Commit c9ffbab3 authored by Marek Ostaszewski's avatar Marek Ostaszewski
Browse files

resources update

parent 46624171
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" level="2" version="4">
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
<model metaid="JNK_signaling_pathway" id="JNK_signaling_pathway">
<annotation>
<celldesigner:extension>
......@@ -246,6 +246,42 @@ alias:MLK1 alias:MEKK9 HGNC:6861 RefSeq:NM_001284230 Ensembl:ENSG00000006432 Uni
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s42" name="S protein">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>
Uniprot:P0QGFD
</body>
</html>
</celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s46</celldesigner:complexSpecies>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr28</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s44" name="N protein">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body/>
</html>
</celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s46</celldesigner:complexSpecies>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr29</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
</celldesigner:listOfIncludedSpecies>
<celldesigner:listOfCompartmentAliases>
<celldesigner:compartmentAlias id="ca1" compartment="c1">
......@@ -366,6 +402,27 @@ alias:MLK1 alias:MEKK9 HGNC:6861 RefSeq:NM_001284230 Ensembl:ENSG00000006432 Uni
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:complexSpeciesAlias>
<celldesigner:complexSpeciesAlias id="csa5" species="s46">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="950.0" y="1174.0" w="192.0" h="186.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:backupSize w="0.0" h="0.0"/>
<celldesigner:backupView state="none"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="192.0" height="186.0"/>
<celldesigner:singleLine width="2.0"/>
<celldesigner:paint color="fff7f7f7" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="2.0"/>
<celldesigner:paint color="fff7f7f7" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:complexSpeciesAlias>
</celldesigner:listOfComplexSpeciesAliases>
<celldesigner:listOfSpeciesAliases>
<celldesigner:speciesAlias id="sa1" species="s1" complexSpeciesAlias="csa1">
......@@ -643,7 +700,7 @@ alias:MLK1 alias:MEKK9 HGNC:6861 RefSeq:NM_001284230 Ensembl:ENSG00000006432 Uni
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="167.0" height="37.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffff0000" scheme="Color"/>
<celldesigner:paint color="ffffcccc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
......@@ -748,6 +805,44 @@ alias:MLK1 alias:MEKK9 HGNC:6861 RefSeq:NM_001284230 Ensembl:ENSG00000006432 Uni
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa37" species="s42" complexSpeciesAlias="csa5">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="962.1764705882354" y="1184.1764705882356" w="95.0" h="36.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="12.176470588235361" y="10.176470588235588"/>
<celldesigner:boxSize width="95.0" height="36.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffffcccc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa38" species="s44" complexSpeciesAlias="csa5">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="963.1764705882354" y="1230.1764705882356" w="95.0" h="36.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="13.176470588235361" y="56.17647058823559"/>
<celldesigner:boxSize width="95.0" height="36.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffffcccc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/>
<celldesigner:listOfProteins>
......@@ -827,6 +922,8 @@ alias:MLK1 alias:MEKK9 HGNC:6861 RefSeq:NM_001284230 Ensembl:ENSG00000006432 Uni
<celldesigner:modificationResidue angle="1.1780972450961724" id="rs1" side="none"/>
</celldesigner:listOfModificationResidues>
</celldesigner:protein>
<celldesigner:protein id="pr28" name="S protein" type="GENERIC"/>
<celldesigner:protein id="pr29" name="N protein" type="GENERIC"/>
</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
......@@ -1163,6 +1260,18 @@ alias:MLK1 alias:MEKK9 HGNC:6861 RefSeq:NM_001284230 Ensembl:ENSG00000006432 Uni
</celldesigner:extension>
</annotation>
</species>
<species metaid="s46" id="s46" name="SARS-CoV-1 proteins" compartment="default" 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:extension>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
<reaction metaid="re1" id="re1" reversible="false">
......
Include,Resource,Type,Name
No,https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4846.gpml,GPML,WP4846
No,https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4853.gpml,GPML,WP4853
Yes,https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4853.gpml,GPML,Linoleic acid metabolism
No,https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4860.gpml,GPML,WP4860
No,https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4861.gpml,GPML,WP4861
No,https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4862.gpml,GPML,WP4862
Yes,https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4863.gpml,GPML,HCoVs autophagy (WP4863)
Yes,https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4868.gpml,GPML,HCoVs ER stress (WP4869)
Yes,https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4869.gpml,GPML,Type I Ifn signaling (WP4868)
Yes,https://git-r3lab.uni.lu/covid/models/raw/master/Curation/Ubiquination%20and%20Protein%20Degradation/Orf10_Cul2_pathway.xml,CellDesigner_SBML,Orf10 Cul2 pathway
Yes,https://git-r3lab.uni.lu/covid/models/raw/master/Curation/Innate%20Immunity%20and%20Proinflammatory%20Response/COVID19_PAMP_signaling.xml,CellDesigner_SBML,PAMP signaling
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/Virus%20replication%20cycle/Virus_replication_cycle_V06.xml,CellDesigner_SBML,Virus replication cycle
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/RTC-and-transcription/RTC-and-transcription-CD.xml,CellDesigner_SBML,RTC and transcription
Yes,https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4868.gpml,GPML,HCoVs Type I Ifn signaling (WP4868)
Yes,https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4880.gpml,GPML,HCoVs Ifn induction (WP4880)
Yes,https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4869.gpml,GPML,HCoVs ER stress (WP4869)
Yes,https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4876.gpml,GPML,SARS-CoV-2 NLRP3 Inflammasome (WP4876)
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/Apoptosis/Apoptosis_VS_SSA_AN.xml,CellDesigner_SBML,Apoptosis
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/Drug%20mechanisms/Role_of_spike_ACE2_interaction_in_pulmonary_blood_pressure_regulation_v3.xml,CellDesigner_SBML,ACE2-Spike-drugs
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/ER%20Stress/ER_Stress_Cov19.xml,CellDesigner_SBML,ER stress
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/Interferon%20pathway/Interferon2.xml,CellDesigner_SBML,Interferon 1 pathway
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/ETC/ETC_Covid19.xml,CellDesigner_SBML,ETC
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/HMOX1%20pathway/HMOX1_Pathway_Updated.xml,CellDesigner_SBML,HMOX1 pathway
Yes,https://git-r3lab.uni.lu/covid/models/raw/master/Curation/Innate%20Immunity%20and%20Proinflammatory%20Response/COVID19_PAMP_signaling.xml,CellDesigner_SBML,PAMP signaling
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.xml,CellDesigner_SBML,JNK pathway
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/RTC-and-transcription/RTC-and-transcription-CD.xml,CellDesigner_SBML,RTC and transcription
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/SARS-CoV-2%20proteins/E/E_SARS_CoV_2_22_05_2020.xml,CellDesigner_SBML,E protein interactions
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/SARS-CoV-2%20proteins/Nsp4_Nsp6/Nsp4_Nsp6_v2.xml,CellDesigner_SBML,Nsp4 and Nsp6 interactions
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/SARS-CoV-2%20proteins/Nsp9/Nsp9.xml,CellDesigner_SBML,Nsp9 interactions
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/SARS-CoV-2%20proteins/Nsp14/Nsp14.xml,CellDesigner_SBML,Nsp14 and metabolism
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/HMOX1%20pathway/HMOX1%20pathway.xml,CellDesigner_SBML,HMOX1 pathway
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/ETC/ETC_Covid19.xml,CellDesigner_SBML,ETC
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/SARS-CoV-2%20proteins/E/E_SARS_CoV_2.xml,CellDesigner_SBML,E protein interactions
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/SARS-CoV-2%20proteins/Orf3a/Orf3a.xml,CellDesigner_SBML,Orf3a interactions
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/SARS-CoV-2%20proteins/Nsp9/Nsp9.xml,CellDesigner_SBML,Nsp9 interactions
Yes,https://git-r3lab.uni.lu/covid/models/raw/master/Curation/Ubiquination%20and%20Protein%20Degradation/Orf10_Cul2_pathway.xml,CellDesigner_SBML,Orf10 Cul2 pathway
Yes,https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/Virus%20replication%20cycle/Virus_replication_cycle_V07.xml,CellDesigner_SBML,Virus replication cycle
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