Home page of a biological database called characterises functional links between proteins[1]
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis.[citation needed] They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics.[2] Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures.
Biological databases can be classified by the kind of data they collect (see below). Broadly, there are molecular databases (for sequences, molecules, etc.), functional databases (for physiology, enzyme activities, phenotypes, ecology etc), taxonomic databases (for species and other taxonomic ranks), images and other media, or specimens (for museum collections etc.)
Databases are important tools in assisting scientists to analyze and explain a host of biological phenomena from the structure of biomolecules and their interaction, to the whole metabolism of organisms and to understanding the evolution of species. This knowledge helps facilitate the fight against diseases, assists in the development of medications, predicting certain genetic diseases and in discovering basic relationships among species in the history of life.
Major biological databases
These tables cover a variety of notable biological databses across a wide swath of fields, specialties, data types, and use-cases. Many of these databases are collated in the ELIXIR Core Data Resource list which collects important European data resources critical to life science research.[3]
Repository of biological images, supporting the deposition and reuse of reference imaging data that underpin published research across the life sciences.
Comprehensive, quality-checked, and regularly updated datasets of aligned small and large subunit ribosomal RNA sequences for all three domains of life (Bacteria, Archaea and Eukarya)
Genomic and functional data for eukaryotic pathogens and invertebrate disease vectors
Access
Most biological databases are available through web sites that organise data such that users can browse through the data online. In addition the underlying data is usually available for download in a variety of formats. Biological data comes in many formats. These formats include text, sequence data, protein structure and links. Each of these can be found from certain sources, for example:[citation needed]
Sequence data is provided by GenBank, in terms of DNA, and UniProt, in terms of protein.
Protein structures are provided by PDB, SCOP, and CATH.
Problems and challenges
Biological knowledge is distributed among countless databases. This sometimes makes it difficult to ensure the consistency of information, e.g. when different names are used for the same species or different data formats. As a consequence, inter-operability is a constant challenge for information exchange. For instance, if a DNA sequence database stores the DNA sequence along the name of a species, a name change of that species may break the links to other databases which may use a different name. Integrative bioinformatics is one field attempting to tackle this problem by providing unified access. One solution is how biological databases cross-reference to other databases with accession numbers to link their related knowledge together (e.g. so that the accession number stays the same even if a species name changes). Redundancy is another problem, as many databases must store the same information, e.g. protein structure databases also contain the sequence of the proteins they cover, their sequence, and their bibliographic information.
Numerous databases attempt to document the diversity of life on earth. A prominent example is the Catalogue of Life, first created in 2001 by Species 2000 and the Integrated Taxonomic Information System.[47] The Catalogue of Life is a collaborative project that aims to document taxonomic categorization of all currently accepted species in the world.[48] The Catalogue of Life provides a consolidated and consistent database for researchers and policymakers to reference. The Catalogue of Life curates up-to-date datasets from other sources such as Conifer Database, ICTV MSL (for viruses), and LepIndex (for butterflies and moths). In total, the Catalogue of Life draws from 165 databases as of May 2022.[49] Operational costs of the Catalogue of Life are paid for by the Global Biodiversity Information Facility, the Illinois Natural History Survey, the Naturalis Biodiversity Center, and the Smithsonian Institution.[50]
Some biological databases also document geographical distribution of different species. Shuang Dai et al. created a new multi-source database to document spatial/geographical distribution of 1,371 bird species in China, as existing databases had been severely lacking in spatial distribution data for many species.[51] Sources for this new database included books, literature, GPS tracking, and online webpage data. The new database displayed taxonomy, distribution, species info, and data sources for each species. After completion of the bird spatial distribution database, it was discovered that 61% of known species in China were found to be distributed in regions beyond where they were previously known.[52]
Medical databases are a special case of biomedical data resource and can range from bibliographies, such as PubMed, to image databases for the development of AI based diagnostic software. For instance, one such image database was developed with the goal of aiding in the development of wound monitoring algorithms.[54] Over 188 multi-modal image sets were curated from 79 patient visits, consisting of photographs, thermal images, and 3D mesh depth maps. Wound outlines were manually drawn and added to the photo datasets.[55] The database was made publicly available in the form of a program called WoundsDB, downloadable from the Chronic Wound Database website.
Publications
Biological databases are commonly described and updated through peer-reviewed publications, which serve both as documentation and as a means of community dissemination.
A major venue for such publications is the annual Nucleic Acids Research (NAR) Database Issue, typically published in January. This special issue presents articles describing new biological databases as well as updates to existing resources, and is accompanied by the NAR online Molecular Biology Database Collection.[56]
In addition, general data-focused journals such as Scientific Data publish descriptions of datasets across a wide range of scientific disciplines, including but not limited to the life sciences.
