title: MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions.
abstract: Prokaryotic protein-protein interactions are underrepresented in currently available databases. Here, we describe a 'gold standard' dataset (MPI-LIT) focusing on microbial binary protein-protein interactions and associated experimental evidence that we have manually curated from 813 abstracts and full texts that were selected from an initial set of 36 852 abstracts. The MPI-LIT dataset comprises 1237 experimental descriptions that describe a non-redundant set of 746 interactions of which 659 (88%) are not reported in public databases. To estimate the curation quality, we compared our dataset with a union of microbial interaction data from IntAct, DIP, BIND and MINT. Among common abstracts, we achieve a sensitivity of up to 66% for interactions and 75% for experimental methods. Compared with these other datasets, MPI-LIT has the lowest fraction of interaction experiments per abstract (0.9) and the highest coverage of strains (92) and scientific articles (813). We compared methods that evaluate functional interactions among proteins (such as genomic context or co-expression) which are implemented in the STRING database. Most of these methods discriminate well between functionally relevant protein interactions (MPI-LIT) and high-throughput data.
  
  
  BACKGROUND
  http://www.jcvi.org/mpidb/interaction.php?dbsource=MPI-LIT.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: J Craig Venter Institute, Rockville, MD 20850, USA. raja@jcvi.org
authors.forename: Seesandra V
authors.initials: SV
authors.lastname: Rajagopala
authors.forename: Johannes
authors.initials: J
authors.lastname: Goll
authors.forename: N D Deve
authors.initials: ND
authors.lastname: Gowda
authors.forename: Kumar C
authors.initials: KC
authors.lastname: Sunil
authors.forename: Björn
authors.initials: B
authors.lastname: Titz
authors.forename: Arnab
authors.initials: A
authors.lastname: Mukherjee
authors.forename: Sharmila S
authors.initials: SS
authors.lastname: Mary
authors.forename: Naresh
authors.initials: N
authors.lastname: Raviswaran
authors.forename: Chetan S
authors.initials: CS
authors.lastname: Poojari
authors.forename: Srinivas
authors.initials: S
authors.lastname: Ramachandra
authors.forename: Svetlana
authors.initials: S
authors.lastname: Shtivelband
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Blazie
authors.forename: Julia
authors.initials: J
authors.lastname: Hofmann
authors.forename: Peter
authors.initials: P
authors.lastname: Uetz
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D019295:Computational Biology; D030562:Databases, Protein; D011485:Protein Binding; D025941:Protein Interaction Mapping
chemical_list: D001426:Bacterial Proteins
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