Commit be673a43 authored by Marek Ostaszewski's avatar Marek Ostaszewski

compartment harmonisation

parent 5d849b0e
......@@ -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="1145.5" y="82.0"/>
<celldesigner:namePoint x="1156.5" 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 &apos;Apoptosis&apos;.
<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="1209.5" y="1064.0"/>
<celldesigner:namePoint x="1230.0" 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 &apos;Apoptosis&apos;.
<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 &apos;Apoptosis&apos;.
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="default" id="default" size="1" units="volume"/>
<compartment metaid="c4" id="c4" name="Plasma membrane" size="1" units="volume" outside="c7">
<compartment metaid="c7" id="c7" name="extracellular space" size="1" units="volume" outside="default">
<annotation>
<celldesigner:extension>
<celldesigner:name>Plasma membrane</celldesigner:name>
<celldesigner:name>extracellular space</celldesigner:name>
</celldesigner:extension>
</annotation>
</compartment>
<compartment metaid="c5" id="c5" name="Cytoplasm" size="0.5" units="volume" outside="c7">
<compartment metaid="c6" id="c6" name="mitochondrion" size="1" units="volume" outside="c5">
<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="c7" id="c7" name="Extracellular space" size="1" units="volume" outside="default">
<compartment metaid="c4" id="c4" name="cell membrane" size="1" units="volume" outside="c7">
<annotation>
<celldesigner:extension>
<celldesigner:name>Extracellular space</celldesigner:name>
<celldesigner:name>cell membrane</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="c6" id="c6" name="Mitochondrion" size="1" units="volume" outside="c5">
<compartment metaid="c5" id="c5" name="cell" size="0.5" units="volume" outside="c7">
<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 &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="0.07210651322633832,0.0028511662646293345 0.07366756609033964,-0.03662814449375329">
<celldesigner:modification type="INHIBITION" modifiers="s156" aliases="csa11" targetLineIndex="-1,2" editPoints="0.07210651322633854,0.0028511662646293345 0.07366756609033986,-0.03662814449375329">
<celldesigner:connectScheme connectPolicy="square">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="vertical"/>
......
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......@@ -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="2773.5" y="1198.5"/>
<celldesigner:namePoint x="2789.0" 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="482.5" y="1358.5"/>
<celldesigner:namePoint x="493.5" 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="917.875" y="1204.0625"/>
<celldesigner:namePoint x="886.375" 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="1084.875" y="1074.5625"/>
<celldesigner:namePoint x="1012.375" 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="885.0" y="1523.5"/>
<celldesigner:namePoint x="843.5" 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="1553.5"/>
<celldesigner:namePoint x="862.0" y="1554.5"/>
<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="c1" id="c1" name="Nucleoplasm" size="1" units="volume" outside="c2">
<compartment metaid="c5" id="c5" name="mitochondrial matrix" size="1" units="volume" outside="c6">
<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="c2" id="c2" name="Cytosol" size="1" units="volume" outside="default">
<compartment metaid="c6" id="c6" 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>
</rdf:RDF>
</annotation>
</compartment>
<compartment metaid="c5" id="c5" name="Matrix" size="1" units="volume" outside="c6">
<compartment metaid="c1" id="c1" name="nucleus" size="1" units="volume" outside="c2">
<annotation>
<celldesigner:extension>
<celldesigner:name>Matrix</celldesigner:name>
<celldesigner:name>nucleus</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="#c1">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0005634"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
<compartment metaid="c6" id="c6" name="Mitochondrion" size="1" units="volume" outside="c2">
<compartment metaid="c2" id="c2" name="cell" size="1" units="volume" outside="default">
<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="#c2">
<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>
......@@ -6485,7 +6539,7 @@ https://identifiers.org/reactome:R-HSA-844612.2
<celldesigner:lineDirection index="3" value="horizontal"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:editPoints>0.011535894963253579,-0.04269850397662012 0.011836428044637248,-0.04261730867147051 0.0683274279638395,-0.25171085471848986</celldesigner:editPoints>
<celldesigner:editPoints>0.011535894963254023,-0.04269850397662012 0.011836428044637692,-0.04261730867147051 0.0683274279638395,-0.25171085471848986</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
</celldesigner:productLink>
<celldesigner:productLink product="s832" alias="sa102" targetLineIndex="-1,1">
......
......@@ -571,7 +571,7 @@ Uniprot:P0QGFD
<celldesigner:compartmentAlias id="ca1" compartment="c1">
<celldesigner:class>SQUARE</celldesigner:class>
<celldesigner:bounds x="953.0" y="675.0" w="317.0" h="155.0"/>
<celldesigner:namePoint x="1103.5" y="792.5"/>
<celldesigner:namePoint x="1099.5" y="792.5"/>
<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
<celldesigner:paint color="ffcccc00" scheme="Color"/>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
......@@ -579,7 +579,7 @@ Uniprot:P0QGFD
<celldesigner:compartmentAlias id="ca2" compartment="c2">
<celldesigner:class>SQUARE</celldesigner:class>
<celldesigner:bounds x="30.0" y="30.0" w="1746.0" h="1069.0"/>
<celldesigner:namePoint x="1243.0" y="977.0"/>
<celldesigner:namePoint x="1237.0" y="977.0"/>
<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
<celldesigner:paint color="ffcccc00" scheme="Color"/>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
......@@ -587,7 +587,7 @@ Uniprot:P0QGFD
<celldesigner:compartmentAlias id="ca3" compartment="c3">
<celldesigner:class>SQUARE</celldesigner:class>
<celldesigner:bounds x="917.0" y="382.0" w="402.0" h="203.0"/>
<celldesigner:namePoint x="1183.5" y="548.5"/>
<celldesigner:namePoint x="1184.5" y="548.5"/>
<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
<celldesigner:paint color="ffcccc00" scheme="Color"/>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
......@@ -595,7 +595,7 @@ Uniprot:P0QGFD
<celldesigner:compartmentAlias id="ca5" compartment="c5">
<celldesigner:class>SQUARE</celldesigner:class>
<celldesigner:bounds x="56.0" y="208.0" w="1661.0" h="814.0"/>
<celldesigner:namePoint x="348.0" y="860.5"/>
<celldesigner:namePoint x="368.5" y="860.5"/>
<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
<celldesigner:paint color="ffcccc00" scheme="Color"/>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
......@@ -1750,32 +1750,59 @@ Uniprot:P0QGFD
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="default" id="default" size="1" units="volume"/>
<compartment metaid="c1" id="c1" name="Mitochondria" size="1" units="volume" outside="c5">
<compartment metaid="c2" id="c2" name="human host" size="1" units="volume" outside="default">
<annotation>
<celldesigner:extension>
<celldesigner:name>Mitochondria</celldesigner:name>
<celldesigner:name>human host</celldesigner:name>
</celldesigner:extension>
</annotation>
</compartment>
<compartment metaid="c3" id="c3" name="Nucleus" size="1" units="volume" outside="c5">
<compartment metaid="c5" id="c5" name="cell" size="1" units="volume" outside="c2">
<annotation>
<celldesigner:extension>
<celldesigner:name>Nucleus</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>
<compartment metaid="c5" id="c5" name="Cytoplasm" size="1" units="volume" outside="c2">
<compartment metaid="c3" id="c3" name="nucleus" size="1" units="volume" outside="c5">
<annotation>
<celldesigner:extension>
<celldesigner:name>Cytoplasm</celldesigner:name>
<celldesigner:name>nucleus</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">
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<rdf:Bag>
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This source diff could not be displayed because it is too large. You can view the blob instead.
......@@ -1085,7 +1085,7 @@ The pathway of PAMP signalling affected by human coronavirus proteins
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......@@ -7924,7 +7951,7 @@ Infection of macrophages with N15m1, which expresses an unstable nsp15, or N15m3
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......@@ -668,7 +668,7 @@ P105
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