://gdc.nci.nih.gov/ >>>>!!!!<<<< The Cancer Genomics Hub (CGHub) is a secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects. Access to CGHub Data: All researchers using CGHub must meet the access and use criteria established by the National Institutes of Health (NIH) to ensure the privacy, security, and integrity of participant data. CGHub also hosts some publicly available data, in particular data from the Cancer Cell Line Encyclopedia. All metadata is publicly available and the catalog of metadata and associated BAMs can be explored using the CGHub Data Browser.