how to parse the annotation of the (species ,compartments) of SBML using libsbml

[cruise h]

I know i shall send this to libsbml-discuss, but i can't join it. Sorry for the inconvient i have caused.

I have use RDFanootation in the libsbml ,but it only return a libsbml-history class, and i can't  get the information i need?

Can experts like you to tell me how to parse the annotation and get the databese URL for species and compartment?

Thankyou!

[cruse hu]

more details, I use libsbml.RDFAnnotationParser_parseRDFAnnotation(a)

It returns:
<libsbml.ModelHistory proxy of <Swig Object of type 'ModelHistory_t *' at 0x0000022D7DFD79C0> >

It just returns a class of model history,  apparently, i can't read the annotation by it.

cruise h <howitwo...@gmail.com> 于2021年3月12日周五 下午7:21写道：

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[Frank Bergmann]

You have not indicated what programming language you use, so i hope it was python. LibSBML does all the work for the SBML supported MIRIAM subset for you, so an example for printing all resources for species / reactions could look like this: 

```

import libsbml


def print_terms(element):
  """prints resources and qualifier for sbase element"""
  num_terms = element.getNumCVTerms()
  for i in range(num_terms):
    term = element.getCVTerm(i)
    if term.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER:
      print('element qualifier is bq_{0}'.format(libsbml.BiolQualifierType_toString(term.getBiologicalQualifierType())))
    else:
      print('element qualifier is model_{0}'.format(libsbml.ModelQualifierType_toString(term.getBiologicalQualifierType())))
    num_resources = term.getNumResources()
    for j in range(num_resources):
      print('  {0}'.format(term.getResourceURI(j)))



doc = libsbml.readSBMLFromFile('BIOMD0000000001.xml')
model = doc.getModel()

for i in range(model.getNumSpecies()):
  species = model.getSpecies(i)
  print('annotatiosn for species {0}'.format(species.getId()))
  print_terms(species)
 
for i in range(model.getNumReactions()):
  reaction = model.getReaction(i)
  print('annotations for reaction {0}'.format(reaction.getId()))
  print_terms(reaction)

```

cheers

Frank

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[Frank Bergmann]

and of course it should have been term.getModelQualifierType() in the else branch. 

We'll try to add an example in a future version of libSBML. 

cheers

Frank

[cruse hu]

Yes, i use libsbml python API. It works! Thank you very much.

Frank Bergmann <frank.thom...@gmail.com> 于2021年3月12日周五 下午10:29写道：

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