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COVID-19
models
Commits
be673a43
Commit
be673a43
authored
Feb 22, 2021
by
Marek Ostaszewski
Browse files
compartment harmonisation
parent
5d849b0e
Changes
22
Expand all
Hide whitespace changes
Inline
Side-by-side
Curation/Apoptosis/Apoptosis_stable.xml
View file @
be673a43
...
...
@@ -389,7 +389,7 @@ MESH Id is provided for the phenotype 'Apoptosis'.
<celldesigner:compartmentAlias
id=
"ca4"
compartment=
"c4"
>
<celldesigner:class>
SQUARE
</celldesigner:class>
<celldesigner:bounds
x=
"80.0"
y=
"75.0"
w=
"1220.0"
h=
"135.0"
/>
<celldesigner:namePoint
x=
"11
4
5.5"
y=
"82.0"
/>
<celldesigner:namePoint
x=
"115
6
.5"
y=
"82.0"
/>
<celldesigner:doubleLine
thickness=
"6.0"
outerWidth=
"5.0"
innerWidth=
"2.0"
/>
<celldesigner:paint
color=
"ffff6666"
scheme=
"Color"
/>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
...
...
@@ -397,7 +397,7 @@ MESH Id is provided for the phenotype 'Apoptosis'.
<celldesigner:compartmentAlias
id=
"ca5"
compartment=
"c5"
>
<celldesigner:class>
SQUARE
</celldesigner:class>
<celldesigner:bounds
x=
"80.0"
y=
"210.0"
w=
"1220.0"
h=
"885.0"
/>
<celldesigner:namePoint
x=
"12
09.5
"
y=
"1064.0"
/>
<celldesigner:namePoint
x=
"12
30.0
"
y=
"1064.0"
/>
<celldesigner:doubleLine
thickness=
"6.0"
outerWidth=
"5.0"
innerWidth=
"2.0"
/>
<celldesigner:paint
color=
"ffff6666"
scheme=
"Color"
/>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
...
...
@@ -405,7 +405,7 @@ MESH Id is provided for the phenotype 'Apoptosis'.
<celldesigner:compartmentAlias
id=
"ca6"
compartment=
"c6"
>
<celldesigner:class>
OVAL
</celldesigner:class>
<celldesigner:bounds
x=
"910.0"
y=
"866.25"
w=
"380.0"
h=
"187.5"
/>
<celldesigner:namePoint
x=
"1080.
5
"
y=
"1008.0"
/>
<celldesigner:namePoint
x=
"1080.
0
"
y=
"1008.0"
/>
<celldesigner:doubleLine
thickness=
"12.0"
outerWidth=
"2.0"
innerWidth=
"1.0"
/>
<celldesigner:paint
color=
"ff333300"
scheme=
"Color"
/>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
...
...
@@ -1829,32 +1829,59 @@ MESH Id is provided for the phenotype 'Apoptosis'.
</listOfUnitDefinitions>
<listOfCompartments>
<compartment
metaid=
"default"
id=
"default"
size=
"1"
units=
"volume"
/>
<compartment
metaid=
"c
4
"
id=
"c
4
"
name=
"
Plasma membran
e"
size=
"1"
units=
"volume"
outside=
"
c7
"
>
<compartment
metaid=
"c
7
"
id=
"c
7
"
name=
"
extracellular spac
e"
size=
"1"
units=
"volume"
outside=
"
default
"
>
<annotation>
<celldesigner:extension>
<celldesigner:name>
Plasma membran
e
</celldesigner:name>
<celldesigner:name>
extracellular spac
e
</celldesigner:name>
</celldesigner:extension>
</annotation>
</compartment>
<compartment
metaid=
"c
5
"
id=
"c
5
"
name=
"
Cytoplasm
"
size=
"
0.5
"
units=
"volume"
outside=
"c
7
"
>
<compartment
metaid=
"c
6
"
id=
"c
6
"
name=
"
mitochondrion
"
size=
"
1
"
units=
"volume"
outside=
"c
5
"
>
<annotation>
<celldesigner:extension>
<celldesigner:name>
Cytoplasm
</celldesigner:name>
<celldesigner:name>
mitochondrion
</celldesigner:name>
</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=
"#c6"
>
<bqbiol:is>
<rdf:Bag>
<rdf:li
rdf:resource=
"urn:miriam:obo.go:GO%3A0005739"
/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
<compartment
metaid=
"c
7
"
id=
"c
7
"
name=
"
Extracellular spac
e"
size=
"1"
units=
"volume"
outside=
"
default
"
>
<compartment
metaid=
"c
4
"
id=
"c
4
"
name=
"
cell membran
e"
size=
"1"
units=
"volume"
outside=
"
c7
"
>
<annotation>
<celldesigner:extension>
<celldesigner:name>
Extracellular spac
e
</celldesigner:name>
<celldesigner:name>
cell membran
e
</celldesigner:name>
</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=
"#c4"
>
<bqbiol:is>
<rdf:Bag>
<rdf:li
rdf:resource=
"urn:miriam:obo.go:GO%3A0005886"
/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
<compartment
metaid=
"c
6
"
id=
"c
6
"
name=
"
Mitochondrion
"
size=
"
1
"
units=
"volume"
outside=
"c
5
"
>
<compartment
metaid=
"c
5
"
id=
"c
5
"
name=
"
cell
"
size=
"
0.5
"
units=
"volume"
outside=
"c
7
"
>
<annotation>
<celldesigner:extension>
<celldesigner:name>
Mitochondrion
</celldesigner:name>
<celldesigner:name>
cell
</celldesigner:name>
</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=
"#c5"
>
<bqbiol:is>
<rdf:Bag>
<rdf:li
rdf:resource=
"urn:miriam:obo.go:GO%3A0005737"
/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
...
...
@@ -3017,7 +3044,7 @@ MESH Id is provided for the phenotype 'Apoptosis'.
</celldesigner:linkTarget>
<celldesigner:line
width=
"3.0"
color=
"ff000000"
/>
</celldesigner:modification>
<celldesigner:modification
type=
"INHIBITION"
modifiers=
"s156"
aliases=
"csa11"
targetLineIndex=
"-1,2"
editPoints=
"0.072106513226338
32
,0.0028511662646293345 0.0736675660903396
4
,-0.03662814449375329"
>
<celldesigner:modification
type=
"INHIBITION"
modifiers=
"s156"
aliases=
"csa11"
targetLineIndex=
"-1,2"
editPoints=
"0.072106513226338
54
,0.0028511662646293345 0.073667566090339
8
6,-0.03662814449375329"
>
<celldesigner:connectScheme
connectPolicy=
"square"
>
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection
index=
"0"
value=
"vertical"
/>
...
...
Curation/Coagulation pathway/Coagulation-pathway_stable.xml
View file @
be673a43
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Click to expand it.
Curation/ER Stress/ER_Stress_stable.xml
View file @
be673a43
This diff is collapsed.
Click to expand it.
Curation/ETC/ETC_stable.xml
View file @
be673a43
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instead.
Curation/HMOX1 pathway/HMOX1_Pathway_stable.xml
View file @
be673a43
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Click to expand it.
Curation/Inflammasomes/NLRP3_Activation_stable.xml
View file @
be673a43
...
...
@@ -689,7 +689,7 @@
<celldesigner:compartmentAlias
id=
"ca1"
compartment=
"c1"
>
<celldesigner:class>
SQUARE
</celldesigner:class>
<celldesigner:bounds
x=
"2411.5"
y=
"1180.0"
w=
"485.0"
h=
"320.0"
/>
<celldesigner:namePoint
x=
"27
73.5
"
y=
"1198.5"
/>
<celldesigner:namePoint
x=
"27
89.0
"
y=
"1198.5"
/>
<celldesigner:doubleLine
thickness=
"12.0"
outerWidth=
"2.0"
innerWidth=
"1.0"
/>
<celldesigner:paint
color=
"ffcccc00"
scheme=
"Color"
/>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
...
...
@@ -697,7 +697,7 @@
<celldesigner:compartmentAlias
id=
"ca2"
compartment=
"c2"
>
<celldesigner:class>
SQUARE
</celldesigner:class>
<celldesigner:bounds
x=
"454.0"
y=
"340.0"
w=
"2640.0"
h=
"2160.0"
/>
<celldesigner:namePoint
x=
"4
82
.5"
y=
"1358.5"
/>
<celldesigner:namePoint
x=
"4
93
.5"
y=
"1358.5"
/>
<celldesigner:doubleLine
thickness=
"12.0"
outerWidth=
"2.0"
innerWidth=
"1.0"
/>
<celldesigner:paint
color=
"ffcccc00"
scheme=
"Color"
/>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
...
...
@@ -705,7 +705,7 @@
<celldesigner:compartmentAlias
id=
"ca3"
compartment=
"c3"
>
<celldesigner:class>
SQUARE
</celldesigner:class>
<celldesigner:bounds
x=
"900.875"
y=
"1177.1875"
w=
"146.25"
h=
"145.625"
/>
<celldesigner:namePoint
x=
"
917.8
75"
y=
"1204.0625"
/>
<celldesigner:namePoint
x=
"
886.3
75"
y=
"1204.0625"
/>
<celldesigner:doubleLine
thickness=
"12.0"
outerWidth=
"2.0"
innerWidth=
"1.0"
/>
<celldesigner:paint
color=
"ffcccc00"
scheme=
"Color"
/>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
...
...
@@ -713,7 +713,7 @@
<celldesigner:compartmentAlias
id=
"ca4"
compartment=
"c4"
>
<celldesigner:class>
SQUARE
</celldesigner:class>
<celldesigner:bounds
x=
"1070.875"
y=
"1046.6875"
w=
"146.25"
h=
"150.625"
/>
<celldesigner:namePoint
x=
"10
84.8
75"
y=
"1074.5625"
/>
<celldesigner:namePoint
x=
"10
12.3
75"
y=
"1074.5625"
/>
<celldesigner:doubleLine
thickness=
"12.0"
outerWidth=
"2.0"
innerWidth=
"1.0"
/>
<celldesigner:paint
color=
"ffcccc00"
scheme=
"Color"
/>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
...
...
@@ -721,7 +721,7 @@
<celldesigner:compartmentAlias
id=
"ca5"
compartment=
"c5"
>
<celldesigner:class>
SQUARE
</celldesigner:class>
<celldesigner:bounds
x=
"834.0"
y=
"1410.0"
w=
"140.0"
h=
"150.0"
/>
<celldesigner:namePoint
x=
"8
85.0
"
y=
"1523.5"
/>
<celldesigner:namePoint
x=
"8
43.5
"
y=
"1523.5"
/>
<celldesigner:doubleLine
thickness=
"12.0"
outerWidth=
"2.0"
innerWidth=
"1.0"
/>
<celldesigner:paint
color=
"ffcccc00"
scheme=
"Color"
/>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
...
...
@@ -729,7 +729,7 @@
<celldesigner:compartmentAlias
id=
"ca6"
compartment=
"c6"
>
<celldesigner:class>
SQUARE
</celldesigner:class>
<celldesigner:bounds
x=
"794.0"
y=
"1380.0"
w=
"220.0"
h=
"210.0"
/>
<celldesigner:namePoint
x=
"862.
5
"
y=
"155
3
.5"
/>
<celldesigner:namePoint
x=
"862.
0
"
y=
"155
4
.5"
/>
<celldesigner:doubleLine
thickness=
"12.0"
outerWidth=
"2.0"
innerWidth=
"1.0"
/>
<celldesigner:paint
color=
"ffcccc00"
scheme=
"Color"
/>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
...
...
@@ -3023,46 +3023,100 @@
</listOfUnitDefinitions>
<listOfCompartments>
<compartment
metaid=
"default"
id=
"default"
size=
"1"
units=
"volume"
/>
<compartment
metaid=
"c
1
"
id=
"c
1
"
name=
"
Nucleoplasm
"
size=
"1"
units=
"volume"
outside=
"c
2
"
>
<compartment
metaid=
"c
5
"
id=
"c
5
"
name=
"
mitochondrial matrix
"
size=
"1"
units=
"volume"
outside=
"c
6
"
>
<annotation>
<celldesigner:extension>
<celldesigner:name>
Nucleoplasm
</celldesigner:name>
<celldesigner:name>
mitochondrial matrix
</celldesigner:name>
</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=
"#c5"
>
<bqbiol:is>
<rdf:Bag>
<rdf:li
rdf:resource=
"urn:miriam:obo.go:GO%3A0005759"
/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
<compartment
metaid=
"c
2
"
id=
"c
2
"
name=
"
Cytosol
"
size=
"1"
units=
"volume"
outside=
"
default
"
>
<compartment
metaid=
"c
6
"
id=
"c
6
"
name=
"
mitochondrion
"
size=
"1"
units=
"volume"
outside=
"
c2
"
>
<annotation>
<celldesigner:extension>
<celldesigner:name>
Cytosol
</celldesigner:name>
<celldesigner:name>
mitochondrion
</celldesigner:name>
</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=
"#c6"
>
<bqbiol:is>
<rdf:Bag>
<rdf:li
rdf:resource=
"urn:miriam:obo.go:GO%3A0005739"
/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
<compartment
metaid=
"c3"
id=
"c3"
name=
"Golgi"
size=
"1"
units=
"volume"
outside=
"c2"
>
<compartment
metaid=
"c3"
id=
"c3"
name=
"Golgi
apparatus
"
size=
"1"
units=
"volume"
outside=
"c2"
>
<annotation>
<celldesigner:extension>
<celldesigner:name>
Golgi
</celldesigner:name>
<celldesigner:name>
Golgi
apparatus
</celldesigner:name>
</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=
"#c3"
>
<bqbiol:is>
<rdf:Bag>
<rdf:li
rdf:resource=
"urn:miriam:obo.go:GO%3A0005794"
/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
<compartment
metaid=
"c4"
id=
"c4"
name=
"
ERGIC
"
size=
"1"
units=
"volume"
outside=
"c2"
>
<compartment
metaid=
"c4"
id=
"c4"
name=
"
endoplasmic reticulum-Golgi intermediate compartment
"
size=
"1"
units=
"volume"
outside=
"c2"
>
<annotation>
<celldesigner:extension>
<celldesigner:name>
ERGIC
</celldesigner:name>
<celldesigner:name>
endoplasmic reticulum-Golgi intermediate compartment
</celldesigner:name>
</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=
"#c4"
>
<bqbiol:is>
<rdf:Bag>
<rdf:li
rdf:resource=
"urn:miriam:obo.go:GO%3A0005793"
/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
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...
...
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...
...
Curation/Interferon lambda pathway/IFN-lambda_stable.xml
View file @
be673a43
This diff is collapsed.
Click to expand it.
Curation/Interferon pathway/Interferon1_stable.xml
View file @
be673a43
...
...
@@ -1130,7 +1130,7 @@ SIGNOR-SCISOVG
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Curation/JNK pathway/JNK_pathway_stable.xml
View file @
be673a43
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