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Found 35 result(s)

FILER: Functional genomics repository

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Harmonized, indexed, searchable large-scale human FG data collection with extensive metadata. Provides scalable, unified way to easily access massive functional genomics (FG) and annotation data collections curated from large-scale genomic studies. Direct integration (API) with custom / high-throughput genetic and genomic analysis workflows.

BioProject

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The BioProject database is a searcheable collection of complete and incomplete (in-progress) large-scale molecular projects including genome sequencing and assembly, transcriptome, metagenomic, annotation, expression and mapping projects. BioProject provides a central point to link to all data associated with a project in the NCBI molecular and literature databases.

BioSample

BioSample at the NCBI

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The BioSample database contains descriptions of biological source materials used in experimental assays.

Deep Carbon Observatory Data Portal

DCO-VIVO

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<<<!!!<<< This repository is no longer available. >>>!!!>>>The Deep Carbon Observatory (DCO) is a global community of multi-disciplinary scientists unlocking the inner secrets of Earth through investigations into life, energy, and the fundamentally unique chemistry of carbon. Deep Carbon Observatory Digital Object Registry (“DCO-VIVO”) is a centrally-managed digital object identification, object registration and metadata management service for the DCO. Digital object registration includes DCO-ID generation based on the global Handle System infrastructure and metadata collection using VIVO. Users will be able to deposit their data into the DCO Data Repository and have that data discoverable and accessible by others.

Electron Microscopy Data Bank

EMDB

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The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.

PeptideAtlas

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The PeptideAtlas validates expressed proteins to provide eukaryotic genome data. Peptide Atlas provides data to advance biological discoveries in humans. The PeptideAtlas accepts proteomic data from high-throughput processes and encourages data submission.

VectorBase

Bioinformatics Resource for Invertebrate Vectors of Human Pathogens

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VectorBase provides data on arthropod vectors of human pathogens. Sequence data, gene expression data, images, population data, and insecticide resistance data for arthropod vectors are available for download. VectorBase also offers genome browser, gene expression and microarray repository, and BLAST searches for all VectorBase genomes. VectorBase Genomes include Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus, Ixodes scapularis, Pediculus humanus, Rhodnius prolixus. VectorBase is one the Bioinformatics Resource Centers (BRC) projects which is funded by National Institute of Allergy and Infectious Diseases (NAID).

Gene Ontology

GO

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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.

The Universal Protein Resource

UniProt

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The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc).

dbSNP

SNV

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The NCBI Short Genetic Variations database, commonly known as dbSNP, catalogs short variations in nucleotide sequences from a wide range of organisms. These variations include single nucleotide variations, short nucleotide insertions and deletions, short tandem repeats and microsatellites. Short Genetic Variations may be common, thus representing true polymorphisms, or they may be rare. Some rare human entries have additional information associated withthem, including disease associations, genotype information and allele origin, as some variations are somatic rather than germline events. ***NCBI will phase out support for non-human organism data in dbSNP and dbVar beginning on September 1, 2017***

ALlele FREquency Database

ALFRED

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We are working on a new version of ALFRED web interface. The current web interface will not be available from December 15th, 2023. There will be a period where a public web interface is not available for viewing ALFRED data. Expected date for the deployment of the new ALFRED web interface with minimum functions is March 1st, 2024 --------------------------------------------- ALFRED is a free, web-accessible, curated compilation of allele frequency data on DNA sequence polymorphisms in anthropologically defined human populations. ALFRED is distinct from such databases as dbSNP, which catalogs sequence variation.

CottonGen

Cotton Database Resources

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CottonGen is a new cotton community genomics, genetics and breeding database being developed to enable basic, translational and applied research in cotton. It is being built using the open-source Tripal database infrastructure. CottonGen consolidates and expands the data from CottonDB and the Cotton Marker Database, providing enhanced tools for easy querying, visualizing and downloading research data.

Antimicrobial Peptide Database

APD

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The Antimicrobial Peptide Database (APD) was originally created by a graduate student, Zhe Wang, as his master's thesis in the laboratory of Dr. Guangshun Wang. The project was initiated in 2002 and the first version of the database was open to the public in August 2003. It contained 525 peptide entries, which can be searched in multiple ways, including APD ID, peptide name, amino acid sequence, original location, PDB ID, structure, methods for structural determination, peptide length, charge, hydrophobic content, antibacterial, antifungal, antiviral, anticancer, and hemolytic activity. Some results of this bioinformatics tool were reported in the 2004 database paper. The peptide data stored in the APD were gleaned from the literature (PubMed, PDB, Google, and Swiss-Prot) manually in over a decade.

GNPS: Global Natural Products Social Molecular Networking

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GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. GNPS aids in identification and discovery throughout the entire life cycle of data; from initial data acquisition/analysis to post publication.

Sequence Read Archive

SRA

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The Sequence Read Archive stores the raw sequencing data from such sequencing platforms as the Roche 454 GS System, the Illumina Genome Analyzer, the Applied Biosystems SOLiD System, the Helicos Heliscope, and the Complete Genomics. It archives the sequencing data associated with RNA-Seq, ChIP-Seq, Genomic and Transcriptomic assemblies, and 16S ribosomal RNA data.

PlasmoDB

Plasmodium Genomics Resource

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PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.

PiroplasmaDB

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A genome database for the genus Piroplasma. PiroplasmaDB is a member of pathogen-databases that are housed under the NIAID-funded EuPathDB Bioinformatics Resource Center (BRC) umbrella.

AmoebaDB

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AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first iteration (released in early 2010), AmoebaDB contains the genomes of three Entamoeba species (see below). AmoebaDB integrates whole genome sequence and annotation and will rapidly expand to include experimental data and environmental isolate sequences provided by community researchers . The database includes supplemental bioinformatics analyses and a web interface for data-mining.

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.

Bioconductor

Open Source Software for Bioinformatics

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Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.

Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer

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The information in the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer relates cytogenetic changes and their genomic consequences, in particular gene fusions, to tumor characteristics, based either on individual cases or associations. All the data have been manually culled from the literature by Felix Mitelman in collaboration with Bertil Johansson and Fredrik Mertens.

GeneWeaver.org

The Ontological Discovery Environment

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GeneWeaver combines cross-species data and gene entity integration, scalable hierarchical analysis of user data with a community-built and curated data archive of gene sets and gene networks, and tools for data driven comparison of user-defined biological, behavioral and disease concepts. Gene Weaver allows users to integrate gene sets across species, tissue and experimental platform. It differs from conventional gene set over-representation analysis tools in that it allows users to evaluate intersections among all combinations of a collection of gene sets, including, but not limited to annotations to controlled vocabularies. There are numerous applications of this approach. Sets can be stored, shared and compared privately, among user defined groups of investigators, and across all users.

MicrosporidiaDB

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MicrosporidiaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for the phylum Microsporidia. In its first iteration (released in early 2010), MicrosporidiaDB contains the genomes of two Encephalitozoon species (see below). MicrosporidiaDB integrates whole genome sequence and annotation and will rapidly expand to include experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining.

Immune Epitope Database

IEDB

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IEDB offers easy searching of experimental data characterizing antibody and T cell epitopes studied in humans, non-human primates, and other animal species. Epitopes involved in infectious disease, allergy, autoimmunity, and transplant are included. The IEDB also hosts tools to assist in the prediction and analysis of B cell and T cell epitopes.

DisProt

Database of Protein Disorder

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The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. DisProt is a community resource annotating protein sequences for intrinsically disorder regions from the literature. It classifies intrinsic disorder based on experimental methods and three ontologies for molecular function, transition and binding partner.