Singular Annotations

There’s a little more to creating new annotations compared to reading and writing them. There are a few additional classes that need to be introduced: Editor, SingleAnnotation, PersonalInformation, PhysicalEntity, PhysicalProcess and EnergyDiff. This document assumes background knowledge in what these different types of annotations are.

To demonstrate libOmexMeta we first generate a sbml document using tellurium and antimony.

import tellurium as te
ant = """
model ToyModel
    compartment cytosol = 1.0;
    A in cytosol;
    B in cytosol
    A = 10;
    B = 0;
    k1 = 0.1;
    k2 = 0.1;
    r1: A => B; k1*A
    r1: B => A; k2*B
end"""
sbml = te.antimonyToSBML(ant)
print(sbml)

Which produces:

<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
  <model metaid="ToyModel" id="ToyModel">
    <listOfCompartments>
      <compartment id="cytosol" spatialDimensions="3" size="1" constant="true"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="A" compartment="cytosol" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
      <species id="B" compartment="cytosol" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter id="k1" value="0.1" constant="true"/>
      <parameter id="k2" value="0.1" constant="true"/>
    </listOfParameters>
    <listOfReactions>
      <reaction id="r1" reversible="false" fast="false">
        <listOfReactants>
          <speciesReference species="B" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="A" stoichiometry="1" constant="true"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k2 </ci>
              <ci> B </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>

Creating Single Annotations

A SingularAnnotation object is a typedef’d omexmeta::Triple object which is essentially a wrapper around the librdf_statement* object from the Redland Libraries. In this example we create a simple singular annotation for the top level model element of the sbml. We also add this annotation to our RDF graph and serialize to Turtle syntax.

Simple example of creating a single annotation

Create a single annotation in Python
from pyomexmeta import RDF, eUriType, SingularAnnotation

sbml = """<?xml version="1.1" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
  <model metaid="ToyModel" id="ToyModel">
    <listOfCompartments>
      <compartment id="cytosol" spatialDimensions="3" size="1" constant="true"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="A" compartment="cytosol" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
      <species id="B" compartment="cytosol" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter id="k1" value="0.1" constant="true"/>
      <parameter id="k2" value="0.1" constant="true"/>
    </listOfParameters>
    <listOfReactions>
      <reaction id="r1" reversible="false" fast="false">
        <listOfReactants>
          <speciesReference species="B" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="A" stoichiometry="1" constant="true"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k2 </ci>
              <ci> B </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>"""

# create an empty RDF object
rdf = RDF()

editor = rdf.to_editor(sbml, True)

print(editor.get_metaids())  # prints out model metaids

with editor.new_singular_annotation() as singular_annotation:
    singular_annotation \
        .about('ToyModel') \
        .predicate("dc", "description") \
        .resource_literal("This is a toy model for demonstration purposes")
print(rdf)
Output
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
['ToyModel', 'compartment0000', 'species0000', 'species0001', 'parameter0000', 'parameter0001', 'reaction0000', 'kineticLaw0000']
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix dc: <http://purl.org/dc/terms/> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .

local:ProcessProperty0000
    bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#reaction0000> ;
    bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .

local:SinkParticipant0000
    semsim:hasMultiplier "1"^^rdf:double ;
    semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#species0000> .

local:SourceParticipant0000
    semsim:hasMultiplier "1"^^rdf:double ;
    semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#species0001> .

<http://omex-library.org/NewOmex.omex/NewModel.xml#ToyModel>
    dc:description "This is a toy model for demonstration purposes" .

<http://omex-library.org/NewOmex.omex/NewModel.xml#reaction0000>
    semsim:hasSinkParticipant local:SinkParticipant0000 ;
    semsim:hasSourceParticipant local:SourceParticipant0000 .

The first thing to notice is that the sbml string only has a single metaid called ToyModel, which is the metaid of the model element. Metaids are essential for annotation, given that you cannot annotate an element that does not have a metaid.

Using the generate_new_metaids argument

If only some of your model elements have metaids, you can use the third argument to toEditor to automatically create metaids

Create a single annotation in Python and create metaids
from pyomexmeta import RDF, eUriType, SingularAnnotation

sbml = """<?xml version="1.1" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
  <model metaid="ToyModel" id="ToyModel">
    <listOfCompartments>
      <compartment id="cytosol" spatialDimensions="3" size="1" constant="true"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="A" compartment="cytosol" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
      <species id="B" compartment="cytosol" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter id="k1" value="0.1" constant="true"/>
      <parameter id="k2" value="0.1" constant="true"/>
    </listOfParameters>
    <listOfReactions>
      <reaction id="r1" reversible="false" fast="false">
        <listOfReactants>
          <speciesReference species="B" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="A" stoichiometry="1" constant="true"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k2 </ci>
              <ci> B </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>"""

# create an empty RDF object
rdf = RDF()

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

print(editor.get_xml()) # prints out sbml with metaids

with editor.new_singular_annotation() as identity:
    identity \
        .about('species0000') \
        .predicate("bqbiol", "is") \
        .resource_uri("uniprot/P01137")
print(rdf)
Output
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
<?xml version="1.1" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
  <model metaid="ToyModel" id="ToyModel">
    <listOfCompartments>
      <compartment id="cytosol" spatialDimensions="3" size="1" constant="true" metaid="compartment0000"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="A" compartment="cytosol" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" metaid="species0000"/>
      <species id="B" compartment="cytosol" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" metaid="species0001"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter id="k1" value="0.1" constant="true" metaid="parameter0000"/>
      <parameter id="k2" value="0.1" constant="true" metaid="parameter0001"/>
    </listOfParameters>
    <listOfReactions>
      <reaction id="r1" reversible="false" fast="false" metaid="reaction0000">
        <listOfReactants>
          <speciesReference species="B" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="A" stoichiometry="1" constant="true"/>
        </listOfProducts>
        <kineticLaw metaid="kineticLaw0000">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k2 </ci>
              <ci> B </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .

local:ProcessProperty0000
    bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#reaction0000> ;
    bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .

local:SinkParticipant0000
    semsim:hasMultiplier "1"^^rdf:double ;
    semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#species0000> .

local:SourceParticipant0000
    semsim:hasMultiplier "1"^^rdf:double ;
    semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#species0001> .

<http://omex-library.org/NewOmex.omex/NewModel.xml#reaction0000>
    semsim:hasSinkParticipant local:SinkParticipant0000 ;
    semsim:hasSourceParticipant local:SourceParticipant0000 .

<http://omex-library.org/NewOmex.omex/NewModel.xml#species0000>
    bqbiol:is <https://identifiers.org/uniprot/P01137> .

Creating and Serializing a Single Annotation without adding to the model

In the previous examples, we added the singular annotation we had just constructed to the RDF graph and then serialized the RDF graph to turtle syntax. It is also possible to serialize a singular annotation (a typedef’d Triple) and a set of annotations (a Triples class) without adding the annotations to the RDF graph.

Create a single annotation in Python and serialize to turtle without commiting the triples to the current RDF graph
from pyomexmeta import RDF, eUriType, SingularAnnotation

sbml = """<?xml version="1.1" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
  <model metaid="ToyModel" id="ToyModel">
    <listOfCompartments>
      <compartment id="cytosol" spatialDimensions="3" size="1" constant="true"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="A" compartment="cytosol" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
      <species id="B" compartment="cytosol" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter id="k1" value="0.1" constant="true"/>
      <parameter id="k2" value="0.1" constant="true"/>
    </listOfParameters>
    <listOfReactions>
      <reaction id="r1" reversible="false" fast="false">
        <listOfReactants>
          <speciesReference species="B" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="A" stoichiometry="1" constant="true"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k2 </ci>
              <ci> B </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>"""

# create an empty RDF object
rdf = RDF()

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


with editor.new_singular_annotation() as singular_annotation:
    singular_annotation \
        .about('species0001') \
        .predicate("bqbiol", "is") \
        .resource_uri("uniprot/P01137")

    # In python, the singular annotation gets committed to the model
    # automatically after the current context manager looses scope (i.e.
    # at the end of the current with block). But serializing (printing)
    # here does so without adding to the current RDF graph.
    # This features makes more sense in C/C++
    print(singular_annotation)
Output
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
<pyomexmeta.pyomexmeta.SingularAnnotation object at 0x0000021E613E5AF0>

Subjects, Predicates and Resources

Singular annotations are Triples or RDF statements. Therefore by definition they are composed of three nodes (or terms): the subject, the predicate and the resource. For a more detailed description of what these are, please refer to the RDF 1.1: Concepts and Abstract Syntax document. The RDF is a very general framework for storing information. In libOmexMeta we have restricted this generality in accordance with the OmexMeta specification 1.1.

Subject

A subject in libOmexMeta is the metaid of the element being element appended onto the local namespace. In RDF, the subject is the value of the about attribute. To set the subject of an annotation in libOmexMeta, use the about() method. Although we focus on singular annotations here, this generalizes to the other of annotations supported by libOmexMeta.

In this example, we have forced the generation of new metaids, which defaults to ##OmexMetaId followed by a 4 digit number. Hence the metaid #OmexMetaId0002 exists and is the metaid for the Species element with the name “A” (see xml above).

Warning

The following example is not a complete example. It will fail because a SingularAnnotation is only valid when all three of subject, predicate and resource are specified. For brevity, we assume sbml is the same as in the above examples.

However, leaving generate_new_metaids=False (the default) causes an error, because the metaid #OmexMetaId0002 was not found in your model.

Raise error whilst setting the subject portion of the RDF triple in Python.
rdf = RDF()

with rdf.to_editor(sbml, generate_new_metaids=True) as editor:
    with editor.new_singular_annotation() as singular_annotation:
        singular_annotation.about('#OmexMetaId0002')

Predicate

Predicates in libOmexMeta are all subclasses of the Predicate class. Existing predicate classes include BiomodelsBiologyQualifier, BiomodelsBiologyQualifier, DCTerm, SemSim and Foaf. For convenience, these predicate classes are only ever instantiated using a Factory method, which takes two string arguments: the namespace and the term, i.e:

Build in namespaces and prefixes for Predicates.

Namespace

Prefix

http://xmlns.cppom/foaf/0.1/

foaf

http://purl.org/dc/terms/

dc

http://biomodels.net/model-qualifiers/”

bqmodel

http://biomodels.net/biology-qualifiers/”

bqbiol

http://www.bhi.washington.edu/semsim#”

semsim

Each of these namespaces are referred to by their prefix. The term portion of the predicates are by defined by the namespace you are using and can easily be googled. An alternative strategy however, is simply to “get it wrong” and run your program and you will be provided with a full list of available terms for the prefix you are using.

Warning

The following example will fail because the singular annotations built are not complete.

Setting the Predicate portion of a singular annotation in Python
rdf = RDF()

with rdf.to_editor(sbml, generate_new_metaids=True) as editor:

    # build an annotation with bqbiol predicate
    with editor.new_singular_annotation() as bqbiol_singular_annotation:
        bqbiol_singular_annotation.set_predicate('bqbiol', 'is')

    # build an annotation with bqmodel predicate
    with editor.new_singular_annotation() as bqmodel_singular_annotation:
        bqmodel_singular_annotation.set_predicate('bqmodel', 'isDerivedFrom')

    # build an annotation with dcterm predicate
    with editor.new_singular_annotation() as dc_singular_annotation:
        dc_singular_annotation.set_predicate('dc', 'date')
Setting the Predicate portion of a singular annotation in C++
RDF rdf;
Editor editor = rdf.toEditor(sbml, "sbml", false);

SingularAnnotation bqbiol_singular_annotation = editor.newSingularAnnotation();
bqbiol_singular_annotation.setPredicate("bqbiol", "is")

SingularAnnotation bqmodel_singular_annotation = editor.newSingularAnnotation();
bqmodel_singular_annotation.setPredicate("bqmodel", "isDerivedFrom")

SingularAnnotation dc_singular_annotation = editor.newSingularAnnotation();
dc_singular_annotation.setPredicate("dc", "date")
Setting the Predicate portion of a singular annotation in C
// create an empty RDF object
RDF *rdf_ptr = RDF_new();

// create editor object
Editor *editor_ptr = RDF_toEditor(rdf_ptr, sbml, OMEXMETA_TYPE_SBML, false);

// create out annotation
SingularAnnotation *bqbiol_singular_annotation = Editor_newSingularAnnotation(editor_ptr);
SingularAnnotation_setPredicate(singular_annotation, "bqbiol", "is);

SingularAnnotation *bqmodel_singular_annotation = Editor_newSingularAnnotation(editor_ptr);
SingularAnnotation_setPredicate(singular_annotation, "bqmodel", "isDerivedFrom);

SingularAnnotation *bqbiol_singular_annotation = Editor_newSingularAnnotation(editor_ptr);
SingularAnnotation_setPredicate(singular_annotation, "dc", "date");

It should be noted that these Predicate subclasses in libOmexMeta are only convenience structures to ease the collection of information from the user. It is also possible and sometimes necessary to manually give libOmexMeta the entire predicate string. In C++, the setPredicate is overloaded to accept a single string, which indicates that this is a full uri. In C and Python, this is a different method call - see below.

Create a single annotation in Python using an arbitrary uri
from pyomexmeta import RDF, eUriType, SingularAnnotation

sbml = """<?xml version="1.1" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
  <model metaid="ToyModel" id="ToyModel">
    <listOfCompartments>
      <compartment id="cytosol" spatialDimensions="3" size="1" constant="true"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="A" compartment="cytosol" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
      <species id="B" compartment="cytosol" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter id="k1" value="0.1" constant="true"/>
      <parameter id="k2" value="0.1" constant="true"/>
    </listOfParameters>
    <listOfReactions>
      <reaction id="r1" reversible="false" fast="false">
        <listOfReactants>
          <speciesReference species="B" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="A" stoichiometry="1" constant="true"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k2 </ci>
              <ci> B </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>"""

# create an empty RDF object
rdf = RDF()

editor = rdf.to_editor(sbml, generate_new_metaids=True)
with editor.new_singular_annotation() as singular_annotation:
    singular_annotation \
        .about('species0000') \
        .predicate_from_uri("https://predicate.com/linker") \
        .resource_literal("New predicate demonstration")
print(rdf)
Output
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .

local:ProcessProperty0000
    bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#reaction0000> ;
    bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .

local:SinkParticipant0000
    semsim:hasMultiplier "1"^^rdf:double ;
    semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#species0000> .

local:SourceParticipant0000
    semsim:hasMultiplier "1"^^rdf:double ;
    semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#species0001> .

<http://omex-library.org/NewOmex.omex/NewModel.xml#reaction0000>
    semsim:hasSinkParticipant local:SinkParticipant0000 ;
    semsim:hasSourceParticipant local:SourceParticipant0000 .

<http://omex-library.org/NewOmex.omex/NewModel.xml#species0000>
    <https://predicate.com/linker> "New predicate demonstration" .

Resources

A resource node can be any of the three types of node: a literal, uri or a blank node. Separate methods exist for each of these. In the next example we create a set of singular annotations that demonstrate the various usages of Resource.

Demonstration of options for the resource node in Python
from pyomexmeta import RDF, eUriType, SingularAnnotation

sbml = """<?xml version="1.1" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
  <model metaid="ToyModel" id="ToyModel">
    <listOfCompartments>
      <compartment id="cytosol" spatialDimensions="3" size="1" constant="true"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="A" compartment="cytosol" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
      <species id="B" compartment="cytosol" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter id="k1" value="0.1" constant="true"/>
      <parameter id="k2" value="0.1" constant="true"/>
    </listOfParameters>
    <listOfReactions>
      <reaction id="r1" reversible="false" fast="false">
        <listOfReactants>
          <speciesReference species="B" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="A" stoichiometry="1" constant="true"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k2 </ci>
              <ci> B </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>"""

# create an empty RDF object
rdf = RDF()

editor = rdf.to_editor(sbml, generate_new_metaids=True)
with editor.new_singular_annotation() as literal:
    literal \
        .about('ToyModel') \
        .predicate("dc", "description") \
        .resource_literal("This is a toy model for demonstration purposes")

with editor.new_singular_annotation() as blank:
    blank \
        .about('species0000') \
        .predicate("dc", "description") \
        .resource_blank("BankIdentifier")

# The `uniprot/PD1234` gets resolved to https://identifier.org/uniprot/PD12345
with editor.new_singular_annotation() as uri:
    uri \
        .about('species0001') \
        .predicate("bqbiol", "is") \
        .resource_uri("uniprot/PD1234")

# In fact, this can be string with a format string1/string2
with editor.new_singular_annotation() as uri:
    uri \
        .about('species0000') \
        .predicate("bqbiol", "is") \
        .resource_uri("string1/string2")

# Colons work too
with editor.new_singular_annotation() as uri:
    uri \
        .about('species0000') \
        .predicate("bqbiol", "is") \
        .resource_uri("FMA:75132")

print(len(rdf))
print(rdf)
Output
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
[16:33:38 +01:00]  warning : XML parser warning: Unsupported version '1.1' 
13
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix dc: <http://purl.org/dc/terms/> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .

local:ProcessProperty0000
    bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#reaction0000> ;
    bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .

local:SinkParticipant0000
    semsim:hasMultiplier "1"^^rdf:double ;
    semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#species0000> .

local:SourceParticipant0000
    semsim:hasMultiplier "1"^^rdf:double ;
    semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#species0001> .

<http://omex-library.org/NewOmex.omex/NewModel.xml#ToyModel>
    dc:description "This is a toy model for demonstration purposes" .

<http://omex-library.org/NewOmex.omex/NewModel.xml#reaction0000>
    semsim:hasSinkParticipant local:SinkParticipant0000 ;
    semsim:hasSourceParticipant local:SourceParticipant0000 .

<http://omex-library.org/NewOmex.omex/NewModel.xml#species0000>
    bqbiol:is <https://identifiers.org/FMA:75132>, <https://identifiers.org/string1/string2> ;
    dc:description _:BankIdentifier .

<http://omex-library.org/NewOmex.omex/NewModel.xml#species0001>
    bqbiol:is <https://identifiers.org/uniprot/PD1234> .