[BioC] rBiopaxParser, Reactome and namespaces

Mon May 27 20:40:26 CEST 2013

Hi Frank,

Thanks for your reply - I apologize for my delayed follow up.   

I think I can now give you a reproducible example, using Reactome's latest "Xenopus laevis" owl file -- one of the smallest files they offer.   I will mail you a gzipped version of this file off-list, just to be sure we are both have the same test data.

I am using  rBiopaxParser_1.1.1 -- full sessionInfo shown below.

library(rBiopaxParser)
frog.bp <- readBiopax("Xenopus_laevis.owl")

   # if I let the "class" arg default to NULL, I get all a data.frame with all instances, totaling 1572
dim (selectInstances(frog.bp))                                                 # 1572    6

   # subset that data.frame to get only the BiochemicalReactions
dim(subset(selectInstances(frog.bp), class=="bp:BiochemicalReaction"))         #  91 6

   # try to replicate this by using the "class" arg to selectInstances.
   # both versions fail,  with and without a namespace
dim(selectInstances(frog.bp, class="bp:BiochemicalReaction"))                  #   0 6
dim(selectInstances(frog.bp, class="BiochemicalReaction"))                     #   0 6

I won't exclude the possibility that I am doing something dumb!

 - Paul

> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] C

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

other attached packages:
[1] rBiopaxParser_1.1.1  RUnit_0.4.26         BiocInstaller_1.11.1

loaded via a namespace (and not attached):
[1] XML_3.95-0.2   compiler_3.0.0 tools_3.0.0   

On May 23, 2013, at 5:30 AM, Frank Kramer wrote:

> Dear Paul,
> 
> thank you for the report. I absolutely agree with you, the namespaces of an OWL (and XML/RDF) file are not fixed and can vary between pathway database providers. Namespace identifiers are, or at least should be, removed from instances during parsing. As you noticed I strip namespaces off the input parameters since you should not be able to find anything if you include them and to add a bit of robustness as well.
> It seems this did not work very well in your case ;-)
> 
> Unfortunately I could not reproduce your problem:
> 
> ####### CODE
> library(rBiopaxParser)
> #reactome urls changed so what used to link to biopax2 is now biopax3.
> #this is for shortness of example code, I also tried this with manually #downloading the owls
> file=downloadBiopaxData(database="reactome",model="reactome",version="biopax2")
> biopax = readBiopax(file, verbose=T)
> head(biopax$df)
> 
> ####### OUTPUT
> Found a BioPAX level 3 OWL. Parsing...
> [Info Verbose] Parsing Biopax-Model as a data.frame...
> (...)
> [Info Verbose] Finished! Created a data.frame with 1000689 rows within only 3591.365 seconds.
> > head(biopax$df)
>                class                   id property property_attr
> 1 BiochemicalReaction BiochemicalReaction1     left  rdf:resource
> 2 BiochemicalReaction BiochemicalReaction1     left  rdf:resource
> 3 BiochemicalReaction BiochemicalReaction1     left  rdf:resource
> 4 BiochemicalReaction BiochemicalReaction1    right  rdf:resource
> 5 BiochemicalReaction BiochemicalReaction1    right  rdf:resource
> 6 BiochemicalReaction BiochemicalReaction1 eCNumber  rdf:datatype
>                      property_attr_value property_value
> 1                               #Complex1
> 2                               #Complex2
> 3                              #Protein12
> 4                         #SmallMolecule1
> 5                               #Complex3
> 6 http://www.w3.org/2001/XMLSchema#string       3.1.3.48
> 
> > head(unique(biopax$df$class))
> [1] BiochemicalReaction        Complex
> [3] CellularLocationVocabulary UnificationXref
> [5] Protein                    ProteinReference
> 33 Levels: BiochemicalReaction BioSource ... UnificationXref
> 
> > head(table(biopax$df$property), n=3)
>          author cellularLocation          comment
>           65131            24758           130936
> 
> > sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8
> [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8
> [7] LC_PAPER=C                 LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] RCurl_1.95-4.1      bitops_1.0-5        rBiopaxParser_1.0.0
> 
> loaded via a namespace (and not attached):
> [1] XML_3.96-1.1
> ####### END
> 
> Can you check biopax$namespaces, to see if any namespaces were detected during parsing? These are saved in order to reuse them if you want to write out a new Biopax OWL file later on.
> 
> Can you check if you are using the current release/devel version of the rBiopaxParser?
> 
> 
> Best wishes,
> Frank
> 
> 
> University Medical Center Göttingen
> Department for Medical Statistics
> Humboldtallee 32
> 37073 Göttingen
> Germany
> 
> Phone: +49 (0) 551 39-10710
> Fax: +49 (0) 551 39-4995
> 
> http://www.ams.med.uni-goettingen.de/amsneu/kramer-en.html
> 
> Am 22.05.2013 05:08, schrieb Paul Shannon:
>> Hi Frank,
>> 
>> I am most happiliy using the rBiopaxParser package, and your vignette, in order to extract detailed (but topologically simple) interaction data from the latest Reactome "Homosapiens.owl".  Your package offers great power and convenience.
>> 
>> However, I run into difficulty with namespaces.
>> 
>> For a simple example, consider this one line from the method listIntances, found in the file R/selectBiopax.R:
>> 
>>    sel = sel & (tolower(biopax$df$class) %in% tolower(stripns(class)))
>> 
>> As parsed from Homosapiens.owl, the class column of biopax$df has values like these, always containing a namespace prefix:
>> 
>>    head(unique(biopax$df$class))
>>      "bp:BiochemicalReaction"        "bp:Protein"
>>      "bp:CellularLocationVocabulary" "bp:UnificationXref"
>>      "bp:ProteinReference"           "bp:BioSource"
>> 
>> By stripping the namespace off of "bp:Protein" (the right hand side of the %in% clause) it cannot match the biopax$df$class value, as parsed from the owl file (which preserves the "bp:").
>> 
>> I believe I see similar logic in other places, with these methods specifically encountered so far:
>> 
>>   selectInstances
>>   listPathwayComponents
>> 
>> Namespaces  are used with the "property" column as well:
>> 
>>    head(table(biopax$df$property), n=3)
>>       bp:author bp:cellularLocation          bp:comment
>>           55654               23838              123750
>> 
>> Speaking from the nickel seats, and not claiming to understand all of the implications:  perhaps these could be neatly avoided if your readBiopax method could optionally eliminate namespaces when reading in an owl file?
>> 
>> Thanks,
>> 
>>  - Paul
>> 
>> 