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Found 19 result(s)

Peptidome

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Peptidome was a public repository that archived tandem mass spectrometry peptide and protein identification data generated by the scientific community. This repository is now offline and is in archival mode. All data may be obtained from the Peptidome FTP site. Due to budgetary constraints NCBI has discontinued the Peptidome Repository. All existing data and metadata files will continue to be made available from our ftp server a ftp://ftp.ncbi.nih.gov/pub/peptidome/ indefinitely. Those files are named according to their Peptidome accession number, allowing cited data to be identified and downloaded. All of the Peptidome studies have been made publicly available at the PRoteomics IDEntifications (PRIDE) database. A map of Peptidome to Pride accessions may be found at ftp://ftp.ncbi.nih.gov/pub/peptidome/peptidome-pride_map.txt. If you have any specific questions, please feel free to contact us at info@ncbi.nlm.nih.gov.

Cellosaurus

Cellosaurus - a knowledge resource on cell lines

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The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines, Naturally immortal cell lines (example: stem cell lines), Finite life cell lines when those are distributed and used widely, Vertebrate cell line with an emphasis on human, mouse and rat cell lines, Invertebrate (insects and ticks) cell lines. Its scope does not include: Primary cell lines (with the exception of the finite life cell lines described above), Plant cell lines. Cellosaurus was initiated to be used as a cell line controlled vocabulary in the context of the neXtProt knowledgebase, but it quickly become apparent that there was a need for a cell line knowledge resource that would serve the needs of individual researchers, cell line distributors and bioinformatic resources. This leads to an increase of the scope and depth of the content of the Cellosaurus. The Cellosaurus is a participant of the Resource Identification Initiative and contributes actively to the work of the International Cell Line Authentication Committee (ICLAC). It is a Global Core Biodata Resource, an ELIXIR Core Data Resource and an IRDiRC Recognized Resource.

OPAL

Open At La Trobe

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Open At LaTrobe (OPAL) is La Trobe University’s official repository for Open Access materials generated by academic and professional staff and HDR students. These include publications and other research outputs, theses, open data, and educational resources. OPAL enables the storage, sharing, and selective publication of files and the assignment of a persistent DOI. Users maintain control over who can see their private files and all uploads are stored in La Trobe University approved storage. Access is via La Trobe University login credentials. La Trobe produces a wide range of useful datasets including supplementary data associated with publications and stand-alone datasets and collections.

Genomic Expression Archive

GEA

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Genomic Expression Archive (GEA) is a public database of functional genomics data such as gene expression, epigenetics and genotyping SNP array. Both microarray- and sequence-based data are accepted in the MAGE-TAB format in compliance with MIAME and MINSEQE guidelines, respectively. GEA issues accession numbers, E-GEAD-n to experiment and A-GEAD-n to array design. Data exchange between GEA and EBI ArrayExpress is planned.

Mouse Genome Informatics

MGI

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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

PubChem

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Pubchem contains 3 databases. 1. PubChem BioAssay: The PubChem BioAssay Database contains bioactivity screens of chemical substances described in PubChem Substance. It provides searchable descriptions of each bioassay, including descriptions of the conditions and readouts specific to that screening procedure. 2. PubChem Compound: The PubChem Compound Database contains validated chemical depiction information provided to describe substances in PubChem Substance. Structures stored within PubChem Compounds are pre-clustered and cross-referenced by identity and similarity groups. 3. PubChem Substance. The PubChem Substance Database contains descriptions of samples, from a variety of sources, and links to biological screening results that are available in PubChem BioAssay. If the chemical contents of a sample are known, the description includes links to PubChem Compound.

Integrated Relational Enzyme database

IntEnz

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IntEnz contains the recommendation of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalyzed reactions. Users can browse by enzyme classification or use advanced search options to search enzymes by class, subclass and sub-subclass information.

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.

RCSB Protein Data Bank

RCSB PDB

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The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. These are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans. Understanding the shape of a molecule helps to understand how it works. This knowledge can be used to help deduce a structure's role in human health and disease, and in drug development. The structures in the archive range from tiny proteins and bits of DNA to complex molecular machines like the ribosome.

NCBI HomoloGene

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The HomoloGene database provides a system for the automated detection of homologs among annotated genes of genomes across multiple species. These homologs are fully documented and organized by homology group. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences.

Array Express

functional genomics data

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ArrayExpress is one of the major international repositories for high-throughput functional genomics data from both microarray and high-throughput sequencing studies, many of which are supported by peer-reviewed publications. Data sets are submitted directly to ArrayExpress and curated by a team of specialist biological curators. In the past (until 2018) datasets from the NCBI Gene Expression Omnibus database were imported on a weekly basis. Data is collected to MIAME and MINSEQE standards.

ProteomeXchange

PX

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The ProteomeXchange consortium has been set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. Current members accepting submissions are: The PRIDE PRoteomics IDEntifications database at the European Bioinformatics Institute focusing mainly on shotgun mass spectrometry proteomics data PeptideAtlas/PASSEL focusing on SRM/MRM datasets.

European Nucleotide Archive

ENA

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The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources. These include submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centres and routine and comprehensive exchange with our partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature.

NCBI dbVar

Database of genomic structural VARiation

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The dbVar is a database of genomic structural variation containing data from multiple gene studies. Users can browse data containing the number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals. ***NCBI will phase out support for non-human organism data in dbSNP and dbVar beginning on September 1, 2017 ***

Nucleic Acid Database

NDB

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The NDB is a resource for nucleic acid research and education. The NDB assembles and distributes information about the three-dimensional structures of nucleic acids through a variety of resources, including a searchable database, Atlas, and software

Protein Data Bank in Europe

PDBe

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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.

Rhea

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Rhea is a freely available and comprehensive resource of expert-curated biochemical reactions. It has been designed to provide a non-redundant set of chemical transformations for applications such as the functional annotation of enzymes, pathway inference and metabolic network reconstruction. There are three types of reaction participants (reactants and products): Small molecules, Rhea polymers, Generic compounds. All three types of reaction participants are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both mass and charge balance of the reactions. We have populated the database with the reactions found in the enzyme classification (i.e. in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalysed reactions, other biochemical reactions (including those that are often termed "spontaneous") also are included.

GenBase

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GenBase is a genetic sequence database that accepts user submissions (mRNA, genomic DNAs, ncRNA, or small genomes such as organelles, viruses, plasmids, phages from any organism) and integrates data from INSDC.

PRoteomics IDEntifications Database

PRIDE

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The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. PRIDE encourages and welcomes direct user submissions of mass spectrometry data to be published in peer-reviewed publications.