STRING v10: protein-protein interaction networks, integrated over the tree of life.
Bottom Line: However, known and predicted interactions are scattered over multiple resources, and the available data exhibit notable differences in terms of quality and completeness.For this purpose, we have introduced hierarchical and self-consistent orthology annotations for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution.Further improvements in version 10.0 include a completely redesigned prediction pipeline for inferring protein-protein associations from co-expression data, an API interface for the R computing environment and improved statistical analysis for enrichment tests in user-provided networks.
Affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.Show MeSH
Related in: MedlinePlus
Mentions: Apart from directly browsing and searching the website, data access in STRING is possible also via a REST-based API (application programing interface) and via wholesale data download. With version 10.0, we have introduced a further option: direct access from the R programming environment, following the Bioconductor standard (39). The corresponding package is named STRINGdb (Figure 3), and can be downloaded from the Bioconductor repository (http://www.bioconductor.org/packages/release/bioc/html/STRINGdb.html). The package interacts with the STRING server via the REST API and via additional, dedicated web services. To optimize the speed of subsequent accesses, the entire interaction network and associated data for a given organism are downloaded from the server and cached locally in the R environment, whenever possible. The package is built around the iGraph framework (40), which handles the complexity of the network data structures and provides fast query/analysis functions. Once a network is loaded/cached into an iGraph object, high-level functions facilitate the most common user tasks, such as mapping protein names onto their corresponding STRING identifiers, retrieving the neighbors of a protein of interest, retrieving PubMed IDs for publications that support a given interaction, finding clusters of proteins in the network and generating stable links back to the STRING website.
Affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.