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@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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