queryPSICQUIC: Use PSICQUIC to query for molecular interactions (using MIQL,...

In vitkl/MItools: Protein interaction data tools: retrieving data from IntAct and most other databases using PSICQUIC service

Description

query_PSICQUIC function queries a specified molecular interaction database using MIQL query language, retrieves the data in a specified format and saves it to a file

Usage

queryPSICQUIC(query, format, database, file)

Arguments

query	search query in MIQL query language, as you would type in PSICQUIC View client: http://www.ebi.ac.uk/Tools/webservices/psicquic/view/home.xhtml
format	output format (most widely used tabular format is tab25, use tab27 for more data columns)
database	PSICQUIC service (full list: http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS), use "imex" shorthand to choose all IMEx databases
file	file name and directory to save the result ("/dir/filename")

Details

See https://psicquic.github.io/MiqlReference.html or https://psicquic.github.io/MiqlReference27.html for the description of MIQL query language.

Unlike rawQuery function from PSICQUIC package this function allows to use all IMEx databases by passing "imex" to database argument and also separates the choice of output format from the query. Output format options: https://psicquic.github.io/formats.html

This function also splits large query result into chunks (2500 interactions) to limit the load on the PSICQUIC servers.

List of data provider names accepted by the function: "imex", "APID Interactomes", "BioGrid", "bhf-ucl", "ChEMBL", "HPIDb", "InnateDB", "InnateDB-All", "IntAct", "mentha", "MPIDB", "MatrixDB", "MINT", "Reactome", "Reactome-FIs", "EBI-GOA-miRNA", "I2D", "I2D-IMEx", "InnateDB-IMEx", "MolCon", "UniProt", "MBInfo", "VirHostNet", "BAR", "EBI-GOA-nonIntAct", "ZINC"

Value

saves query result to a file, returns the query settings, how many interactions per database retrieved and which databases are inactive

Author(s)

Vitalii Kleshchevnikov

Vitalii Kleshchevnikov

Examples

queryPSICQUIC(query = "id:P74565 AND detmethod:\"MI:0018\"",
               format = "tab27",
               database = "imex",
               file = "P74565_2H_interactions_imex_tab27.tsv")

queryPSICQUIC(query = "id:P74565 AND detmethod:\"MI:0018\"",
               format = "tab25",
               database = "mentha",
               file = "P74565_2H_interactions_mentha_tab25.tsv")

queryPSICQUIC(query = "id:P74565",
               format = "tab25",
               database = "mentha",
               file = "P74565_2H_interactions_mentha_tab25.tsv")

queryPSICQUIC(query = "id:156",
               format = "tab25",
               database = "BioGrid",
               file = "entrezgene156_interactions_BioGrid_tab25.tsv")

vitkl/MItools documentation built on May 29, 2019, 2:55 p.m.