Use prefix for `hasTaxon` in turtle syntax

[aram148]

Suggested that compact forms be used where possible. For example:

bqbiol:hasTaxon https://identifiers.org/taxonomy:9895 ;

should be

bqbiol:hasTaxon 9895 or something similar

[nickerso]

bqbiol:hasTaxon taxon:9895 (using the namespace as is being defined in the annotation file/graph)

[CiaranWelsh]

Do you have a code example that demonstrates where libOmexMeta uses long form where it should use short? This can be used as the basis of a new test.

[CiaranWelsh]

from pyomexmeta import RDF, Editor
import tellurium as te

r = te.loada("""
R1: S1 => S2; k1*S1;
R2: S2 => S2; k2*S2
k1 = 0.1; 
k2 = 0.3
S1 = 5;
S1 = 3
""")

sbml = r.getSBML()

rdf = RDF()

editor = rdf.to_editor(sbml, True, False)

editor.add_taxon("9896")

print(rdf)

produces

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix NCBI_Taxon: <https://identifiers.org/taxonomy:> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .

<http://omex-library.org/NewOmex.omex/NewModel.xml>
    bqbiol:hasTaxon <https://identifiers.org/taxonomy:9896> .

Where it should produce

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix NCBI_Taxon: <https://identifiers.org/taxonomy:> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .

<http://omex-library.org/NewOmex.omex/NewModel.xml>
    bqbiol:hasTaxon NCBI_Taxon:9896 .

[CiaranWelsh]

This appears to be a bug, as it should already be using the NCBI_Taxon prefix.

[CiaranWelsh]

@nickerso @jhgennari @maxneal @hsauro Okay, so whether this is a bug in the redland libraries or a bug in the spec, I don't know; but its seems that prefixes do not get used in Turtle syntax if the subsequent uri portion begins with a number.

For example, the following code works as expected. I've used the low level libOmexMeta interface for directly creating nodes, triples and adding a namespace:

    LibrdfNode subject = LibrdfNode::fromUriString("http://omex-library.org/NewOmex.omex/NewModel.xml#model0000");
    LibrdfNode predicate = LibrdfNode::fromUriString("http://biomodels.net/biology-qualifiers/hasTaxon");
    LibrdfNode resource = LibrdfNode::fromUriString("https://identifiers.org/taxonomy:AnIdThatDoesNotStartWithANumber"); // <-- important line

    RDF rdf;
    Editor editor = rdf.toEditor(SBMLFactory::getSBML(SBML_NOT_ANNOTATED2), true, false); // arbitrary sbml model, contents not relevant here. 

    SingularAnnotation singularAnnotation = editor.newSingularAnnotation();
    singularAnnotation.setSubject(subject.getWithoutIncrement()); // get* returns a raw librdf_node* pointer. No reference counter incremented
    singularAnnotation.setPredicate(predicate.getWithoutIncrement());/ get* returns a raw librdf_node* pointer. No reference counter incremented
    singularAnnotation.setResource(resource.getWithoutIncrement());/ get* returns a raw librdf_node* pointer. No reference counter incremented

    editor.addSingleAnnotation(singularAnnotation);
    editor.addNamespace("https://identifiers.org/taxonomy:", "NCBI_Taxon"); // Manually add the namespace

    std::cout << rdf.toString("turtle") << std::endl;

As we expect, this will output:

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix NCBI_Taxon: <https://identifiers.org/taxonomy:> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .

<http://omex-library.org/NewOmex.omex/NewModel.xml#model0000>
    bqbiol:hasTaxon NCBI_Taxon:AnIdThatDoesNotStartWithANumber .

But if we instead use a number, i.e. an actual taxon id:

    LibrdfNode subject = LibrdfNode::fromUriString("http://omex-library.org/NewOmex.omex/NewModel.xml#model0000");
    LibrdfNode predicate = LibrdfNode::fromUriString("http://biomodels.net/biology-qualifiers/hasTaxon");
    LibrdfNode resource = LibrdfNode::fromUriString("https://identifiers.org/taxonomy:9696");

    RDF rdf;
    Editor editor = rdf.toEditor(SBMLFactory::getSBML(SBML_NOT_ANNOTATED2), true, false);

    SingularAnnotation singularAnnotation = editor.newSingularAnnotation();
    singularAnnotation.setSubject(subject.getWithoutIncrement());

    singularAnnotation.setPredicate(predicate.getWithoutIncrement());
    singularAnnotation.setResource(resource.getWithoutIncrement());

    editor.addSingleAnnotation(singularAnnotation);
    editor.addNamespace("https://identifiers.org/taxonomy:", "NCBI_Taxon");

    std::cout << rdf.toString("turtle") << std::endl;

we get

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix NCBI_Taxon: <https://identifiers.org/taxonomy:> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .

<http://omex-library.org/NewOmex.omex/NewModel.xml#model0000>
    bqbiol:hasTaxon <https://identifiers.org/taxonomy:9696> .

In the past, there was a mistake in the spec regarding the prefix for "myOmexLib" and I spent a lot of effort trying to figure out why we couldn't get the turtle serializer to use the prefix, when the actual problem was that we had a subtle syntax error in the spec.

So, is this a bug in the redland libraries or a bug in the spec? If its a problem with the redland libraries, it may be possible for me to go digging around in the C code but this could be a can of worms.

[CiaranWelsh]

Begin PR #61 for this issue

[nickerso]

@CiaranWelsh - this is sounding like a non-urgent issue and we can stick with the full URI version of the taxon annotations for now. And then loop back to this one in future.