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Commit 87c2d14f authored by cylon-x's avatar cylon-x 🤖
Browse files

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

parents ecd699d5 29f4e76f
Pipeline #37180 passed with stages
in 3 minutes and 34 seconds
......@@ -1782,7 +1782,6 @@ MESH Id is provided for the phenotype 'Apoptosis'.
<celldesigner:protein id="pr28" name="Orf3a" type="GENERIC"/>
<celldesigner:protein id="pr29" name="MAPK14" type="GENERIC"/>
<celldesigner:protein id="pr32" name="E" type="GENERIC"/>
<celldesigner:protein id="pr33" name="Orf7a" type="GENERIC"/>
<celldesigner:protein id="pr34" name="M" type="GENERIC"/>
<celldesigner:protein id="pr36" name="Orf3b" type="GENERIC"/>
<celldesigner:protein id="pr37" name="Orf8a" type="GENERIC"/>
......@@ -1790,6 +1789,7 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:protein id="pr39" name="Orf6" type="GENERIC"/>
<celldesigner:protein id="pr40" name="S" type="GENERIC"/>
<celldesigner:protein id="pr41" name="Orf9b" type="GENERIC"/>
<celldesigner:protein id="pr33" name="Orf7a" type="GENERIC"/>
</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
......@@ -2056,6 +2056,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:catalyzed reaction="re19"/>
</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="#s45">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59637"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s94" id="s94" name="E" compartment="c5" initialAmount="0">
......@@ -2070,20 +2079,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:catalyzed reaction="re23"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s39" id="s39" name="Orf7a" compartment="c5" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr33</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re23"/>
</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="#s94">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59637"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s38" id="s38" name="M" compartment="c5" initialAmount="0">
......@@ -2214,6 +2218,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:proteinReference>pr36</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="#s144">
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59633"/>
</rdf:Bag>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s145" id="s145" name="Orf8a" compartment="c5" initialAmount="0">
......@@ -2225,6 +2238,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:proteinReference>pr37</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="#s145">
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:Q7TFA0"/>
</rdf:Bag>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s146" id="s146" name="N" compartment="c5" initialAmount="0">
......@@ -2236,6 +2258,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:proteinReference>pr38</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="#s146">
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59595"/>
</rdf:Bag>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s147" id="s147" name="Orf6" compartment="c5" initialAmount="0">
......@@ -2247,6 +2278,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:proteinReference>pr39</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="#s147">
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59634"/>
</rdf:Bag>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s148" id="s148" name="S" compartment="c5" initialAmount="0">
......@@ -2258,6 +2298,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:proteinReference>pr40</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="#s148">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59594"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s149" id="s149" name="Orf9b" compartment="c5" initialAmount="0">
......@@ -2269,6 +2318,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:proteinReference>pr41</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="#s149">
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59636"/>
</rdf:Bag>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s150" id="s150" name="BAD" compartment="c5" initialAmount="0">
......@@ -2361,6 +2419,38 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
</celldesigner:extension>
</annotation>
</species>
<species metaid="s39" id="s39" name="Orf7a" compartment="c5" initialAmount="0" charge="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>COVID19 Disease Map
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr33</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re23"/>
</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="#s39">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:Q19QW4"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
<reaction metaid="re1" id="re1" reversible="false">
......@@ -2738,7 +2828,7 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
</celldesigner:linkTarget>
<celldesigner:line width="3.0" color="ff000000"/>
</celldesigner:modification>
<celldesigner:modification type="INHIBITION" modifiers="s116" aliases="sa29" targetLineIndex="-1,7" editPoints="0.0025603618302028064,0.020742578188163163 0.9875528009624692,-0.1008400438617616">
<celldesigner:modification type="INHIBITION" modifiers="s116" aliases="sa29" targetLineIndex="-1,7" editPoints="0.0025603618302028064,0.020742578188163385 0.9875528009624693,-0.10084004386176137">
<celldesigner:connectScheme connectPolicy="square">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="vertical"/>
......@@ -2927,7 +3017,7 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
</celldesigner:linkTarget>
<celldesigner:line width="3.0" color="ff000000"/>
</celldesigner:modification>
<celldesigner:modification type="INHIBITION" modifiers="s156" aliases="csa11" targetLineIndex="-1,2" editPoints="0.07210651322633788,0.0028511662646293345 0.0736675660903392,-0.03662814449375329">
<celldesigner:modification type="INHIBITION" modifiers="s156" aliases="csa11" targetLineIndex="-1,2" editPoints="0.07210651322633832,0.0028511662646293345 0.07366756609033964,-0.03662814449375329">
<celldesigner:connectScheme connectPolicy="square">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="vertical"/>
......
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......@@ -1022,23 +1022,6 @@ Uniprot O14561
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s209" name="Fe-S">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body/>
</html>
</celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s210</celldesigner:complexSpecies>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>Fe-S</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s206" name="SDHA">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
......@@ -1163,23 +1146,6 @@ Uniprot O14561
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s255" name="BCS1">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body/>
</html>
</celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s267</celldesigner:complexSpecies>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr107</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s256" name="UQCR10">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
......@@ -1758,7 +1724,7 @@ Uniprot O14561
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s357" name="ATPIF1">
<celldesigner:species id="s357" name="ATP5IF1">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
......@@ -2251,7 +2217,7 @@ Uniprot O14561
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s459" name="GARS">
<celldesigner:species id="s459" name="GARS1">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
......@@ -2268,7 +2234,7 @@ Uniprot O14561
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s460" name="KARS">
<celldesigner:species id="s460" name="KARS1">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
......@@ -2353,7 +2319,7 @@ Uniprot O14561
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s467" name="MTRNR1">
<celldesigner:species id="s467" name="MT-RNR1">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
......@@ -2693,23 +2659,6 @@ Uniprot O14561
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s490" name="POLG1">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body/>
</html>
</celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s1111</celldesigner:complexSpecies>
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<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr241</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s491" name="POLG2">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
......@@ -3105,23 +3054,6 @@ Uniprot P49821
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s536" name="Fe-S">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body/>
</html>
</celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s263</celldesigner:complexSpecies>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>Fe-S</celldesigner:name>
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</celldesigner:species>
<celldesigner:species id="s537" name="FAD">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
......@@ -3241,23 +3173,6 @@ Uniprot P49821
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s674" name="Fe-S">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body/>
</html>
</celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s667</celldesigner:complexSpecies>
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<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>Fe-S</celldesigner:name>
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</celldesigner:species>
<celldesigner:species id="s675" name="FAD">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
......@@ -3438,23 +3353,6 @@ Uniprot P49821
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s686" name="Fe-S">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body/>
</html>
</celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s684</celldesigner:complexSpecies>
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<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>Fe-S</celldesigner:name>
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<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
......@@ -4588,7 +4486,7 @@ Mutations in COX15 produce a defect in the mitochondrial heme biosynthetic pathw
</celldesigner:speciesIdentity>
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<celldesigner:species id="s1156" name="TIMM54">
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<html xmlns="http://www.w3.org/1999/xhtml">
<head>
......@@ -4598,14 +4496,14 @@ Mutations in COX15 produce a defect in the mitochondrial heme biosynthetic pathw
</html>
</celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s1153</celldesigner:complexSpecies>
<celldesigner:complexSpecies>s1154</celldesigner:complexSpecies>
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<html xmlns="http://www.w3.org/1999/xhtml">
<head>
......@@ -4615,14 +4513,14 @@ Mutations in COX15 produce a defect in the mitochondrial heme biosynthetic pathw
</html>
</celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s1153</celldesigner:complexSpecies>
<celldesigner:complexSpecies>s1154</celldesigner:complexSpecies>
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<html xmlns="http://www.w3.org/1999/xhtml">
<head>
......@@ -4632,14 +4530,14 @@ Mutations in COX15 produce a defect in the mitochondrial heme biosynthetic pathw
</html>
</celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s1153</celldesigner:complexSpecies>
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<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
......@@ -4649,14 +4547,14 @@ Mutations in COX15 produce a defect in the mitochondrial heme biosynthetic pathw
</html>
</celldesigner:notes>
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