PSICQUIC-compliant services typically return verbose protein identifiers for the interactions they report. However, we often wish to know the entrez geneID or HUGO symbol of the gene associated with the interacting protein. The IDMapper class, using biomaRt, provides that mapping. The addGeneInfo method adds four columns to the data.frame it is passed: gene symbol and geneID for both interacting proteins.
PSICQUIC is an effort from the HUPO Proteomics Standard Initiative (HUPO-PSI) to standardise programmatic access to molecular interaction databases. The Bioconductor PSICQUIC package provides a traditional R interface layered on top of the PSICQUIC REST interface. Gene symbols are most commonly used in queries; interactions are returned in a data.frame, characterized by interaction type, detection method, and publication references. Confidence scores are sometimes avaialable. Queries may be constrained by many of these same attributes, i.e., interaction type, detection method, species, publication identifier, and source database.
This is the primary interface to the PSICQUIC services, in which approximately thirty interaction providers return annotated molecular (often protein-protein) interactions in response to a standard query language ("MIQL" – the molecular interaction query language). This method is thus an R interface to MIQL, with several conveniences added.
The central PSICQUIC server has only one purpose: to return a list of, and metadata about, the currently "live" PSICQUIC-compliant MI-QL websites. A list of these providers by the PSICQUIC object you create, and is returned by this method.
For exploratory situations, or by personal preference, one can bypass the interactions API (which we expect will be used by most people most of the time). The rawQuery method allows you to craft your own MIQL (molecular interaction query language) query but without needing to obtain per-provider URLs. The sixteen columns of data are returned in a data.frame without column titles.
PSICQUIC uses standard codes to identify species, detection methods, and interaction types. In the absence of easy-to-use data files which we could store with, and provide from this package, we instead offer methods which drive your web browser to pages which offer the relevant information.
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