queryPSICQUIC.Rdquery_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
queryPSICQUIC(query, format, database, file)
| 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") |
saves query result to a file, returns the query settings, how many interactions per database retrieved and which databases are inactive
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"
queryPSICQUIC(query = "id:P74565 AND detmethod:\"MI:0018\"", format = "tab27", database = "imex", file = "P74565_2H_interactions_imex_tab27.tsv")#> Warning: the condition has length > 1 and only the first element will be used#> Warning: number of items to replace is not a multiple of replacement length#> query file #> 1: id:P74565 AND detmethod:%22MI:0018%22 P74565_2H_interactions_imex_tab27.tsv #> 2: id:P74565 AND detmethod:%22MI:0018%22 P74565_2H_interactions_imex_tab27.tsv #> 3: id:P74565 AND detmethod:%22MI:0018%22 P74565_2H_interactions_imex_tab27.tsv #> 4: id:P74565 AND detmethod:%22MI:0018%22 P74565_2H_interactions_imex_tab27.tsv #> 5: id:P74565 AND detmethod:%22MI:0018%22 P74565_2H_interactions_imex_tab27.tsv #> 6: id:P74565 AND detmethod:%22MI:0018%22 P74565_2H_interactions_imex_tab27.tsv #> 7: id:P74565 AND detmethod:%22MI:0018%22 P74565_2H_interactions_imex_tab27.tsv #> 8: id:P74565 AND detmethod:%22MI:0018%22 P74565_2H_interactions_imex_tab27.tsv #> 9: id:P74565 AND detmethod:%22MI:0018%22 P74565_2H_interactions_imex_tab27.tsv #> 10: id:P74565 AND detmethod:%22MI:0018%22 P74565_2H_interactions_imex_tab27.tsv #> 11: id:P74565 AND detmethod:%22MI:0018%22 P74565_2H_interactions_imex_tab27.tsv #> format all.databases n.interactions.in.database database.not.active #> 1: tab27 IntAct 44 #> 2: tab27 MINT 0 #> 3: tab27 bhf-ucl 0 #> 4: tab27 MPIDB 0 #> 5: tab27 MatrixDB <html> #> 6: tab27 HPIDb 0 #> 7: tab27 I2D-IMEx I2D-IMEx #> 8: tab27 InnateDB-IMEx InnateDB-IMEx #> 9: tab27 MolCon MolCon #> 10: tab27 UniProt 0 #> 11: tab27 MBInfo 0queryPSICQUIC(query = "id:P74565 AND detmethod:\"MI:0018\"", format = "tab25", database = "mentha", file = "P74565_2H_interactions_mentha_tab25.tsv")#> query #> 1: id:P74565 AND detmethod:%22MI:0018%22 #> file format all.databases #> 1: P74565_2H_interactions_mentha_tab25.tsv tab25 mentha #> n.interactions.in.database database.not.active #> 1: 44queryPSICQUIC(query = "id:P74565", format = "tab25", database = "mentha", file = "P74565_2H_interactions_mentha_tab25.tsv")#> query file format all.databases #> 1: id:P74565 P74565_2H_interactions_mentha_tab25.tsv tab25 mentha #> n.interactions.in.database database.not.active #> 1: 44queryPSICQUIC(query = "id:156", format = "tab25", database = "BioGrid", file = "entrezgene156_interactions_BioGrid_tab25.tsv")#> query file format all.databases #> 1: id:156 entrezgene156_interactions_BioGrid_tab25.tsv tab25 BioGrid #> n.interactions.in.database database.not.active #> 1: 82