Databases (free)

With the rapid increase of biological data, it has become even more important to organize and structure the data in a way so that information can easily be retrieved. As a result, the number of databases has also increased rapidly over the past few years. Most of these databases have a web interface and can be accessed from everywhere in the world, which is an enormously important service for the scientific community.

Short description

General-purpose data resources and Model collections
PubMed comprises more than 26 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.
In BioNumbers we aim to enable you to find in one minute any useful molecular biology number that can be important for your research.
Pathguide contains information about 547 biological pathway related resources and molecular interaction related resources.
BioModels Database is a repository of computational models of biological processes. Models described from literature are manually curated and enriched with cross-references.

Nucleotide Sequence Databases
National Center for Biotechnology Information (NCBI) advances science and health by providing access to biomedical and genomic information.
GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI.

Protein Databases
The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
Protein Data Bank
URL A Structural View of Biology. This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease.

Pathway Databases
URL KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
BioCyc is a collection of 7615 Pathway/Genome Databases (PGDBs), plus software tools for understanding their data.
MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2453 pathways from 2788 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.
URL Reactome is a free, open-source, curated and peer reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education.

Enzyme Reaction Kinetics Databases
URL Comprehensive enzyme information system
URL SABIO-RK is a curated database that contains information about biochemical reactions, their kinetic rate equations with parameters and experimental conditions.

Transcription Factor Databases
URL The high-quality transcription factor binding profile database
URL In order to understand gene regulation, accurate and comprehensive knowledge of transcriptional regulatory elements is essential. Transcriptional Regulatory Element Database (TRED) has been built in response to increasing needs of an integrated repository for both cis- and trans- regulatory elements in mammals, and the lack of such resources at present.
Transc Factor Encyclopedia
URL The long-term goal of TFe is to create an online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes, combining a mixture of both expert-curated and automatically-populated content to provide users with a wide set of information relevant to a transcription factor protein of their interest.

Microarray and Sequencing Databases
Gene Expression Omnibus (GEO). GEO is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles.
Array Express
URL ArrayExpress Archive of Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data for reuse to the research community.

Compound and Drug Databases
URL Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
Guide to Pharmacology
URL An expert-driven guide to pharmacological targets and the substances that act on them.

Last version

September 2016