SingularAnnotation

class pyomexmeta.SingularAnnotation(singular_annotation_ptr: ctypes.c_longlong)

Interface for handling single annotations or Triples (or rdf statements).

This is the lowest level interface exposed to users. It allows you to create arbitrary RDF triples and add them to the RDF graph.

SingularAnnotation objects are created using the Editor.new_singular_annotation() method.

All SingularAnnotation objects need to call the SingularAnnotation.about() method to set the subject portion of the triple object being created.

The predicate portion may be set with the predicate factory, invoked with the SingularAnnotation.predicate() method or directly from a full uri using SingularAnnotation.set_predicate_from_uri() method

The resource portion of the triple may be set with one of

SingularAnnotation.set_resource_literal()
SingularAnnotation.set_resource_uri()
SingularAnnotation.set_resource_blank()

for creating a literal, uri or blank note respectively.

From section 2.3.6 in the OmexMeta specification:

Singular annotations within COMBINE archive annotation files should be encoded as a single RDF triple. The subject of the triple is the annotated element and should be formatted as a relative URI. The predicate is the URI of a BioModels.net qualifier linking the subject to a URI from a knowledge resource or the Dublin Core Metadata Terms qualifier description. The object of the triple should be an identifiers.org-formatted URI indicating a concept in a knowledge resource, or a text string for free-text definitions of model elements.

The following is an example singular semantic annotation indicating that the model element with meta- data ID “meta0013” from the model file “MyModel.sbml” represents adenosine tri-phosphate:

The following is an example free-text description of a model variable with metadata ID “meta0014”:

__init__(singular_annotation_ptr: ctypes.c_longlong)

Constructor for a SingularAnnotation() object.

This constructor should not be used directly by users. Instead use the Editor.new_singular_annotation() method.

Methods in this class implement a builder interface, by returning a a reference to self. This allows optional chaining of methods together.

Parameters: singular_annotation_ptr – A pointer to an SingularAnnotation which exist in memory

__weakref__: list of weak references to the object (if defined)

about(about: str) → pyomexmeta.pyomexmeta.SingularAnnotation 

Create a subject node with the string about

Parameters: about – a metaid that exists in the model. Errors when this metaid does not exist in the model you are annotating, and presents you with available metaids.
Returns: SingularAnnotation reference to self object

delete() → None: clean up resources associated with this SingularAnnotation

get_about() → str: Returns the about (subject) portion of rdf triple

get_predicate() → str: Return the predicate portion of the rdf triple

get_ptr() → ctypes.c_longlong: returns the underlying pointer to the memory address that stores this SingularAnnotation

get_resource() → str: return the resource portion of the rdf triple

predicate(namespace: str, term: str) → pyomexmeta.pyomexmeta.SingularAnnotation 

This method provides a factory interface for predicate node creation.

Parameters

namespace – One of * “bqbiol” BiomodelsBiologyQualifier. http://biomodels.net/biology-qualifiers/ * “bqmodel” BiomodelsModelQualifier. http://biomodels.net/model-qualifiers/ * “dc” DCTerm. http://purl.org/dc/terms/ * “semsim” SemSim. http://bime.uw.edu/semsim/ * “foaf” Foaf. http://xmlns.com/foaf/0.1/
term – the string of the term in namespace that you would like to use. All terms are supported but there are a finite set from which you cannot deviate. Attempts to create a term in namespace that does not exist results in an error, with a list of available terms in namespace namespace

Returns