Possible issue with the .setAnnotation method (Python)?

[woosubs]

Hi, I was trying to set the annotation of a model.species instance from an SBML model, using the .setAnnotation method with the string below:

After this, I retrieved the annotation using .getAnnotationString to check whether it was successfully updated, and found below was returned:

So all the information exists, but the part between <rdf:Description> …. </rdf:Description> was duplicated except the nested content. It seemed weird, for example because the meta id was duplicated as well. Could you check this and let me know whether it is behaving correctly? I ran the methods on Jupiter Lab with Python version 3.9.15.

Thank you,
Woosub

[fbergmann]

Could you send us the complete example you were using? (or the sbml model (it is fine to have it reduced to just the element in question with the annotation). the setAnnotation function, replaces existing annotations.

[woosubs]

Hello, Please find the files attached. The other two files are used for the .ipynb example. I learned that the setAnnotation method indeed replaces the existing annotation, but also found the new annotation was slightly different from what I had provided. Best, Woosub Shin

On Fri, Feb 17, 2023 at 8:29 PM Frank Bergmann ***@***.***> wrote: Could you send us the complete example you were using? (or the sbml model (it is fine to have it reduced to just the element in question with the annotation). the setAnnotation function, replaces existing annotations. — Reply to this email directly, view it on GitHub <#296 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGBDWGN3EHS6HPKNHX3KGSDWX5OIRANCNFSM6AAAAAAU7DKASI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

<annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vcard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#metaid_0000036"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:59789"/> <bqbiol:hasProperty> <rdf:Bag> <rdf:li rdf:resource="http://property_information"/> </rdf:Bag> </bqbiol:hasProperty> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation>

[fbergmann]

I'm afraid we still have enough information (maybe attachments from your email reply did not get added to the github issue). Maybe you can manually attach them, or send a link to an online resource, so we can look at the issue. We need:

• the python code you tried
• the input sbml file and annotation string you tried to set.
• ideally the result you hoped to get rather than the one you received.

thanks

[fbergmann]

Ok, through googling i found your Notebook. So looking at what happens here, is that setAnnotation does indeed unset the annotation first.

However, after setting the annotation that you provide, libsbml then goes ahead an parses the RDF provided. Since you use RDF that does not correspond to the subset that is described in the SBML specification this causes the issue that you see.

that will require a new version of COPASI, where setAnnotation gets an additional flag, whether to parse the annotations after setting it. You'd have to set it to false.

Note that while it is fine for you to use any RDF you'd like within SBML. Most tools wont be able to read the information that does not conform to the SBML subset. It might be better to use another annotation / RDF node to store these information in.

I'll make a PR, to handle the setAnnotation part. We might have to think about disabling processing the CVTerms during read as well. What do you think @skeating ?

[fbergmann]

just in case here the test case, requiring python-libsbml and copasi-basico:

import libsbml
import os

_TARGET_ANNOTATION = """
<annotation>
  <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vcard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
    <rdf:Description rdf:about="#metaid_0000036">
      <bqbiol:is>
        <rdf:Bag>
          <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:59789"/>
          <bqbiol:hasProperty>
            <rdf:Bag>
              <rdf:li rdf:resource="http://amas/match_score/by_name/1.0"/>
            </rdf:Bag>
          </bqbiol:hasProperty>
          <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:15414"/>
          <bqbiol:hasProperty>
            <rdf:Bag>
              <rdf:li rdf:resource="http://amas/match_score/by_name/1.0"/>
            </rdf:Bag>
          </bqbiol:hasProperty>
        </rdf:Bag>
      </bqbiol:is>
    </rdf:Description>
  </rdf:RDF>
</annotation>
""".strip()


def main():
    if os.path.exists('bm190.xml'):
        with open('bm190.xml', 'r', encoding='utf8') as f:
            sbml = f.read()
    else:
        import basico.biomodels as bm
        sbml = bm.get_content_for_model(190)
        with open('bm190.xml', 'w', encoding='utf8') as f:
            f.write(sbml)

    doc = libsbml.readSBMLFromString(sbml)
    model = doc.getModel()
    one_s = model.getSpecies('SAM')

    one_s.setAnnotation(_TARGET_ANNOTATION)
    print(one_s.getAnnotationString())


if __name__ == '__main__':
    main()

yields:

<annotation>
  <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vcard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
    <rdf:Description rdf:about="#metaid_0000036">
      <bqbiol:is>
        <rdf:Bag>
          <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:59789"/>
          <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:15414"/>
        </rdf:Bag>
      </bqbiol:is>
    </rdf:Description>
    <rdf:Description rdf:about="#metaid_0000036">
      <bqbiol:is>
        <rdf:Bag>
          <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:59789"/>
          <bqbiol:hasProperty>
            <rdf:Bag>
              <rdf:li rdf:resource="http://amas/match_score/by_name/1.0"/>
            </rdf:Bag>
          </bqbiol:hasProperty>
          <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:15414"/>
          <bqbiol:hasProperty>
            <rdf:Bag>
              <rdf:li rdf:resource="http://amas/match_score/by_name/1.0"/>
            </rdf:Bag>
          </bqbiol:hasProperty>
        </rdf:Bag>
      </bqbiol:is>
    </rdf:Description>
  </rdf:RDF>
</annotation>

with 2 instead of just the one rdf:Descriptions.

[woosubs]

Sorry for getting back to you so late and thank you very much for your response! It was really helpful. Woosub

…

On Fri, Mar 17, 2023 at 12:17 AM Frank Bergmann ***@***.***> wrote: just in case here the test case, requiring python-libsbml and copasi-basico: import libsbmlimport os _TARGET_ANNOTATION = """<annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vcard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#metaid_0000036"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:59789"/> <bqbiol:hasProperty> <rdf:Bag> <rdf:li rdf:resource="http://amas/match_score/by_name/1.0"/> </rdf:Bag> </bqbiol:hasProperty> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:15414"/> <bqbiol:hasProperty> <rdf:Bag> <rdf:li rdf:resource="http://amas/match_score/by_name/1.0"/> </rdf:Bag> </bqbiol:hasProperty> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF></annotation>""".strip() def main(): if os.path.exists('bm190.xml'): with open('bm190.xml', 'r', encoding='utf8') as f: sbml = f.read() else: import basico.biomodels as bm sbml = bm.get_content_for_model(190) with open('bm190.xml', 'w', encoding='utf8') as f: f.write(sbml) doc = libsbml.readSBMLFromString(sbml) model = doc.getModel() one_s = model.getSpecies('SAM') one_s.setAnnotation(_TARGET_ANNOTATION) print(one_s.getAnnotationString()) if __name__ == '__main__': main() yields: <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vcard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#metaid_0000036"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:59789"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:15414"/> </rdf:Bag> </bqbiol:is> </rdf:Description> <rdf:Description rdf:about="#metaid_0000036"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:59789"/> <bqbiol:hasProperty> <rdf:Bag> <rdf:li rdf:resource="http://amas/match_score/by_name/1.0"/> </rdf:Bag> </bqbiol:hasProperty> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:15414"/> <bqbiol:hasProperty> <rdf:Bag> <rdf:li rdf:resource="http://amas/match_score/by_name/1.0"/> </rdf:Bag> </bqbiol:hasProperty> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> with 2 instead of just the one rdf:Descriptions. — Reply to this email directly, view it on GitHub <#296 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGBDWGKAQZIDKYKIJV3JX4DW4MVG7ANCNFSM6AAAAAAU7DKASI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[skeating]

Is this sorted and can be closed ?

[woosubs]

Closed. Thank you!