@prefix OMEXlib: <http://omex-library.org/> .
@prefix myOMEX: <http://omex-library.org/NewOmex.omex/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:OmexMetaId0001
bqbiol:isPropertyOf local:EntityProperty0000 ;
bqbiol:isVersionOf <https://identifiers.org/OPB/OPB_00340> .
local:EntityProperty0000
bqbiol:is <https://identifiers.org/uniprot/P84022> ;
bqbiol:isPartOf <https://identifiers.org/fma/FMA:24178>, <https://identifiers.org/fma/FMA:63877>, <https://identifiers.org/fma/FMA:70737>, <https://identifiers.org/fma/FMA:7163> .
"""
# remember that the default parser is "guess".
# the parser will try to figure out which syntax is being used.
# but if it doesn't guess well, you can use the format argument for `from_string`
rdf = RDF.from_string(turtle_string)
formats = [
"ntriples", "turtle", "rdfxml-abbrev", "rdfxml", "dot", "json-triples",
"json", "nquads", "html"
]
for syntax in formats:
print("Serializing to {}".format(syntax))
print(rdf.to_string(syntax))
print("\n\n")
# Note: printing the rdf object is the same as rdf.to_string("turtle")
from pyomexmeta import RDF
rdf_str = """@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix myOMEX: <http://omex-library.org/NewOmex.omex/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#>
<http://purl.org/dc/terms/creator> <https://orchid.org/1234-1234-1234-1234> ."""
# read the annotations into RDF graph
rdf = RDF.from_string(rdf_str, format="turtle")
# serialize the string to rdfxml-abbrev
xml_string = rdf.to_string("rdfxml-abbrev")
print(f"RDF graph serialized to rdfxml abbreviated is:\n\n{xml_string}")
import os
from pyomexmeta import RDF, eUriType
rdf_str = """@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix myOMEX: <http://omex-library.org/NewOmex.omex/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#OmexMetaId0000>
bqbiol:is <https://identifiers.org/uniprot/PD12345> ."""
# download model xml, scan for rdf, create rdf graph and store in sqlite database
rdf = RDF.from_string(rdf_str, syntax="turtle")
# pick a filename (this can be anywhere on your system)
docs_dir = os.path.join(os.path.dirname(__file__), "source")
diagrams_dir = os.path.join(docs_dir, "diagrams")
fname = os.path.join(diagrams_dir, "Diagram")
# draw a diagram
rdf.draw(fname)
print(f"file saved to {fname}.pdf")