BiNoM files (Cytoscape plugin)
Presence in each of the biopax objects of the whole hierarchy of the parent classes in the ontology. Each object is mostly described according to the most generic type possible (Entity, Conversion, Interaction, Control). Its true type is in its properties via rdf:type.
Main problems:
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When we query objects with the rdfs:subClassOf* property (rdfs:subClassOf is an instance of rdf:Property), objects appear as many times as they have parent classes.
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Since the BioPAX superclass is "Entity" we have reactions that are then considered as entities.
Sound illustration: link
This project is in an unusable state (unless you remove the wrong types and restore the correct types). It's a misunderstanding of how to query an RDF Schema based ontology (RDFS).
Example of Protein:
<bp:PhysicalEntity rdf:about="http://www.biopax.org/release/biopax-level3.owl#PRKCZ_at_Cytosol">
<bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PRKCZ@Cytosol</bp:name>
<rdf:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#Entity"/>
<rdf:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#Protein"/>
</bp:PhysicalEntity>
Example of Catalysis:
<bp:Control rdf:about="http://www.biopax.org/release/biopax-level3.owl#emtc_emtc_re28_c_emtc_emtc_s3983">
<bp:controlType rdf:datatype="http://www.w3.org/2001/XMLSchema#string">INHIBITION</bp:controlType>
<bp:controller rdf:resource="http://www.biopax.org/release/biopax-level3.owl#CTBP1_2__HDAC1_HDAC3_SNAI2_at_Nucleus"/>
<bp:controlled rdf:resource="http://www.biopax.org/release/biopax-level3.owl#emtc_emtc_re28"/>
<rdf:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#Interaction"/>
<rdf:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#Entity"/>
<rdf:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#Catalysis"/>
</bp:Control>