Biological databases are stores of biological information.[1] The journal Nucleic Acids Research regularly publishes special issues on biological databases and has a list of such databases. The 2018 issue has a list of about 180 such databases and updates to previously described databases.[2]Omics Discovery Index can be used to browse and search several biological databases.
Meta databases
Meta databases are databases of databases that collect data about data to generate new data. They are capable of merging information from different sources and making it available in a new and more convenient form, or with an emphasis on a particular disease or organism.[metadatabase is a database model for metadata management, global query of independent database, and distributed data processing. The word metadatabase is an addition to the dictionary]. originally ,metadata was only common term referring simply to data about data such a tags ,keywords, and markup headers.
ConsensusPathDB: a molecular functional interaction database, integrating information from 12 other
DDBJ (Japan), GenBank (USA) and European Nucleotide Archive (Europe) are repositories for nucleotide sequence data from all organisms. All three accept nucleotide sequence submissions, and then exchange new and updated data on a daily basis to achieve optimal synchronisation between them. These three databases are primary databases, as they house original sequence data. They collaborate with Sequence Read Archive (SRA), which archives raw reads from high-throughput sequencing instruments.
1000 Genomes Project: launched in January 2008. The genomes of more than a thousand anonymous participants from a number of different ethnic groups were analyzed and made publicly available.
EggNOG Database: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. It provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation.[5][6]
These databases collect genome sequences, annotate and analyze them, and provide public access. Some add curation of experimental literature to improve computed annotations. These databases may hold many species genomes, or a single model organism genome.
ArrayExpress:[7] archive of functional genomics data; stores data from high-throughput functional genomics experiments from EMBL
Ensembl: provides automatic annotation databases for human, mouse, other vertebrate and eukaryote genomes
Ensembl Genomes: provides genome-scale data for bacteria, protists, fungi, plants and invertebrate metazoa, through a unified set of interactive and programmatic interfaces (using the Ensembl software platform)
Gene Expression Omnibus (GEO[8]): a public functional genomics data repository from the U.S. National Cancer Institute (NCI), which supports array- and sequence-based data. Tools for querying and downloading gene expression profiles are provided.
Human Protein Atlas (HPA[9]): a public database with expression profiles of human protein coding genes both on mRNA and protein level in tissues, cells, subcellular compartments, and cancer tumors.
PHI-base: pathogen-host interaction database. It links gene information to phenotypic information from microbial pathogens on their hosts. Information is manually curated from peer reviewed literature.
The Cancer Genome Atlas (TCGA): provides data from hundreds of cancer samples obtained using high-throughput techniques such as gene expression profiling, copy number variation profiling, SNP genotyping, genome-wide DNA methylation profiling, microRNA profiling, and exon sequencing of at least 1,200 genes
DiProDB: a database to collect and analyse thermodynamic, structural and other dinucleotide properties
Housekeeping and Reference Transcript Atlas (HRT Atlas)[17]web-based tool for searching cell specific candidate reference genes/transcripts suitable for qPCR experiment normalization. HRT Atlas also describes a complete list of human and mouse housekeeping genes and transcripts
Dryad: repository of data underlying scientific publications in the basic and applied biosciences
FINDbase (the Frequency of INherited Disorders database)
GigaDB: repository of large scale datasets underlying scientific publications in the biological and biomedical research
HGNC (HUGO Gene Nomenclature Committee): a resource for approved human gene nomenclature
International Human Epigenome Consortium:[18] integrates epigenomic reference data from well-known national endeavors such as the Canadian CEEHRC,[19] European Blueprint,[20] European Genome-phenome Archive (EGA[21]), US ENCODE and NIH Roadmap, German DEEP,[22] Japanese CREST,[23] Korean KNIH, Singapore's GIS and China's EpiHK[24]
TDR Targets: a chemogenomics database focused on drug discovery in tropical diseases
TRANSFAC: a database about eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles
JASPAR: a database of manually curated, non-redundant transcription factor binding profiles.
MetOSite: a database about methionine sulfoxidation sites and its functional roles in proteins[25]
Healthcare Cost and Utilization Project (HCUP) is the largest collection of hospital care data in the United States. It includes hundreds of millions of inpatient, outpatient, and emergency records.
