title: PRIMOS: an integrated database of reassessed protein-protein interactions providing web-based access to in silico validation of experimentally derived data.
abstract: Steady improvements in proteomics present a bioinformatic challenge to retrieve, store, and process the accumulating and often redundant amount of information. In particular, a large-scale comparison and analysis of protein-protein interaction (PPI) data requires tools for data interpretation as well as validation. At this juncture, the Protein Interaction and Molecule Search (PRIMOS) platform represents a novel web portal that unifies six primary PPI databases (BIND, Biomolecular Interaction Network Database; DIP, Database of Interacting Proteins; HPRD, Human Protein Reference Database; IntAct; MINT, Molecular Interaction Database; and MIPS, Munich Information Center for Protein Sequences) into a single consistent repository, which currently includes more than 196,700 redundancy-removed PPIs. PRIMOS supports three advanced search strategies centering on disease-relevant PPIs, on inter- and intra-organismal crosstalk relations (e.g., pathogen-host interactions), and on highly connected protein nodes analysis ("hub" identification). The main novelties distinguishing PRIMOS from other secondary PPI databases are the reassessment of known PPIs, and the capacity to validate personal experimental data by our peer-reviewed, homology-based validation. This article focuses on definite PRIMOS use cases (presentation of embedded biological concepts, example applications) to demonstrate its broad functionality and practical value. PRIMOS is publicly available at http://primos.fh-hagenberg.at.
authors.affiliation: Division of Molecular Dermatology, Department of Dermatology, Paracelsus Medical University Salzburg, Salzburg, Austria.
authors.forename: Raphaela
authors.initials: R
authors.lastname: Rid
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Strasser
authors.forename: Doris
authors.initials: D
authors.lastname: Siegl
authors.forename: Christian
authors.initials: C
authors.lastname: Frech
authors.forename: Michael
authors.initials: M
authors.lastname: Kommenda
authors.forename: Thomas
authors.initials: T
authors.lastname: Kern
authors.forename: Helmut
authors.initials: H
authors.lastname: Hintner
authors.forename: Johann W
authors.initials: JW
authors.lastname: Bauer
authors.forename: Kamil
authors.initials: K
authors.lastname: Önder
mesh_terms: D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism*; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D020543:Proteome