Serializing RDF Graphs
Serializing is just a fancy term for writing the information in an RDF graph to a string or file. There are several syntaxes that are supported by libOmexMeta, including:
ntriples, turtle, rdfxml-xmp, rdfxml-abbrev, rdfxml, dot, json-triples, json, nquads, html
Writing to string
Write to a string in Python
from pyomexmeta import RDF, eUriType
turtle_string = """@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#> .
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")
Output
Serializing to ntriples
<http://omex-library.org/NewOmex.omex/NewModel.rdf#OmexMetaId0001> <http://biomodels.net/biology-qualifiers/isPropertyOf> <http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000> .
<http://omex-library.org/NewOmex.omex/NewModel.rdf#OmexMetaId0001> <http://biomodels.net/biology-qualifiers/isVersionOf> <https://identifiers.org/OPB/OPB_00340> .
<http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000> <http://biomodels.net/biology-qualifiers/is> <https://identifiers.org/uniprot/P84022> .
<http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:24178> .
<http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:63877> .
<http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:70737> .
<http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:7163> .
Serializing to turtle
@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 local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
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> .
local:OmexMetaId0001
bqbiol:isPropertyOf local:EntityProperty0000 ;
bqbiol:isVersionOf <https://identifiers.org/OPB/OPB_00340> .
Serializing to rdfxml-abbrev
<?xml version="1.1" encoding="utf-8"?>
<rdf:RDF xmlns:OMEXlib="http://omex-library.org/"
xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
xmlns:local="http://omex-library.org/NewOmex.omex/NewModel.rdf#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000">
<bqbiol:is rdf:resource="https://identifiers.org/uniprot/P84022"/>
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:24178"/>
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:63877"/>
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:70737"/>
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:7163"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/NewOmex.omex/NewModel.rdf#OmexMetaId0001">
<bqbiol:isPropertyOf rdf:resource="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/OPB/OPB_00340"/>
</rdf:Description>
</rdf:RDF>
Serializing to rdfxml
<?xml version="1.1" encoding="utf-8"?>
<rdf:RDF xmlns:OMEXlib="http://omex-library.org/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:local="http://omex-library.org/NewOmex.omex/NewModel.rdf#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="http://omex-library.org/NewOmex.omex/NewModel.rdf#OmexMetaId0001">
<bqbiol:isPropertyOf rdf:resource="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/NewOmex.omex/NewModel.rdf#OmexMetaId0001">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/OPB/OPB_00340"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000">
<bqbiol:is rdf:resource="https://identifiers.org/uniprot/P84022"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000">
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:24178"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000">
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:63877"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000">
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:70737"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000">
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:7163"/>
</rdf:Description>
</rdf:RDF>
Serializing to dot
digraph {
rankdir = LR;
charset="utf-8";
"ROMEXlib:NewOmex.omex/NewModel.rdf#OmexMetaId0001" -> "ROMEXlib:NewOmex.omex/NewModel.rdf#EntityProperty0000" [ label="bqbiol:isPropertyOf" ];
"ROMEXlib:NewOmex.omex/NewModel.rdf#OmexMetaId0001" -> "Rhttps://identifiers.org/OPB/OPB_00340" [ label="bqbiol:isVersionOf" ];
"ROMEXlib:NewOmex.omex/NewModel.rdf#EntityProperty0000" -> "Rhttps://identifiers.org/uniprot/P84022" [ label="bqbiol:is" ];
"ROMEXlib:NewOmex.omex/NewModel.rdf#EntityProperty0000" -> "Rhttps://identifiers.org/fma/FMA:24178" [ label="bqbiol:isPartOf" ];
"ROMEXlib:NewOmex.omex/NewModel.rdf#EntityProperty0000" -> "Rhttps://identifiers.org/fma/FMA:63877" [ label="bqbiol:isPartOf" ];
"ROMEXlib:NewOmex.omex/NewModel.rdf#EntityProperty0000" -> "Rhttps://identifiers.org/fma/FMA:70737" [ label="bqbiol:isPartOf" ];
"ROMEXlib:NewOmex.omex/NewModel.rdf#EntityProperty0000" -> "Rhttps://identifiers.org/fma/FMA:7163" [ label="bqbiol:isPartOf" ];
// Resources
"ROMEXlib:NewOmex.omex/NewModel.rdf#OmexMetaId0001" [ label="OMEXlib:NewOmex.omex/NewModel.rdf#OmexMetaId0001", shape = ellipse, color = blue ];
"ROMEXlib:NewOmex.omex/NewModel.rdf#EntityProperty0000" [ label="OMEXlib:NewOmex.omex/NewModel.rdf#EntityProperty0000", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/OPB/OPB_00340" [ label="https://identifiers.org/OPB/OPB_00340", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/uniprot/P84022" [ label="https://identifiers.org/uniprot/P84022", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/fma/FMA:24178" [ label="https://identifiers.org/fma/FMA:24178", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/fma/FMA:63877" [ label="https://identifiers.org/fma/FMA:63877", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/fma/FMA:70737" [ label="https://identifiers.org/fma/FMA:70737", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/fma/FMA:7163" [ label="https://identifiers.org/fma/FMA:7163", shape = ellipse, color = blue ];
// Anonymous nodes
// Literals
label="\n\nModel:\nbase\n\nNamespaces:\nbqbiol: http://biomodels.net/biology-qualifiers/\nOMEXlib: http://omex-library.org/\nlocal: http://omex-library.org/NewOmex.omex/NewModel.rdf#\n";
}
Serializing to json-triples
{
"triples" : [
{
"subject" : {
"value" : "http://omex-library.org/NewOmex.omex/NewModel.rdf#OmexMetaId0001",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isPropertyOf",
"type" : "uri"
},
"object" : {
"value" : "http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/NewOmex.omex/NewModel.rdf#OmexMetaId0001",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isVersionOf",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/OPB/OPB_00340",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/is",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/uniprot/P84022",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isPartOf",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/fma/FMA:24178",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isPartOf",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/fma/FMA:63877",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isPartOf",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/fma/FMA:70737",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isPartOf",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/fma/FMA:7163",
"type" : "uri"
}
}
]
}
Serializing to json
{
"http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000" : {
"http://biomodels.net/biology-qualifiers/is" : [ {
"value" : "https://identifiers.org/uniprot/P84022",
"type" : "uri"
}
],
"http://biomodels.net/biology-qualifiers/isPartOf" : [ {
"value" : "https://identifiers.org/fma/FMA:24178",
"type" : "uri"
}
,
{
"value" : "https://identifiers.org/fma/FMA:63877",
"type" : "uri"
}
,
{
"value" : "https://identifiers.org/fma/FMA:70737",
"type" : "uri"
}
,
{
"value" : "https://identifiers.org/fma/FMA:7163",
"type" : "uri"
}
]
}
,
"http://omex-library.org/NewOmex.omex/NewModel.rdf#OmexMetaId0001" : {
"http://biomodels.net/biology-qualifiers/isPropertyOf" : [ {
"value" : "http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000",
"type" : "uri"
}
],
"http://biomodels.net/biology-qualifiers/isVersionOf" : [ {
"value" : "https://identifiers.org/OPB/OPB_00340",
"type" : "uri"
}
]
}
}
Serializing to nquads
<http://omex-library.org/NewOmex.omex/NewModel.rdf#OmexMetaId0001> <http://biomodels.net/biology-qualifiers/isPropertyOf> <http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000> .
<http://omex-library.org/NewOmex.omex/NewModel.rdf#OmexMetaId0001> <http://biomodels.net/biology-qualifiers/isVersionOf> <https://identifiers.org/OPB/OPB_00340> .
<http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000> <http://biomodels.net/biology-qualifiers/is> <https://identifiers.org/uniprot/P84022> .
<http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:24178> .
<http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:63877> .
<http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:70737> .
<http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:7163> .
Serializing to html
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN"
"http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>Raptor Graph Serialisation</title>
</head>
<body>
<table id="triples" border="1">
<tr>
<th>Subject</th>
<th>Predicate</th>
<th>Object</th>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/NewOmex.omex/NewModel.rdf#OmexMetaId0001">http://omex-library.org/NewOmex.omex/NewModel.rdf#OmexMetaId0001</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isPropertyOf">http://biomodels.net/biology-qualifiers/isPropertyOf</a></span></td>
<td><span class="uri"><a href="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000">http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/NewOmex.omex/NewModel.rdf#OmexMetaId0001">http://omex-library.org/NewOmex.omex/NewModel.rdf#OmexMetaId0001</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isVersionOf">http://biomodels.net/biology-qualifiers/isVersionOf</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/OPB/OPB_00340">https://identifiers.org/OPB/OPB_00340</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000">http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/is">http://biomodels.net/biology-qualifiers/is</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/uniprot/P84022">https://identifiers.org/uniprot/P84022</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000">http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isPartOf">http://biomodels.net/biology-qualifiers/isPartOf</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/fma/FMA:24178">https://identifiers.org/fma/FMA:24178</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000">http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isPartOf">http://biomodels.net/biology-qualifiers/isPartOf</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/fma/FMA:63877">https://identifiers.org/fma/FMA:63877</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000">http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isPartOf">http://biomodels.net/biology-qualifiers/isPartOf</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/fma/FMA:70737">https://identifiers.org/fma/FMA:70737</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000">http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isPartOf">http://biomodels.net/biology-qualifiers/isPartOf</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/fma/FMA:7163">https://identifiers.org/fma/FMA:7163</a></span></td>
</tr>
</table>
<p>Total number of triples: <span class="count">7</span>.</p>
</body>
</html>
Write to a string in C++
#include "omexmeta/OmexMeta.h"
#include <vector>
using namespace omexmeta;
int main() {
std::string turtle_string = "@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .\n"
"@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .\n"
"@prefix OMEXlib: <http://omex-library.org/> .\n"
"@prefix myOMEX: <http://omex-library.org/NewOmex.omex/> .\n"
"@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .\n"
"\n"
"<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001>\n"
" bqbiol:isPropertyOf local:EntityProperty0000 ;\n"
" bqbiol:isVersionOf <https://identifiers.org/OPB/OPB_00340> .\n"
"\n"
"<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000>\n"
" bqbiol:is <https://identifiers.org/uniprot/P84022> ;\n"
" 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> .\n";
// 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 `fromString`
RDF rdf = RDF::fromString(turtle_string);
std::vector<std::string> formats = {
"ntriples",
"turtle",
"rdfxml-abbrev",
"rdfxml",
"dot",
"json-triples",
"json",
"nquads",
"html"
};
for (auto &syntax: formats){
std::cout << "Serializing to " << syntax << ":" << std::endl;
std::cout << rdf.toString(syntax) << std::endl;
std::cout << std::endl;
std::cout << std::endl;
}
return 0;
}
Output
Serializing to ntriples:
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001> <http://biomodels.net/biology-qualifiers/isPropertyOf> <http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001> <http://biomodels.net/biology-qualifiers/isVersionOf> <https://identifiers.org/OPB/OPB_00340> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/is> <https://identifiers.org/uniprot/P84022> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:24178> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:63877> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:70737> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:7163> .
Serializing to turtle:
@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 local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#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> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001>
bqbiol:isPropertyOf local:EntityProperty0000 ;
bqbiol:isVersionOf <https://identifiers.org/OPB/OPB_00340> .
Serializing to rdfxml-abbrev:
<?xml version="1.1" encoding="utf-8"?>
<rdf:RDF xmlns:OMEXlib="http://omex-library.org/"
xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
xmlns:local="http://omex-library.org/NewOmex.omex/NewModel.rdf#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">
<bqbiol:is rdf:resource="https://identifiers.org/uniprot/P84022"/>
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:24178"/>
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:63877"/>
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:70737"/>
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:7163"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001">
<bqbiol:isPropertyOf rdf:resource="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/OPB/OPB_00340"/>
</rdf:Description>
</rdf:RDF>
Serializing to rdfxml:
<?xml version="1.1" encoding="utf-8"?>
<rdf:RDF xmlns:OMEXlib="http://omex-library.org/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:local="http://omex-library.org/NewOmex.omex/NewModel.rdf#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001">
<bqbiol:isPropertyOf rdf:resource="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/OPB/OPB_00340"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">
<bqbiol:is rdf:resource="https://identifiers.org/uniprot/P84022"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:24178"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:63877"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:70737"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:7163"/>
</rdf:Description>
</rdf:RDF>
Serializing to dot:
digraph {
rankdir = LR;
charset="utf-8";
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#OmexMetaId0001" -> "ROMEXlib:NewOmex.omex/NewModel.rdf#EntityProperty0000" [ label="bqbiol:isPropertyOf" ];
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#OmexMetaId0001" -> "Rhttps://identifiers.org/OPB/OPB_00340" [ label="bqbiol:isVersionOf" ];
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#EntityProperty0000" -> "Rhttps://identifiers.org/uniprot/P84022" [ label="bqbiol:is" ];
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#EntityProperty0000" -> "Rhttps://identifiers.org/fma/FMA:24178" [ label="bqbiol:isPartOf" ];
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#EntityProperty0000" -> "Rhttps://identifiers.org/fma/FMA:63877" [ label="bqbiol:isPartOf" ];
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#EntityProperty0000" -> "Rhttps://identifiers.org/fma/FMA:70737" [ label="bqbiol:isPartOf" ];
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#EntityProperty0000" -> "Rhttps://identifiers.org/fma/FMA:7163" [ label="bqbiol:isPartOf" ];
// Resources
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#OmexMetaId0001" [ label="OMEXlib:Welsh2020.omex/Welsh2020.xml#OmexMetaId0001", shape = ellipse, color = blue ];
"ROMEXlib:NewOmex.omex/NewModel.rdf#EntityProperty0000" [ label="OMEXlib:NewOmex.omex/NewModel.rdf#EntityProperty0000", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/OPB/OPB_00340" [ label="https://identifiers.org/OPB/OPB_00340", shape = ellipse, color = blue ];
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#EntityProperty0000" [ label="OMEXlib:Welsh2020.omex/Welsh2020.xml#EntityProperty0000", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/uniprot/P84022" [ label="https://identifiers.org/uniprot/P84022", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/fma/FMA:24178" [ label="https://identifiers.org/fma/FMA:24178", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/fma/FMA:63877" [ label="https://identifiers.org/fma/FMA:63877", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/fma/FMA:70737" [ label="https://identifiers.org/fma/FMA:70737", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/fma/FMA:7163" [ label="https://identifiers.org/fma/FMA:7163", shape = ellipse, color = blue ];
// Anonymous nodes
// Literals
label="\n\nModel:\nbase\n\nNamespaces:\nbqbiol: http://biomodels.net/biology-qualifiers/\nOMEXlib: http://omex-library.org/\nlocal: http://omex-library.org/NewOmex.omex/NewModel.rdf#\n";
}
Serializing to json-triples:
{
"triples" : [
{
"subject" : {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isPropertyOf",
"type" : "uri"
},
"object" : {
"value" : "http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isVersionOf",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/OPB/OPB_00340",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/is",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/uniprot/P84022",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isPartOf",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/fma/FMA:24178",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isPartOf",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/fma/FMA:63877",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isPartOf",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/fma/FMA:70737",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isPartOf",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/fma/FMA:7163",
"type" : "uri"
}
}
]
}
Serializing to json:
{
"http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000" : {
"http://biomodels.net/biology-qualifiers/is" : [ {
"value" : "https://identifiers.org/uniprot/P84022",
"type" : "uri"
}
],
"http://biomodels.net/biology-qualifiers/isPartOf" : [ {
"value" : "https://identifiers.org/fma/FMA:24178",
"type" : "uri"
}
,
{
"value" : "https://identifiers.org/fma/FMA:63877",
"type" : "uri"
}
,
{
"value" : "https://identifiers.org/fma/FMA:70737",
"type" : "uri"
}
,
{
"value" : "https://identifiers.org/fma/FMA:7163",
"type" : "uri"
}
]
}
,
"http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001" : {
"http://biomodels.net/biology-qualifiers/isPropertyOf" : [ {
"value" : "http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000",
"type" : "uri"
}
],
"http://biomodels.net/biology-qualifiers/isVersionOf" : [ {
"value" : "https://identifiers.org/OPB/OPB_00340",
"type" : "uri"
}
]
}
}
Serializing to nquads:
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001> <http://biomodels.net/biology-qualifiers/isPropertyOf> <http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001> <http://biomodels.net/biology-qualifiers/isVersionOf> <https://identifiers.org/OPB/OPB_00340> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/is> <https://identifiers.org/uniprot/P84022> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:24178> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:63877> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:70737> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:7163> .
Serializing to html:
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN"
"http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>Raptor Graph Serialisation</title>
</head>
<body>
<table id="triples" border="1">
<tr>
<th>Subject</th>
<th>Predicate</th>
<th>Object</th>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001">http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isPropertyOf">http://biomodels.net/biology-qualifiers/isPropertyOf</a></span></td>
<td><span class="uri"><a href="http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000">http://omex-library.org/NewOmex.omex/NewModel.rdf#EntityProperty0000</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001">http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isVersionOf">http://biomodels.net/biology-qualifiers/isVersionOf</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/OPB/OPB_00340">https://identifiers.org/OPB/OPB_00340</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/is">http://biomodels.net/biology-qualifiers/is</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/uniprot/P84022">https://identifiers.org/uniprot/P84022</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isPartOf">http://biomodels.net/biology-qualifiers/isPartOf</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/fma/FMA:24178">https://identifiers.org/fma/FMA:24178</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isPartOf">http://biomodels.net/biology-qualifiers/isPartOf</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/fma/FMA:63877">https://identifiers.org/fma/FMA:63877</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isPartOf">http://biomodels.net/biology-qualifiers/isPartOf</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/fma/FMA:70737">https://identifiers.org/fma/FMA:70737</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isPartOf">http://biomodels.net/biology-qualifiers/isPartOf</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/fma/FMA:7163">https://identifiers.org/fma/FMA:7163</a></span></td>
</tr>
</table>
<p>Total number of triples: <span class="count">7</span>.</p>
</body>
</html>
Write to a string in C
#include "omexmeta/OmexMeta.h"
#include "omexmeta/OmexMetaCApi.h"
using namespace omexmeta;
int main() {
const char* turtle_string = "@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .\n"
"@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .\n"
"@prefix OMEXlib: <http://omex-library.org/> .\n"
"@prefix local: <http://omex-library.org/Welsh2020.omex/Welsh2020.rdf#> .\n"
"\n"
"<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001>\n"
" bqbiol:isPropertyOf local:EntityProperty0000 ;\n"
" bqbiol:isVersionOf <https://identifiers.org/OPB/OPB_00340> .\n"
"\n"
"<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000>\n"
" bqbiol:is <https://identifiers.org/uniprot/P84022> ;\n"
" 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> .\n";
// 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 `fromString`
RDF* rdf = RDF_fromString(turtle_string, "guess");
const char* formats[9] = {
"ntriples",
"turtle",
"rdfxml-abbrev",
"rdfxml",
"dot",
"json-triples",
"json",
"nquads",
"html"
};
for (int i=0; i<9; i++){
printf("Serializing to %s: \n", formats[i]);
char* string = RDF_toString(rdf, formats[i]);
printf("%s\n", string );
printf("\n\n");
free(string);
}
RDF_delete(rdf);
return 0;
}
Output
Serializing to ntriples:
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001> <http://biomodels.net/biology-qualifiers/isPropertyOf> <http://omex-library.org/Welsh2020.omex/Welsh2020.rdf#EntityProperty0000> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001> <http://biomodels.net/biology-qualifiers/isVersionOf> <https://identifiers.org/OPB/OPB_00340> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/is> <https://identifiers.org/uniprot/P84022> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:24178> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:63877> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:70737> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:7163> .
Serializing to turtle:
@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 local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#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> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001>
bqbiol:isPropertyOf <http://omex-library.org/Welsh2020.omex/Welsh2020.rdf#EntityProperty0000> ;
bqbiol:isVersionOf <https://identifiers.org/OPB/OPB_00340> .
Serializing to rdfxml-abbrev:
<?xml version="1.1" encoding="utf-8"?>
<rdf:RDF xmlns:OMEXlib="http://omex-library.org/"
xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
xmlns:local="http://omex-library.org/NewOmex.omex/NewModel.rdf#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">
<bqbiol:is rdf:resource="https://identifiers.org/uniprot/P84022"/>
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:24178"/>
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:63877"/>
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:70737"/>
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:7163"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001">
<bqbiol:isPropertyOf rdf:resource="http://omex-library.org/Welsh2020.omex/Welsh2020.rdf#EntityProperty0000"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/OPB/OPB_00340"/>
</rdf:Description>
</rdf:RDF>
Serializing to rdfxml:
<?xml version="1.1" encoding="utf-8"?>
<rdf:RDF xmlns:OMEXlib="http://omex-library.org/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:local="http://omex-library.org/NewOmex.omex/NewModel.rdf#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001">
<bqbiol:isPropertyOf rdf:resource="http://omex-library.org/Welsh2020.omex/Welsh2020.rdf#EntityProperty0000"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/OPB/OPB_00340"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">
<bqbiol:is rdf:resource="https://identifiers.org/uniprot/P84022"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:24178"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:63877"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:70737"/>
</rdf:Description>
<rdf:Description rdf:about="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">
<bqbiol:isPartOf rdf:resource="https://identifiers.org/fma/FMA:7163"/>
</rdf:Description>
</rdf:RDF>
Serializing to dot:
digraph {
rankdir = LR;
charset="utf-8";
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#OmexMetaId0001" -> "ROMEXlib:Welsh2020.omex/Welsh2020.rdf#EntityProperty0000" [ label="bqbiol:isPropertyOf" ];
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#OmexMetaId0001" -> "Rhttps://identifiers.org/OPB/OPB_00340" [ label="bqbiol:isVersionOf" ];
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#EntityProperty0000" -> "Rhttps://identifiers.org/uniprot/P84022" [ label="bqbiol:is" ];
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#EntityProperty0000" -> "Rhttps://identifiers.org/fma/FMA:24178" [ label="bqbiol:isPartOf" ];
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#EntityProperty0000" -> "Rhttps://identifiers.org/fma/FMA:63877" [ label="bqbiol:isPartOf" ];
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#EntityProperty0000" -> "Rhttps://identifiers.org/fma/FMA:70737" [ label="bqbiol:isPartOf" ];
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#EntityProperty0000" -> "Rhttps://identifiers.org/fma/FMA:7163" [ label="bqbiol:isPartOf" ];
// Resources
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#OmexMetaId0001" [ label="OMEXlib:Welsh2020.omex/Welsh2020.xml#OmexMetaId0001", shape = ellipse, color = blue ];
"ROMEXlib:Welsh2020.omex/Welsh2020.rdf#EntityProperty0000" [ label="OMEXlib:Welsh2020.omex/Welsh2020.rdf#EntityProperty0000", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/OPB/OPB_00340" [ label="https://identifiers.org/OPB/OPB_00340", shape = ellipse, color = blue ];
"ROMEXlib:Welsh2020.omex/Welsh2020.xml#EntityProperty0000" [ label="OMEXlib:Welsh2020.omex/Welsh2020.xml#EntityProperty0000", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/uniprot/P84022" [ label="https://identifiers.org/uniprot/P84022", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/fma/FMA:24178" [ label="https://identifiers.org/fma/FMA:24178", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/fma/FMA:63877" [ label="https://identifiers.org/fma/FMA:63877", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/fma/FMA:70737" [ label="https://identifiers.org/fma/FMA:70737", shape = ellipse, color = blue ];
"Rhttps://identifiers.org/fma/FMA:7163" [ label="https://identifiers.org/fma/FMA:7163", shape = ellipse, color = blue ];
// Anonymous nodes
// Literals
label="\n\nModel:\nbase\n\nNamespaces:\nbqbiol: http://biomodels.net/biology-qualifiers/\nOMEXlib: http://omex-library.org/\nlocal: http://omex-library.org/NewOmex.omex/NewModel.rdf#\n";
}
Serializing to json-triples:
{
"triples" : [
{
"subject" : {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isPropertyOf",
"type" : "uri"
},
"object" : {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.rdf#EntityProperty0000",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isVersionOf",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/OPB/OPB_00340",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/is",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/uniprot/P84022",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isPartOf",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/fma/FMA:24178",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isPartOf",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/fma/FMA:63877",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isPartOf",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/fma/FMA:70737",
"type" : "uri"
}
},
{
"subject" : {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000",
"type" : "uri"
},
"predicate" : {
"value" : "http://biomodels.net/biology-qualifiers/isPartOf",
"type" : "uri"
},
"object" : {
"value" : "https://identifiers.org/fma/FMA:7163",
"type" : "uri"
}
}
]
}
Serializing to json:
{
"http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000" : {
"http://biomodels.net/biology-qualifiers/is" : [ {
"value" : "https://identifiers.org/uniprot/P84022",
"type" : "uri"
}
],
"http://biomodels.net/biology-qualifiers/isPartOf" : [ {
"value" : "https://identifiers.org/fma/FMA:24178",
"type" : "uri"
}
,
{
"value" : "https://identifiers.org/fma/FMA:63877",
"type" : "uri"
}
,
{
"value" : "https://identifiers.org/fma/FMA:70737",
"type" : "uri"
}
,
{
"value" : "https://identifiers.org/fma/FMA:7163",
"type" : "uri"
}
]
}
,
"http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001" : {
"http://biomodels.net/biology-qualifiers/isPropertyOf" : [ {
"value" : "http://omex-library.org/Welsh2020.omex/Welsh2020.rdf#EntityProperty0000",
"type" : "uri"
}
],
"http://biomodels.net/biology-qualifiers/isVersionOf" : [ {
"value" : "https://identifiers.org/OPB/OPB_00340",
"type" : "uri"
}
]
}
}
Serializing to nquads:
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001> <http://biomodels.net/biology-qualifiers/isPropertyOf> <http://omex-library.org/Welsh2020.omex/Welsh2020.rdf#EntityProperty0000> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001> <http://biomodels.net/biology-qualifiers/isVersionOf> <https://identifiers.org/OPB/OPB_00340> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/is> <https://identifiers.org/uniprot/P84022> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:24178> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:63877> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:70737> .
<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000> <http://biomodels.net/biology-qualifiers/isPartOf> <https://identifiers.org/fma/FMA:7163> .
Serializing to html:
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN"
"http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>Raptor Graph Serialisation</title>
</head>
<body>
<table id="triples" border="1">
<tr>
<th>Subject</th>
<th>Predicate</th>
<th>Object</th>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001">http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isPropertyOf">http://biomodels.net/biology-qualifiers/isPropertyOf</a></span></td>
<td><span class="uri"><a href="http://omex-library.org/Welsh2020.omex/Welsh2020.rdf#EntityProperty0000">http://omex-library.org/Welsh2020.omex/Welsh2020.rdf#EntityProperty0000</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001">http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isVersionOf">http://biomodels.net/biology-qualifiers/isVersionOf</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/OPB/OPB_00340">https://identifiers.org/OPB/OPB_00340</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/is">http://biomodels.net/biology-qualifiers/is</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/uniprot/P84022">https://identifiers.org/uniprot/P84022</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isPartOf">http://biomodels.net/biology-qualifiers/isPartOf</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/fma/FMA:24178">https://identifiers.org/fma/FMA:24178</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isPartOf">http://biomodels.net/biology-qualifiers/isPartOf</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/fma/FMA:63877">https://identifiers.org/fma/FMA:63877</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isPartOf">http://biomodels.net/biology-qualifiers/isPartOf</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/fma/FMA:70737">https://identifiers.org/fma/FMA:70737</a></span></td>
</tr>
<tr class="triple">
<td><span class="uri"><a href="http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000">http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000</a></span></td>
<td><span class="uri"><a href="http://biomodels.net/biology-qualifiers/isPartOf">http://biomodels.net/biology-qualifiers/isPartOf</a></span></td>
<td><span class="uri"><a href="https://identifiers.org/fma/FMA:7163">https://identifiers.org/fma/FMA:7163</a></span></td>
</tr>
</table>
<p>Total number of triples: <span class="count">7</span>.</p>
</body>
</html>
Writing to a file
Write to a file in Python
from pyomexmeta import RDF, eUriType
import os
turtle_string = """@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#> .
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)
syntax = "ntriples"
filename = os.path.join(os.path.dirname(__file__), "write_to_file.rdf")
print("Serializing to {}:".format(syntax))
print(rdf.to_file(filename, syntax))
print(f"RDF graph serialized to \"{filename}\"")
print(f"Counted \"{len(rdf)}\" triples")
# clear up file
if os.path.isfile(filename):
os.remove(filename)
# Note: printing the rdf object is the same as rdf.to_string("turtle")
Output
Serializing to ntriples:
0
RDF graph serialized to "D:\libOmexMeta\docs\write_to_file.rdf"
Counted "7" triples
Write to a file in C++
#include "omexmeta/OmexMeta.h"
#include <vector>
#include <filesystem>
using namespace omexmeta;
int main() {
std::string turtle_string = "@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .\n"
"@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .\n"
"@prefix OMEXlib: <http://omex-library.org/> .\n"
"@prefix myOMEX: <http://omex-library.org/NewOmex.omex/> .\n"
"@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .\n"
"\n"
"<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001>\n"
" bqbiol:isPropertyOf local:EntityProperty0000 ;\n"
" bqbiol:isVersionOf <https://identifiers.org/OPB/OPB_00340> .\n"
"\n"
"<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000>\n"
" bqbiol:is <https://identifiers.org/uniprot/P84022> ;\n"
" 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> .\n";
// 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 `fromString`
RDF rdf = RDF::fromString(turtle_string);
std::string syntax = "ntriples";
std::filesystem::path filename = std::filesystem::current_path() /+ "annotations.rdf";
std::cout << "Serializing to " << syntax << ":" << std::endl;
rdf.toFile(filename.string(), syntax);
std::cout << "RDF graph serialized to \"" << filename << "\"" << std::endl;
std::cout << "Counted \""<< rdf.size() <<"\" triples" << std::endl;
// clean up
if(std::filesystem::exists(filename)){
std::filesystem::remove(filename);
}
return 0;
}
Output
Serializing to ntriples:
RDF graph serialized to ""D:\\libOmexMeta\\cmake-build-release\\docs\\annotations.rdf""
Counted "7" triples
Write to a file in C
#include "omexmeta/OmexMeta.h"
#include "omexmeta/OmexMetaCApi.h"
using namespace omexmeta;
int main() {
const char* turtle_string = "@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .\n"
"@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .\n"
"@prefix OMEXlib: <http://omex-library.org/> .\n"
"@prefix local: <http://omex-library.org/Welsh2020.omex/Welsh2020.rdf#> .\n"
"\n"
"<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#OmexMetaId0001>\n"
" bqbiol:isPropertyOf local:EntityProperty0000 ;\n"
" bqbiol:isVersionOf <https://identifiers.org/OPB/OPB_00340> .\n"
"\n"
"<http://omex-library.org/Welsh2020.omex/Welsh2020.xml#EntityProperty0000>\n"
" bqbiol:is <https://identifiers.org/uniprot/P84022> ;\n"
" 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> .\n";
// 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 `fromString`
RDF* rdf = RDF_fromString(turtle_string, "guess");
const char* syntax = "ntriples";
// we cheat and use c++ for system independent filepath
std::filesystem::path p = std::filesystem::current_path() / "annotations.rdf";
std::string fname = p.string();
printf("Serializing to %s \n", syntax);
int failed = RDF_toFile(rdf, syntax, fname.c_str()); // 1 if failed else 0
if (failed) {
printf("You broke C");
exit(1);
}
printf("RDF graph serialized to \"%s\"", fname.c_str());
printf("Counted \"%d\" triples", RDF_size(rdf));
// clean up (more cheating)
if(std::filesystem::exists(fname)){
std::filesystem::remove(fname);
}
RDF_delete(rdf);
return 0;
}
Output
Serializing to ntriples
RDF graph serialized to "D:\libOmexMeta\cmake-build-release\docs\annotations.rdf"Counted "7" triples