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] read SBML file from BiGG database, unit consistency check
3 messages · hettling, Michael Lawrence
1 day later
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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,
Hannes
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
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