Databases

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Collection of External Databases

BioGPS

BioGPS is a gene portal built with two guiding principles in mind -- customizability and extensibility. Check out our BioGPS publication in Genome Biology!

First, although every scientist who visits a gene portal wants to view gene annotation, the specific reasons are different for every person. A geneticist may be here to find candidate genes in a genomic interval. A cell biologist may be here to view our Gene Atlas expression profiles. A molecular biologist may want to find information on protein domains. If everyone has their unique interests, gene portals should be adaptable to suit your individual needs. Therefore, BioGPS offers a customizable gene report layout, where you can control which pieces of data are displayed and how they're displayed. Select from our extensive plugin library only the sources that are relevant to you.

Second, are you tired of visiting a dozen different gene portals, each of which have 80% of the same data, for the 20% unique content? Or are you a web developer whose website doesn't quite have the visibility you think it deserves? We designed BioGPS to solve both of these problems by creating a simple plugin interface which allows anyone to add new plugins to BioGPS, completely autonomously. Our goal is to completely remove ourselves from the critical path of extending BioGPS. With other portals, you can beg and plead with the portal administrators to add new content. In BioGPS, if you see data that's missing (or have data that others would be interested in), you can do it all yourself. (Note that we're still finalizing this plugin architecture, so stay tuned!)

biogps.gnf.org/#goto=welcome

BioPortal

Use BioPortal to access and share ontologies that are actively used in biomedical communities. You can search for terms in ontologies, browse a list of ontologies in BioPortal, search biomedical resources that we automatically annotated with ontology terms. You can create ontology-based annotations for your own text , link your own project that uses ontologies to the description of those ontologies , find and create relations between terms in different ontologies, review and comment on ontologies and their components as you browse them.

bioportal.bioontology.org/

BioGRID

BioGRID is an online interaction repository with data compiled through comprehensive curation efforts. Our current index is version 3.1.69 and searches 23,755 publications for 355,947 raw protein and genetic interactions from major model organism species. All interaction data are freely provided through our search index and available via download in a wide variety of standardized formats.

thebiogrid.org/

ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

[1]www.ebi.ac.uk/chebi/init.do

Database of Interacting Proteins

The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Please, check the reference page to find articles describing the DIP database in greater detail.

This page serves also as an access point to other projects related to DIP, such as The Database of Ligand-Receptor Partners (DLRP) and JDIP.

dip.doe-mbi.ucla.edu/dip/Main.cgi

EnsEMBL

The Ensembl project aims to provide:

  • Accurate, automatic analysis of genome data.
  • Analysis and annotation maintained on the current data.
  • Presentation of the analysis to all via the web.
  • Distribution of the analysis to other bioinformatics laboratories.

Ensembl will concentrate on vertebrate genomes, but other groups have adapted the system for use with plant and fungal genomes. Please see Powered by Ensembl for a list of projects that use Ensembl technology.

www.ensembl.org

GeneCards: The human gene compendium

GeneCards is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes. Information is featured in 18 GeneCards sections as shown below.

The GeneCards human gene database extracts and integrates a carefully selected subset of gene related information from dozens of relevant sources. It provides robust user-friendly access to up-to-date knowledge. GeneCards overcomes barriers of data format heterogeneity, and uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each gene, and provides the means to obtain a deep understanding of biology and medicine.

www.genecards.org/

Human Protein Reference Database

The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data. HPRD has been created using an object oriented database in Zope, an open source web application server, that provides versatility in query functions and allows data to be displayed dynamically.

www.hprd.org/

IUPHAR DATABASE

The IUPHAR Committee on Receptor Nomenclature and Drug Classification (NC-IUPHAR) was founded in 1987, with the mission of:

  • issuing guidelines for receptor and ion channel classification, and addressing the main issues in pharmacology today,
  • classifying the major receptor and ion channel systems,
  • facilitating the interface between the discovery of new sequences from the Human Genome Project and the designation of the derived proteins as functional receptors and ion channels – also designating the receptor polymorphisms which are functionally important,
  • setting up a website with access to data on all known receptor systems, freely available to all scientists throughout the world.

www.iuphar-db.org/DATABASE/ReceptorFamiliesForward

KEGG: Kyoto Encyclopedia of Genes and Genomes

A grand challenge in the post-genomic era is a complete computer representation of the cell, the organism, the ecosystem, and the biosphere, which will enable computational prediction of higher-level complexity of cellular processes and organism behaviors from genomic and molecular information. Towards this end we have been developing a bioinformatics resource named KEGG as part of the research projects of the Kanehisa Laboratories in the Bioinformatics Center of Kyoto University and the Human Genome Center of the University of Tokyo.

www.genome.jp/kegg/

Kinase: Genomics, evolution, and function of protein kinases

kinase.com explores the functions, evolution and diversity of protein kinases, the key controllers of cell behavior. We focus on the kinome, the full complement of protein kinases in any sequenced genome. This includes our extensive KinBase database, and papers and supporting material for our published work from Sugen and the Salk Institute.

www.kinase.com

Molecular INTeraction database

The Molecular INTeraction database. MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The full MINT dataset can be freely downloaded.

mint.bio.uniroma2.it/mint/Welcome.do

MITOP - Library

The aim of this database is to provide a comprehensive list of mitochondrial proteins of yeast, mouse, Arabidopsis thaliana, neurospora and human. Datasets relevant to the study of the mitochondrial proteome are integrated and accessible via search tools and links. They include computational predictions of signalling sequences and summarize results from proteome mapping, mutant screening, expression profiling, protein-protein interaction and cellular sublocalisation studies. Predictive scores (score based on support vector machine prediction) are given and are calculated using the integration of the included datasets and annotated reference sets of mitochondrial proteins.

http://www.mitop.de:8080/mitop2/

Obesity genes database

Obesity Gene Map Database

Pathguide: the pathway resource list

Pathguide contains information about 325 biological pathway related resources and molecular interaction related resources. Click on a link to go to the resource home page or 'Details' for a description page. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated.

www.pathguide.org/

Pfam

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
There are two components to Pfam: Pfam-A and Pfam-B. Pfam-A entries are high quality, manually curated families. Although these Pfam-A entries cover a large proportion of the sequences in the underlying sequence database, in order to give a more comprehensive coverage of known proteins we also generate a supplement using the ADDA database. These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found.

Pfam also generates higher-level groupings of related families, known as clans. A clan is a collection of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM.

pfam.janelia.org/

RSCB Protein Data Base: A Resource for Studying Biological Macromolecules

The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards.

The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.

www.pdb.org/pdb/home/home.do

String

STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources: Genomic Context, High-throughput Experiments, (Conserved) Coexpression, and Previous Knowledge.
STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. The database currently covers 2,590,259 proteins from 630 organisms

string-db.org/

SysZNF: the C2H2 zinc finger gene database

SysZNF, an information resource for C2H2 Zinc Finger genes in human and mouse.

epgd.biosino.org/SysZNF/

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