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

hettling j.hettling at vu.nl
Mon Aug 5 15:23:13 CEST 2013

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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