title: STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
abstract: Complete knowledge of all direct and indirect interactions between proteins in a given cell would represent an important milestone towards a comprehensive description of cellular mechanisms and functions. Although this goal is still elusive, considerable progress has been made-particularly for certain model organisms and functional systems. Currently, protein interactions and associations are annotated at various levels of detail in online resources, ranging from raw data repositories to highly formalized pathway databases. For many applications, a global view of all the available interaction data is desirable, including lower-quality data and/or computational predictions. The STRING database (http://string-db.org/) aims to provide such a global perspective for as many organisms as feasible. Known and predicted associations are scored and integrated, resulting in comprehensive protein networks covering >1100 organisms. Here, we describe the update to version 9.1 of STRING, introducing several improvements: (i) we extend the automated mining of scientific texts for interaction information, to now also include full-text articles; (ii) we entirely re-designed the algorithm for transferring interactions from one model organism to the other; and (iii) we provide users with statistical information on any functional enrichment observed in their networks.
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland.
authors.forename: Andrea
authors.initials: A
authors.lastname: Franceschini
authors.forename: Damian
authors.initials: D
authors.lastname: Szklarczyk
authors.forename: Sune
authors.initials: S
authors.lastname: Frankild
authors.forename: Michael
authors.initials: M
authors.lastname: Kuhn
authors.forename: Milan
authors.initials: M
authors.lastname: Simonovic
authors.forename: Alexander
authors.initials: A
authors.lastname: Roth
authors.forename: Jianyi
authors.initials: J
authors.lastname: Lin
authors.forename: Pablo
authors.initials: P
authors.lastname: Minguez
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.forename: Christian
authors.initials: C
authors.lastname: von Mering
authors.forename: Lars J
authors.initials: LJ
authors.lastname: Jensen
mesh_terms: D000465:Algorithms; D003627:Data Interpretation, Statistical; D057225:Data Mining; D030562:Databases, Protein; D020407:Internet; D025941:Protein Interaction Mapping; D018511:Systems Integration; D014584:User-Computer Interface