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issue #121, #89 - test questionable water annotations
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‎src/test/java/edu/ucsd/sbrg/bigg/annotation/SpeciesAnnotationTest.java

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package edu.ucsd.sbrg.bigg.annotation;
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import edu.ucsd.sbrg.TestUtils;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import org.sbml.jsbml.CVTerm;
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import org.sbml.jsbml.Model;
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import org.sbml.jsbml.ext.fbc.FBCConstants;
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import org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin;
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import java.util.Set;
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import static edu.ucsd.sbrg.TestUtils.assertCVTermIsPresent;
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import static edu.ucsd.sbrg.TestUtils.assertCVTermsArePresent;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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public class SpeciesAnnotationTest extends BiGGDBTest {
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@BeforeEach
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public void init() {
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TestUtils.initParameters();
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}
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@Test
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public void basicAnnotationTest() {
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var m = new Model(3, 2);
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var s = m.createSpecies("atp");
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var sFbcPlugin = (FBCSpeciesPlugin) s.getPlugin(FBCConstants.shortLabel);
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var annotator = new SpeciesAnnotation(s);
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annotator.annotate();
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assertEquals("atp", s.getId());
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assertEquals("ATP C10H12N5O13P3", s.getName());
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assertEquals("SBO:0000240", s.getSBOTermID());
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assertCVTermIsPresent(s,
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CVTerm.Type.BIOLOGICAL_QUALIFIER,
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CVTerm.Qualifier.BQB_IS,
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"https://identifiers.org/bigg.metabolite/atp");
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assertEquals(null, sFbcPlugin.getChemicalFormula());
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}
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@Test
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public void unknownMetaboliteCanBeInferredFromId() {
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var m = new Model(3, 2);
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var s = m.createSpecies("atp_c");
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var annotator = new SpeciesAnnotation(s);
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annotator.annotate();
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assertEquals("atp_c", s.getId());
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assertEquals("ATP C10H12N5O13P3", s.getName());
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assertEquals("SBO:0000240", s.getSBOTermID());
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assertCVTermsArePresent(s,
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CVTerm.Type.BIOLOGICAL_QUALIFIER,
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CVTerm.Qualifier.BQB_IS,
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expectedATPAnnotations,
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"Expected annotations are not present.");
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}
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@Test
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public void unknownMetaboliteCanBeInferredFromCV() {
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var m = new Model(3, 2);
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var s = m.createSpecies("big_chungus");
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var cvTerm = new CVTerm();
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cvTerm.setQualifier(CVTerm.Qualifier.BQB_IS);
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cvTerm.addResource("http://identifiers.org/reactome.compound/113592");
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s.addCVTerm(cvTerm);
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var annotator = new SpeciesAnnotation(s);
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annotator.annotate();
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assertEquals("big_chungus", s.getId());
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assertEquals("ATP C10H12N5O13P3", s.getName());
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assertEquals("SBO:0000240", s.getSBOTermID());
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assertEquals(1, s.getCVTermCount());
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assertEquals(30, s.getCVTerm(0).getNumResources());
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assertCVTermIsPresent(s,
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CVTerm.Type.BIOLOGICAL_QUALIFIER,
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CVTerm.Qualifier.BQB_IS,
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"http://identifiers.org/reactome.compound/113592");
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assertCVTermsArePresent(s,
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CVTerm.Type.BIOLOGICAL_QUALIFIER,
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CVTerm.Qualifier.BQB_IS,
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expectedATPAnnotations,
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"Expected uris are not present.");
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}
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private static Set<String> expectedATPAnnotations = Set.of(
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"https://identifiers.org/bigg.metabolite/atp",
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"https://identifiers.org/biocyc/META:ATP",
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"https://identifiers.org/chebi/CHEBI:10789",
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"https://identifiers.org/chebi/CHEBI:10841",
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"https://identifiers.org/chebi/CHEBI:13236",
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"https://identifiers.org/chebi/CHEBI:15422",
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"https://identifiers.org/chebi/CHEBI:22249",
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"https://identifiers.org/chebi/CHEBI:2359",
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"https://identifiers.org/chebi/CHEBI:237958",
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"https://identifiers.org/chebi/CHEBI:30616",
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"https://identifiers.org/chebi/CHEBI:40938",
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"https://identifiers.org/chebi/CHEBI:57299",
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"https://identifiers.org/hmdb/HMDB00538",
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"https://identifiers.org/inchikey/ZKHQWZAMYRWXGA-KQYNXXCUSA-J",
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"https://identifiers.org/kegg.compound/C00002",
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"https://identifiers.org/kegg.drug/D08646",
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"https://identifiers.org/metanetx.chemical/MNXM3",
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"https://identifiers.org/reactome/R-ALL-113592",
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"https://identifiers.org/reactome/R-ALL-113593",
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"https://identifiers.org/reactome/R-ALL-211579",
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"https://identifiers.org/reactome/R-ALL-29358",
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"https://identifiers.org/reactome/R-ALL-389573",
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"https://identifiers.org/reactome/R-ALL-5632460",
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"https://identifiers.org/reactome/R-ALL-5696069",
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"https://identifiers.org/reactome/R-ALL-6798184",
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"https://identifiers.org/reactome/R-ALL-8869363",
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"https://identifiers.org/reactome/R-ALL-8878982",
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"https://identifiers.org/reactome/R-ALL-8938081",
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"https://identifiers.org/seed.compound/cpd00002");
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/**
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* Note this serves to document the behaviour discussed in
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* https://github.com/draeger-lab/ModelPolisher/issues/89
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*
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* The annotations as are should likely not be considered correct.
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*/
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@Test
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public void H2OAnnotationTest() {
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var m = new Model(3, 2);
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var s = m.createSpecies("h2o");
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var sFbcPlugin = (FBCSpeciesPlugin) s.getPlugin(FBCConstants.shortLabel);
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var annotator = new SpeciesAnnotation(s);
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annotator.annotate();
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assertEquals("h2o", s.getId());
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assertEquals("H2O H2O", s.getName());
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assertEquals("SBO:0000240", s.getSBOTermID());
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assertEquals(null, sFbcPlugin.getChemicalFormula());
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assertCVTermsArePresent(s,
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CVTerm.Type.BIOLOGICAL_QUALIFIER,
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CVTerm.Qualifier.BQB_IS,
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Set.of("https://identifiers.org/bigg.metabolite/h2o",
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"https://identifiers.org/biocyc/META:CPD-15815",
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"https://identifiers.org/biocyc/META:HYDROXYL-GROUP",
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"https://identifiers.org/biocyc/META:OH",
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"https://identifiers.org/biocyc/META:OXONIUM",
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"https://identifiers.org/biocyc/META:WATER",
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"https://identifiers.org/chebi/CHEBI:10743",
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"https://identifiers.org/chebi/CHEBI:13352",
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"https://identifiers.org/chebi/CHEBI:13365",
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"https://identifiers.org/chebi/CHEBI:13419",
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"https://identifiers.org/chebi/CHEBI:15377",
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"https://identifiers.org/chebi/CHEBI:16234",
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"https://identifiers.org/chebi/CHEBI:27313",
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"https://identifiers.org/chebi/CHEBI:29356",
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"https://identifiers.org/chebi/CHEBI:29412",
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"https://identifiers.org/chebi/CHEBI:30490",
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"https://identifiers.org/chebi/CHEBI:33813",
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"https://identifiers.org/chebi/CHEBI:42043",
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"https://identifiers.org/chebi/CHEBI:42857",
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"https://identifiers.org/chebi/CHEBI:43228",
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"https://identifiers.org/chebi/CHEBI:44292",
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"https://identifiers.org/chebi/CHEBI:44641",
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"https://identifiers.org/chebi/CHEBI:44701",
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"https://identifiers.org/chebi/CHEBI:44819",
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"https://identifiers.org/chebi/CHEBI:5585",
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"https://identifiers.org/chebi/CHEBI:5594",
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"https://identifiers.org/hmdb/HMDB01039",
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"https://identifiers.org/hmdb/HMDB02111",
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"https://identifiers.org/inchikey/XLYOFNOQVPJJNP-UHFFFAOYSA-N",
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"https://identifiers.org/kegg.compound/C00001",
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"https://identifiers.org/kegg.compound/C01328",
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"https://identifiers.org/kegg.drug/D00001",
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"https://identifiers.org/kegg.drug/D06322",
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"https://identifiers.org/metanetx.chemical/MNXM2",
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"https://identifiers.org/reactome/R-ALL-109276",
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"https://identifiers.org/reactome/R-ALL-113518",
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"https://identifiers.org/reactome/R-ALL-113519",
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"https://identifiers.org/reactome/R-ALL-113521",
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"https://identifiers.org/reactome/R-ALL-141343",
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"https://identifiers.org/reactome/R-ALL-1605715",
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"https://identifiers.org/reactome/R-ALL-189422",
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"https://identifiers.org/reactome/R-ALL-2022884",
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"https://identifiers.org/reactome/R-ALL-29356",
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"https://identifiers.org/reactome/R-ALL-351603",
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"https://identifiers.org/reactome/R-ALL-5278291",
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"https://identifiers.org/reactome/R-ALL-5668574",
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"https://identifiers.org/reactome/R-ALL-5693747",
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"https://identifiers.org/reactome/R-ALL-8851517",
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"https://identifiers.org/seed.compound/cpd00001",
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"https://identifiers.org/seed.compound/cpd15275",
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"https://identifiers.org/seed.compound/cpd27222"),
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"Expected annotations not on H2O.");
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}
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}

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