List of biological databases from Wikipedia, the free encyclopedia
BioSharing - a curated web-based searchable portal of linked information on content standards, databases, and data policies in the life sciences, broadly covering the biological, natural and biomedical sciences.
The Bioinformatics Links Directory features curated links to molecular resources, tools and databases.
Major Databases and Resources
The National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/) advances science and health by providing access to biomedical and genomic information.
PubMed (https://www.ncbi.nlm.nih.gov/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.
BioMedSearch (http://www.biomedsearch.com/) is a biomedical search engine that contains NIH/PubMed documents, a large collection of theses, dissertations, and other proprietary publications not found anywhere else for free, making it one of the most comprehensive and powerful free biomedical searches.
Gene Ontology Consortium (GO) (http://geneontology.org) project is a major bioinformatics initiative to develop a computational representation of our evolving knowledge of how genes encode biological functions at the molecular, cellular and tissue system levels. The project has developed formal ontologies that represent over 40,000 biological concepts, and are constantly being revised to reflect new discoveries. To date, these concepts have been used to "annotate" gene functions based on experiments reported in over 100,000 peer-reviewed scientific papers.
GeneCards:The Human Gene Database (http://www.genecards.org/) 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.
MalaCards: The human disease database (http://www.malacards.org/) is an integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human genes.
The European Bioinformatics Institute (http://www.ebi.ac.uk/) helps scientists realise the potential of ‘big data’ in biology by exploiting complex information to make discoveries that benefit mankind and provides freely available data and bioinformatics services to the scientific community.
Ensembl (http://useast.ensembl.org/index.html) is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
UCSC Genome Browser (http://genome.ucsc.edu/) includes a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data.
KEGG: Kyoto Encyclopedia of Genes and Genomes (http://www.genome.jp/kegg/) - 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.
Information Hyperlinked over Proteins (iHOP) (http://www.ihop-net.org/UniPub/iHOP/) A network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. IHOP provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research.
Reactome (http://www.reactome.org/) is a free, open-source, curated and peer reviewed pathway database. The 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.
ExPASy (http://www.expasy.org/) is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. On this portal you find resources from many different SIB groups as well as external institutions.
The Universal Protein Resource (UniProt) (http://www.uniprot.org/) is a comprehensive resource for protein sequence and annotation data.
The Eukaryotic Promoter Database (http://epd.vital-it.ch/) allows the access to several databases of experimentally validated promoters: EPD and EPDnew databases.
STRING (http://string-db.org/) is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations.
Human Ageing Genomic Resources (HAGR) (http://genomics.senescence.info/) - a collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses.
Gene Aging Nexus (GAN) (http://gan.usc.edu/public/index.jsp) - a data mining platform for the biogerontological-geriatric research community. It enables users to analyze, query, and visualize the aging-related genomic data.
The Human Mortality Database (HMD) (http://www.mortality.org/) provides detailed mortality and population data to researchers, students, journalists, policy analysts, and others interested in the history of human longevity.