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Conversion to RDF for internal annotations (PATTERN and LIST annotations) was never implemented. As a result, those annotations can be in the source BEL file, but not in the converted RDF.
Question to discuss: how should those annotations be represented/modeled in RDF?
Example:
DEFINE ANNOTATION ExternalID AS LIST {"-12345","6789"}
SET ExternalID = "-12345"
SET Evidence = "Some Evidence String"
SET Citation = {"PubMed","12-O-tetradecanoyl-phorbol-13-acetate-induced ACTH secretion in pituitary tumor cells.","6325215","","Heisler S","European journal of pharmacology 1984 Feb 17;98(2):177-83"}
The text was updated successfully, but these errors were encountered:
For LIST we could model as a skos:ConceptScheme. This annotation resource could even be a blank node, document relative, or UUID URI since it is internal to the document.
In RDF turtle we might say:
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
# Document relative URI for ExternalID concept scheme.<#annotations-externalID>a belv:AnnotationConceptScheme , skos:ConceptScheme ;
belv:prefix "ExternalID" ;
skos:prefLabel "External Identifiers" .
# Blank node representing the -12345 value as a concept.
_:externalID_1 a belv:AnnotationConcept , skos:Concept , rdfs:Resource ;
skos:inScheme <#annotations-externalID> ;
dcterms:identifier "-12345" ;
skos:prefLabel "-12345" .
# Blank node representing the 6789 value as a concept.
_:externalID_2 a belv:AnnotationConcept , skos:Concept , rdfs:Resource ;
skos:inScheme <#annotations-externalID> ;
dcterms:identifier "6789" ;
skos:prefLabel "6789" .
It starts to look the same as how we model external namespaces and annotation as SKOS Concept Schemes apart from the anonymous vs well-known resource URIs.
For PATTERN annotation it does not seem to fit in as a SKOS thesaurus. It feels like a type of belv Annotation but with a regular expression literal. For example identifiers.org created their own RDF property to convey a regular expression pattern:
We have BEL content where we do not have these custom annotations defined in a LIST
It would be essential to link custom annotations to a statemente. e.g.
Conversion to RDF for internal annotations (PATTERN and LIST annotations) was never implemented. As a result, those annotations can be in the source BEL file, but not in the converted RDF.
Question to discuss: how should those annotations be represented/modeled in RDF?
Example:
DEFINE ANNOTATION ExternalID AS LIST {"-12345","6789"}
SET ExternalID = "-12345"
SET Evidence = "Some Evidence String"
SET Citation = {"PubMed","12-O-tetradecanoyl-phorbol-13-acetate-induced ACTH secretion in pituitary tumor cells.","6325215","","Heisler S","European journal of pharmacology 1984 Feb 17;98(2):177-83"}
The text was updated successfully, but these errors were encountered: