diff --git a/service/testFiles/export_with_artifitial_comp.xml b/service/testFiles/export_with_artifitial_comp.xml index 4f66b8045188b4d56bb9f9e1c889bb486534b914..72a9a9e799cb173b0ec55b71906563eb0a6879b3 100644 --- a/service/testFiles/export_with_artifitial_comp.xml +++ b/service/testFiles/export_with_artifitial_comp.xml @@ -3422,90 +3422,6 @@ Y <title/> </head> <body> -<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"> -<rdf:Description rdf:about="#s2616"> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:refseq:NP_115903.1"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family:MAP1_LC3"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family:PTHR10969"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:ncbigene:84557"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:84557"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:isVersionOf> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pubmed:17580304"/> -</rdf:Bag> -</bqbiol:isVersionOf> -<bqbiol:isDescribedBy> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pubmed:17580304"/> -</rdf:Bag> -</bqbiol:isDescribedBy> -<bqbiol:isVersionOf> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pubmed:8833088"/> -</rdf:Bag> -</bqbiol:isVersionOf> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:refseq:NP_852610.1"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:entrez.gene:84557"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:isDescribedBy> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pubmed:8833088"/> -</rdf:Bag> -</bqbiol:isDescribedBy> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA30582"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A84557"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:hgnc:6838"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family%3AMAP1_LC3"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR10969"/> -</rdf:Bag> -</bqbiol:hasVersion> -</rdf:Description> -</rdf:RDF> </body> </html> </notes> @@ -3610,80 +3526,6 @@ Y <title/> </head> <body> -<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"> -<rdf:Description rdf:about="#s2612"> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family:APG12"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:entrez.gene:9140"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:isVersionOf> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pubmed:9852036"/> -</rdf:Bag> -</bqbiol:isVersionOf> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family:PTHR13385"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:reactome:REACT_25642"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A9140"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:refseq:NP_004698.3"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR13385"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA24879"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:isDescribedBy> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pubmed:9852036"/> -</rdf:Bag> -</bqbiol:isDescribedBy> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:ncbigene:9140"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family%3AAPG12"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:9140"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:hgnc:588"/> -</rdf:Bag> -</bqbiol:hasVersion> -</rdf:Description> -</rdf:RDF> </body> </html> </notes> @@ -3778,85 +3620,6 @@ Y <title/> </head> <body> -<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"> -<rdf:Description rdf:about="#s1747"> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:refseq:NP_115903.1"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family:MAP1_LC3"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family:PTHR10969"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:ncbigene:84557"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:84557"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:isVersionOf> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pubmed:17580304"/> -</rdf:Bag> -</bqbiol:isVersionOf> -<bqbiol:isDescribedBy> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pubmed:17580304"/> -</rdf:Bag> -</bqbiol:isDescribedBy> -<bqbiol:isVersionOf> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pubmed:8833088"/> -</rdf:Bag> -</bqbiol:isVersionOf> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:refseq:NP_852610.1"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:isDescribedBy> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pubmed:8833088"/> -</rdf:Bag> -</bqbiol:isDescribedBy> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA30582"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A84557"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:hgnc:6838"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family%3AMAP1_LC3"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR10969"/> -</rdf:Bag> -</bqbiol:hasVersion> -</rdf:Description> -</rdf:RDF> </body> </html> </notes> @@ -3976,8 +3739,19 @@ Y <title/> </head> <body> -<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"> -<rdf:Description rdf:about="#s2615"> +</body> +</html> +</notes> +<annotation> +<celldesigner:extension> +<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> +<celldesigner:speciesIdentity> +<celldesigner:class>PROTEIN</celldesigner:class> +<celldesigner:proteinReference>pr664</celldesigner:proteinReference> +</celldesigner:speciesIdentity> +</celldesigner:extension> +<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> +<rdf:Description rdf:about="#s2481"> <bqbiol:hasVersion> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:refseq:NP_001177196.1"/> @@ -3990,7 +3764,7 @@ Y </bqbiol:hasVersion> <bqbiol:hasVersion> <rdf:Bag> -<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:55054"/> +<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A55054"/> </rdf:Bag> </bqbiol:hasVersion> <bqbiol:hasVersion> @@ -4030,139 +3804,15 @@ Y </bqbiol:hasVersion> </rdf:Description> </rdf:RDF> -</body> -</html> -</notes> -<annotation> -<celldesigner:extension> -<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> -<celldesigner:speciesIdentity> -<celldesigner:class>PROTEIN</celldesigner:class> -<celldesigner:proteinReference>pr664</celldesigner:proteinReference> -</celldesigner:speciesIdentity> -</celldesigner:extension> -<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> -<rdf:Description rdf:about="#s2481"> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:refseq:NP_001177196.1"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A55054"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A55054"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:refseq:NP_110430.5"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:refseq:NP_001177195.1"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:refseq:NP_060444.3"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:refseq:NP_942593.2"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:ncbigene:55054"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:isVersionOf> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:entrez.gene:20959619"/> -</rdf:Bag> -</bqbiol:isVersionOf> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:hgnc:21498"/> -</rdf:Bag> -</bqbiol:hasVersion> -</rdf:Description> -</rdf:RDF> -</annotation> -</species> -<species metaid="s2480" id="s2480" name="ATG5" compartment="c1" initialAmount="0" charge="0"> -<notes> -<html xmlns="http://www.w3.org/1999/xhtml"> -<head> -<title/> -</head> -<body> -<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"> -<rdf:Description rdf:about="#s2614"> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR13040"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:ncbigene:9474"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:reactome:REACT_25578"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A9474"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:9474"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family%3AAPG5"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:refseq:NP_004840.1"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family:PTHR13040"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:isDescribedBy> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pubmed:9474"/> -</rdf:Bag> -</bqbiol:isDescribedBy> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:panther.family:APG5"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:hgnc:589"/> -</rdf:Bag> -</bqbiol:hasVersion> -</rdf:Description> -</rdf:RDF> +</annotation> +</species> +<species metaid="s2480" id="s2480" name="ATG5" compartment="c1" initialAmount="0" charge="0"> +<notes> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<title/> +</head> +<body> </body> </html> </notes> @@ -4242,45 +3892,6 @@ Y <title/> </head> <body> -<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"> -<rdf:Description rdf:about="#s2610"> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA134861090"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:10490"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:ncbigene:10490"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:isVersionOf> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:entrez.gene:10490"/> -</rdf:Bag> -</bqbiol:isVersionOf> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:refseq:NP_006361.1"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:hgnc:17793"/> -</rdf:Bag> -</bqbiol:hasVersion> -<bqbiol:hasVersion> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A10490"/> -</rdf:Bag> -</bqbiol:hasVersion> -</rdf:Description> -</rdf:RDF> </body> </html> </notes> @@ -4343,70 +3954,6 @@ Y <title/> </head> <body> -<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"> -<rdf:Description rdf:about="#s2609"> -<bqbiol:isDescribedBy> -<rdf:Bag> -<rdf:li rdf:resource="urn:miriam:pubmed:9614193"/> -</rdf:Bag> -</bqbiol:isDescribedBy> 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xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"> -<rdf:Description rdf:about="#s1743"> +</body> +</html> +</notes> +<annotation> +<celldesigner:extension> +<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> +<celldesigner:speciesIdentity> +<celldesigner:class>PROTEIN</celldesigner:class> +<celldesigner:proteinReference>pr649</celldesigner:proteinReference> +</celldesigner:speciesIdentity> +</celldesigner:extension> +<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> +<rdf:Description rdf:about="#s1785"> <bqbiol:isVersionOf> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:pubmed:9765397"/> @@ -5043,7 +4404,7 @@ Y </bqbiol:hasVersion> <bqbiol:hasVersion> <rdf:Bag> -<rdf:li 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