[Bioc-devel] read SBML file from BiGG database, unit consistency check

hettling j.hettling at vu.nl
Wed Aug 7 13:11:40 CEST 2013

I contacted the BiGG maintainers and it turns out that the units they
have in the SBML document are technically correct for the reconstruction
databases, although the validator complains. Since we don't need the
units in our package, I found a workaround by just parsing them out:

     file <- "SBML_export.xml" #file from BiGG
     string <- paste(readLines(file),collapse="\n")
     ##Parse out units to avoid validation error
     string <- gsub("units=\".+?\"", "", string)
     H.sapiens_Recon_1 <- rsbml_read(text=string) 

This works fine for importing all files.

Many thanks,


On Tue, 2013-08-06 at 11:03 -0700, Michael Lawrence wrote:
> In terms of reproducibility, if you still have the SBML files, you
> could keep an archive of those, along with their download date (or
> version of BiGG if it has one). 
> Of course, it would be a good idea to tell the BiGG people about their
> invalid SBML.
> On Mon, Aug 5, 2013 at 6:23 AM, hettling <j.hettling at vu.nl> wrote:
>         Dear all,
>         We are developing a package (BiGGR) which includes rsbml
>         objects
>         generated from SBML exports of the BiGG database. For the
>         Bioconductor
>         revisions I was asked to describe for each dataset how it was
>         made in
>         the .Rd file.
>         Datasets were made a few months ago by downloading the SBML
>         files (for
>         example the metabolic reconstruction H.Pylori) from
>         http://bigg.ucsd.edu/bigg/exportSelect.pl and then we used the
>         rsbml_read function to parse the SBML and store the
>         reconstruction as a
>         rsbml dataset.
>         This worked fine when we were creating the datasets. Now,
>         however, maybe
>         due to an update in BiGG, I get an error reading the SBML
>         files from
>         BiGG that there is an inconsistency in the units.
>         Indeed, if I check the validity of the documents at
>         http://sbml.org/validator/ and include a unit check, it gives
>         me errors
>         which are correctly identified by rsbml.
>         How can I describe how my datasets were made now? My rsbml
>         objects work
>         fine, the problem is that it would be difficult for the user
>         to
>         reproduce how the datasets were made.
>         I hope someone can help me,
>         many thanks in advance
>         Hannes Hettling
>         _______________________________________________
>         Bioc-devel at r-project.org mailing list
>         https://stat.ethz.ch/mailman/listinfo/bioc-devel

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