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Posts: 6
Registered:
March 2012
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Re: unable to add CVTerm to model
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20 Mar '12 11:41
 
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Hi all,
I am trying to put a inchi line to a general species just like the example
bellow (the line is the one underlined):
<species metaid="metaid_M_13" id="M_13" sboTerm="SBO:0000299">
<annotation>
* <in:inchi xmlns:in="http://biomodels.net/inchi"
metaid="metaid_M_13_inchi">InChI=1/C6H12O4/c1-6(2,3-7)4(8)5(9)10/h4,7-8H,3H2,1-2H3,(H,9,10)/p-1/t4-/m0/s1/fC6H11O4/q-1</in:inchi>
*
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="
http://purl.org/dc/terms/" xmlns:vCard="
http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="
http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="
http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_M_13">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="#metaid_M_13_inchi"/>
<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A15980"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
So far, my code is:
sp = model.createSpecies()
sp.setId(comp)
sp.setMetaId(comp)
sp.setName(comp)
sp.setSBOTerm(299)
sp.setCompartment("C_1")
new_cvt = CVTerm()
new_cvt.setQualifierType(1)
new_cvt.setBiologicalQualifierType(BQB_IS)
new_cvt.addResource("urn:miriam:kegg.compound:"+comp)
sp.addCVTerm(new_cvt)
Can you give me a clue to what to do next?
Thank you,
Rodrigo
On 20 March 2012 16:50, Rodrigo Liberal <rodrigolf@gmail.com> wrote:
> of course. :)
> thanks,
> Rodrigo
>
>
> On 20 March 2012 15:50, Frank T. Bergmann <fbergman@caltech.edu> wrote:
>
>> >
>> > model.setNotes("<body xmlns='http://www.w3.org/1999/xhtml'>here is my
>> > note</p></body>")
>>
>> this was rejected, as it is invalid XML .. if you modify it to read:
>>
>> model.setNotes("<body xmlns='http://www.w3.org/1999/xhtml'><p>here is my
>> note</p></body>"
>>
>> you are good to go …
>>
>> Cheers
>> Frank
>>
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