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 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.
The Bioinformatics Resource Centers (BRCs) are a group of five Internet-based research centers established in 2004 and funded by NIAID The BRCs were formed in response to the threats posed by emerging and re-emerging pathogens, particularly Centers for Disease Control and Prevention (CDC) Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them.
The National Microbial Pathogen Data Resource was one of the eight Bioinformatics Resource Centers funded by the National Institutes of Allergy and Infectious Diseases, NIAID a component of the National Institutes of Health (NIH), which is an agency of the United States Department of Health and Human Services. The NMPDR was funded for five years from 2004 through a grant to co-PI's Rick Stevens from the Computation Institute at the University of Chicago, and Ross Overbeek at the Fellowship for the Interpretation of Genomes.
VectorBase is one of the five Bioinformatics Resource Centers (BRC) funded by the National Institute of Allergy and Infectious Diseases (NIAID), a component of the National Institutes of Health (NIH), which is an agency of the United States Department of Health and Human Services. VectorBase is focused on invertebrate vectors of human pathogens working with the sequencing centers and the research community to curate vector genomes.
Pathogenomics is a field which uses high-throughput screening technology and bioinformatics to study encoded microbe resistance, as well as virulence factors (VFs), which enable a microorganism to infect a host and possibly cause disease. This includes studying genomes of pathogens which cannot be cultured outside of a host. In the past, researchers and medical professionals found it difficult to study and understand pathogenic traits of infectious organisms. With newer technology, pathogen genomes can be identified and sequenced in a much shorter time and at a lower cost, thus improving the ability to diagnose, treat, and even predict and prevent pathogenic infections and disease. It has also allowed researchers to better understand genome evolution events - gene loss, gain, duplication, rearrangement - and how those events impact pathogen resistance and ability to cause disease. This influx of information has created a need for bioinformatics tools and databases to analyze and make the vast amounts of data accessible to researchers, and it has raised ethical questions about the wisdom of reconstructing previously extinct and deadly pathogens in order to better understand virulence.
Pathema was one of the eight bioinformatics resource centers funded by the National Institute of Allergy and Infectious Diseases (NIAID), a component of the National Institute of Health (NIH), which is an agency of the United States Department of Health and Human Services.
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.S. National Institute of Allergy and Infectious Diseases (NIAID) Category A-C Priority Pathogen lists for biodefense research, and other viral pathogens causing emerging/reemerging infectious diseases. ViPR is one of the five Bioinformatics Resource Centers (BRC) funded by NIAID, a component of the National Institutes of Health (NIH), which is an agency of the United States Department of Health and Human Services.
The Influenza Research Database (IRD) is an integrative and comprehensive publicly available database and analysis resource to search, analyze, visualize, save and share data for influenza virus research. IRD is one of the five Bioinformatics Resource Centers (BRC) funded by the National Institute of Allergy and Infectious Diseases (NIAID), a component of the National Institutes of Health (NIH), which is an agency of the United States Department of Health and Human Services.
PhytoPath was a joint scientific project between the European Bioinformatics Institute and Rothamsted Research, running from January 2012 to May 30, 2017. The project aimed to enable the exploitation of the growing body of “-omics” data being generated for phytopathogens, their plant hosts and related model species. Gene mutant phenotypic information is directly displayed in genome browsers.
The Eukaryotic Pathgen Database, or EuPathDB, is a database of bioinformatic and experimental data related to a variety of eukaryotic pathogens. It was established in 2006 under a National Institutes of Health program to create Bioinformatics Resource Centers to facilitate research on pathogens that may pose biodefense threats. EuPathDB stores data related to its organisms of interest and provides tools for searching through and analyzing the data. It currently consists of 14 component databases, each dedicated to a certain research topic. EuPathDB includes:
Hahella gaghwensis is a marine strain of Gram-negative, aerobic, and obligately halophilic bacteria of the gammaproteobacteria. Unlike its relative, H. chejuensis, H. ganghwensis is obligately halophilic, and both have distinctly different metabolic capabilities and fatty acid content.
Multiomics, multi-omics, integrative omics, "panomics" or "pan-omics" is a biological analysis approach in which the data sets are multiple "omes", such as the genome, proteome, transcriptome, epigenome, metabolome, and microbiome ; in other words, the use of multiple omics technologies to study life in a concerted way. By combining these "omes", scientists can analyze complex biological big data to find novel associations between biological entities, pinpoint relevant biomarkers and build elaborate markers of disease and physiology. In doing so, multiomics integrates diverse omics data to find a coherently matching geno-pheno-envirotype relationship or association. The OmicTools service lists more than 99 softwares related to multiomic data analysis, as well as more than 99 databases on the topic.
BacDive is a bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity.
The Monarch Initiative is a large scale bioinformatics web resource focused on leveraging existing biomedical knowledge to connect genotypes with phenotypes in an effort to aid research that combats genetic diseases. Monarch does this by integrating multi-species genotype, phenotype, genetic variant and disease knowledge from various existing biomedical data resources into a centralized and structured database. While this integration process has been traditionally done manually by basic researchers and clinicians on a case-by-case basis, The Monarch Initiative provides an aggregated and structured collection of data and tools that make biomedical knowledge exploration more efficient and effective.
PathoPhenoDB is a biological database. The database connects pathogens to their phenotypes using multiple databases such as NCBI, Human Disease Ontology Human Phenotype Ontology, Mammalian Phenotype Ontology, PubChem, SIDER and CARD. Pathogen-disease associations were gathered mainly through the CDC and the List of Infectious Diseases page on Wikipedia. The manner by which they assigned taxonomy was semi-automatic. When mapped against NCBI Taxonomy, if the pathogen was not an exact match, it was then mapped to the parent class. PathoPhenoDB employs NPMI in order to filter pairs based on their co-occurrence statistics.
Jessica Kissinger is a Distinguished Research Professor at the Franklin College of Arts and Sciences, University of Georgia and director of the Institute of Bioinformatics. Her research focus is on the evolution, assembly and data curation of protozoan parasite genomes, particularly Cryptosporidium, Toxoplasma gondii and Plasmodium.
Zhang Zhang (章张) is a Distinguished Professor of Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS) & China National Center for Bioinformation (CNCB), and acts as Associate Director of the National Genomics Data Center (NGDC), which is part of BIG & CNCB.
