Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization, clinical effects of mutations as well as similarities of biological sequences and structures.
In genetics, an expressed sequence tag (EST) is a short sub-sequence of a cDNA sequence. ESTs may be used to identify gene transcripts, and were instrumental in gene discovery and in gene-sequence determination. The identification of ESTs has proceeded rapidly, with approximately 74.2 million ESTs now available in public databases. EST approaches have largely been superseded by whole genome and transcriptome sequencing and metagenome sequencing.
In academia, computational immunology is a field of science that encompasses high-throughput genomic and bioinformatics approaches to immunology. The field's main aim is to convert immunological data into computational problems, solve these problems using mathematical and computational approaches and then convert these results into immunologically meaningful interpretations.
The Pathogen-Host Interactions database (PHI-base) is a biological database that contains manually curated information on genes experimentally proven to affect the outcome of pathogen-host interactions. The database has been maintained by researchers at Rothamsted Research and external collaborators since 2005. PHI-base has been part of the UK node of ELIXIR, the European life-science infrastructure for biological information, since 2016.
Mouse Genome Informatics (MGI) is a free, online database and bioinformatics resource hosted by The Jackson Laboratory, with funding by the National Human Genome Research Institute (NHGRI), the National Cancer Institute (NCI), and the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). MGI provides access to data on the genetics, genomics and biology of the laboratory mouse to facilitate the study of human health and disease. The database integrates multiple projects, with the two largest contributions coming from the Mouse Genome Database and Mouse Gene Expression Database (GXD). As of 2018, MGI contains data curated from over 230,000 publications.
In molecular biology, snoRNA U102 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
MicrobesOnline is a publicly and freely accessible website that hosts multiple comparative genomic tools for comparing microbial species at the genomic, transcriptomic and functional levels. MicrobesOnline was developed by the Virtual Institute for Microbial Stress and Survival, which is based at the Lawrence Berkeley National Laboratory in Berkeley, California. The site was launched in 2005, with regular updates until 2011.
Gene Expression Omnibus (GEO) is a database for gene expression profiling and RNA methylation profiling managed by the National Center for Biotechnology Information (NCBI). These high-throughput screening genomics data are derived from microarray or RNA-Seq experimental data. These data need to conform to the minimum information about a microarray experiment (MIAME) format.
Computational Resources for Drug Discovery (CRDD) is one of the important silico modules of Open Source for Drug Discovery (OSDD). The CRDD web portal provides computer resources related to drug discovery on a single platform. It provides computational resources for researchers in computer-aided drug design, a discussion forum, and resources to maintain a wiki related to drug discovery, predict inhibitors, and predict the ADME-Tox property of molecules. One of the major objectives of CRDD is to promote open source software in the field of chemoinformatics and pharmacoinformatics.
COSMIC is an online database of somatically acquired mutations found in human cancer. Somatic mutations are those that occur in non-germline cells that are not inherited by children. COSMIC, an acronym of Catalogue Of Somatic Mutations In Cancer, curates data from papers in the scientific literature and large scale experimental screens from the Cancer Genome Project at the Sanger Institute. The database is freely available to academic researchers and commercially licensed to others.
This microRNA database and microRNA targets databases is a compilation of databases and web portals and servers used for microRNAs and their targets. MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (ncRNAs) that regulate gene expression by targeting messenger RNAs.
EMAGE is an online biological database of gene expression data in the developing mouse embryo. The data held in EMAGE is spatially annotated to a framework of 3D mouse embryo models produced by EMAP. These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. EMAGE is a freely available web-based resource funded by the Medical Research Council (UK) and based at the MRC Human Genetics Unit in the Institute of Genetics and Molecular Medicine, Edinburgh, UK.
The human gene Chromosome 3 open reading frame 14 is a gene of uncertain function located at 3p14.2 near fragile site FRBA3—which falls between this gene and the centromere. Its protein is expected to localize to the nucleus and bind DNA. Orthologs have been identified in all of the major animal groups, minus amphibians and insects, tracing as far back as the sea anemone; indicating an origin of over 1000 mya, highlighting its importance in the animal genome.
Experimental factor ontology, also known as EFO, is an open-access ontology of experimental variables particularly those used in molecular biology. The ontology covers variables which include aspects of disease, anatomy, cell type, cell lines, chemical compounds and assay information. EFO is developed and maintained at the EMBL-EBI as a cross-cutting resource for the purposes of curation, querying and data integration in resources such as Ensembl, ChEMBL and Expression Atlas.
The CyberCell Database (CCDB) is a freely available, web-accessible database that provides quantitative genomic, proteomic as well metabolomic data on Escherichia coli. Escherichia coli is perhaps the best-studied bacterium on the planet and has been the organism of choice for several international efforts in cell simulation. These cell simulation efforts require up-to-date web-accessible resources that provide comprehensive, non-redundant, and quantitative data on this bacterium. The intent of CCDB is to facilitate the collection, revision, coordination and storage of the key information required for in silico E. coli simulation.
The Expression Atlas is a database maintained by the European Bioinformatics Institute that provides information on gene expression patterns from RNA-Seq and Microarray studies, and protein expression from Proteomics studies. The Expression Atlas allows searches by gene, splice variant, protein attribute, disease, treatment or organism part. Individual genes or gene sets can be searched for. All datasets in Expression Atlas have its metadata manually curated and its data analysed through standardised analysis pipelines. There are two components to the Expression Atlas, the Baseline Atlas and the Differential Atlas:
Model organism databases (MODs) are biological databases, or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied model organisms. MODs allow researchers to easily find background information on large sets of genes, plan experiments efficiently, combine their data with existing knowledge, and construct novel hypotheses. They allow users to analyse results and interpret datasets, and the data they generate are increasingly used to describe less well studied species. Where possible, MODs share common approaches to collect and represent biological information. For example, all MODs use the Gene Ontology (GO) to describe functions, processes and cellular locations of specific gene products. Projects also exist to enable software sharing for curation, visualization and querying between different MODs. Organismal diversity and varying user requirements however mean that MODs are often required to customize capture, display, and provision of data.
Biocuration is the field of life sciences dedicated to organizing biomedical data, information and knowledge into structured formats, such as spreadsheets, tables and knowledge graphs. The biocuration of biomedical knowledge is made possible by the cooperative work of biocurators, software developers and bioinformaticians and is at the base of the work of biological databases.
