{core}
MIRIAM-compliant RDF annotation reader/writer.
This class of objects is defined by libSBML only and has no direct
equivalent in terms of SBML components. This class is not prescribed by
the SBML specifications, although it is used to implement features
defined in SBML.
RDFAnnotationParser is a libSBML construct used as part of the libSBML support for annotations conforming to the guidelines specified by MIRIAM ('Minimum Information Requested in the Annotation of biochemical Models', Nature Biotechnology, vol. 23, no. 12, Dec. 2005). Section 6 of the SBML Level 2 and Level 3 specification documents defines a recommended way of encoding MIRIAM information using a subset of RDF (Resource Description Format). The general scheme is as follows. A set of RDF-based annotations attached to a given SBML <annotation>
element are read by RDFAnnotationParser and converted into a list of CVTerm objects. There are different versions of the main method,and RDFAnnotationParser::parseRDFAnnotation(XMLNode annotation), used depending on whether the annotation in question concerns the MIRIAM model history or other MIRIAM resource annotations. A special object class, ModelHistory, is used to make it easier to manipulate model history annotations.
All of the methods on RDFAnnotationParser are static; the class exists only to encapsulate the annotation and CVTerm parsing and manipulation functionality.
|
static XMLNode | createAnnotation () |
| Creates a blank annotation and returns its root XMLNode object. More...
|
|
static XMLNode | createCVTerms (SBase obj) |
| Takes a list of CVTerm objects and creates a the RDF 'Description' element. More...
|
|
static XMLNode | createRDFAnnotation (long level, long version) |
| Creates a blank RDF element suitable for use in SBML annotations. More...
|
|
static XMLNode | createRDFAnnotation (long level) |
| Creates a blank RDF element suitable for use in SBML annotations. More...
|
|
static XMLNode | createRDFAnnotation () |
| Creates a blank RDF element suitable for use in SBML annotations. More...
|
|
static XMLNode | deleteRDFAnnotation (XMLNode annotation) |
| Deletes any SBML MIRIAM RDF annotation found in the given XMLNode tree and returns any remaining annotation content. More...
|
|
static XMLNode | deleteRDFCVTermAnnotation (XMLNode annotation) |
| Deletes any SBML MIRIAM RDF 'CVTerm' annotation found in the given XMLNode tree and returns any remaining annotation content. More...
|
|
static XMLNode | deleteRDFHistoryAnnotation (XMLNode annotation) |
| Deletes any SBML MIRIAM RDF 'History' annotation found in the given XMLNode tree and returns any remaining annotation content. More...
|
|
static XMLNode | parseCVTerms (SBase obj) |
| Takes a list of CVTerm objects and creates a complete SBML annotation around it. More...
|
|
static XMLNode | parseModelHistory (SBase obj) |
| Reads the model history and cvTerms stored in obj and creates the XML structure for an SBML annotation representing that metadata if there is a model history stored in obj . More...
|
|
static XMLNode | parseOnlyModelHistory (SBase obj) |
| Reads the model history stored in obj and creates the XML structure for an SBML annotation representing that history. More...
|
|
static ModelHistory | parseRDFAnnotation (XMLNode annotation, string metaId, XMLInputStream stream) |
| Parses an annotation into a ModelHistory class instance. More...
|
|
static ModelHistory | parseRDFAnnotation (XMLNode annotation, string metaId) |
| Parses an annotation into a ModelHistory class instance. More...
|
|
static ModelHistory | parseRDFAnnotation (XMLNode annotation) |
| Parses an annotation into a ModelHistory class instance. More...
|
|
static void | parseRDFAnnotation (XMLNode annotation, CVTermList CVTerms) |
|
static void | parseRDFAnnotation (XMLNode annotation, CVTermList CVTerms, string metaId, XMLInputStream stream) |
|
static void | parseRDFAnnotation (XMLNode annotation, CVTermList CVTerms, string metaId) |
|
static XMLNode libsbmlcs.RDFAnnotationParser.createAnnotation |
( |
| ) |
|
|
static |
Creates a blank annotation and returns its root XMLNode object.
This creates a completely empty SBML <annotation>
element. It is not attached to any SBML element. An example of how this might be used is illustrated in the following code fragment. In this example, suppose that content
is an XMLNode object previously created, containing MIRIAM-style annotations, and that sbmlObject
is an SBML object derived from SBase (e.g., a Model, or a Species, or a Compartment, etc.). Then: The SBML specification contains more information about the format of annotations. We urge readers to consult Section 6 of the SBML Level 2 (Versions 2–4) and SBML Level 3 specification documents.
- Returns
- a pointer to an XMLNode for the annotation
- See also
- RDFAnnotationParser::createRDFAnnotation()
static XMLNode libsbmlcs.RDFAnnotationParser.createRDFAnnotation |
( |
long |
level, |
|
|
long |
version |
|
) |
| |
|
static |
Creates a blank RDF element suitable for use in SBML annotations.
The annotation created by this method has namespace declarations for all the relevant XML namespaces used in RDF annotations and also has an empty RDF element. The result is the following XML:
<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:RDF>
Note that this does not create the containing SBML <annotation>
element; the method RDFAnnotationParser::createAnnotation() is available for creating the container.
- Returns
- a pointer to an XMLNode
- See also
- RDFAnnotationParser::createAnnotation()
static XMLNode libsbmlcs.RDFAnnotationParser.createRDFAnnotation |
( |
long |
level | ) |
|
|
static |
Creates a blank RDF element suitable for use in SBML annotations.
The annotation created by this method has namespace declarations for all the relevant XML namespaces used in RDF annotations and also has an empty RDF element. The result is the following XML:
<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:RDF>
Note that this does not create the containing SBML <annotation>
element; the method RDFAnnotationParser::createAnnotation() is available for creating the container.
- Returns
- a pointer to an XMLNode
- See also
- RDFAnnotationParser::createAnnotation()
static XMLNode libsbmlcs.RDFAnnotationParser.createRDFAnnotation |
( |
| ) |
|
|
static |
Creates a blank RDF element suitable for use in SBML annotations.
The annotation created by this method has namespace declarations for all the relevant XML namespaces used in RDF annotations and also has an empty RDF element. The result is the following XML:
<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:RDF>
Note that this does not create the containing SBML <annotation>
element; the method RDFAnnotationParser::createAnnotation() is available for creating the container.
- Returns
- a pointer to an XMLNode
- See also
- RDFAnnotationParser::createAnnotation()