Hi Sara,

  Thanks for reporting the issue. Could you please send me a copy of the
file you used? I will try to reproduce the error and find the fix then.

  Best wishes,
David

2009/12/7 Sara JC Gosline <sara.gosline@mail.mcgill.ca>

> Hello again,
>
> I have recently installed and used RpsiXML to successfully parse the latest
> xml files from intact. However, when I try the same functions with the
> latest version of Biogrid (to obtain assay-specific interactions instead of
> experiment-specific), I get a graph with a single node “NA” and 1
> interaction. SessionInfo is at the end of the email.
>
> ***Parsing xml files to graph:
> I used the ‘PCA’ file since it is relatively short:
>
>>
>> g<-psimi25XML2Graph('../biogrid/psiml25/BIOGRID-SYSTEM-PCA-2.0.59.psi25.xml',BIOGRID.PSIMI25,type='interaction',verbose=T)
> 1 Entries found
> Parsing entry 1
> Parsing experiments: ...............................................
> Parsing interactors:
> 100% ========================================>
> Parsing interactions:
> 100% ========================================>
>
>>  g
>>
> [1] "psimi25Graph"
> attr(,"package")
> [1] "RpsiXML"
>
>>  nodes(g)
>>
> [1] "NA"
>
>>  edges(g)
>>
> $`NA`
> [1] "NA"
>
> ***Parsing xml file without graph:
> To determine if this is something wrong with the parsing, I redo the
> parsing without formatting to a graph object:
>
>>
>> g<-parsePsimi25Interaction('../biogrid/psiml25/BIOGRID-SYSTEM-PCA-2.0.59.psi25.xml',BIOGRID.PSIMI25,verbose=T)
>
> Here is the first bit of output:
>
>>  g
>>
> ==================================
> interaction entry ( 2009-11-25 ):
> ==================================
> [ organism ]: Arabidopsis thaliana Saccharomyces cerevisiae
> Schizosaccharomyces pombe
> [ taxonomy ID ]: 3702 4932 4896
> [ interactors ]: there are 1214 interactors in total, here are the first
> few ones:
> sourceDb sourceId shortLabel uniprotId organismName taxId
> <NA> "" "1" "BZR1" NA "Arabidopsis thaliana" "3702"
> <NA> "" "2" "GRF6" NA "Arabidopsis thaliana" "3702"
> <NA> "" "3" "FUN14" NA "Saccharomyces cerevisiae" "4932"
> <NA> "" "4" "UIP4" NA "Saccharomyces cerevisiae" "4932"
> <NA> "" "5" "ALO1" NA "Saccharomyces cerevisiae" "4932"
> <NA> "" "6" "SPO7" NA "Saccharomyces cerevisiae" "4932"
> ...
> [ interactions ]: there are 2736 interactions in total, here are the first
> few ones:
> [[1]]
> interaction ( NA ):
> ---------------------------------
> [ source database ]:
> [ source experiment ID ]: 1
> [ interaction type ]: protein complementation assay
> [ experiment ]: pubmed 17681130
> [ participant ]: NA NA
> [ bait ]: 1
> [ bait UniProt ]: NA
> [ prey ]: 2
> [ prey UniProt ]: NA
>
> So the interactors and interactions are being parsed correctly, but not
> being retrieved properly. When I look at the attributes of each interaction
> I get mostly NA’s:
> attributes(g@interactions[[1]])
> $sourceDb
> [1] ""
>
> $sourceId
> [1] NA
>
> $interactionType
> [1] "protein complementation assay"
>
> $expPubMed
> [1] "17681130"
>
> $expSourceId
> [1] "1"
>
> $confidenceValue
> [1] NA
>
> $participant
> <NA> <NA>
> NA NA
>
> $bait
> [1] "1"
>
> $baitUniProt
> [1] NA
>
> $prey
> [1] "2"
>
> $preyUniProt
> [1] NA
>
> $inhibitor
> [1] NA
>
> $neutralComponent
> [1] NA
>
> $class
> [1] "psimi25Interaction"
> attr(,"package")
> [1] "RpsiXML"
>
>
>
> ***Conclusion:
> Is there an easy workaround for this? Maybe where I can manually look up
> identifiers?
>
> Thanks,
> sara
>
>
> ***SessionInfo:
>
>   sessionInfo()
>>
> R version 2.8.1 (2008-12-22)
> x86_64-unknown-linux-gnu
>
> locale:
>
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid splines tools stats graphics grDevices utils
> [8] datasets methods base
>
> other attached packages:
> [1] gtools_2.5.0-1 multicore_0.1-3 ppiStats_1.8.0
> [4] RColorBrewer_1.0-2 lattice_0.17-17 ScISI_1.14.0
> [7] apComplex_2.8.0 ppiData_0.1.13 Rgraphviz_1.20.4
> [10] org.Sc.sgd.db_2.2.6 GOstats_2.8.0 Category_2.8.4
> [13] genefilter_1.22.0 survival_2.34-1 GO.db_2.2.5
> [16] RSQLite_0.7-1 DBI_0.2-4 RpsiXML_1.0.0
> [19] RBGL_1.20.0 hypergraph_1.14.0 graph_1.20.0
> [22] XML_2.3-0 annotate_1.20.1 xtable_1.5-6
> [25] AnnotationDbi_1.4.3 Biobase_2.2.2
>
> loaded via a namespace (and not attached):
> [1] cluster_1.11.11 GSEABase_1.4.0
>
> _______________________________________________
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>



-- 
Jitao David Zhang
Biological Statistics and Computational Biology Ph.D.
Division of Molecular Genome Analysis
DKFZ, Heidelberg D-69120, Germany

http://www.NextBioMotif.com/

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