Tag: data integration and warehousing

Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. This resource uses the IntAct database framework to help reduce the effort of scientists and improve on IT development. MINT ...

The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).

DisGeNET is a discovery platform containing one of the largest collections available of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models, and the scientific liter ...

The Genome-Wide Association Studies (GWAS) Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, ...

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts publish ...

Genome Aggregation Database (gnomAD) - browser that aggregates exome and whole-genome sequencing data from a wide variety of large-scale sequencing projects. It enables search of genetic variation information by gene, variant or region.

GeneCards is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes.

The Human Gene Mutation Database (HGMD) - comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. It is a flexible resource that can be adapted to a broad range of applications i ...

InterMine was formed in 2002 at the University of Cambridge, originally as a Drosophila-dedicated resource, before expanding to become organism-agnostic, enabling a large range of organisations around the world to create their own InterMines. There a ...

The Chemical Effects in Biological Systems (CEBS) database houses data of interest to environmental health scientists. CEBS is a public resource, and has received depositions of data from academic, industrial, and governmental laboratories.

PubMed® comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

EpiFactors is a web-accessible database that provides broad information about human proteins and complexes involved in epigenetic regulation. It also lists corresponding genes and their expression levels in several samples, in particular 458 human pr ...

The DGVa team accepts direct submissions from researchers and also curates data from the published literature. As part of a regular exchange, DGVa data is sent to its partner archive, dbVar (hosted by the National Center for Biotechnology Information ...

NCBI information retrieval system, including GenBank, MMDB (structures), genomes, population sets, OMIM, taxonomy and PubMed.

The MAR databases is a collection of manually curated marine microbial contextual and sequence databases, based at the Marine Metagenomics Portal. This was developed as a part of the ELIXIR EXCELERATE project in 2017 and is maintained by The Center f ...

Repository for clinicians and scientists working in the rare disorder community. It enables secure sharing of case records by clinicians and rare disease scientists and helps the user to find additional cases of the same unnamed disorder. The reposit ...

Semantic web application network that combines a set of algorithms to streamline the creation of new semantic web-based knowledge management systems. In a single package, it provides the tools to create new applications, including advanced integratio ...

Information retrieval tool for accessing and integrating genetic and medical information for health applications. Resorting to this integrated environment, clinicians are able to access and relate diseases data already available in the Internet, scat ...

The International Protein Index (IPI) provides a top level guide to the main databases that describe the human, mouse and rat proteomes. IPI is built from the protein sequence data taken from the UniProt Knowledgebase, Ensembl and RefSeq databases, w ...

A repository of protein interaction data from mass spectrometry experiments.

An open source database(s) for genetics, genomics and functional research in rice species

CompoundDB4j is an Integrated Drug Resource of Heterogeneous Chemical Databases.

CovidMine is an InterMine dedicated to COVID-19 / SARS-CoV-2 data which integrates confirmed Covid-19 cases, deaths, Sars-CoV-2 reference genome and nucleotide sequences from isolates deposited in Genbank

CRITTERBASE, a publicly accessible data warehouse and interactive portal that currently hosts quality-controlled and taxonomically standardized presence/absence, abundance, and biomass data for 18,644 samples and 3,664 benthic taxa (2,824 of which at ...

Biomedical Research Software as a Service that enables biomedical & translational researchers to securely manage and combine datasets, typically for patient cohorts. A suite of cloud enabled & integrated open source applications can be accessed in a ...

Web based application designed to integrate protein structure, protein sequence and protein annotations in a unique graphical environment. The current version of the application offers a unified, enriched and interactive view of EMDB volumes, PDB str ...

Diagnostic Variant Database (DVD) is a nation-wide human genomic variant database launched by Dutch University Medical Centers. Its purpose is to share all genetic variants detected in the course of next-generation sequencing (NGS) applications betwe ...