Does bqmodel have 'hasProperty' or only bqbiol?
luciansmith opened this issue · comments
I'm running into an issue when parsing annotations with libsbml, and I'm not sure if the issue is with the models, or with libsbml.
The issue is that there's a number of Biomodels with the annotation 'bqmodel:hasProperty'. Libsbml parses that as 'unknown'. It may well simply be a typo on the model creator's part, and they meant to type 'bqbiol:hasProperty'.
However, when trying to track down the actual list, all I could find was
https://www.ebi.ac.uk/rdf/documentation/biomodels/
which doesn't match libsbml's implementation: on that web page, bqmodel has three entries: 'is' 'isDerivedFrom' and 'isDescribedBy'.
In contrast, libsbml has two more entries: 'isInstanceOf', and 'hasInstance'. So presumably, the list was expanded some time after the image in that web page was created? Which means that perhaps 'hasProperty' was also added at some point after that? Is there an active list somewhere?
Update: Rahuman guesses that the annotations are being added by COPASI. @fbergmann , can you verify?
Also, the full list used to be at http://co.mbine.org/specifications/qualifiers which recently died; so hopefully there's a backup.
first, here is the backup:
https://web.archive.org/web/20211204231945/http://co.mbine.org/specifications/qualifiers
as far as COPASI is concerned, it only ever sets bqbiol qualifiers so it wasn't us. But I know that in the past the biomodels team has post processed the sbml files, to change some qualifiers that way.
So overall i'd say the issue is not with libSBML, and not with COPASI either.
Great! Thanks for tracking all this down; I really appreciate it. So, yes, the upshot is that it's the models that need to be fixed. Which I can do!