Missing annotations when converting from SBML3 to SBtab

[smoretti]

Hi

I found several issues when converting from SBML3 to SBtab (or ObjTables) with sbtab_sbml2sbtab.py:

• When several annotations are provided for the same entity (e.g. CHEBI) only the last one is reported in SBtab.

<bqbiol:isRelatedTo>
    <rdf:Bag>
         <rdf:li rdf:resource="https://identifiers.org/CHEBI:29234"/>
         <rdf:li rdf:resource="https://identifiers.org/CHEBI:5584"/>
    </rdf:Bag>
</bqbiol:isRelatedTo>

returns only

!Identifiers:obo.chebi
CHEBI:5584

• Long and/or with / identifiers.org annotations look to break the annotation parsing
  https://identifiers.org/envipath:32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/41e4c903-407f-49f7-bf6b-0a94d39fa3a7
  returns

!Identifiers:envipath:32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound
41e4c903-407f-49f7-bf6b-0a94d39fa3a7

instead of (expect)

!Identifiers:envipath
32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/41e4c903-407f-49f7-bf6b-0a94d39fa3a7

• Not sure the is qualifier is parsed in SBML annotations.

<bqbiol:is>
    <rdf:Bag>
        <rdf:li rdf:resource="https://identifiers.org/CHEBI:28938"/>
    </rdf:Bag>
</bqbiol:is>

I joined an SBML example file.
bigg_e_coli_core.sbml3.xml.zip

I tested on Linux CentOS 7.4, with Python 3.5.2.

[eladnoor]

@tlubitz - could you take a look at this?
These identifiers are important for equilibrator in order to map the compounds in metanetx correctly.

[tlubitz]

@eladnoor
I do have it on my list! Alas, my working time right now is reduced to an absolute minimum, due to lockdown