OWL File Formats

The instances of a BioPAX ontology, represented in RDF, that conform to an OWL ontology can be expressed in a number of file formats. BioPAX recommends the use of RDF/XML-ABBREV because it generally results in smaller file sizes compared to other ways of writing out RDF/XML and is more human readable. It is also the default format for OWL in Protege, likely for similar reasons. For instance, the Protege OWL editor and the Jena OWL API both support input and output of 4 formats:

RDF/XML-ABBREV
The abbreviated form of RDF/XML attempts to make the RDF graph or network into a hierarchy. It is usually not possible to do this, so the output file is usually only partially hierarchical. This format follows the rules of the RDF/XML specification, but additional rules are built into Jena to make the format more hierarchical.

Protege 3.0 enforces the file extension ".owl" for this OWL format, reflecting the fact that this is the de facto standard way of writing RDF/XML in the context of OWL.

Example:       Escherichia coli   562 taxon   </bp:bioSource> <bp:dataSource rdf:ID="dataSource16"> <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Swiss-Prot/TrEMBL</bp:NAME> </bp:dataSource> <bp:protein rdf:ID="protein45"> <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >PHI</bp:SYNONYMS> <bp:DATA-SOURCE rdf:resource="#dataSource16"/> <bp:XREF> <bp:unificationXref rdf:ID="unificationXref47"> <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Q9KH85</bp:ID> Swiss-Prot/TrEMBL</bp:DB> </bp:unificationXref> </bp:XREF> <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >PGI</bp:SHORT-NAME> <bp:DATA-SOURCE> <bp:dataSource rdf:ID="dataSource14"> <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >aMAZE</bp:NAME> </bp:dataSource> </bp:DATA-SOURCE> <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GPI</bp:SYNONYMS> <bp:AVAILABILITY rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY> <bp:XREF> <bp:unificationXref rdf:ID="unificationXref46"> <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >aMAZEPolypeptide0000050740</bp:ID> aMAZE</bp:DB> </bp:unificationXref> </bp:XREF> <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Phosphohexose isomerase</bp:SYNONYMS> <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >phosphoglucose isomerase</bp:NAME> <bp:SEQUENCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >KTFSEAIISGEWKGYTGKAITDVVNIGIGGSDLGPYMVTEALRPYKNHLNMHFVSNVDGTHIAEVLKKVNPETTLFLVASKTFTTQETMTNAHSARDWFLKAAGDEKHVAKHFAALSTNAKAVGEFGIDTANMFEFWDWVGGRYSLWSAIGLSIVLSIGFDNFVELLSGAHAMDKHFSTTPAEKNLPVLLALIGIWYNNFFGAETEAILPYDQYMHRFAAYFQQGNMESNGKYVDRNGNVVDYQTGPIIWGEPGTNGQHAFYQLIHQGTKMVPCDFIAPAITHNPLFDHHQKLLSKFFAQTEALAFGKSREVVEQEYRDQGKDPAT</bp:SEQUENCE> <bp:ORGANISM rdf:resource="#bioSource33"/> <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Glucose-6-phosphate isomerase</bp:SYNONYMS> </bp:protein> <bp:dataSource rdf:ID="dataSource15"> <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >KEGG</bp:NAME> </bp:dataSource> <bp:unificationXref rdf:ID="unificationXref16"> <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0005737</bp:ID> Gene Ontology</bp:DB> </bp:unificationXref> <bp:openControlledVocabulary rdf:ID="openControlledVocabulary15"> <bp:XREF rdf:resource="#unificationXref16"/> <bp:TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >cytoplasm</bp:TERM> </bp:openControlledVocabulary> </rdf:RDF>

RDF/XML
The simple (or normal) way of writing out RDF/XML according to the RDF/XML specification separates each BioPAX instance so that no instance is nested inside of another instance.

Protege 3.0 enforces the file extension ".rdf-xml.owl" for this OWL format.

Example: <rdf:Description rdf:about="#bioSource33"> <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Escherichia coli</bp:NAME> <bp:TAXON-XREF rdf:resource="#unificationXref34"/> <rdf:type rdf:resource="http://www.biopax.org/release/biopax-level1.owl#bioSource"/> </rdf:Description> <rdf:Description rdf:about="#dataSource16"> <rdf:type rdf:resource="http://www.biopax.org/release/biopax-level1.owl#dataSource"/> <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Swiss-Prot/TrEMBL</bp:NAME> </rdf:Description> <rdf:Description rdf:about="#protein45"> <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHI</bp:SYNONYMS> <bp:DATA-SOURCE rdf:resource="#dataSource16"/> <bp:XREF rdf:resource="#unificationXref47"/> <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PGI</bp:SHORT-NAME> <bp:DATA-SOURCE rdf:resource="#dataSource14"/> <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GPI</bp:SYNONYMS> <bp:AVAILABILITY rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY> <bp:XREF rdf:resource="#unificationXref46"/> <rdf:type rdf:resource="http://www.biopax.org/release/biopax-level1.owl#protein"/> <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphohexose isomerase</bp:SYNONYMS> <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">phosphoglucose isomerase</bp:NAME> <bp:SEQUENCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KTFSEAIISGEWKGYTGKAITDVVNIGIGGSDLGPYMVTEALRPYKNHLNMHFVSNVDGTHIAEVLKKVNPETTLFLVASKTFTTQETMTNAHSARDWFLKAAGDEKHVAKHFAALSTNAKAVGEFGIDTANMFEFWDWVGGRYSLWSAIGLSIVLSIGFDNFVELLSGAHAMDKHFSTTPAEKNLPVLLALIGIWYNNFFGAETEAILPYDQYMHRFAAYFQQGNMESNGKYVDRNGNVVDYQTGPIIWGEPGTNGQHAFYQLIHQGTKMVPCDFIAPAITHNPLFDHHQKLLSKFFAQTEALAFGKSREVVEQEYRDQGKDPAT</bp:SEQUENCE> <bp:ORGANISM rdf:resource="#bioSource33"/> <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glucose-6-phosphate isomerase</bp:SYNONYMS> </rdf:Description> <rdf:Description rdf:about="#unificationXref46"> <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZEPolypeptide0000050740</bp:ID> aMAZE</bp:DB> <rdf:type rdf:resource="http://www.biopax.org/release/biopax-level1.owl#unificationXref"/> </rdf:Description> <rdf:Description rdf:about=""> <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level1.owl"/> <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Ontology"/> </rdf:Description> <rdf:Description rdf:about="#dataSource15"> <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:NAME> <rdf:type rdf:resource="http://www.biopax.org/release/biopax-level1.owl#dataSource"/> </rdf:Description> <rdf:Description rdf:about="#unificationXref16"> <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO:0005737</bp:ID> Gene Ontology</bp:DB> <rdf:type rdf:resource="http://www.biopax.org/release/biopax-level1.owl#unificationXref"/> </rdf:Description> <rdf:Description rdf:about="#unificationXref34"> <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">562</bp:ID> <rdf:type rdf:resource="http://www.biopax.org/release/biopax-level1.owl#unificationXref"/> taxon</bp:DB> </rdf:Description> <rdf:Description rdf:about="#openControlledVocabulary15"> <bp:XREF rdf:resource="#unificationXref16"/> <rdf:type rdf:resource="http://www.biopax.org/release/biopax-level1.owl#openControlledVocabulary"/> <bp:TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cytoplasm</bp:TERM> </rdf:Description> <rdf:Description rdf:about="#unificationXref47"> <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q9KH85</bp:ID> Swiss-Prot/TrEMBL</bp:DB> <rdf:type rdf:resource="http://www.biopax.org/release/biopax-level1.owl#unificationXref"/> </rdf:Description> <rdf:Description rdf:about="#dataSource14"> <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:NAME> <rdf:type rdf:resource="http://www.biopax.org/release/biopax-level1.owl#dataSource"/> </rdf:Description> </rdf:RDF>

N-TRIPLE
See the N-TRIPLE specification for more information.

Protege 3.0 enforces the file extension ".ntriple.owl" for this OWL format.

Example: <http://www.biopax.org/examples/simple-demo-pathway#bioSource33> <http://www.biopax.org/release/biopax-level1.owl#NAME> "Escherichia coli"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#bioSource33> <http://www.biopax.org/release/biopax-level1.owl#TAXON-XREF> <http://www.biopax.org/examples/simple-demo-pathway#unificationXref34>. <http://www.biopax.org/examples/simple-demo-pathway#bioSource33> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.biopax.org/release/biopax-level1.owl#bioSource>. <http://www.biopax.org/examples/simple-demo-pathway#protein45> <http://www.biopax.org/release/biopax-level1.owl#SYNONYMS> "PHI"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#protein45> <http://www.biopax.org/release/biopax-level1.owl#DATA-SOURCE> <http://www.biopax.org/examples/simple-demo-pathway#dataSource16>. <http://www.biopax.org/examples/simple-demo-pathway#protein45> <http://www.biopax.org/release/biopax-level1.owl#XREF> <http://www.biopax.org/examples/simple-demo-pathway#unificationXref47>. <http://www.biopax.org/examples/simple-demo-pathway#protein45> <http://www.biopax.org/release/biopax-level1.owl#SHORT-NAME> "PGI"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#protein45> <http://www.biopax.org/release/biopax-level1.owl#DATA-SOURCE> <http://www.biopax.org/examples/simple-demo-pathway#dataSource14>. <http://www.biopax.org/examples/simple-demo-pathway#protein45> <http://www.biopax.org/release/biopax-level1.owl#SYNONYMS> "GPI"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#protein45> <http://www.biopax.org/release/biopax-level1.owl#AVAILABILITY> "see http://www.amaze.ulb.ac.be/"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#protein45> <http://www.biopax.org/release/biopax-level1.owl#XREF> <http://www.biopax.org/examples/simple-demo-pathway#unificationXref46>. <http://www.biopax.org/examples/simple-demo-pathway#protein45> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.biopax.org/release/biopax-level1.owl#protein>. <http://www.biopax.org/examples/simple-demo-pathway#protein45> <http://www.biopax.org/release/biopax-level1.owl#SYNONYMS> "Phosphohexose isomerase"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#protein45> <http://www.biopax.org/release/biopax-level1.owl#NAME> "phosphoglucose isomerase"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#protein45> <http://www.biopax.org/release/biopax-level1.owl#SEQUENCE> "KTFSEAIISGEWKGYTGKAITDVVNIGIGGSDLGPYMVTEALRPYKNHLNMHFVSNVDGTHIAEVLKKVNPETTLFLVASKTFTTQETMTNAHSARDWFLKAAGDEKHVAKHFAALSTNAKAVGEFGIDTANMFEFWDWVGGRYSLWSAIGLSIVLSIGFDNFVELLSGAHAMDKHFSTTPAEKNLPVLLALIGIWYNNFFGAETEAILPYDQYMHRFAAYFQQGNMESNGKYVDRNGNVVDYQTGPIIWGEPGTNGQHAFYQLIHQGTKMVPCDFIAPAITHNPLFDHHQKLLSKFFAQTEALAFGKSREVVEQEYRDQGKDPAT"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#protein45> <http://www.biopax.org/release/biopax-level1.owl#ORGANISM> <http://www.biopax.org/examples/simple-demo-pathway#bioSource33>. <http://www.biopax.org/examples/simple-demo-pathway#protein45> <http://www.biopax.org/release/biopax-level1.owl#SYNONYMS> "Glucose-6-phosphate isomerase"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#dataSource16> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.biopax.org/release/biopax-level1.owl#dataSource>. <http://www.biopax.org/examples/simple-demo-pathway#dataSource16> <http://www.biopax.org/release/biopax-level1.owl#NAME> "Swiss-Prot/TrEMBL"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#unificationXref46> <http://www.biopax.org/release/biopax-level1.owl#ID> "aMAZEPolypeptide0000050740"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#unificationXref46> <http://www.biopax.org/release/biopax-level1.owl#DB> "aMAZE"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#unificationXref46> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.biopax.org/release/biopax-level1.owl#unificationXref>. <http://www.biopax.org/examples/simple-demo-pathway#dataSource15> <http://www.biopax.org/release/biopax-level1.owl#NAME> "KEGG"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#dataSource15> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.biopax.org/release/biopax-level1.owl#dataSource>. <http://www.biopax.org/examples/simple-demo-pathway> <http://www.w3.org/2002/07/owl#imports> <http://www.biopax.org/release/biopax-level1.owl>. <http://www.biopax.org/examples/simple-demo-pathway> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Ontology>. <http://www.biopax.org/examples/simple-demo-pathway#unificationXref16> <http://www.biopax.org/release/biopax-level1.owl#ID> "GO:0005737"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#unificationXref16> <http://www.biopax.org/release/biopax-level1.owl#DB> "Gene Ontology"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#unificationXref16> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.biopax.org/release/biopax-level1.owl#unificationXref>. <http://www.biopax.org/examples/simple-demo-pathway#unificationXref47> <http://www.biopax.org/release/biopax-level1.owl#ID> "Q9KH85"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#unificationXref47> <http://www.biopax.org/release/biopax-level1.owl#DB> "Swiss-Prot/TrEMBL"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#unificationXref47> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.biopax.org/release/biopax-level1.owl#unificationXref>. <http://www.biopax.org/examples/simple-demo-pathway#openControlledVocabulary15> <http://www.biopax.org/release/biopax-level1.owl#XREF> <http://www.biopax.org/examples/simple-demo-pathway#unificationXref16>. <http://www.biopax.org/examples/simple-demo-pathway#openControlledVocabulary15> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.biopax.org/release/biopax-level1.owl#openControlledVocabulary>. <http://www.biopax.org/examples/simple-demo-pathway#openControlledVocabulary15> <http://www.biopax.org/release/biopax-level1.owl#TERM> "cytoplasm"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#unificationXref34> <http://www.biopax.org/release/biopax-level1.owl#ID> "562"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#unificationXref34> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.biopax.org/release/biopax-level1.owl#unificationXref>. <http://www.biopax.org/examples/simple-demo-pathway#unificationXref34> <http://www.biopax.org/release/biopax-level1.owl#DB> "taxon"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#dataSource14> <http://www.biopax.org/release/biopax-level1.owl#NAME> "aMAZE"^^<http://www.w3.org/2001/XMLSchema#string>. <http://www.biopax.org/examples/simple-demo-pathway#dataSource14> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.biopax.org/release/biopax-level1.owl#dataSource>.

N3
N3 is a shorthand notation for writing RDF/XML (+ some non-RDF/XML constructs) that Tim Berners-Lee invented in 1998. It is not a standard, but a number of tools support this format, since it is easy to manually write out. Some BioPAX users have found this format easier to comprehend and write out using Perl scripts, which can then convert the N3 to abbreviated RDF/XML.

See the N3 specification for more information.

Protege 3.0 enforces the file extension ".n3.owl" for this OWL format.

Example: default:bioSource33 a      bp:bioSource ; bp:NAME "Escherichia coli"^^xs:string ; bp:TAXON-XREF default:unificationXref34.

default:dataSource16 a      bp:dataSource ; bp:NAME "Swiss-Prot/TrEMBL"^^xs:string.

default:protein45 a      bp:protein ; bp:AVAILABILITY "see http://www.amaze.ulb.ac.be/"^^xs:string ; bp:DATA-SOURCE default:dataSource16, default:dataSource14 ; bp:NAME "phosphoglucose isomerase"^^xs:string ; bp:ORGANISM default:bioSource33 ; bp:SEQUENCE "KTFSEAIISGEWKGYTGKAITDVVNIGIGGSDLGPYMVTEALRPYKNHLNMHFVSNVDGTHIAEVLKKVNPETTLFLVASKTFTTQETMTNAHSARDWFLKAAGDEKHVAKHFAALSTNAKAVGEFGIDTANMFEFWDWVGGRYSLWSAIGLSIVLSIGFDNFVELLSGAHAMDKHFSTTPAEKNLPVLLALIGIWYNNFFGAETEAILPYDQYMHRFAAYFQQGNMESNGKYVDRNGNVVDYQTGPIIWGEPGTNGQHAFYQLIHQGTKMVPCDFIAPAITHNPLFDHHQKLLSKFFAQTEALAFGKSREVVEQEYRDQGKDPAT"^^xs:string ; bp:SHORT-NAME "PGI"^^xs:string ; bp:SYNONYMS "GPI"^^xs:string, "Phosphohexose isomerase"^^xs:string , "PHI"^^xs:string , "Glucose-6-phosphate isomerase"^^xs:string ; bp:XREF default:unificationXref46, default:unificationXref47.

default:unificationXref46 a      bp:unificationXref ; bp:DB  "aMAZE"^^xs:string ; bp:ID  "aMAZEPolypeptide0000050740"^^xs:string.

<http://www.biopax.org/examples/simple-demo-pathway> a      owl:Ontology ; owl:imports <http://www.biopax.org/release/biopax-level1.owl>.

default:dataSource15 a      bp:dataSource ; bp:NAME "KEGG"^^xs:string.

default:unificationXref16 a      bp:unificationXref ; bp:DB  "Gene Ontology"^^xs:string ; bp:ID  "GO:0005737"^^xs:string.

default:unificationXref34 a      bp:unificationXref ; bp:DB  "taxon"^^xs:string ; bp:ID  "562"^^xs:string.

default:openControlledVocabulary15 a      bp:openControlledVocabulary ; bp:TERM "cytoplasm"^^xs:string ; bp:XREF default:unificationXref16.

default:unificationXref47 a      bp:unificationXref ; bp:DB  "Swiss-Prot/TrEMBL"^^xs:string ; bp:ID  "Q9KH85"^^xs:string.

default:dataSource14 a      bp:dataSource ; bp:NAME "aMAZE"^^xs:string.