- From: Matt Halstead <matt.halstead@auckland.ac.nz>
- Date: Tue, 20 Dec 2005 11:08:14 +1300
- To: www-rdf-validator@w3.org
report=Rdf validator won't draw graphs of the following RDF document. RDF=<?xml version="1.0"> <?xml version="1.0"?> <rdf:RDF xmlns:biopax="http://www.biopax.org/release/biopax-level2.owl#" xmlns="http://www.cellml.org/ontologies/cAMP_PKA_Cascade#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:psimi="http://www.biopax.org/external/psimi#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:daml="http://www.daml.org/2001/03/daml+oil#" xmlns:dc="http://purl.org/dc/elements/1.1/" xml:base="http://www.cellml.org/ontologies/cAMP_PKA_Cascade"> <owl:Ontology rdf:about=""> <owl:imports rdf:resource="http://www.biopax.org/release/biopax- level2.owl"/> <owl:imports rdf:resource="http://www.biopax.org/external/psimi"/> </owl:Ontology> <biopax:protein rdf:ID="active_gi"/> <biopax:physicalEntityParticipant rdf:ID="reaction_3_active_ac"> <biopax:PHYSICAL-ENTITY> <biopax:protein rdf:ID="active_ac"/> </biopax:PHYSICAL-ENTITY> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> <biopax:protein rdf:ID="inactive_pka"/> <biopax:protein rdf:ID="pp2a"/> <biopax:physicalEntityParticipant rdf:ID="reaction_13_active_PKA"> <biopax:PHYSICAL-ENTITY> <biopax:protein rdf:ID="active_pka"/> </biopax:PHYSICAL-ENTITY> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> <biopax:smallMolecule rdf:ID="adrenaline"/> <biopax:biochemicalReaction rdf:ID="formation_of_active_gs"> <biopax:PARTICIPANTS> <biopax:physicalEntityParticipant rdf:ID="reaction_7_inactive_gs"> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> <biopax:PHYSICAL-ENTITY> <biopax:protein rdf:ID="gs"> <rdfs:comment rdf:datatype="http://www.w3.org/2001/ XMLSchema#string" >also termed inactive_gs in the context of this model.</ rdfs:comment> </biopax:protein> </biopax:PHYSICAL-ENTITY> </biopax:physicalEntityParticipant> </biopax:PARTICIPANTS> <biopax:LEFT> <biopax:physicalEntityParticipant rdf:ID="reaction_7_adrenaline_beta_2_ar_complex"> <biopax:PHYSICAL-ENTITY> <biopax:complex rdf:ID="adrenaline_beta_2_ar_complex"/> </biopax:PHYSICAL-ENTITY> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> <rdfs:comment rdf:datatype="http://www.w3.org/2001/ XMLSchema#string" >Adrenaline needs to be bound to the beta 1 adrenaergic receptor before it can bind to the Gs. So this is a reactant.</ rdfs:comment> </biopax:physicalEntityParticipant> </biopax:LEFT> <biopax:RIGHT> <biopax:physicalEntityParticipant rdf:ID="reaction_7_active_gs"> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> <biopax:PHYSICAL-ENTITY> <biopax:protein rdf:ID="active_gs"> <rdfs:comment rdf:datatype="http://www.w3.org/2001/ XMLSchema#string" >This is an abstraction on the activation inactivation cycle of Gs.</rdfs:comment> </biopax:protein> </biopax:PHYSICAL-ENTITY> </biopax:physicalEntityParticipant> </biopax:RIGHT> <biopax:LEFT rdf:resource="#reaction_7_inactive_gs"/> <biopax:PARTICIPANTS> <biopax:physicalEntityParticipant rdf:ID="reaction_7_adrenaline_beta_1_ar_complex"> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> <biopax:PHYSICAL-ENTITY> <biopax:complex rdf:ID="adrenaline_beta_1_ar_complex"/> </biopax:PHYSICAL-ENTITY> </biopax:physicalEntityParticipant> </biopax:PARTICIPANTS> <rdfs:comment rdf:datatype="http://www.w3.org/2001/ XMLSchema#string" >This is really the formation of active_gs from inactive gs in the model.</rdfs:comment> </biopax:biochemicalReaction> <biopax:physicalEntityParticipant rdf:ID="reaction_1_adrenaline_beta_1_ar_complex"> <biopax:PHYSICAL-ENTITY rdf:resource="#adrenaline_beta_1_ar_complex"/> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> <biopax:biochemicalReaction rdf:ID="formation_of_adrenaline_beta_2_ar_complex"> <biopax:LEFT> <biopax:physicalEntityParticipant rdf:ID="reaction_2_beta_2_ar"> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> <biopax:PHYSICAL-ENTITY> <biopax:protein rdf:ID="beta_2_ar"/> </biopax:PHYSICAL-ENTITY> </biopax:physicalEntityParticipant> </biopax:LEFT> <biopax:LEFT> <biopax:physicalEntityParticipant rdf:ID="reaction_2_adrenaline"> <biopax:PHYSICAL-ENTITY rdf:resource="#adrenaline"/> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> </biopax:LEFT> <biopax:RIGHT> <biopax:physicalEntityParticipant rdf:ID="reaction_2_adrenaline_beta_2_ar_complex"> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> <biopax:PHYSICAL-ENTITY rdf:resource="#adrenaline_beta_2_ar_complex"/> </biopax:physicalEntityParticipant> </biopax:RIGHT> </biopax:biochemicalReaction> <biopax:physicalEntityParticipant rdf:ID="reaction_3_ATP"> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> <biopax:PHYSICAL-ENTITY> <biopax:smallMolecule rdf:ID="ATP"/> </biopax:PHYSICAL-ENTITY> </biopax:physicalEntityParticipant> <biopax:physicalEntityParticipant rdf:ID="reaction_3_cAMP"> <biopax:PHYSICAL-ENTITY> <biopax:smallMolecule rdf:ID="cAMP"/> </biopax:PHYSICAL-ENTITY> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> <biopax:physicalEntityParticipant rdf:ID="reaction_4_active_ac"> <biopax:PHYSICAL-ENTITY rdf:resource="#active_ac"/> </biopax:physicalEntityParticipant> <biopax:protein rdf:ID="PDE"/> <biopax:physicalEntityParticipant rdf:ID="reaction_0_ach"> <biopax:PHYSICAL-ENTITY> <biopax:smallMolecule rdf:ID="ACH"/> </biopax:PHYSICAL-ENTITY> </biopax:physicalEntityParticipant> <biopax:biochemicalReaction rdf:ID="formation_of_AMP"> <biopax:LEFT> <biopax:physicalEntityParticipant rdf:ID="reaction_12_cAMP"> <biopax:PHYSICAL-ENTITY rdf:resource="#cAMP"/> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> </biopax:LEFT> <biopax:PARTICIPANTS> <biopax:physicalEntityParticipant rdf:ID="reaction_12_pde"> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> <biopax:PHYSICAL-ENTITY rdf:resource="#PDE"/> </biopax:physicalEntityParticipant> </biopax:PARTICIPANTS> <rdfs:comment rdf:datatype="http://www.w3.org/2001/ XMLSchema#string" >The cycling out of cAMP by PDE.</rdfs:comment> <biopax:RIGHT> <biopax:physicalEntityParticipant rdf:ID="reaction_12_AMP"> <biopax:PHYSICAL-ENTITY> <biopax:smallMolecule rdf:ID="AMP"/> </biopax:PHYSICAL-ENTITY> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> </biopax:RIGHT> </biopax:biochemicalReaction> <biopax:biochemicalReaction rdf:ID="formation_of_active_pka"> <biopax:LEFT> <biopax:physicalEntityParticipant rdf:ID="reaction_14_inactive_pka"> <biopax:PHYSICAL-ENTITY rdf:resource="#inactive_pka"/> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> </biopax:LEFT> <biopax:LEFT> <biopax:physicalEntityParticipant rdf:ID="reaction_14_camp"> <biopax:PHYSICAL-ENTITY rdf:resource="#cAMP"/> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> </biopax:LEFT> <biopax:RIGHT> <biopax:physicalEntityParticipant rdf:ID="reaction_14_active_pka"> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> <biopax:PHYSICAL-ENTITY rdf:resource="#active_pka"/> </biopax:physicalEntityParticipant> </biopax:RIGHT> <rdfs:comment rdf:datatype="http://www.w3.org/2001/ XMLSchema#string" >reaction 14</rdfs:comment> </biopax:biochemicalReaction> <biopax:protein rdf:ID="l_type_calcium_channel"/> <biopax:biochemicalReaction rdf:ID="formation_of_phosphorylated_active_l_type_calcium_channel"> <biopax:LEFT> <biopax:physicalEntityParticipant rdf:ID="reaction_13_l_type_calcium_channel"> <biopax:PHYSICAL-ENTITY rdf:resource="#l_type_calcium_channel"/> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> </biopax:LEFT> <biopax:RIGHT> <biopax:physicalEntityParticipant rdf:ID="reaction_13_phosphorylated_active_l_type_calcium_channel"> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> <biopax:PHYSICAL-ENTITY> <biopax:protein rdf:ID="phosphorylated_active_l_type_calcium_channel"/> </biopax:PHYSICAL-ENTITY> </biopax:physicalEntityParticipant> </biopax:RIGHT> <biopax:PARTICIPANTS rdf:resource="#reaction_13_active_PKA"/> <rdfs:comment rdf:datatype="http://www.w3.org/2001/ XMLSchema#string" >Activation of the l type calcium channel by phosphorylation.</ rdfs:comment> <biopax:LEFT> <biopax:physicalEntityParticipant rdf:ID="reaction_13_phospahte"> <biopax:PHYSICAL-ENTITY> <biopax:smallMolecule rdf:ID="phosphate"/> </biopax:PHYSICAL-ENTITY> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> </biopax:LEFT> </biopax:biochemicalReaction> <biopax:catalysis rdf:ID="catalysis_by_ach_m2_complex_of_formation_of_active_gi"> <biopax:CONTROLLED> <biopax:biochemicalReaction rdf:ID="formation_of_active_gi"> <biopax:PARTICIPANTS> <biopax:physicalEntityParticipant rdf:ID="reaction_10_ach_m2_complex"> <biopax:PHYSICAL-ENTITY> <biopax:complex rdf:ID="ach_m2_complex"/> </biopax:PHYSICAL-ENTITY> <rdfs:comment rdf:datatype="http://www.w3.org/2001/ XMLSchema#string" >The enzyme for this reaction</rdfs:comment> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> </biopax:PARTICIPANTS> <biopax:LEFT> <biopax:physicalEntityParticipant rdf:ID="reaction_10_inactive_gi"> <biopax:PHYSICAL-ENTITY> <biopax:protein rdf:ID="inactive_gi"/> </biopax:PHYSICAL-ENTITY> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> </biopax:LEFT> <biopax:RIGHT> <biopax:physicalEntityParticipant rdf:ID="reaction_10_active_gi"> <biopax:PHYSICAL-ENTITY rdf:resource="#active_gi"/> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> </biopax:RIGHT> </biopax:biochemicalReaction> </biopax:CONTROLLED> <biopax:CONTROLLER rdf:resource="#reaction_10_ach_m2_complex"/> </biopax:catalysis> <biopax:physicalEntityParticipant rdf:ID="reaction_1_adrenaline"> <biopax:PHYSICAL-ENTITY rdf:resource="#adrenaline"/> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> <biopax:catalysis rdf:ID="catalysis_of_formation_of_AMP"> <biopax:CONTROLLED rdf:resource="#formation_of_AMP"/> <biopax:CONTROLLER rdf:resource="#reaction_12_pde"/> </biopax:catalysis> <biopax:biochemicalReaction rdf:ID="formation_of_adrenaline_beta_1_ar_complex"> <biopax:RIGHT rdf:resource="#reaction_1_adrenaline_beta_1_ar_complex"/> <biopax:LEFT rdf:resource="#reaction_1_adrenaline"/> <biopax:LEFT> <biopax:physicalEntityParticipant rdf:ID="reaction_1_beta_1_ar"> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> <biopax:PHYSICAL-ENTITY> <biopax:protein rdf:ID="beta_1_ar"/> </biopax:PHYSICAL-ENTITY> </biopax:physicalEntityParticipant> </biopax:LEFT> </biopax:biochemicalReaction> <biopax:biochemicalReaction rdf:ID="formation_of_cAMP"> <biopax:RIGHT rdf:resource="#reaction_3_cAMP"/> <biopax:PARTICIPANTS rdf:resource="#reaction_3_active_ac"/> <biopax:LEFT rdf:resource="#reaction_3_ATP"/> </biopax:biochemicalReaction> <biopax:physicalEntityParticipant rdf:ID="reaction_4_active_gs"> <biopax:PHYSICAL-ENTITY rdf:resource="#active_gs"/> </biopax:physicalEntityParticipant> <biopax:physicalEntityParticipant rdf:ID="reaction_4_inactive_ac"> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> <biopax:PHYSICAL-ENTITY> <biopax:protein rdf:ID="inactive_ac"/> </biopax:PHYSICAL-ENTITY> </biopax:physicalEntityParticipant> <biopax:smallMolecule rdf:ID="extracellular_ca"/> <biopax:physicalEntityParticipant rdf:ID="reaction_4_active_gi"> <biopax:PHYSICAL-ENTITY rdf:resource="#active_gi"/> </biopax:physicalEntityParticipant> <biopax:biochemicalReaction rdf:ID="formation_of_active_ac"> <biopax:RIGHT rdf:resource="#reaction_4_active_ac"/> <biopax:PARTICIPANTS rdf:resource="#reaction_4_active_gs"/> <biopax:LEFT rdf:resource="#reaction_4_inactive_ac"/> <biopax:PARTICIPANTS rdf:resource="#reaction_4_active_gi"/> </biopax:biochemicalReaction> <biopax:protein rdf:ID="pp1"/> <biopax:modulation rdf:ID="reaction_4_inactivation_of_ac"> <biopax:CONTROLLER rdf:resource="#reaction_4_active_gi"/> <biopax:CONTROLLED> <biopax:catalysis rdf:ID="catalysis_of_formation_of_cAMP"> <biopax:CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/ XMLSchema#string" >ACTIVATION</biopax:CONTROL-TYPE> <biopax:CONTROLLED rdf:resource="#formation_of_cAMP"/> <biopax:DIRECTION rdf:datatype="http://www.w3.org/2001/ XMLSchema#string" >IRREVERSIBLE-LEFT-TO-RIGHT</biopax:DIRECTION> <biopax:PARTICIPANTS rdf:resource="#reaction_3_active_ac"/> <biopax:CONTROLLER rdf:resource="#reaction_3_active_ac"/> </biopax:catalysis> </biopax:CONTROLLED> </biopax:modulation> <biopax:modulation rdf:ID="reaction_4_activation_of_ac"> <biopax:CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/ XMLSchema#string" >ACTIVATION</biopax:CONTROL-TYPE> <biopax:CONTROLLED rdf:resource="#catalysis_of_formation_of_cAMP"/> <biopax:CONTROLLER rdf:resource="#reaction_4_active_gs"/> </biopax:modulation> <biopax:protein rdf:ID="m2"/> <biopax:biochemicalReaction rdf:ID="formation_of_ach_m2_complex"> <biopax:LEFT> <biopax:physicalEntityParticipant rdf:ID="reaction_0_m2"> <biopax:PHYSICAL-ENTITY rdf:resource="#m2"/> </biopax:physicalEntityParticipant> </biopax:LEFT> <biopax:RIGHT> <biopax:physicalEntityParticipant rdf:ID="reaction_0_ach_m2_complex"> <biopax:PHYSICAL-ENTITY rdf:resource="#ach_m2_complex"/> <biopax:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http:// www.w3.org/2001/XMLSchema#double" >1</biopax:STOICHIOMETRIC-COEFFICIENT> </biopax:physicalEntityParticipant> </biopax:RIGHT> <biopax:LEFT rdf:resource="#reaction_0_ach"/> </biopax:biochemicalReaction> <biopax:catalysis rdf:ID="catalysis_by_adrenaline_beta_1_ar_complex_of_formation_of_active _gs"> <biopax:CONTROLLER rdf:resource="#reaction_7_adrenaline_beta_1_ar_complex"/> <biopax:CONTROLLED rdf:resource="#formation_of_active_gs"/> <biopax:DIRECTION rdf:datatype="http://www.w3.org/2001/ XMLSchema#string" >PHYSIOL-LEFT-TO-RIGHT</biopax:DIRECTION> </biopax:catalysis> <biopax:catalysis rdf:ID="catalysis_by_adrenaline_beta_2_ar_complex_of_formation_of_active _gs"> <biopax:CONTROLLED rdf:resource="#formation_of_active_gs"/> <biopax:CONTROLLER rdf:resource="#reaction_7_adrenaline_beta_2_ar_complex"/> <biopax:DIRECTION rdf:datatype="http://www.w3.org/2001/ XMLSchema#string" >PHYSIOL-LEFT-TO-RIGHT</biopax:DIRECTION> </biopax:catalysis> <biopax:smallMolecule rdf:ID="intracellular_ca"/> <biopax:catalysis rdf:ID="catalysis_of_formation_of_phosphorylated_active_l_type_calcium_c hannel"> <biopax:CONTROLLED rdf:resource="#formation_of_phosphorylated_active_l_type_calcium_channel "/> <biopax:DIRECTION rdf:datatype="http://www.w3.org/2001/ XMLSchema#string" >PHYSIOL-LEFT-TO-RIGHT</biopax:DIRECTION> <biopax:CONTROLLER rdf:resource="#reaction_13_active_PKA"/> </biopax:catalysis> </rdf:RDF> <!-- Created with Protege (with OWL Plugin 2.1, Build 284) http:// protege.stanford.edu -->
Received on Monday, 19 December 2005 22:08:33 UTC