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Commit f4281908 authored by Piotr Gawron's avatar Piotr Gawron
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comparison against null filxed

parent e701559a
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CHANGELOG
View file @ f4281908
minerva (14.0.3) stable; urgency=medium
* Bug fix: sbml parser had sometimes problems with combining layout and multi
packages (#966)
* Bug fix: parsing of CellDesigner files that contained substanceUnits could
crash the upload (#985)
* Bug fix: verificatin of version length added when uploading project
......
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
View file @ f4281908
......@@ -13,6 +13,8 @@ import org.sbml.jsbml.ext.layout.*;
import org.sbml.jsbml.ext.multi.*;
import org.sbml.jsbml.ext.render.LocalStyle;
import com.google.common.base.Objects;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
......@@ -317,7 +319,8 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
if (((GeneralGlyph) graphicalObject).getListOfReferenceGlyphs().size() > 0) {
// find a reference to the alias in layout, so we know it's the proper value
ReferenceGlyph referenceGlyph = ((GeneralGlyph) graphicalObject).getListOfReferenceGlyphs().get(0);
if (referenceGlyph.getGlyph().equals(mr.getSpecies().getElementId())) {
if (Objects.equal(referenceGlyph.getGlyph(), mr.getSpecies().getElementId())) {
// if (referenceGlyph.getGlyph().equals(mr.getSpecies().getElementId())) {
residueGlyph = (GeneralGlyph) graphicalObject;
}
} else {
......
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
View file @ f4281908
......@@ -62,6 +62,13 @@ public class SbmlParserTest extends SbmlTestFunctions {
assertEquals(2, model.getMiriamData().size());
}
@Test
public void testParseProblematicMultiLayout() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(
new ConverterParams().filename("testFiles/small/problematic_inflamation_sbml_layout.xml"));
assertNotNull(model);
}
@Test
public void testParseKinetics() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/layoutExample/SBML.xml"));
......
converter-sbml/testFiles/small/problematic_inflamation_sbml_layout.xml 0 → 100644
View file @ f4281908
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<!-- Created by minerva version Unknown on 2019-01-21 at 13:07:15 UTC with
JSBML version 1.4. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core"
layout:required="false" level="3" multi:required="true"
render:required="false" version="2"
xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1"
xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1">
<model id="A_comprehensive_Parkinsons_disease_map">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p />
</body>
</notes>
<layout:listOfLayouts
xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<layout:layout layout:id="minerva_layout">
<render:listOfRenderInformation
xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1">
<render:renderInformation
render:id="minerva_definitions">
<render:listOfColorDefinitions>
<render:colorDefinition
render:id="color_FFCCFFCC" render:value="#CCFFCCFF" />
<render:colorDefinition
render:id="color_FFF7F7F7" render:value="#F7F7F7FF" />
<render:colorDefinition
render:id="color_FFFFCCCC" render:value="#FFCCCCFF" />
<render:colorDefinition
render:id="color_FFCCFF66" render:value="#CCFF66FF" />
<render:colorDefinition
render:id="color_FFCC99FF" render:value="#CC99FFFF" />
<render:colorDefinition
render:id="color_FF000000" render:value="#000000FF" />
</render:listOfColorDefinitions>
<render:listOfStyles>
<render:style render:roleList="style_sa3974">
<render:g render:fill="color_FFCCFFCC"
render:font-size="12" render:stroke-width="1.0" />
</render:style>
</render:listOfStyles>
</render:renderInformation>
</render:listOfRenderInformation>
<layout:dimensions layout:height="1269"
layout:width="2203.889936028838" />
<layout:listOfAdditionalGraphicalObjects>
<layout:generalGlyph
layout:id="modification_131"
layout:reference="modification_residue_0">
<layout:boundingBox>
<layout:position layout:x="517.2555341788755"
layout:y="402.9447283484171" />
<layout:dimensions layout:height="12"
layout:width="12" />
</layout:boundingBox>
<layout:listOfReferenceGlyphs>
<layout:referenceGlyph
layout:id="modification_reference_132" layout:reference="sa3974" />
</layout:listOfReferenceGlyphs>
</layout:generalGlyph>
<layout:generalGlyph
layout:id="modification_133"
layout:reference="modification_residue_1">
<layout:boundingBox>
<layout:position layout:x="516.7320671347599"
layout:y="368.38146801737145" />
<layout:dimensions layout:height="12"
layout:width="12" />
</layout:boundingBox>
<layout:listOfReferenceGlyphs>
<layout:referenceGlyph
layout:id="modification_reference_134" layout:reference="sa3974" />
</layout:listOfReferenceGlyphs>
</layout:generalGlyph>
<layout:generalGlyph
layout:id="modification_135"
layout:reference="modification_residue_2">
<layout:boundingBox>
<layout:position layout:x="594.7121704912977"
layout:y="385.4013646608727" />
<layout:dimensions layout:height="12"
layout:width="12" />
</layout:boundingBox>
<layout:listOfReferenceGlyphs>
<layout:referenceGlyph
layout:id="modification_reference_136" layout:reference="sa3974" />
</layout:listOfReferenceGlyphs>
</layout:generalGlyph>
</layout:listOfAdditionalGraphicalObjects>
<layout:listOfCompartmentGlyphs>
<layout:compartmentGlyph
layout:compartment="default" layout:id="default_compartment">
<layout:boundingBox>
<layout:position layout:x="0" layout:y="0" />
<layout:dimensions layout:height="1269"
layout:width="2203.889936028838" />
</layout:boundingBox>
</layout:compartmentGlyph>
</layout:listOfCompartmentGlyphs>
<layout:listOfSpeciesGlyphs>
<layout:speciesGlyph layout:id="sa3974"
layout:species="species_0" render:objectRole="style_sa3974">
<layout:boundingBox>
<layout:position layout:x="520.7121704912979"
layout:y="371.4013646608364" />
<layout:dimensions layout:height="40"
layout:width="80" />
</layout:boundingBox>
</layout:speciesGlyph>
</layout:listOfSpeciesGlyphs>
<layout:listOfReactionGlyphs>
</layout:listOfReactionGlyphs>
</layout:layout>
</layout:listOfLayouts>
<multi:listOfSpeciesTypes
xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1">
<multi:speciesType
multi:id="minerva_species_type_GenericProtein"
multi:name="GenericProtein" sboTerm="SBO:0000252">
<multi:listOfSpeciesFeatureTypes>
<multi:speciesFeatureType
multi:id="minerva_position_to_compartment_GenericProtein"
multi:name="Position to compartment">
<multi:listOfPossibleSpeciesFeatureValues>
<multi:possibleSpeciesFeatureValue
multi:id="minerva_position_to_compartment_GenericProtein_0"
multi:name="NULL" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_position_to_compartment_GenericProtein_1"
multi:name="inside" />
</multi:listOfPossibleSpeciesFeatureValues>
</multi:speciesFeatureType>
<multi:speciesFeatureType
multi:id="minerva_modification_type_GenericProtein_Residue_PHOSPHORYLATED"
multi:name="phosphorylated">
<multi:listOfPossibleSpeciesFeatureValues>
<multi:possibleSpeciesFeatureValue
multi:id="minerva_modification_type_GenericProtein_Residue_PHOSPHORYLATED_2"
multi:name="S32" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_modification_type_GenericProtein_Residue_PHOSPHORYLATED_3"
multi:name="S36" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_modification_type_GenericProtein_Residue_PHOSPHORYLATED_98"
multi:name="S176" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_modification_type_GenericProtein_Residue_PHOSPHORYLATED_99"
multi:name="S180" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_modification_type_GenericProtein_Residue_PHOSPHORYLATED_102"
multi:name="T838" />
</multi:listOfPossibleSpeciesFeatureValues>
</multi:speciesFeatureType>
<multi:speciesFeatureType
multi:id="minerva_modification_type_GenericProtein_Residue_UBIQUITINATED"
multi:name="ubiquitinated">
<multi:listOfPossibleSpeciesFeatureValues>
<multi:possibleSpeciesFeatureValue
multi:id="minerva_modification_type_GenericProtein_Residue_UBIQUITINATED_4" />
</multi:listOfPossibleSpeciesFeatureValues>
</multi:speciesFeatureType>
<multi:speciesFeatureType
multi:id="minerva_synonym_GenericProtein" multi:name="Synonym">
<multi:listOfPossibleSpeciesFeatureValues>
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_5" multi:name="IKBA" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_6"
multi:name="IkappaBalpha" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_7" multi:name="MAD-3" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_16" multi:name="DJ-1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_17" multi:name="DJ1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_18" multi:name="GATD2" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_29" multi:name="GSTP" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_35" multi:name="ASK1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_36"
multi:name="MAPKKK5" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_42"
multi:name="IKK-beta" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_43" multi:name="IKK2" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_44" multi:name="IKKB" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_45"
multi:name="NFKBIKB" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_48" multi:name="KBF1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_49" multi:name="NF-kB1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_50"
multi:name="NF-kappaB" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_51"
multi:name="NFKB-p50" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_52"
multi:name="NFkappaB" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_53" multi:name="p105" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_54" multi:name="p50" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_70" multi:name="p65" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_77" multi:name="RNF117" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_78" multi:name="TRAP3" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_81" multi:name="RNF85" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_84" multi:name="DAP6" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_88" multi:name="FIP-3" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_89" multi:name="FIP3" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_90" multi:name="Fip3p" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_91"
multi:name="IKK-gamma" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_92" multi:name="NEMO" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_93" multi:name="ZC2HC9" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_104" multi:name="TRX" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_107"
multi:name="FBXW1A" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_108" multi:name="Fwd1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_109" multi:name="bTrCP" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_110"
multi:name="bTrCP1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_111"
multi:name="beta-TrCP1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_112"
multi:name="betaTrCP" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_116" multi:name="PP5" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_120"
multi:name="IKK-alpha" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_121" multi:name="IKK1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_122" multi:name="IKKA" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_123" multi:name="IkBKA" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_synonym_GenericProtein_124"
multi:name="NFKBIKA" />
</multi:listOfPossibleSpeciesFeatureValues>
</multi:speciesFeatureType>
<multi:speciesFeatureType
multi:id="minerva_former_symbol_GenericProtein"
multi:name="Former symbol">
<multi:listOfPossibleSpeciesFeatureValues>
<multi:possibleSpeciesFeatureValue
multi:id="minerva_former_symbol_GenericProtein_8"
multi:name="NFKBI" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_former_symbol_GenericProtein_30"
multi:name="FAEES3" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_former_symbol_GenericProtein_31"
multi:name="GST3" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_former_symbol_GenericProtein_37"
multi:name="MEKK5" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_former_symbol_GenericProtein_71"
multi:name="NFKB3" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_former_symbol_GenericProtein_74"
multi:name="PARK6" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_former_symbol_GenericProtein_94"
multi:name="IP2" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_former_symbol_GenericProtein_95"
multi:name="IP1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_former_symbol_GenericProtein_117"
multi:name="PPP5" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_former_symbol_GenericProtein_125"
multi:name="TCF16" />
</multi:listOfPossibleSpeciesFeatureValues>
</multi:speciesFeatureType>
<multi:speciesFeatureType
multi:id="minerva_symbol_GenericProtein" multi:name="Symbol">
<multi:listOfPossibleSpeciesFeatureValues>
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_9" multi:name="NFKBIA" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_19" multi:name="PARK7" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_32" multi:name="GSTP1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_38" multi:name="MAP3K5" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_46" multi:name="IKBKB" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_55" multi:name="NFKB1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_72" multi:name="RELA" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_75" multi:name="PINK1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_79" multi:name="TRAF2" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_82" multi:name="TRAF6" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_85" multi:name="DAXX" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_96" multi:name="IKBKG" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_105" multi:name="TXN" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_113" multi:name="BTRC" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_118" multi:name="PPP5C" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_symbol_GenericProtein_126" multi:name="CHUK" />
</multi:listOfPossibleSpeciesFeatureValues>
</multi:speciesFeatureType>
<multi:speciesFeatureType
multi:id="minerva_full_name_GenericProtein" multi:name="Full name">
<multi:listOfPossibleSpeciesFeatureValues>
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_10"
multi:name="NFKB inhibitor alpha" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_20"
multi:name="Parkinsonism associated deglycase" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_33"
multi:name="glutathione S-transferase pi 1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_39"
multi:name="mitogen-activated protein kinase kinase kinase 5" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_47"
multi:name="inhibitor of nuclear factor kappa B kinase subunit beta" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_56"
multi:name="nuclear factor kappa B subunit 1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_73"
multi:name="RELA proto-oncogene, NF-kB subunit" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_76"
multi:name="PTEN induced putative kinase 1" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_80"
multi:name="TNF receptor associated factor 2" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_83"
multi:name="TNF receptor associated factor 6" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_86"
multi:name="death domain associated protein" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_97"
multi:name="inhibitor of nuclear factor kappa B kinase subunit gamma" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_106"
multi:name="thioredoxin" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_114"
multi:name="beta-transducin repeat containing E3 ubiquitin protein ligase" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_119"
multi:name="protein phosphatase 5 catalytic subunit" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_full_name_GenericProtein_127"
multi:name="conserved helix-loop-helix ubiquitous kinase" />
</multi:listOfPossibleSpeciesFeatureValues>
</multi:speciesFeatureType>
<multi:speciesFeatureType
multi:id="minerva_charge_GenericProtein" multi:name="Charge">
<multi:listOfPossibleSpeciesFeatureValues>
<multi:possibleSpeciesFeatureValue
multi:id="minerva_charge_GenericProtein_11" multi:name="0" />
</multi:listOfPossibleSpeciesFeatureValues>
</multi:speciesFeatureType>
<multi:speciesFeatureType
multi:id="minerva_activity_GenericProtein" multi:name="Activity">
<multi:listOfPossibleSpeciesFeatureValues>
<multi:possibleSpeciesFeatureValue
multi:id="minerva_activity_GenericProtein_12" multi:name="false" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_activity_GenericProtein_21" multi:name="true" />
</multi:listOfPossibleSpeciesFeatureValues>
</multi:speciesFeatureType>
<multi:speciesFeatureType
multi:id="minerva_structural_state_GenericProtein"
multi:name="Structural state">
<multi:listOfPossibleSpeciesFeatureValues>
<multi:possibleSpeciesFeatureValue
multi:id="minerva_structural_state_GenericProtein_13" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_structural_state_GenericProtein_14"
multi:name="SOH@C106" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_structural_state_GenericProtein_103"
multi:name="oxidized" />
</multi:listOfPossibleSpeciesFeatureValues>
</multi:speciesFeatureType>
<multi:speciesFeatureType
multi:id="minerva_modification_type_GenericProtein_Residue_null">
<multi:listOfPossibleSpeciesFeatureValues>
<multi:possibleSpeciesFeatureValue
multi:id="minerva_modification_type_GenericProtein_Residue_null_15" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_modification_type_GenericProtein_Residue_null_34"
multi:name="T838" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_modification_type_GenericProtein_Residue_null_40"
multi:name="S176" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_modification_type_GenericProtein_Residue_null_41"
multi:name="S180" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_modification_type_GenericProtein_Residue_null_68"
multi:name="S276" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_modification_type_GenericProtein_Residue_null_69"
multi:name="S529" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_modification_type_GenericProtein_Residue_null_100"
multi:name="S32" />
<multi:possibleSpeciesFeatureValue
multi:id="minerva_modification_type_GenericProtein_Residue_null_101"
multi:name="S36" />
</multi:listOfPossibleSpeciesFeatureValues>
</multi:speciesFeatureType>
</multi:listOfSpeciesFeatureTypes>
</multi:speciesType>
</multi:listOfSpeciesTypes>
<listOfUnitDefinitions>
<unitDefinition id="substance" name="substance">
<listOfUnits>
<unit exponent="1" kind="mole" multiplier="1" scale="0" />
</listOfUnits>
</unitDefinition>
<unitDefinition id="area" name="area">
<listOfUnits>
<unit exponent="2" kind="metre" multiplier="1" scale="0" />
</listOfUnits>
</unitDefinition>
<unitDefinition id="volume" name="volume">
<listOfUnits>
<unit exponent="1" kind="litre" multiplier="1" scale="0" />
</listOfUnits>
</unitDefinition>
<unitDefinition id="length" name="length">
<listOfUnits>
<unit exponent="1" kind="metre" multiplier="1" scale="0" />
</listOfUnits>
</unitDefinition>
<unitDefinition id="time" name="time">
<listOfUnits>
<unit exponent="1" kind="second" multiplier="1" scale="0" />
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment constant="false" id="default">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p />
</body>
</notes>
<annotation>
<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="#">
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species compartment="default" id="species_0"
initialAmount="0"
multi:speciesType="minerva_species_type_GenericProtein"
name="NFKBIA" sboTerm="SBO:0000252">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p />
</body>
</notes>
<annotation>
<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="#">
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:hgnc:7797" />
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:refseq:NM_020529" />
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li
rdf:resource="urn:miriam:ensembl:ENSG00000100906" />
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P25963" />
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>