Merge branch 'repo_update' of https://git-r3lab.uni.lu/covid/models into repo_update

Curation/JNK pathway/JNK_pathway_stable.xml

@@ -2330,6 +2330,15 @@ Uniprot:P0QGFD
 <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="#s105">
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P59632"/>
+</rdf:Bag>
+</bqmodel:is>
+</rdf:Description>
+</rdf:RDF>
 </annotation>
 </species>
 <species metaid="s104" id="s104" name="7a" compartment="c2" initialAmount="0">
@@ -2344,6 +2353,15 @@ Uniprot:P0QGFD
 <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="#s104">
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P59635"/>
+</rdf:Bag>
+</bqmodel:is>
+</rdf:Description>
+</rdf:RDF>
 </annotation>
 </species>
 <species metaid="s106" id="s106" name="S" compartment="c2" initialAmount="0">
@@ -2368,6 +2386,15 @@ Uniprot:P0QGFD
 <celldesigner:catalyzed reaction="re42"/>
 </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="#s106">
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P59594"/>
+</rdf:Bag>
+</bqmodel:is>
+</rdf:Description>
+</rdf:RDF>
 </annotation>
 </species>
 <species metaid="s103" id="s103" name="3b" compartment="c2" initialAmount="0">
@@ -2382,6 +2409,15 @@ Uniprot:P0QGFD
 <celldesigner:catalyzed reaction="re36"/>
 </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="#s103">
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P59633"/>
+</rdf:Bag>
+</bqmodel:is>
+</rdf:Description>
+</rdf:RDF>
 </annotation>
 </species>
 </listOfSpecies>
@@ -2414,7 +2450,7 @@ Uniprot:P0QGFD
 </celldesigner:connectScheme>
 <celldesigner:line width="1.0" color="ff000000"/>
 <celldesigner:listOfModification>
-<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="s49" aliases="csa2" targetLineIndex="-1,4" editPoints="0.6490041839468192,-0.29949358690347117">
+<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="s49" aliases="csa2" targetLineIndex="-1,4" editPoints="0.6490041839468192,-0.29949358690347183">
 <celldesigner:connectScheme connectPolicy="direct">
 <celldesigner:listOfLineDirection>
 <celldesigner:lineDirection index="0" value="unknown"/>
@@ -3290,7 +3326,7 @@ Uniprot:P0QGFD
 </celldesigner:linkTarget>
 <celldesigner:line width="1.0" color="ff000000"/>
 </celldesigner:modification>
-<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="s6" aliases="sa5" targetLineIndex="-1,4" editPoints="0.3049969275981761,-0.14963021895091022">
+<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="s6" aliases="sa5" targetLineIndex="-1,4" editPoints="0.3049969275981761,-0.14963021895091067">
 <celldesigner:connectScheme connectPolicy="direct">
 <celldesigner:listOfLineDirection>
 <celldesigner:lineDirection index="0" value="unknown"/>

Executable Modules/SBML_qual_build/sif/Apoptosis_stable.sif

-# Generated by CaSQ v0.9.5
+# Generated by CaSQ v0.9.6
 FAS/FASL_complex POSITIVE FADD
 BAD/BBC3/BCL2L11_complex POSITIVE BAX
 BCL2/MCL1/BCL2L1_complex POSITIVE BAD/BBC3/BCL2L11_complex

Executable Modules/SBML_qual_build/sif/Apoptosis_stable_raw.sif

-# Generated by CaSQ v0.9.5
+# Generated by CaSQ v0.9.6
 csa2 POSITIVE sa9
 csa3 POSITIVE sa30
 csa11 POSITIVE csa3

Executable Modules/SBML_qual_build/sif/Coagulation-pathway_stable.sif

-# Generated by CaSQ v0.9.5
+# Generated by CaSQ v0.9.6
 KNG1:KLKB1_complex POSITIVE Kininogen
 KNG1:KLKB1_complex POSITIVE Kallikrein
 KNG1:KLKB1_complex POSITIVE Bradykinin
@@ -160,11 +160,11 @@ cytokine_storm_phenotype POSITIVE IL1B
 cytokine_storm_phenotype POSITIVE IL8
 cytokine_storm_phenotype POSITIVE IL2RA
 IL1B POSITIVE Thrombosis_phenotype_Blood
+IL8 POSITIVE Thrombosis_phenotype_Blood
+IL2RA POSITIVE Thrombosis_phenotype_Blood
+CRP POSITIVE Thrombosis_phenotype_Blood
 C4d POSITIVE Thrombosis_phenotype_Blood
 C4d POSITIVE C4d_deposition_phenotype
-CRP POSITIVE Thrombosis_phenotype_Blood
-IL2RA POSITIVE Thrombosis_phenotype_Blood
-IL8 POSITIVE Thrombosis_phenotype_Blood
 C3 POSITIVE C3a
 C3 POSITIVE C3b
 MASP1 POSITIVE C2a
@@ -185,8 +185,8 @@ ACE2_Endothelium,_vascular POSITIVE angiotensin_I-7_simple_molecule
 Fibrin_monomer POSITIVE Fibrin_polymer
 F13a POSITIVE Fibrin_polymer
 platelet_activation_phenotype POSITIVE thrombus_formation_phenotype
+MAS1 NEGATIVE thrombus_formation_phenotype
 AGTR1_Platelet POSITIVE thrombus_formation_phenotype
-MAS1 POSITIVE thrombus_formation_phenotype
 K+_ion POSITIVE aldosterone_simple_molecule_Blood
 ACTH_simple_molecule POSITIVE aldosterone_simple_molecule_Blood
 aldosterone_simple_molecule_Endothelium,_vascular POSITIVE NR3C2