Filter
Reset all

Subjects

Content Types

Countries

AID systems

API

Data access

Data access restrictions

Database access

Database access restrictions

Database licenses

Data licenses

Data upload

Data upload restrictions

Enhanced publication

Institution responsibility type

Institution type

Keywords

Metadata standards

PID systems

Provider types

Quality management

Repository languages

Software

Syndications

Repository types

Versioning

  • * at the end of a keyword allows wildcard searches
  • " quotes can be used for searching phrases
  • + represents an AND search (default)
  • | represents an OR search
  • - represents a NOT operation
  • ( and ) implies priority
  • ~N after a word specifies the desired edit distance (fuzziness)
  • ~N after a phrase specifies the desired slop amount
  • 1 (current)
Found 17 result(s)

NCBI Datasets

Subject(s)
Content type(s)
Country
NCBI Datasets is a continually evolving platform designed to provide easy and intuitive access to NCBI’s sequence data and metadata. NCBI Datasets is part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.

Human Proteinpedia

Subject(s)
Content type(s)
Country
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.

Project Achilles

Subject(s)
Content type(s)
Country
Project Achilles is a systematic effort aimed at identifying and cataloging genetic vulnerabilities across hundreds of genomically characterized cancer cell lines. The project uses genome-wide genetic perturbation reagents (shRNAs or Cas9/sgRNAs) to silence or knock-out individual genes and identify those genes that affect cell survival. Large-scale functional screening of cancer cell lines provides a complementary approach to those studies that aim to characterize the molecular alterations (e.g. mutations, copy number alterations) of primary tumors, such as The Cancer Genome Atlas (TCGA). The overall goal of the project is to identify cancer genetic dependencies and link them to molecular characteristics in order to prioritize targets for therapeutic development and identify the patient population that might benefit from such targets. Project Achilles data is hosted on the Cancer Dependency Map Portal (DepMap) where it has been harmonized with our genomics and cellular models data. You can access the latest and all past datasets here: https://depmap.org/portal/download/all/

Bacterial and Viral Bioinformatics Resource Center

BV-BRC

Subject(s)
Content type(s)
Country
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.

GeneCards

The Human Gene Database

Subject(s)
Content type(s)
Country
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.

SWISS-MODEL Repository

SMR

Subject(s)
Content type(s)
Country
The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.

Human Protein Reference Database

HPRD

Subject(s)
Content type(s)
Country
Human Protein Reference Database (HPRD) has been established by a team of biologists, bioinformaticists and software engineers. This is a joint project between the PandeyLab at Johns Hopkins University, and Institute of Bioinformatics, Bangalore. HPRD is a definitive repository of human proteins. This database should serve as a ready reckoner for researchers in their quest for drug discovery, identification of disease markers and promote biomedical research in general. Human Proteinpedia (www.humanproteinpedia.org) is its associated data portal.

Small Molecule Pathway Database

formerly: PathBank

Subject(s)
Content type(s)
Country
The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.

AnimalGenome.ORG

BioMart AnimalGenome.ORG

Subject(s)
Content type(s)
Country
This is a animal and human genome database that uses the BioMart software.

Clinical Proteomic Tumor Analysis Consortium Data Portal

CPTAC Data Portal

Subject(s)
Content type(s)
Country
The CPTAC Data Portal is the centralized repository for the dissemination of proteomic data collected by the Proteome Characterization Centers (PCCs) for the CPTAC program. The portal also hosts analyses of the mass spectrometry data (mapping of spectra to peptide sequences and protein identification) from the PCCs and from a CPTAC-sponsored common data analysis pipeline (CDAP).

The Global Proteome Machine

GPM

Subject(s)
Content type(s)
Country
The Global Proteome Machine (GPM) is a protein identification database. This data repository allows users to post and compare results. GPM's data is provided by contributors like The Informatics Factory, University of Michigan, and Pacific Northwestern National Laboratories. The GPM searchable databases are: GPMDB, pSYT, SNAP, MRM, PEPTIDE and HOT.

1000 Genomes

Thousand Genomes

Subject(s)
Content type(s)
Country
The 1000 Genomes Project is an international collaboration to produce an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts. This resource will support genome-wide association studies and other medical research studies. The genomes of about 2500 unidentified people from about 25 populations around the world will be sequenced using next-generation sequencing technologies. The results of the study will be freely and publicly accessible to researchers worldwide. The International Genome Sample Resource (IGSR) has been established at EMBL-EBI to continue supporting data generated by the 1000 Genomes Project, supplemented with new data and new analysis.

Biomedical Informatics Research Network

BIRN

Subject(s)
Content type(s)
Country
>>>!!!<<< As stated 2017-05-16 The BIRN project was finished a few years ago. The web portal is no longer live.>>>!!!<<< BIRN is a national initiative to advance biomedical research through data sharing and online collaboration. It supports multi-site, and/or multi-institutional, teams by enabling researchers to share significant quantities of data across geographic distance and/or incompatible computing systems. BIRN offers a library of data-sharing software tools specific to biomedical research, best practice references, expert advice and other resources.

PATRIC

Pathosystems Resource Integration Center

Subject(s)
Content type(s)
Country
<<<!!!<<< This repository is no longer available. >>>!!!>>> PATRIC will go offline by mid-December2022. Here is what you need to know. As announced previously, PATRIC, the bacterial BRC, and IRD / ViPR, the viral BRCs, are being merged into the new Bacterial and Viral Bioinformatics Resource Center (BV-BRC). BV-BRC combines the data, tools, and technologies from these BRCs to provide an integrated resource for bacterial and viral genomics-based infectious disease research.

QTL Archive

Subject(s)
Content type(s)
Country
This site provides access to raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data.

Leiden Open Variation Database

LOVD

Subject(s)
Content type(s)
Country
LOVD portal provides LOVD software and access to a list of worldwide LOVD applications through Locus Specific Database list and List of Public LOVD installations. The LOVD installations that have indicated to be included in the global LOVD listing are included in the overall LOVD querying service, which is based on an API.

Ensembl

e!

Subject(s)
Content type(s)
Country
The Ensembl project produces genome databases for vertebrates and other eukaryotic species. Ensembl is a joint project between the European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute (WTSI) to develop a software system that produces and maintains automatic annotation on selected genomes.The Ensembl project was started in 1999, some years before the draft human genome was completed. Even at that early stage it was clear that manual annotation of 3 billion base pairs of sequence would not be able to offer researchers timely access to the latest data. The goal of Ensembl was therefore to automatically annotate the genome, integrate this annotation with other available biological data and make all this publicly available via the web. Since the website's launch in July 2000, many more genomes have been added to Ensembl and the range of available data has also expanded to include comparative genomics, variation and regulatory data. Ensembl is a joint project between European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL), and the Wellcome Trust Sanger Institute (WTSI). Both institutes are located on the Wellcome Trust Genome Campus in Hinxton, south of the city of Cambridge, United Kingdom.