The Protein Information Resource (PIR), located at Georgetown University Medical Center (GUMC), is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies.
The DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets. As both a bioinformatics and a cheminformatics resource, DrugBank combines detailed drug data with comprehensive drug target information. DrugBank uses a fair bit of content from Wikipedia. Wikipedia also often links to Drugbank.
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 32.0, was released in September 2018 and contains 17,929 families.
Amos Bairoch is a Swiss bioinformatician and Professor of Bioinformatics at the Department of Human Protein Sciences of the University of Geneva where he leads the CALIPHO group at the Swiss Institute of Bioinformatics (SIB) combining bioinformatics, curation, and experimental efforts to functionally characterize human proteins.
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.
28S ribosomal RNA is the structural ribosomal RNA (rRNA) for the large component, or large subunit (LSU) of eukaryotic cytoplasmic ribosomes, and thus one of the basic components of all eukaryotic cells. It is the eukaryotic nuclear homologue of the prokaryotic 23S and mitochondrial 16S ribosomal RNAs.
60S ribosomal protein L10-like is a protein that in humans is encoded by the RPL10L gene.
Richard Michael Durbin, FRS, born 30 December 1960, is a British computational biologist. He is currently an Associate Faculty member at the Wellcome Trust Sanger Institute and Professor of Genetics at the University of Cambridge. Previously, he was Senior Group Leader at the Wellcome Trust Sanger Institute for over 20 years and an Honorary Professor of Computational genomics at the University of Cambridge.
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.
MatrixDB is a biological database focused on molecular interactions between extracellular proteins and polysaccharides. MatrixDB takes into account the multimeric nature of the extracellular proteins. The database was initially released in 2009 and is maintained by the research group of Sylvie Ricard-Blum at UMR5246, Claude Bernard University Lyon 1.
PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank. The original version of the database was developed around 1995 by Roman Laskowski and collaborators at University College London. As of 2014, PDBsum is maintained by Laskowski and collaborators in the laboratory of Janet Thornton at the European Bioinformatics Institute (EBI).
The Human Metabolome Database (HMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body. Created by the Human Metabolome Project funded by Genome Canada. One of the first dedicated metabolomics databases, the HMDB facilitates human metabolomics research, including the identification and characterization of human metabolites using NMR spectroscopy, GC-MS spectrometry and LC/MS spectrometry. To aid in this discovery process, the HMDB contains three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. The chemical data includes 41,514 metabolite structures with detailed descriptions along with nearly 10,000 NMR, GC-MS and LC/MS spectra.
The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of sequence assembly and other metadata related to sequencing projects. The archive is composed of three main databases: the Sequence Read Archive, the Trace Archive and the EMBL Nucleotide Sequence Database. The ENA is produced and maintained by the European Bioinformatics Institute and is a member of the International Nucleotide Sequence Database Collaboration (INSDC) along with the DNA Data Bank of Japan and GenBank.
Alexander George Bateman is a computational biologist and Head of Protein Sequence Resources at the European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL) in Cambridge, UK. He has led the development of the Pfam biological database and introduced the Rfam database of RNA families. He has also been involved in the use of Wikipedia for community-based annotation of biological databases.
BacDive is a bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity.
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 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.
