Biological databases

Fossilworks is a portal which provides query, download, and analysis tools to facilitate access to the Paleobiology Database, a large relational database assembled by hundreds of paleontologists from around the world.

UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects.

PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics.

The HUGO Gene Nomenclature Committee (HGNC) is a committee of the Human Genome Organisation (HUGO) that sets the standards for human gene nomenclature.

The BTO (BRENDA Tissue Ontology) represents a comprehensive structured encyclopedia.

The following is the plants sublist of the list of the codes for MeSH (Medical Subject Headings), a comprehensive controlled vocabulary for the purpose of indexing journal articles and books in the life sciences; it can also serve as a thesaurus that facilitates searching.

Plant ontology (PO) is a collection of ontologies developed by the Plant Ontology Consortium.

The appearance and content of the output can be customized in numerous ways using a variety of online options.

Polbase (DNA Polymerase Database) is an open repository of DNA polymerase information.

The UCSC Genome Browser is an on-line genome browser hosted by the University of California, Santa Cruz (UCSC).

Uberon is a comparative anatomy ontology representing a variety of structures found in animals, such as lungs, muscles, bones, feathers and fins.

The Virus Pathogen Database and Analysis Resource (ViPR) is an integrative and comprehensive publicly available database and analysis resource to search, analyze, visualize, save and share data for viral pathogens in the U.

The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships.

The Re-referenced Protein Chemical shift Database (RefDB) is a NMR spectroscopy database of carefully corrected or re-referenced chemical shifts, derived from the BioMagResBank (BMRB) (Fig. 1).

BacMap is a freely available web-accessible database containing fully annotated, fully zoomable and fully searchable chromosome maps from more than 2500 prokaryotic (archaebacterial and eubacterial) species.

CGView (Circular Genome Viewer) is a freely available downloadable Java software program, applet and API (application programming interface) for generating colorful, zoomable, hyperlinked, richly annotated images of circular genomes such as bacterial chromosomes, mitochondrial DNA and plasmids.

CollecTF is a database of transcription factor binding sites in the Bacteria domain.

The IUPHAR/BPS Guide to PHARMACOLOGY is an open-access website, acting as a portal to information on the biological targets of licensed drugs and other small molecules.

PREDITOR (PREDIction of TORsion angles) is a freely available web-server for the prediction of protein torsion angles from chemical shifts.

The Human Proteome Project (HPP) is a collaborative effort coordinated by the Human Proteome Organization.

METAGENassist is a freely available web server for comparative metagenomic analysis.

SuperPose is a freely available web server designed to perform both pairwise and multiple protein structure superpositions.

In Bioinformatics, a Gene Disease Database is a systematized collection of data, typically structured to model aspects of reality, in a way to comprehend the underlying mechanisms of complex diseases, by understanding multiple composite interactions between phenotype-genotype relationships and gene-disease mechanisms.

Volume, Area, Dihedral Angle Reporter (VADAR) is a freely available protein structure validation web server that was developed as a collaboration between Dr.

BrainMaps is an NIH-funded interactive zoomable high-resolution digital brain atlas and virtual microscope that is based on more than 20 million megapixels (60 terabytes) of scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet.

PSORTdb is a database of protein subcellular localization (SCL) for bacteria and archaea.

The Biomolecule Stretching Database contains information about the mechanostability of proteins based on their resistance to stretching.

Basic taste qualities like sour, salty, sweet, bitter and umami serve specific functions in identifying food components found in the diet of humans and animals, and are recognized by proteins in the oral cavity.

deCODE genetics, Inc.

Linear motifs are specified as patterns using regular expression rules.

The Functional Element SNPs Database (FESD) is a biological database of SNPs in Molecular biology.

GeneNetwork is a database and open source bioinformatics software resource for systems genetics.

SeaLifeBase is a global online database of information about marine life.

The Sequence Read Archive (SRA, previously known as the Short Read Archive) is a bioinformatics database that provides a public repository for DNA sequencing data, especially the "short reads" generated by High-throughput sequencing, which are typically less than 1,000 base pairs in length.

Xenbase is a Model Organism Database (MOD), providing informatics resources, as well as genomic and biological data on Xenopus frogs.

The International Mouse Phenotyping Consortium (IMPC) is an international scientific endeavour to create and characterize the phenotype of 20,000 knockout mouse strains.

NetPath hosts 20 signaling pathways including 10 pathways with a major role in the regulation of immune system and 10 pathways with relevance to regulation of cancer.

The website can be used to browse pathways and submit data to a suite of data analysis tools.

SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-accessible database storing information about biochemical reactions and their kinetic properties.

PubMed Central (PMC) is a free digital repository that archives publicly accessible full-text scholarly articles that have been published within the biomedical and life sciences journal literature.

DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a free online bioinformatics resource developed by the Laboratory of Immunopathogenesis and Bioinformatics (LIB).

It was developed by the Wodak Lab at the Hospital for Sick Children.

Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane protein structures with respect to the lipid bilayer.

MetaboLights is a data repository founded in 2012 for cross-species and cross-platform metabolomic studies that provides primary research data and meta data for metabolomic studies as well as a knowledge base for properties of individual metabolites.

MatrixDB is a biological database focused on molecular interactions between extracellular proteins and polysaccharides.

ModBase is developed in the laboratory of Andrej Sali at UCSF.

The Multi-Omics Profiling Expression Database (MOPED) is an expanding multi-omics resource that supports rapid browsing of transcriptomics and proteomics information from publicly available studies on model organisms and humans.

The ChemDB HIV, Opportunistic Infection and Tuberculosis Therapeutics Database is a publicly available tool developed by the National Institute of Allergy and Infectious Diseases to compile preclinical data on small molecules with potential therapeutic action against HIV/AIDS and related opportunistic infections.

The Small Molecule Pathway Database (SMPDB) is a comprehensive, high-quality, freely accessible, online database containing more than 600 small molecule (i.e. metabolic) pathways found in humans.

The Ciona intestinalis protein database (CIPRO) is a protein database for the tunicate species C.

The Colocalization Benchmark Source (CBS) is a free collection of downloadable images to test and validate the degree of colocalization of markers in any fluorescence microscopy studies.

dictyBase is an online bioinformatics database for the model organism Dictyostelium discoideum.

Dryad is an international disciplinary repository of data underlying scientific and medical publications.

SNPedia (pronounced "snipedia") is a wiki-based bioinformatics web site that serves as a database of single nucleotide polymorphisms (SNPs).

TopFIND is the Termini oriented protein Function Inferred Database (TopFIND) is an integrated knowledgebase focused on protein termini, their formation by proteases and functional implications.

The Toxin and Toxin-Target Database (T3DB), also known as the Toxic Exposome Database, is a freely accessible online database of common substances that are toxic to humans, along with their protein, DNA or organ targets.

Allostery is the most direct and efficient way for regulation of biological macromolecule function induced by the binding of a ligand at an allosteric site topographically distinct from the orthosteric site.

The name CATH is an acronym of the four main levels in the classification.

The COSMIC database was designed to collect and display information on somatic mutations in cancer.

ConoServer is a database of toxins that are expressed by the predatory sea snails in the family Conidae, the cone snails.

The Consensus Coding Sequence (CCDS) Project is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies.

The Conserved Domain Database (CDD) is a database of well-annotated multiple sequence alignment models and derived database search models, for ancient domains and full-length proteins.

The Database of protein conformational diversity (PCDB) is a database of diversity of protein tertiary structures within protein domains as determined by X-ray crystallography.

As of build 131 (available February 2010), dbSNP had amassed over 184 million submissions representing more than 64 million distinct variants for 55 organisms, including Homo sapiens, Mus musculus, Oryza sativa, and many other species.

DiProDB is a database designed to collect and analyse thermodynamic, structural and other dinucleotide properties.

Effective is a database of predicted bacterial secreted proteins.

The Human Metabolome Database (HMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body.

InSatDb is a database of microsatellites of sequenced insect genomes

The Integrated Microbial Genomes (IMG) system is a genome browsing and annotation platform developed by the U.