Times Reported Time consuming queries #1

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SELECT distinct viaChemPTR.via_term_id, -- chem #015 viaGenePTR.via_term_id, -- gene #015 viaChemPTR.phenotype_id, -- phenotype #015 viaChemPTR.term_id -- disease #015 FROM pub2.PHENOTYPE_TERM_REFERENCE viaChemPTR # 015, pub2.PHENOTYPE_TERM_REFERENCE viaGenePTR # 015 WHERE viaChemPTR.term_id = viaGenePTR.term_id # 015 AND viaChemPTR.term_object_type_id = 3 # 015 AND viaChemPTR.phenotype_id = viaGenePTR.phenotype_id # 015 AND viaChemPTR.via_term_object_type_id = 2 # 015 AND viaGenePTR.via_term_object_type_id = 4 # 015;

Date: 2024-09-23 11:05:43
Duration: 1m53s
Bind query: yes

SELECT distinct viaChemPTR.via_term_id, -- chem #015 viaGenePTR.via_term_id, -- gene #015 viaChemPTR.phenotype_id, -- phenotype #015 viaChemPTR.term_id -- disease #015 FROM pub2.PHENOTYPE_TERM_REFERENCE viaChemPTR # 015, pub2.PHENOTYPE_TERM_REFERENCE viaGenePTR # 015 WHERE viaChemPTR.term_id = viaGenePTR.term_id # 015 AND viaChemPTR.term_object_type_id = 3 # 015 AND viaChemPTR.phenotype_id = viaGenePTR.phenotype_id # 015 AND viaChemPTR.via_term_object_type_id = 2 # 015 AND viaGenePTR.via_term_object_type_id = 4 # 015;

Date: 2024-09-23 11:11:32
Duration: 1m49s
Bind query: yes

SELECT distinct viaChemPTR.via_term_id, -- chem #015 viaGenePTR.via_term_id, -- gene #015 viaChemPTR.phenotype_id, -- phenotype #015 viaChemPTR.term_id -- disease #015 FROM pub2.PHENOTYPE_TERM_REFERENCE viaChemPTR # 015, pub2.PHENOTYPE_TERM_REFERENCE viaGenePTR # 015 WHERE viaChemPTR.term_id = viaGenePTR.term_id # 015 AND viaChemPTR.term_object_type_id = 3 # 015 AND viaChemPTR.phenotype_id = viaGenePTR.phenotype_id # 015 AND viaChemPTR.via_term_object_type_id = 2 # 015 AND viaGenePTR.via_term_object_type_id = 4 # 015;

Date: 2024-09-23 10:52:31
Duration: 1m43s
Bind query: yes

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Times Reported Time consuming queries #2

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[ User: pub1 - Total duration: 1m46s - Times executed: 3 ]

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SELECT gene_id # 015, chem_id # 015, acc_txt # 015 FROM pub2.GENE_CHEM_REFERENCE transactionalReferenceTabler # 015 LEFT OUTER JOIN pub2.REFERENCE r ON transactionalReferenceTabler.reference_id = r.id # 015 # 015;

Date: 2024-09-23 11:03:04
Duration: 35s987ms
Database: ctddev51
User: pub1
Bind query: yes

SELECT gene_id # 015, chem_id # 015, acc_txt # 015 FROM pub2.GENE_CHEM_REFERENCE transactionalReferenceTabler # 015 LEFT OUTER JOIN pub2.REFERENCE r ON transactionalReferenceTabler.reference_id = r.id # 015 # 015;

Date: 2024-09-23 10:50:00
Duration: 35s452ms
Database: ctddev51
User: pub1
Bind query: yes

SELECT gene_id # 015, chem_id # 015, acc_txt # 015 FROM pub2.GENE_CHEM_REFERENCE transactionalReferenceTabler # 015 LEFT OUTER JOIN pub2.REFERENCE r ON transactionalReferenceTabler.reference_id = r.id # 015 # 015;

Date: 2024-09-23 11:08:54
Duration: 34s675ms
Database: ctddev51
User: pub1
Bind query: yes

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Times Reported Time consuming queries #3

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SELECT distinct go_term_id # 015, gene_id # 015, evidence_cd # 015 FROM pub2.GENE_GO_ANNOT transactionalReferenceTabler # 015 where is_not = 'f' # 015;

Date: 2024-09-23 11:09:33
Duration: 27s269ms
Bind query: yes

SELECT distinct go_term_id # 015, gene_id # 015, evidence_cd # 015 FROM pub2.GENE_GO_ANNOT transactionalReferenceTabler # 015 where is_not = 'f' # 015;

Date: 2024-09-23 11:03:41
Duration: 26s763ms
Bind query: yes

SELECT distinct go_term_id # 015, gene_id # 015, evidence_cd # 015 FROM pub2.GENE_GO_ANNOT transactionalReferenceTabler # 015 where is_not = 'f' # 015;

Date: 2024-09-23 10:50:38
Duration: 25s865ms
Bind query: yes

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Times Reported Time consuming queries #4

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SELECT phenotype_id # 015, term_id # 015, acc_txt # 015 FROM pub2.PHENOTYPE_TERM_REFERENCE transactionalReferenceTabler # 015 LEFT OUTER JOIN pub2.REFERENCE r ON transactionalReferenceTabler.reference_id = r.id # 015 where source_cd = 'C' and term_object_type_id = 2 # 015;

Date: 2024-09-23 11:09:06
Duration: 7s211ms
Bind query: yes

SELECT phenotype_id # 015, term_id # 015, acc_txt # 015 FROM pub2.PHENOTYPE_TERM_REFERENCE transactionalReferenceTabler # 015 LEFT OUTER JOIN pub2.REFERENCE r ON transactionalReferenceTabler.reference_id = r.id # 015 where source_cd = 'C' and term_object_type_id = 2 # 015;

Date: 2024-09-23 10:50:12
Duration: 4s230ms
Bind query: yes

SELECT phenotype_id # 015, term_id # 015, acc_txt # 015 FROM pub2.PHENOTYPE_TERM_REFERENCE transactionalReferenceTabler # 015 LEFT OUTER JOIN pub2.REFERENCE r ON transactionalReferenceTabler.reference_id = r.id # 015 where source_cd = 'C' and term_object_type_id = 2 # 015;

Date: 2024-09-23 11:03:13
Duration: 4s16ms
Bind query: yes

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Times Reported Time consuming queries #5

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SELECT chem_id # 015, disease_id # 015, acc_txt # 015 FROM pub2.CHEM_DISEASE_REFERENCE transactionalReferenceTabler # 015 LEFT OUTER JOIN pub2.REFERENCE r ON transactionalReferenceTabler.reference_id = r.id # 015 where source_cd = 'C' # 015;

Date: 2024-09-23 11:08:58
Duration: 2s220ms
Bind query: yes

SELECT chem_id # 015, disease_id # 015, acc_txt # 015 FROM pub2.CHEM_DISEASE_REFERENCE transactionalReferenceTabler # 015 LEFT OUTER JOIN pub2.REFERENCE r ON transactionalReferenceTabler.reference_id = r.id # 015 where source_cd = 'C' # 015;

Date: 2024-09-23 11:03:08
Duration: 1s850ms
Bind query: yes

SELECT chem_id # 015, disease_id # 015, acc_txt # 015 FROM pub2.CHEM_DISEASE_REFERENCE transactionalReferenceTabler # 015 LEFT OUTER JOIN pub2.REFERENCE r ON transactionalReferenceTabler.reference_id = r.id # 015 where source_cd = 'C' # 015;

Date: 2024-09-23 10:50:07
Duration: 1s849ms
Bind query: yes

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Times Reported Time consuming queries #6

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select ID, OBJECT_TYPE_ID, ACC_TXT, t.ACC_DB_CD, NM, NM_SORT, SECONDARY_NM, DESCRIPTION, NOTE from pub2.term t where object_type_id = 4 and t.id in ( select distinct gene_id from pub2.gene_chem_reference r where r.id NOT in ( SELECT gene_chem_reference_id FROM pub2.GENE_CHEM_REFERENCE_AXN WHERE action_degree_type_nm = 'does not affect') union select distinct gene_id from pub2.gene_disease_reference r where source_cd in ('C', 'O'));

Date: 2024-09-23 11:03:46
Duration: 1s568ms
Bind query: yes

select ID, OBJECT_TYPE_ID, ACC_TXT, t.ACC_DB_CD, NM, NM_SORT, SECONDARY_NM, DESCRIPTION, NOTE from pub2.term t where object_type_id = 4 and t.id in ( select distinct gene_id from pub2.gene_chem_reference r where r.id NOT in ( SELECT gene_chem_reference_id FROM pub2.GENE_CHEM_REFERENCE_AXN WHERE action_degree_type_nm = 'does not affect') union select distinct gene_id from pub2.gene_disease_reference r where source_cd in ('C', 'O'));

Date: 2024-09-23 11:09:38
Duration: 1s539ms
Bind query: yes

select ID, OBJECT_TYPE_ID, ACC_TXT, t.ACC_DB_CD, NM, NM_SORT, SECONDARY_NM, DESCRIPTION, NOTE from pub2.term t where object_type_id = 4 and t.id in ( select distinct gene_id from pub2.gene_chem_reference r where r.id NOT in ( SELECT gene_chem_reference_id FROM pub2.GENE_CHEM_REFERENCE_AXN WHERE action_degree_type_nm = 'does not affect') union select distinct gene_id from pub2.gene_disease_reference r where source_cd in ('C', 'O'));

Date: 2024-09-23 10:50:43
Duration: 1s457ms
Bind query: yes

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Times Reported Time consuming queries #7

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[ User: pubeu - Total duration: 3s411ms - Times executed: 1 ]

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WITH recursive sub_node ( object_id, id, path, lvl ) AS ( SELECT n.object_id, n.id, ARRAY[n.nm_sort], 1 FROM dag_node n WHERE n.object_id = '589967' UNION ALL SELECT n.object_id, n.id, CAST(path || n.nm_sort AS varchar(600)[]), sn.lvl + 1 FROM dag_node n INNER JOIN sub_node sn ON (n.parent_id = sn.id)) SELECT /* TreeTermBasicsDAO.getDescendants */ DISTINCT t.nm priNm, t.nm_html priNmHtml, t.secondary_nm secondaryNm, t.acc_db_cd accDbCd, t.acc_txt termAcc, t.is_leaf isLeaf, t.has_chems hasChems, t.has_diseases hasDiseases, t.has_exposures hasExposures, t.has_genes hasGenes, sn.lvl, sn.path, MAX(sn.lvl) OVER () maxLvl, t.has_phenotypes hasPhenotypes FROM sub_node sn INNER JOIN term t ON sn.object_id = t.id WHERE sn.lvl <= 2 ORDER BY sn.path;

Date: 2024-09-23 05:45:12
Duration: 3s411ms
Database: ctddev51
User: pubeu
Bind query: yes

WITH recursive sub_node ( object_id, id, path, lvl ) AS ( SELECT n.object_id, n.id, ARRAY[n.nm_sort], 1 FROM dag_node n WHERE n.object_id = '1432724' UNION ALL SELECT n.object_id, n.id, CAST(path || n.nm_sort AS varchar(600)[]), sn.lvl + 1 FROM dag_node n INNER JOIN sub_node sn ON (n.parent_id = sn.id)) SELECT /* TreeTermBasicsDAO.getDescendants */ DISTINCT t.nm priNm, t.nm_html priNmHtml, t.secondary_nm secondaryNm, t.acc_db_cd accDbCd, t.acc_txt termAcc, t.is_leaf isLeaf, t.has_chems hasChems, t.has_diseases hasDiseases, t.has_exposures hasExposures, t.has_genes hasGenes, sn.lvl, sn.path, MAX(sn.lvl) OVER () maxLvl, t.has_phenotypes hasPhenotypes FROM sub_node sn INNER JOIN term t ON sn.object_id = t.id WHERE sn.lvl <= 2 ORDER BY sn.path;

Date: 2024-09-23 05:45:13
Duration: 1s43ms
Bind query: yes

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Times Reported Time consuming queries #8

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SELECT /* BatchChemGODAO */ 'ddt' "Input", sqi.chem_nm "ChemicalName", sqi.chem_acc_txt "ChemicalID", sqi.casRN "CasRN", sqi.gene_symbol "GeneSymbol", sqi.gene_acc_txt "GeneID", sqi.ontology_nm "Ontology", sqi.go_term_nm "GoTermName", sqi.go_acc_txt "GoTermID" FROM ( WITH sq AS ( SELECT DISTINCT c.id chem_id, c.nm chem_nm, c.acc_txt chem_acc_txt, c.secondary_nm casRN, c.nm_sort chem_nm_sort, gcr.gene_id, g.nm gene_symbol, g.acc_txt gene_acc_txt, g.nm_sort gene_symbol_sort FROM term c INNER JOIN gene_chem_reference gcr ON c.id = gcr.chem_id INNER JOIN term g ON gcr.gene_id = g.id WHERE (c.id = 1291235)) SELECT DISTINCT sq.chem_nm, sq.chem_acc_txt, sq.casRN, sq.gene_symbol, sq.gene_acc_txt, gt.nm go_term_nm, gt.acc_txt go_acc_txt, sq.chem_nm_sort, sq.gene_symbol_sort, gt.nm_sort, d.nm ontology_nm FROM sq INNER JOIN gene_go_annot gga ON sq.gene_id = gga.gene_id INNER JOIN dag_node gt ON gga.go_term_id = gt.object_id INNER JOIN dag d ON gt.dag_id = d.id WHERE gga.is_not = false AND (d.id = 5 OR d.id = 4) ORDER BY sq.chem_nm_sort, sq.gene_symbol_sort, d.nm, gt.nm_sort) sqi;

Date: 2024-09-23 05:48:28
Duration: 4s304ms
Bind query: yes

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Times Reported Time consuming queries #9

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select distinct /* ChemPhenotypesAssnsDAO */ associatedTerm.nm || '^' || o.cd || '^' || associatedTerm.nm_html || '^' || associatedTerm.acc_txt || '^' || associatedTerm.acc_db_cd as associatedTerm, associatedTerm.id associatedTermId, ptr.ixn_id ixnId, associatedTerm.object_type_id || '|' || associatedTerm.nm_sort associatedTermNmSort, COALESCE(associatedTerm.secondary_nm, '') casRN, phenotypeTerm.nm || '^' || 'go' || '^' || phenotypeTerm.nm_html || '^' || phenotypeTerm.acc_txt || '^' || phenotypeTerm.acc_db_cd as phenotype, phenotypeTerm.id phenotypeId, ( SELECT STRING_AGG(distinct taxonTerm.nm || '^' || 'taxon' || '^' || taxonTerm.nm_html || '^' || taxonTerm.acc_txt || '^' || taxonTerm.acc_db_cd || '^' || COALESCE(taxonTerm.secondary_nm, ''), '|')) as taxonTerms, ( SELECT STRING_AGG(distinct anatomyTerm.nm_html || '^' || anatomyTerm.acc_txt || '^' || ia.level_seq || '^' || anatomyTerm.acc_db_cd || '^' || anatomyTerm.nm, '|')) as anatomyTerms, COUNT(DISTINCT taxonTerm.nm) taxonCount, i.ixn_prose_html ixnProseHtml, i.ixn_prose_txt ixnProse, i.sort_txt ixnSort, ( SELECT STRING_AGG(distinct r.acc_txt, '|')) as references, COUNT(DISTINCT ptr.reference_id) refCount, pt.indirect_term_qty inferredCount, COUNT(*) OVER () fullRowCount from phenotype_term_reference ptr inner join phenotype_term pt on ptr.term_id = pt.term_id and ptr.phenotype_id = pt.phenotype_id inner join term associatedTerm on ptr.term_id = associatedTerm.id inner join term phenotypeTerm on ptr.phenotype_id = phenotypeTerm.id left outer join term taxonTerm on ptr.taxon_id = taxonTerm.id inner join reference r on ptr.reference_id = r.id inner join ixn i on ptr.ixn_id = i.id inner join object_type o on associatedTerm.object_type_id = o.id left outer join ixn_anatomy ia on ptr.ixn_id = ia.ixn_id left outer join term anatomyTerm on ia.anatomy_id = anatomyTerm.id where ptr.term_id IN ( select /* DBConstants.getDAGTermSQL */ distinct dp.descendant_object_id from dag_path dp WHERE dp.ancestor_object_id in ( select distinct id from term baseTerm where object_type_id = 2 and upper(baseTerm.nm) LIKE 'ZINC')) and ptr.term_object_type_id = 2 and ptr.phenotype_id IN ( select /* DBConstants.getDAGTermSQL */ distinct dp.descendant_object_id from dag_path dp WHERE dp.ancestor_object_id in ( select distinct id from term baseTerm where object_type_id = 5 and baseTerm.id in ( select object_id from db_link l where l.acc_txt = 'GO:0006915' AND l.type_cd = 'A' AND l.object_type_id = 5))) and taxonTerm.id in ( select /* DBConstants.getDAGTermSQL */ distinct dp.descendant_object_id from dag_path dp WHERE dp.ancestor_object_id in ( select distinct id from term baseTerm where object_type_id = 1 and baseTerm.id in ( select object_id from db_link l where l.acc_txt = '9606' AND l.type_cd = 'A' AND l.object_type_id = 1))) and i.id in ( select ixn_id from ixn_axn where action_type_nm = 'phenotype' and action_degree_type_nm in ('increases')) group by associatedTerm, associatedTermNmSort, phenotype, casRN, ixnId, ixnProseHtml, ixnProse, ixnSort, associatedTermId, phenotypeId, inferredCount ORDER BY associatedTermNmSort LIMIT 50;

Date: 2024-09-23 05:48:48
Duration: 4s23ms
Bind query: yes

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Times Reported Time consuming queries #10

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select distinct /* ChemPhenotypesAssnsDAO */ associatedTerm.nm || '^' || o.cd || '^' || associatedTerm.nm_html || '^' || associatedTerm.acc_txt || '^' || associatedTerm.acc_db_cd as associatedTerm, associatedTerm.id associatedTermId, ptr.ixn_id ixnId, associatedTerm.object_type_id || '|' || associatedTerm.nm_sort associatedTermNmSort, COALESCE(associatedTerm.secondary_nm, '') casRN, phenotypeTerm.nm || '^' || 'go' || '^' || phenotypeTerm.nm_html || '^' || phenotypeTerm.acc_txt || '^' || phenotypeTerm.acc_db_cd as phenotype, phenotypeTerm.id phenotypeId, ( SELECT STRING_AGG(distinct taxonTerm.nm || '^' || 'taxon' || '^' || taxonTerm.nm_html || '^' || taxonTerm.acc_txt || '^' || taxonTerm.acc_db_cd || '^' || COALESCE(taxonTerm.secondary_nm, ''), '|')) as taxonTerms, ( SELECT STRING_AGG(distinct anatomyTerm.nm_html || '^' || anatomyTerm.acc_txt || '^' || ia.level_seq || '^' || anatomyTerm.acc_db_cd || '^' || anatomyTerm.nm, '|')) as anatomyTerms, COUNT(DISTINCT taxonTerm.nm) taxonCount, i.ixn_prose_html ixnProseHtml, i.ixn_prose_txt ixnProse, i.sort_txt ixnSort, ( SELECT STRING_AGG(distinct r.acc_txt, '|')) as references, COUNT(DISTINCT ptr.reference_id) refCount, pt.indirect_term_qty inferredCount, COUNT(*) OVER () fullRowCount from phenotype_term_reference ptr inner join phenotype_term pt on ptr.term_id = pt.term_id and ptr.phenotype_id = pt.phenotype_id inner join term associatedTerm on ptr.term_id = associatedTerm.id inner join term phenotypeTerm on ptr.phenotype_id = phenotypeTerm.id left outer join term taxonTerm on ptr.taxon_id = taxonTerm.id inner join reference r on ptr.reference_id = r.id inner join ixn i on ptr.ixn_id = i.id inner join object_type o on associatedTerm.object_type_id = o.id left outer join ixn_anatomy ia on ptr.ixn_id = ia.ixn_id left outer join term anatomyTerm on ia.anatomy_id = anatomyTerm.id where ptr.term_id IN ( select /* DBConstants.getDAGTermSQL */ distinct dp.descendant_object_id from dag_path dp WHERE dp.ancestor_object_id in ( select distinct id from term baseTerm where object_type_id = 2 and upper(baseTerm.nm) LIKE 'ACETYLCYSTEINE')) and ptr.term_object_type_id = 2 and ptr.phenotype_id IN ( select /* DBConstants.getDAGTermSQL */ distinct dp.descendant_object_id from dag_path dp WHERE dp.ancestor_object_id in ( select distinct id from term baseTerm where object_type_id = 5 and baseTerm.id in ( select object_id from db_link l where l.acc_txt = 'GO:0006979' AND l.type_cd = 'A' AND l.object_type_id = 5))) and i.id in ( select ixn_id from ixn_anatomy where anatomy_id IN ( select /* DBConstants.getDAGTermSQL */ distinct dp.descendant_object_id from dag_path dp WHERE dp.ancestor_object_id in ( select distinct id from term baseTerm where object_type_id = 10 and upper(baseTerm.nm) LIKE 'CARDIOVASCULAR SYSTEM'))) and taxonTerm.id in ( select /* DBConstants.getDAGTermSQL */ distinct dp.descendant_object_id from dag_path dp WHERE dp.ancestor_object_id in ( select distinct id from term baseTerm where object_type_id = 1 and baseTerm.id in ( select object_id from db_link l where l.acc_txt = '9605' AND l.type_cd = 'A' AND l.object_type_id = 1))) and i.id in ( select ixn_id from ixn_axn where action_type_nm = 'phenotype' and action_degree_type_nm in ('increases')) group by associatedTerm, associatedTermNmSort, phenotype, casRN, ixnId, ixnProseHtml, ixnProse, ixnSort, associatedTermId, phenotypeId, inferredCount ORDER BY associatedTermNmSort LIMIT 50;

Date: 2024-09-23 05:48:53
Duration: 3s983ms
Bind query: yes

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Times Reported Time consuming queries #11

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[ User: pubeu - Total duration: 3s965ms - Times executed: 1 ]

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SELECT /* CIQH.getIxnCacheQuery */ gcr.ixn_id, NULL, NULL, NULL FROM gene_chem_reference gcr WHERE /* CIQH.getIxnWhereCore */ gcr.gene_id = ANY (ARRAY (( SELECT /* IQH.getMasterDiseaseWhereEquals.Name.Gene */ gd.gene_id FROM term t INNER JOIN dag_path dp ON t.id = dp.ancestor_object_id INNER JOIN gene_disease gd ON dp.descendant_object_id = gd.disease_id WHERE UPPER(t.nm) LIKE 'ASTHMA' AND t.object_type_id = 3))) AND gcr.id IN ( SELECT gcra.gene_chem_reference_id FROM gene_chem_reference_axn gcra WHERE (gcra.action_degree_type_nm = 'increases'));

Date: 2024-09-23 05:47:19
Duration: 3s965ms
Database: ctddev51
User: pubeu
Bind query: yes

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Times Reported Time consuming queries #12

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SELECT /* AdvancedGeneQueryDAO.getData */ g.id geneId, g.acc_txt acc, g.nm nm, g.nm nmHtml, g.secondary_nm secondaryNm, g.has_chems hasChems, g.has_diseases hasDiseases, g.has_exposures hasExposures, g.has_phenotypes hasPhenotypes, COUNT(*) OVER () fullRowCount FROM term g WHERE g.id IN ( SELECT gcr.gene_id FROM gene_chem_reference gcr WHERE /* CIQH.getIxnWhereCore */ gcr.gene_id = ANY (ARRAY (( SELECT /* IQH.getMasterDiseaseWhereEquals.Name.Gene */ gd.gene_id FROM term t INNER JOIN dag_path dp ON t.id = dp.ancestor_object_id INNER JOIN gene_disease gd ON dp.descendant_object_id = gd.disease_id WHERE UPPER(t.nm) LIKE 'ASTHMA' AND t.object_type_id = 3))) AND gcr.id IN ( SELECT gcra.gene_chem_reference_id FROM gene_chem_reference_axn gcra WHERE (gcra.action_degree_type_nm = 'increases'))) ORDER BY g.nm_sort, g.id LIMIT 50;

Date: 2024-09-23 05:47:24
Duration: 3s794ms
Bind query: yes