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+<celldesigner:extension> +<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> +<celldesigner:speciesIdentity> +<celldesigner:class>PHENOTYPE</celldesigner:class> +<celldesigner:name>Apoptosis</celldesigner:name> +</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="#s20"> +<bqbiol:isEncodedBy> +<rdf:Bag> +<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0006915"/> +</rdf:Bag> +</bqbiol:isEncodedBy> +</rdf:Description> +</rdf:RDF> +</annotation> +</species> +<species metaid="s21" id="s21" name="Autophagy" compartment="c5" initialAmount="0"> +<notes> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<title/> +</head> +<body>GO:0006914 Autophagy +</body> +</html> +</notes> +<annotation> +<celldesigner:extension> +<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> +<celldesigner:speciesIdentity> +<celldesigner:class>PHENOTYPE</celldesigner:class> +<celldesigner:name>Autophagy</celldesigner:name> +</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="#s21"> +<bqbiol:isEncodedBy> +<rdf:Bag> +<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0006914"/> +</rdf:Bag> +</bqbiol:isEncodedBy> +</rdf:Description> +</rdf:RDF> +</annotation> +</species> +<species metaid="s15" id="s15" name="BCL2" compartment="c1" initialAmount="0"> +<notes> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<title/> +</head> +<body>HGNC:990 RefSeq:NM_000633 Ensembl:ENSG00000171791 Uniprot:P10415 +</body> +</html> +</notes> +<annotation> +<celldesigner:extension> +<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> +<celldesigner:speciesIdentity> +<celldesigner:class>PROTEIN</celldesigner:class> +<celldesigner:proteinReference>pr12</celldesigner:proteinReference> +<celldesigner:state> +<celldesigner:listOfModifications> +<celldesigner:modification residue="rs1" state="phosphorylated"/> +</celldesigner:listOfModifications> +</celldesigner:state> +</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="#s15"> +<bqbiol:is> +<rdf:Bag> +<rdf:li rdf:resource="urn:miriam:ncbigene:596"/> +</rdf:Bag> +</bqbiol:is> +</rdf:Description> +</rdf:RDF> +</annotation> +</species> +<species metaid="s5" id="s5" name="MAP2K4" compartment="c5" initialAmount="0"> +<notes> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<title/> +</head> +<body>alias:MEK4 alias:MKK4 HGNC:6844 RefSeq:NM_001281435 Ensembl:ENSG00000065559 Uniprot:P45985 Entrez:6416 +</body> +</html> +</notes> +<annotation> +<celldesigner:extension> +<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> +<celldesigner:speciesIdentity> +<celldesigner:class>PROTEIN</celldesigner:class> +<celldesigner:proteinReference>pr4</celldesigner:proteinReference> +<celldesigner:state> +<celldesigner:listOfModifications> +<celldesigner:modification residue="rs1" state="phosphorylated"/> +</celldesigner:listOfModifications> +</celldesigner:state> +</celldesigner:speciesIdentity> +<celldesigner:listOfCatalyzedReactions> +<celldesigner:catalyzed reaction="re4"/> +</celldesigner:listOfCatalyzedReactions> +</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="#s5"> +<bqbiol:is> +<rdf:Bag> +<rdf:li rdf:resource="urn:miriam:ncbigene:6416"/> +</rdf:Bag> +</bqbiol:is> +</rdf:Description> +</rdf:RDF> +</annotation> +</species> +<species metaid="s6" id="s6" name="MAP2K7" compartment="c5" initialAmount="0"> +<notes> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<title/> +</head> +<body>alias:MKK7 HGNC:6847 RefSeq:NM_001297555 Ensembl:ENSG00000076984 Uniprot:O14733 Entrez:5609 +</body> +</html> +</notes> +<annotation> +<celldesigner:extension> +<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> +<celldesigner:speciesIdentity> +<celldesigner:class>PROTEIN</celldesigner:class> +<celldesigner:proteinReference>pr5</celldesigner:proteinReference> +<celldesigner:state> +<celldesigner:listOfModifications> +<celldesigner:modification residue="rs1" state="phosphorylated"/> +</celldesigner:listOfModifications> +</celldesigner:state> +</celldesigner:speciesIdentity> +<celldesigner:listOfCatalyzedReactions> +<celldesigner:catalyzed reaction="re4"/> +</celldesigner:listOfCatalyzedReactions> +</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="#s6"> +<bqmodel:is> +<rdf:Bag> +<rdf:li rdf:resource="urn:miriam:ncbigene:5609"/> +</rdf:Bag> +</bqmodel:is> +</rdf:Description> +</rdf:RDF> +</annotation> +</species> +<species metaid="s37" id="s37" name="ATF2" compartment="c5" initialAmount="0"> +<notes> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<title/> +</head> +<body>HGNC:784 RefSeq:NM_001880 Ensembl:ENSG00000115966 Uniprot:P15336 Entrez:1386 +</body> +</html> +</notes> +<annotation> +<celldesigner:extension> +<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> +<celldesigner:speciesIdentity> +<celldesigner:class>PROTEIN</celldesigner:class> +<celldesigner:proteinReference>pr26</celldesigner:proteinReference> +<celldesigner:state> +<celldesigner:listOfModifications> +<celldesigner:modification residue="rs1" state="phosphorylated"/> +</celldesigner:listOfModifications> +</celldesigner:state> +</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="#s37"> +<bqbiol:is> +<rdf:Bag> +<rdf:li rdf:resource="urn:miriam:ncbigene:1386"/> +</rdf:Bag> +</bqbiol:is> +</rdf:Description> +</rdf:RDF> +</annotation> +</species> +<species metaid="s38" id="s38" name="TP53" compartment="c5" initialAmount="0"> +<notes> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<title/> +</head> +<body>alias:p53 HGNC:11998 RefSeq:NM_000546 Ensembl:ENSG00000141510 Uniprot:P04637 Entrez:7157 +</body> +</html> +</notes> +<annotation> +<celldesigner:extension> +<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> +<celldesigner:speciesIdentity> +<celldesigner:class>PROTEIN</celldesigner:class> +<celldesigner:proteinReference>pr27</celldesigner:proteinReference> +<celldesigner:state> +<celldesigner:listOfModifications> +<celldesigner:modification residue="rs1" state="phosphorylated"/> +</celldesigner:listOfModifications> +</celldesigner:state> +</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="#s38"> +<bqbiol:is> +<rdf:Bag> +<rdf:li rdf:resource="urn:miriam:ncbigene:7157"/> +</rdf:Bag> +</bqbiol:is> +</rdf:Description> +</rdf:RDF> +</annotation> +</species> +<species metaid="s46" id="s46" name="SARS-CoV-1 proteins" compartment="c2" initialAmount="0"> +<annotation> +<celldesigner:extension> +<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> +<celldesigner:speciesIdentity> +<celldesigner:class>COMPLEX</celldesigner:class> +<celldesigner:hypothetical>true</celldesigner:hypothetical> +<celldesigner:name>SARS-CoV-1 proteins</celldesigner:name> +</celldesigner:speciesIdentity> +<celldesigner:listOfCatalyzedReactions> +<celldesigner:catalyzed reaction="re2"/> +<celldesigner:catalyzed reaction="re23"/> +<celldesigner:catalyzed reaction="re37"/> +<celldesigner:catalyzed reaction="re39"/> +</celldesigner:listOfCatalyzedReactions> +</celldesigner:extension> +</annotation> +</species> +<species metaid="s40" id="s40" name="TP53 signalling" compartment="c5" initialAmount="0"> +<notes> +<html xmlns="http://www.w3.org/1999/xhtml"> +<head> +<title/> +</head> +<body>GO:0072331 signal transduction by p53 class mediator +</body> +</html> +</notes> +<annotation> +<celldesigner:extension> +<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> +<celldesigner:speciesIdentity> +<celldesigner:class>PHENOTYPE</celldesigner:class> +<celldesigner:name>TP53 signalling</celldesigner:name> +</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="#s40"> +<bqbiol:isEncodedBy> +<rdf:Bag> +<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0072331"/> +</rdf:Bag> +</bqbiol:isEncodedBy> +</rdf:Description> +</rdf:RDF> +</annotation> +</species> +<species metaid="s49" id="s49" name="MLK1/2/3" compartment="c5" initialAmount="0"> +<annotation> +<celldesigner:extension> 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name="MAP2K7" compartment="c5" initialAmount="0"> +<annotation> +<celldesigner:extension> +<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> +<celldesigner:speciesIdentity> +<celldesigner:class>PROTEIN</celldesigner:class> +<celldesigner:proteinReference>pr5</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="#s60"> +<bqmodel:is> +<rdf:Bag> +<rdf:li rdf:resource="urn:miriam:ncbigene:5609"/> +</rdf:Bag> +</bqmodel:is> +</rdf:Description> +</rdf:RDF> +</annotation> +</species> +<species metaid="s71" id="s71" name="BCL2" compartment="c1" initialAmount="0"> +<annotation> 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+<celldesigner:class>COMPLEX</celldesigner:class> +<celldesigner:hypothetical>true</celldesigner:hypothetical> +<celldesigner:name>AP-1</celldesigner:name> +</celldesigner:speciesIdentity> +</celldesigner:extension> +</annotation> +</species> +<species metaid="s90" id="s90" name="AP-1" compartment="c3" initialAmount="0"> +<annotation> +<celldesigner:extension> +<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> +<celldesigner:speciesIdentity> +<celldesigner:class>COMPLEX</celldesigner:class> +<celldesigner:hypothetical>true</celldesigner:hypothetical> +<celldesigner:name>AP-1</celldesigner:name> +</celldesigner:speciesIdentity> +</celldesigner:extension> +</annotation> +</species> +<species metaid="s94" id="s94" name="MEKK1/4" compartment="c5" initialAmount="0"> +<annotation> +<celldesigner:extension> +<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment> +<celldesigner:speciesIdentity> 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Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/ETC/ETC_stable.xml,CellDesigner_SBML,ETC Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/HMOX1%20pathway/HMOX1_Pathway_stable.xml,CellDesigner_SBML,HMOX1 pathway -Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/Interferon%20pathway/Interferon1.xml,CellDesigner_SBML,Interferon 1 pathway -Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/JNK%20pathway/JNK_pathway_V3.xml,CellDesigner_SBML,JNK pathway +Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/Interferon%20pathway/Interferon1_stable.xml,CellDesigner_SBML,Interferon 1 pathway +Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/JNK%20pathway/JNK_pathway_stable.xml,CellDesigner_SBML,JNK pathway Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/PAMP%20signalling/PAMP_signaling_stable.xml,CellDesigner_SBML,PAMP signaling Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/Pyrimidine%20deprivation/Pyrimidine_deprivation_stable.xml,CellDesigner_SBML,Pyrimidine deprivation Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/Renin-angiotensin%20pathway/Renin_angiotensin_stable.xml,CellDesigner_SBML,Renin-angiotensin pathway