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 14 result(s)

IsoArcH

Subject(s)
Content type(s)
Country
IsoArcH is an open access isotope web-database for bioarchaeological samples from prehistoric and historical periods all over the world. With 40,000+ isotope related data obtained on 13,000+ specimens (i.e., humans, animals, plants and organic residues) coming from 500+ archaeological sites, IsoArcH is now one of the world's largest repositories for isotopic data and metadata deriving from archaeological contexts. IsoArcH allows to initiate big data initiatives but also highlights research lacks in certain regions or time periods. Among others, it supports the creation of sound baselines, the undertaking of multi-scale analysis, and the realization of extensive studies and syntheses on various research issues such as paleodiet, food production, resource management, migrations, paleoclimate and paleoenvironmental changes.

Human Genetic Variation Repository

HGVD

Subject(s)
Content type(s)
Country
The Human Genetic Variation Database (HGVD) aims to provide a central resource to archive and display Japanese genetic variation and association between the variation and transcription level of genes. The database currently contains genetic variations determined by exome sequencing of 1,208 individuals and genotyping data of common variations obtained from a cohort of 3,248 individuals.

NetPath

Subject(s)
Content type(s)
Country
<<<!!!<<< This repository is no longer available. >>>!!!>>> NetPath is currently one of the largest open-source repository of human signaling pathways that is all set to become a community standard to meet the challenges in functional genomics and systems biology. Signaling networks are the key to deciphering many of the complex networks that govern the machinery inside the cell. Several signaling molecules play an important role in disease processes that are a direct result of their altered functioning and are now recognized as potential therapeutic targets. Understanding how to restore the proper functioning of these pathways that have become deregulated in disease, is needed for accelerating biomedical research. This resource is aimed at demystifying the biological pathways and highlights the key relationships and connections between them. Apart from this, pathways provide a way of reducing the dimensionality of high throughput data, by grouping thousands of genes, proteins and metabolites at functional level into just several hundreds of pathways for an experiment. Identifying the active pathways that differ between two conditions can have more explanatory power than just a simple list of differentially expressed genes and proteins.

AceView

AceView genes

Subject(s)
Content type(s)
Country
AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals’ transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated.

Brain-CODE

Brain-Centre for Ontario Data Exploration

Subject(s)
Content type(s)
Country
Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders.

Mammalian Transcriptomic Database

MTD

Subject(s)
Content type(s)
Country
MTD is focused on mammalian transcriptomes with a current version that contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exons, transcripts, and genes by integrating them into a genome browser. We developed a novel nomenclature for each transcript that considers its genomic position and transcriptional features.

circBase

Subject(s)
Content type(s)
Country
Thousands of circular RNAs (circRNAs) have recently been shown to be expressed in eukaryotic cells [Salzman et al. 2012, Jeck et al. 2013, Memczak et al. 2013, Salzman et al. 2013]. Here you can explore public circRNA datasets and download the custom python scripts needed to discover circRNAs in your own (ribominus) RNA-seq data.

Nuclear Receptor Signaling Atlas

NURSA Hub

Subject(s)
Content type(s)
Country
>>> !!! the repository is offline !!! <<< More information see: https://dknet.org/about/NURSA_Archive All NURSA-biocurated transcriptomic datasets have been preserved for data mining in SPP through an enhanced and expanded version of Transcriptomine named Ominer. To access these datasets, dkNET provides users with the information of 527 transcriptomic datasets that contain data related to nuclear receptors and nuclear receptor coregulators in the NURSA Datasets table view and redirects users to the current SPP dataset page. Once users find the specific dataset of research interest, users can download the dataset by clicking DOI and then clicking the Download Dataset button at the Signaling Pathways Project webpage. See https://www.re3data.org/repository/r3d100013650

Canadian Open Neuroscience Platform Portal

CONP

Subject(s)
Content type(s)
Country
The CONP portal is a web interface for the Canadian Open Neuroscience Platform (CONP) to facilitate open science in the neuroscience community. CONP simplifies global researcher access and sharing of datasets and tools. The portal internalizes the cycle of a typical research project: starting with data acquisition, followed by processing using already existing/published tools, and ultimately publication of the obtained results including a link to the original dataset. From more information on CONP, please visit https://conp.ca

The Human Protein Atlas

HPA

Subject(s)
Content type(s)
Country
The Swedish Human Protein Atlas project has been set up to allow for a systematic exploration of the human proteome using Antibody-Based Proteomics. This is accomplished by combining high-throughput generation of affinity-purified antibodies with protein profiling in a multitude of tissues and cells assembled in tissue microarrays. Confocal microscopy analysis using human cell lines is performed for more detailed protein localization. The program hosts the Human Protein Atlas portal with expression profiles of human proteins in tissues and cells. The main objective of the resource centre is to produce specific antibodies to human target proteins using a high-throughput production method involving the cloning and protein expression of Protein Epitope Signature Tags (PrESTs). After purification, the antibodies are used to study expression profiles in cells and tissues and for functional analysis of the corresponding proteins in a wide range of platforms.

IMGT/HLA Database

IPD-IMGT/HLA

Subject(s)
Content type(s)
Country
The IPD-IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (MHC) and includes the official sequences named by the WHO Nomenclature Committee For Factors of the HLA System. The IPD-IMGT/HLA Database is part of the international ImMunoGeneTics project (IMGT). The database uses the 2010 naming convention for HLA alleles in all tools herein. To aid in the adoption of the new nomenclature, all search tools can be used with both the current and pre-2010 allele designations. The pre-2010 nomenclature designations are only used where older reports or outputs have been made available for download.

NCBI dbVar

Database of genomic structural VARiation

Subject(s)
Content type(s)
Country
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 ***

IMGT/GENE-DB

ImMunoGeneTics / Gene-DB

Subject(s)
Content type(s)
Country
IMGT/GENE-DB is the IMGT genome database for IG and TR genes from human, mouse and other vertebrates. IMGT/GENE-DB provides a full characterization of the genes and of their alleles: IMGT gene name and definition, chromosomal localization, number of alleles, and for each allele, the IMGT allele functionality, and the IMGT reference sequences and other sequences from the literature. IMGT/GENE-DB allele reference sequences are available in FASTA format (nucleotide and amino acid sequences with IMGT gaps according to the IMGT unique numbering, or without gaps).

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.