STRING 7—recent developments in the integration and prediction of protein interactions

By C. von Mering, Lars Juhl Jensen, Michael Kuhn, Samuel Chaffron, Tobias Doerks, Beate Krüger, Berend Snel, Peer Bork. Nucleic Acids Res., 2006

715 citations recorded by the source corpus.

Information on protein–protein interactions is still mostly limited to a small number of model organisms, and originates from a wide variety of experimental and computational techniques. The database and online resource STRING generalizes access to protein interaction data, by integrating known and predicted interactions from a variety of sources. The underlying infrastructure includes a consistent body of completely sequenced genomes and exhaustive orthology classifications, based on which interaction evidence is transferred between organisms. Although primarily developed for protein interaction analysis, the resource has also been successfully applied to comparative genomics, phylogenetics and network studies, which are all facilitated by programmatic access to the database backend and the availability of compact download files. As of release 7, STRING has almost doubled to 373 distinct organisms, and contains more than 1.5 million proteins for which associations have been pre-computed. Novel features include AJAX-based web-navigation, inclusion of additional resources such as BioGRID, and detailed protein domain annotation. STRING is available at

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3e0adeef1c2b9c2cd77e4cfe204bb2a2906448c2

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Citations in the corpus

SMART 6: recent updates and new developments (2008, methodology): “The data has been imported from the STRING database ( 13 ), and is synchronized with its version 8 release.”
Human Protein Reference Database—2009 update (2008, background): “Web resources that display or have made use of HPRD data include Entrez-Gene, VisANT (11) Genes2Networks (12), Cerebral (13), BioNetBuilder (14), COXPRESdb (15), STRING 7 (16) and UniHI (17).”
eggNOG: automated construction and annotation of orthologous groups of genes (2007, background): “The eggNOG assignments for 373 complete genomes [19] were mapped onto the tree of life.”
NetworKIN: a resource for exploring cellular phosphorylation networks (2007, methodology): “Second, we capture the kinase and substrate context using a probabilistic functional association network from the STRING database ( 12 ).”
STITCH: interaction networks of chemicals and proteins (2007, background): “The associations derived here are combined with protein–protein interactions stored in the STRING database (18) to form one large network.”
A Bioinformatician's Guide to Metagenomics (2008, methodology): “Alternative approaches to address the problem include making separate trees for each metagenomic gene only in the context of the reference data set, subdividing the alignment into smaller parts to produce more complete subalignments that can still contain multiple metagenome-derived genes, or insert”
ConsensusPathDB—a database for integrating human functional interaction networks (2008, methodology): “in the STRING database ( 30 ) and can be integrated into ConsensusPathDB.”
Dynamic modularity in protein interaction networks predicts breast cancer outcome (2009, background): “1b ) or a different high-confidence human PPI databas”
Data Mining Techniques for the Life Sciences (2010, methodology): “STRING STRING was first introduced in the year 2000 (50) and evolved from a Web server of predicted functional association between proteins into a comprehensive Web portal of protein–protein interactions (28, 51).”
Tn-seq; high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms (2009, methodology): “4 ) and supplemented these data with 41 additional interactions from the STRIN”
STRING 8—a global view on proteins and their functional interactions in 630 organisms (2008, background): “Here, we describe new features that have been added since our report on the previous release, STRING 7 (16).”