[Bioc-devel] Problem with constrained PSICQUIC queries

[Laurent Gatto]

Dear all,

I am querying the PSICQUIC resource using the identically names
Bioconductor package. The query described in the vignette works as
expected.

> options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE)
> suppressPackageStartupMessages(library(PSICQUIC))
> psicquic <- PSICQUIC()
> tbl <- interactions(psicquic, id=c("TP53", "MYC"), species="9606")
> dim(tbl)
[1]  8 16
> tbl[, c("A", "B", "detectionMethod", "provider")]
                           A                                     B
1 entrez gene/locuslink:4609            entrez gene/locuslink:7157
2        innatedb:IDBG-26364                   innatedb:IDBG-35442
3        innatedb:IDBG-35442                   innatedb:IDBG-26364
4           uniprotkb:P01106                      uniprotkb:P04637
5           uniprotkb:P04637                      uniprotkb:P01106
6           uniprotkb:P04637                      uniprotkb:P01106
7           uniprotkb:P01106                      uniprotkb:P04637
8         refseq:NP_002458.1 entrezgene/locuslink:7157|omim:191170
                                     detectionMethod     provider
1 psi-mi:MI:0004(affinity chromatography technology)      BioGrid
2 psi-mi:MI:0004(affinity chromatography technology) InnateDB-All
3                psi-mi:MI:0030(cross-linking study) InnateDB-All
4       psi-mi:MI:0676(tandem affinity purification)       IntAct
5       psi-mi:MI:0676(tandem affinity purification)       mentha
6 psi-mi:MI:0004(affinity chromatography technology)       mentha
7       psi-mi:MI:0046(experimental knowledge based) Reactome-FIs
8                          psi-mi:MI:0030(crosslink)         BIND


My next attempt is to query only relevant detection methods

> tbl2 <- interactions(psicquic, id=c("TP53", "MYC"), species="9606",
                       detectionMethod = list("psi-mi:MI:0004", "psi-mi:MI:0676"))

This query however does never stops.

I then tried to reproduce the PSICQUIC::interactions call (by setting
quiet = FALE). From what I can see, PSICQUIC::interactions creates calls
to the individual resources behind the common PSICQUIC interface. I only
show the query for one of these, namely BioGrid, which indeed works.

$curl 'http://tyersrest.tyerslab.com:8805/psicquic/webservices/current/search/query/identifier:%28TP53%20AND%20MYC%29%20AND%20species:9606'

In clear text, this is 

  http://tyersrest.tyerslab.com:8805/psicquic/webservices/current/search/query/identifier:(TP53 AND MYC) AND species:9606

The second query

$curl 'http://tyersrest.tyerslab.com:8805/psicquic/webservices/current/search/query/identifier:%28TP53%20AND%20MYC%29%20AND%20species:9606%20AND%20detmethod:%28psi-mi:MI:0004%20OR%20psi-mi:MI:0676%29'

in clear text, this is

  http://tyersrest.tyerslab.com:8805/psicquic/webservices/current/search/query/identifier:(TP53 AND MYC) AND species:9606 AND detmethod:(psi-mi:MI:0004 OR psi-mi:MI:0676)

continuously retrieves MB of data - I eventually killed the process.

As a positive control, I performed the same queries

  'identifier:(TP53 AND MYC) AND species:9606 '
  
  'identifier:(TP53 AND MYC) AND species:9606 AND detmethod:(psi-mi:MI:0004 OR psi-mi:MI:0676)'

using the PSICQUIC online form, which worked fine.

What I will do for now is to run the search using all interaction
methods and filter the results, but I believe I should be able to
constrain the query by specifying a detection method. I hope I'm not
missing anything obvious.

Thank you very much in advance.

Best wishes,

Laurent


R Under development (unstable) (2015-12-17 r69781)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] PSICQUIC_1.9.3      plyr_1.8.3          httr_1.0.0         
[4] biomaRt_2.27.2      IRanges_2.5.22      S4Vectors_0.9.22   
[7] BiocGenerics_0.17.2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.3          XML_3.98-1.3         bitops_1.0-6        
 [4] R6_2.1.2             DBI_0.3.1            magrittr_1.5        
 [7] RSQLite_1.0.0        stringi_1.0-1        tools_3.3.0         
[10] stringr_1.0.0        Biobase_2.31.3       RCurl_1.95-4.7      
[13] compiler_3.3.0       AnnotationDbi_1.33.6