Examples with AnnotationEvidence org.nextprot.api.core.domain.annotation.AnnotationEvidence used on opensource projects

Example 21 with AnnotationEvidence

use of org.nextprot.api.core.domain.annotation.AnnotationEvidence in project nextprot-api by calipho-sib.

the class DbXrefServiceIntegrationTest method shouldReturn_1_ReactomeXrefAsAnnotation.

/*
 * This query finds entries having a single xref among 'Orphanet', 'KEGGPathway' , 'Reactome' and 'DrugBank'
 * It is convenient for tests: we know we get a single annotation from xrefs for a given entry
 * Example:
 * NX_A0AVF1 for Reactome
 * NX_A1L167 for Kegg
 * NX_A0PJY2 for Orphanet
 * NX_Q9Y2D1 for DrugBank

select a.unique_name, string_agg(a.acs, ',') as acs, string_agg(a.cv_name, ',') as dbs, count(*) as dbcount, sum(a.cnt) as xrcount from (
select si.unique_name, db.cv_name, count(*) as cnt, string_agg(x.accession, ',') as acs
from sequence_identifiers si
inner join identifier_resource_assoc ira on (si.identifier_id=ira.identifier_id)
inner join db_xrefs x on (ira.resource_id=x.resource_id)
inner join cv_databases db on (x.cv_database_id=db.cv_id)
where si.cv_type_id=1 and si.cv_status_id=1 
and db.cv_name in ('Orphanet', 'DrugBank','KEGGPathway','Reactome')
group by si.unique_name, db.cv_name
) a
group by a.unique_name
having sum(a.cnt)=1
;


 */
@Test
public void shouldReturn_1_ReactomeXrefAsAnnotation() {
    List<Annotation> annotations = this.xrefService.findDbXrefsAsAnnotationsByEntry("NX_A0AVF1");
    assertTrue(annotations.size() == 1);
    Annotation annot = annotations.get(0);
    assertTrue(annot.getCategory().equals(AnnotationCategory.PATHWAY.getDbAnnotationTypeName()));
    assertTrue(annot.getAPICategory() == AnnotationCategory.PATHWAY);
    assertTrue(annot.getQualityQualifier().equals("GOLD"));
    Assert.assertEquals("Intraflagellar transport", annot.getDescription());
    for (AnnotationIsoformSpecificity spec : annot.getTargetingIsoformsMap().values()) {
        assertTrue(spec.getSpecificity().equals("UNKNOWN"));
    }
    assertTrue(annot.getEvidences().size() == 1);
    AnnotationEvidence evi = annot.getEvidences().get(0);
    assertTrue(evi.getAssignedBy().equals("Reactome"));
    assertTrue(evi.getEvidenceCodeAC().equals("ECO:0000305"));
    assertTrue(evi.getResourceAccession().equals("R-HSA-5620924"));
    assertTrue(evi.getResourceDb().equals("Reactome"));
    Assert.assertTrue(annotations.get(0).getProperties().isEmpty());
}

Example 22 with AnnotationEvidence

use of org.nextprot.api.core.domain.annotation.AnnotationEvidence in project nextprot-api by calipho-sib.

the class DbXrefServiceIntegrationTest method shouldFindTransportActivityAnnotation.

@Test
public void shouldFindTransportActivityAnnotation() {
    List<Annotation> annotations = this.xrefService.findDbXrefsAsAnnotationsByEntry("NX_Q86VW1").stream().filter(a -> a.getAPICategory() == AnnotationCategory.TRANSPORT_ACTIVITY).collect(Collectors.toList());
    Assert.assertEquals(1, annotations.size());
    Annotation annotation = annotations.get(0);
    Assert.assertEquals("AN_Q86VW1_XR_6580312", annotation.getUniqueName());
    Assert.assertEquals("the major facilitator superfamily (mfs)", annotation.getDescription());
    List<AnnotationEvidence> evidences = annotation.getEvidences().stream().filter(e -> e.getResourceDb().equals("TCDB")).collect(Collectors.toList());
    // Assert Evidence
    Assert.assertEquals(1, evidences.size());
    AnnotationEvidence evidence = evidences.get(0);
    Assert.assertEquals("database", evidence.getResourceType());
    Assert.assertEquals("2.A.1.19.12", evidence.getResourceAccession());
    Assert.assertEquals("ECO:0000305", evidence.getEvidenceCodeAC());
    Assert.assertEquals(QualityQualifier.GOLD.toString(), evidence.getQualityQualifier());
    // Assert Xref
    Assert.assertNotNull(annotation.getParentXref());
    Assert.assertEquals("2.A.1.19.12", annotation.getParentXref().getAccession());
    Assert.assertEquals("TCDB", annotation.getParentXref().getDatabaseName());
    Assert.assertNotNull(annotation.getParentXref().getProperties());
    List<DbXref.DbXrefProperty> props = annotation.getParentXref().getProperties().stream().filter(p -> p.getName().equals("family name")).collect(Collectors.toList());
    Assert.assertEquals(1, props.size());
    Assert.assertEquals("the major facilitator superfamily (mfs)", props.get(0).getValue());
}

Example 23 with AnnotationEvidence

use of org.nextprot.api.core.domain.annotation.AnnotationEvidence in project nextprot-api by calipho-sib.

the class InteractionServiceIntegrationTest method shouldDealWithAnyInteractionSpecialInteraction.

/*
 * This queries retrieves entries with their 
 * - count of xeno interactions
 * - count of self interactions
 * - count of interactions with another protein entry defined in nextprot
 * - count of interactions whih another protein isoform defined in nextprot
 * - count of isoform specific interactions 
 * 
 *  and can be used to find test examples
 *  
select entry_ac, sum(is_iso_spec) as iso_spec_interactions, sum(has_xeno) as with_xeno, sum(has_self) as with_self, sum(has_iso) as with_isos, 
sum(has_entry) as entries, sum(has_xeno)+ sum(has_self)+ sum(has_iso)+ sum(has_entry) as interaction_count from (
select xr1.accession, 
(regexp_split_to_array(xr1.accession,'-'))[1]  as entry_ac,
case when xr1.accession like '%-%' then 1 else 0 end as is_iso_spec,
case when inter.is_xeno then 1 else 0 end as has_xeno,
case when interactant1.is_self_interaction then 1 else 0 end as has_self,
case when inter.is_xeno is false and interactant1.is_self_interaction is false and xr2.accession ilike '%-%' then 1 else 0 end as has_iso,
case when inter.is_xeno is false and interactant1.is_self_interaction is false and xr2.accession not ilike '%-%' then 1 else 0 end as has_entry
from partnerships inter 
inner join partnership_partner_assoc interactant1 on (inter.partnership_id=interactant1.partnership_id)
inner join db_xrefs xr1 on (interactant1.db_xref_id=xr1.resource_id)
left outer join partnership_partner_assoc interactant2 on (inter.partnership_id=interactant2.partnership_id and interactant1.assoc_id != interactant2.assoc_id or interactant2.assoc_id is null)
left outer join db_xrefs xr2 on (interactant2.db_xref_id=xr2.resource_id)
) a 
group by entry_ac
having sum(has_xeno)>0 and sum(has_self)>0 and sum(has_iso)>0 and sum(has_entry)>0
order by sum(has_xeno)+ sum(has_self)+ sum(has_iso)+ sum(has_entry) 
*/
/*
	 * NX_Q9UNQ0 should contain at least 1 interactions of each type:
	 * - self interaction 
	 * - xeno interaction (interaction with a protein not defined in nextprot, see resourceinternalrefs
	 * - interaction with another nextprot entry
	 * - interaction with another nextprot specific isoform
	 * and there should at least 1 interaction declared as isoform specific
	 * 
	 * see query above to find other examples if necessary in future releases
	 * 
	 */
@Test
public void shouldDealWithAnyInteractionSpecialInteraction() {
    String entry_ac = "NX_Q9UNQ0";
    List<Annotation> annots = this.interactionService.findInteractionsAsAnnotationsByEntry(entry_ac);
    int numberOfExperiments = 0;
    int withNxEntries = 0;
    int withNxIsos = 0;
    int withSelf = 0;
    int withXrefs = 0;
    int isoSpecs = 0;
    for (Annotation annot : annots) {
        /*
			System.out.println("partner " + annot.getBioObject().getAccession() +
					" " + annot.getBioObject().getBioType() + " / " + annot.getBioObject().getResourceType());
			*/
        // basic checks
        assertTrue(annot.getCategory().equals("BinaryInteraction"));
        assertTrue(annot.getAPICategory() == AnnotationCategory.BINARY_INTERACTION);
        // partners
        if (isAnnotationASelfInteraction(annot, entry_ac))
            withSelf++;
        if (isAnnotationAnInteractionWithAnExternalXrefAsPartner(annot))
            withXrefs++;
        if (isAnnotationAnInteractionWithaNextprotEntryAsPartner(annot, entry_ac))
            withNxEntries++;
        if (isAnnotationAnInteractionWithANextprotIsoformAsPartner(annot))
            withNxIsos++;
        // specificity of annotation subject
        if (isAnnotationAnInteractionWithANextprotIsoformAsSubject(annot))
            isoSpecs++;
        // evidences
        assertTrue(annot.getEvidences().size() == 1);
        AnnotationEvidence evi = annot.getEvidences().get(0);
        assertTrue(evi.getQualityQualifier().equals("GOLD") || evi.getQualityQualifier().equals("SILVER"));
        assertTrue(evi.getResourceDb().equals("IntAct"));
        if (annot.getEvidences().get(0).getPropertyValue("numberOfExperiments") != null)
            numberOfExperiments++;
    }
    /*
		System.out.println("numberOfExperiments:" + numberOfExperiments);
		System.out.println("withNxEntries:" + withNxEntries);
		System.out.println("withNxIsos:" + withNxIsos);
		System.out.println("withSelf:" + withSelf );
		System.out.println("withXrefs:" + withXrefs );
		System.out.println("isoSpecs:" + isoSpecs );
		*/
    // should exist for each interaction
    assertTrue(numberOfExperiments == annots.size());
    // 8 cases
    assertTrue(withNxEntries >= 1);
    // 1 case
    assertTrue(withNxIsos >= 1);
    // 10 cases
    assertTrue(withXrefs >= 1);
    // 1 case
    assertTrue(withSelf == 1);
    // 16 cases
    assertTrue(isoSpecs > 1);
}

Example 24 with AnnotationEvidence

use of org.nextprot.api.core.domain.annotation.AnnotationEvidence in project nextprot-api by calipho-sib.

the class AnnotationTest method testTwoNegative.

@Test
public void testTwoNegative() {
    Annotation a = new Annotation();
    List<AnnotationEvidence> evidences = new ArrayList<>();
    evidences.add(buildEvidence("negative"));
    evidences.add(buildEvidence("negative"));
    a.setEvidences(evidences);
    Assert.assertTrue(a.isExpressionLevelDetected().isPresent());
    Assert.assertTrue(!a.isExpressionLevelDetected().get());
}

Example 25 with AnnotationEvidence

use of org.nextprot.api.core.domain.annotation.AnnotationEvidence in project nextprot-api by calipho-sib.

the class AnnotationTest method testOneNegative.

@Test
public void testOneNegative() {
    Annotation a = new Annotation();
    List<AnnotationEvidence> evidences = new ArrayList<>();
    evidences.add(buildEvidence("negative"));
    a.setEvidences(evidences);
    Assert.assertTrue(a.isExpressionLevelDetected().isPresent());
    Assert.assertTrue(!a.isExpressionLevelDetected().get());
}