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. Originally, metadata was only a common term referring simply to data about data such as tags, keywords, and markup headers.
ConsensusPathDB: a molecular functional interaction database, integrating information from 12 others
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.[6][7]
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:[8] 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[9]): 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[10]): 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.
Several publicly available data repositories and resources have been developed to support and manage protein related information, biological knowledge discovery and data-driven hypothesis generation.[15] The databases in the table below are selected from the databases listed in the Nucleic Acids Research (NAR) databases issues and database collection and the databases cross-referenced in the UniProtKB. Most of these databases are cross-referenced with UniProt / UniProtKB so that identifiers can be mapped to each other.[15]
Proteins in human:
There are about ~20,000 protein coding genes in the standard human genome. (Roughly ~1200 already have Wikipedia articles - the Gene Wiki - about them) if we are Including splice variants, there could be as many as 500,000 unique human proteins[16]
The human Proteinpedia is based on HPRD (Human protein reference database)which is a repository hosting over 30,000 human proteins. However it is unclear how many of these are unique proteins
Swiss-Prot has collected over 81 000 variants in roughly 13,000 human protein sequence records from peer-reviewed literature. It is unclear how many unique proteins types are present in the database.
Numerous databases collect information about species and other taxonomic categories. The Catalogue of Life is a special case as it is a meta-database of about 150 specialized "global species databases" (GSDs) that have collected the names and other information on (almost) all described and thus "known" species.
BacDive: bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity, including taxonomy information
EzTaxon-e: database for the identification of prokaryotes based on 16S ribosomal RNA gene sequences
NCBI Taxonomy: a taxonomic database operated by NCBI and concentrating on all taxa for which DNA sequences are available (those sequences are stored by GenBank, another database operated by NCBI).
Image databases
Images play a critical role in biomedicine, ranging from images of anthropological specimens to zoology. However, there are relatively few databases dedicated to image collection, although some projects such as iNaturalist collect photos as a main part of their data. A special case of "images" are 3-dimensional images such as protein structures or 3D-reconstructions of anatomical structures. Image databases include, among others:[22]
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)[27] 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:[28] integrates epigenomic reference data from well-known national endeavors such as the Canadian CEEHRC,[29] European Blueprint,[30] European Genome-phenome Archive (EGA[31]), US ENCODE and NIH Roadmap, German DEEP,[32] Japanese CREST,[33] Korean KNIH, Singapore's GIS and China's EpiHK[34]
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[35]
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.
LEXAS curates descriptions of biological experiments from PMC articles.
^ abChen C, Huang H, Wu CH (2017). "Protein Bioinformatics Databases and Resources". In Wu CH, Arighi CN, Ross KE (eds.). Protein Bioinformatics. Methods in Molecular Biology. Vol. 1558. New York, NY: Springer New York. pp. 3–39. doi:10.1007/978-1-4939-6783-4_1. ISBN978-1-4939-6781-0. PMC5506686. PMID28150231.
^Iudin A, Korir PK, Salavert-Torres J, Kleywegt GJ, Patwardhan A (May 2016). "EMPIAR: a public archive for raw electron microscopy image data". Nature Methods. 13 (5): 387–388. doi:10.1038/nmeth.3806. PMID27067018. S2CID38996040.
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