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Commit d175914c authored by Marek Ostaszewski's avatar Marek Ostaszewski
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Curation/Inflammasomes/NLRP3_Activation_COVID19_V3.xml 0 → 100644
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Curation/SARS-CoV-2 proteins/Orf3a/Orf3a_stable.xml
View file @ d175914c
......@@ -6,8 +6,11 @@
<head>
<title/>
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<body>Author(s):
<body>
Author:
Muhammed Naveez, Riga Technical University, Latvia
Description:
Interactions of the SARS-CoV-2 Orf3a with human proteins, especially in the context of the HOPS Complex.
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......@@ -3252,7 +3255,7 @@ ORF3A Map
<title/>
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<body>CHNAGE NAME IRF6=LPS
TNFRSF1A=TNKFa
TNFRSF1A=TNKFa
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</notes>
......@@ -4860,7 +4863,7 @@ A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Pote
<head>
<title/>
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<body>TRIM59 inhibition
<body>TRIM59 inhibition
PMID 22588174
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......@@ -4944,7 +4947,7 @@ PMID 22588174
<title/>
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<body>TRAF6 PMID:20724660
TRIM 38 PMID: 22539786
TRIM 38 PMID: 22539786
TRIM 23 PMID: 20724660
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......
Curation/Virus replication cycle/Virus_replication_cycle_stable.xml
View file @ d175914c
......@@ -225,7 +225,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
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<species metaid="s3582" id="s3582" name="NRP1" compartment="c182" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr68</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s3583" id="s3583" name="cholesterol" compartment="c182" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>cholesterol</celldesigner:name>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re855"/>
</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="#s3583">
<bqbiol:isEncodedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A16113"/>
</rdf:Bag>
</bqbiol:isEncodedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s3586" id="s3586" name="S1:NRP1 complex" compartment="c182" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>COMPLEX</celldesigner:class>
<celldesigner:name>S1:NRP1 complex</celldesigner:name>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re855"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s2597" id="s2597" name="S1" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>http://www.ebi.ac.uk/interpro/entry/InterPro/IPR002551/
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr16</celldesigner:proteinReference>
<celldesigner:state>
<celldesigner:listOfStructuralStates>
<celldesigner:structuralState structuralState="CendR"/>
</celldesigner:listOfStructuralStates>
</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="#s2597">
<bqbiol:isEncodedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:interpro:IPR002551"/>
</rdf:Bag>
</bqbiol:isEncodedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
<reaction metaid="re838" id="re838" reversible="false">
......@@ -8214,8 +8470,8 @@ N: P0DTC9
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s3575" alias="csa430">
<celldesigner:linkAnchor position="W"/>
<celldesigner:baseProduct species="s3578" alias="csa430">
<celldesigner:linkAnchor position="WNW"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:listOfReactantLinks>
......@@ -8244,8 +8500,21 @@ N: P0DTC9
<celldesigner:lineDirection index="1" value="horizontal"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:editPoints>0.007305296885112722,-0.08657327589951591</celldesigner:editPoints>
<celldesigner:editPoints>0.01829671538654365,-0.08341579853126224</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ff000000"/>
<celldesigner:listOfModification>
<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="s3581" aliases="sa2369" targetLineIndex="-1,3">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:linkTarget species="s3581" alias="sa2369">
<celldesigner:linkAnchor position="N"/>
</celldesigner:linkTarget>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:modification>
</celldesigner:listOfModification>
</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="#re838">
......@@ -8264,6 +8533,11 @@ N: P0DTC9
<rdf:li rdf:resource="urn:miriam:taxonomy:2697049"/>
</rdf:Bag>
</bqbiol:occursIn>
<bqmodel:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:32970989"/>
</rdf:Bag>
</bqmodel:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
......@@ -8291,7 +8565,7 @@ N: P0DTC9
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00003" species="s3575">
<speciesReference metaid="CDMT00003" species="s3578">
<annotation>
<celldesigner:extension>
<celldesigner:alias>csa430</celldesigner:alias>
......@@ -8299,6 +8573,15 @@ N: P0DTC9
</annotation>
</speciesReference>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference metaid="CDMT00004" species="s3581">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa2369</celldesigner:alias>
</celldesigner:extension>
</annotation>
</modifierSpeciesReference>
</listOfModifiers>
</reaction>
<reaction metaid="re841" id="re841" reversible="false">
<annotation>
......@@ -8324,14 +8607,14 @@ N: P0DTC9
<celldesigner:editPoints>-0.02834811847187066,-0.23528938331652638 0.9573436829303237,-0.3540474316783113</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ff000000"/>
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<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="s3575" aliases="csa430" targetLineIndex="-1,3" editPoints="0.006061686025350621,-0.07762049979148866">
<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="s3578" aliases="csa430" targetLineIndex="-1,3" editPoints="0.006061686025350621,-0.07762049979148866">
<celldesigner:connectScheme connectPolicy="square">
<celldesigner:listOfLineDirection>