Times Reported Time consuming queries #1

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[ User: editeu - Total duration: 1m15s - Times executed: 21 ]

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select t.ID, t.OBJECT_TYPE_ID, t.ACC_TXT, t.ACC_DB_CD, t.NM, t.NM_SORT, t.SECONDARY_NM, t.DESCRIPTION, t.NOTE, l.NM from pub2.TERM t, pub2.TERM_LABEL l where t.OBJECT_TYPE_ID = 4 and t.id = l.TERM_ID;

Date: 2025-01-14 10:58:34
Duration: 5s484ms
Database: ctddev51
User: editeu
Bind query: yes

select t.ID, t.OBJECT_TYPE_ID, t.ACC_TXT, t.ACC_DB_CD, t.NM, t.NM_SORT, t.SECONDARY_NM, t.DESCRIPTION, t.NOTE, l.NM from pub2.TERM t, pub2.TERM_LABEL l where t.OBJECT_TYPE_ID = 4 and t.id = l.TERM_ID;

Date: 2025-01-14 08:32:30
Duration: 5s458ms
Database: ctddev51
User: editeu
Bind query: yes

select t.ID, t.OBJECT_TYPE_ID, t.ACC_TXT, t.ACC_DB_CD, t.NM, t.NM_SORT, t.SECONDARY_NM, t.DESCRIPTION, t.NOTE, l.NM from pub2.TERM t, pub2.TERM_LABEL l where t.OBJECT_TYPE_ID = 4 and t.id = l.TERM_ID;

Date: 2025-01-14 11:12:05
Duration: 5s389ms
Database: ctddev51
User: editeu
Bind query: yes

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Times Reported Time consuming queries #2

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[ User: pub2 - Total duration: 7s526ms - Times executed: 1 ]

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[ Application: pgAdmin 4 - CONN:5561680 - Total duration: 7s526ms - Times executed: 1 ]

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select distinct source_cd from PHENOTYPE_TERM_REFERENCE;

Date: 2025-01-14 15:17:19
Duration: 7s526ms
Database: ctddev51
User: pub2
Application: pgAdmin 4 - CONN:5561680

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Times Reported Time consuming queries #3

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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: 2025-01-14 05:48:49
Duration: 6s801ms
Bind query: yes

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Times Reported Time consuming queries #4

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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: 2025-01-14 05:48:55
Duration: 6s716ms
Bind query: yes

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Times Reported Time consuming queries #5

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[ User: pubeu - Total duration: 4s625ms - Times executed: 1 ]

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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 = 1302084)) 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: 2025-01-14 05:48:26
Duration: 4s625ms
Database: ctddev51
User: pubeu
Bind query: yes

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Times Reported Time consuming queries #6

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[ User: pubeu - Total duration: 4s152ms - 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: 2025-01-14 05:47:20
Duration: 4s152ms
Database: ctddev51
User: pubeu
Bind query: yes

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Times Reported Time consuming queries #7

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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: 2025-01-14 05:47:24
Duration: 4s54ms
Bind query: yes

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Times Reported Time consuming queries #8

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[ User: pub2 - Total duration: 3s876ms - Times executed: 1 ]

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select distinct geneTerm.acc_txt, geneTerm.nm, 'gene', goTerm.acc_txt, goTerm.nm, 'phenotype' from pub2.GENE_GO_ANNOT gga, pub2.TERM geneTerm, pub2.TERM goTerm where gga.gene_id = geneTerm.id and gga.go_term_id = goTerm.id and (gga.go_term_id IN ( SELECT id FROM term WHERE nm IN ( -- TOP_CURATED_CHEMICALS 'Valproic Acid', 'Tetrachlorodibenzodioxin', 'bisphenol A', 'Benzo(a)pyrene', '(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine', '4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide', 'Acetaminophen', 'Dexamethasone', 'pirinixic acid', 'Estradiol', 'Lipopolysaccharides', 'Cisplatin' -- TOP_CURATED_GENES 'NOG', 'INS', 'TNF', 'CASP3', 'IL1B', 'PPARA', 'AHR', 'CYP1A1', 'IL6', 'MAPK1', 'PTGS2', 'MAPK3', -- TOP_CURATED_DISEASES 'Hypertension', 'Chemical and Drug Induced Liver Injury', 'Hypotension', 'Pain', 'Kidney Diseases', 'Breast Neoplasms', 'Acute Kidney Injury', 'Necrosis', 'Cocaine-Related Disorders', 'Drug-Related Side Effects and Adverse Reactions', 'Substance Withdrawal Syndrome', -- GO: 'cell proliferation', 'cell death', 'lipid oxidation', 'regulation of blood pressure', 'lipid catabolic process', 'positive regulation of cell death', 'positive regulation of apoptotic process', 'glutathione metabolic process', 'reactive oxygen species biosynthetic process', 'positive regulation of reactive oxygen species biosynthetic process', 'vasoconstriction')) or gga.gene_id IN ( SELECT id FROM term WHERE nm IN ( -- TOP_CURATED_CHEMICALS 'Valproic Acid', 'Tetrachlorodibenzodioxin', 'bisphenol A', 'Benzo(a)pyrene', '(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine', '4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide', 'Acetaminophen', 'Dexamethasone', 'pirinixic acid', 'Estradiol', 'Lipopolysaccharides', 'Cisplatin' -- TOP_CURATED_GENES 'NOG', 'INS', 'TNF', 'CASP3', 'IL1B', 'PPARA', 'AHR', 'CYP1A1', 'IL6', 'MAPK1', 'PTGS2', 'MAPK3', -- TOP_CURATED_DISEASES 'Hypertension', 'Chemical and Drug Induced Liver Injury', 'Hypotension', 'Pain', 'Kidney Diseases', 'Breast Neoplasms', 'Acute Kidney Injury', 'Necrosis', 'Cocaine-Related Disorders', 'Drug-Related Side Effects and Adverse Reactions', 'Substance Withdrawal Syndrome', -- GO: 'cell proliferation', 'cell death', 'lipid oxidation', 'regulation of blood pressure', 'lipid catabolic process', 'positive regulation of cell death', 'positive regulation of apoptotic process', 'glutathione metabolic process', 'reactive oxygen species biosynthetic process', 'positive regulation of reactive oxygen species biosynthetic process', 'vasoconstriction'))) and (gga.go_term_id, gga.gene_id) in ( select phenotype_id, gene_id from tetramer) LIMIT 200;

Date: 2025-01-14 15:36:55
Duration: 3s876ms
Database: ctddev51
User: pub2
Bind query: yes

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Times Reported Time consuming queries #9

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[ User: pub2 - Total duration: 3s857ms - Times executed: 1 ]

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select distinct chemTerm.acc_txt # 015, chemTerm.nm # 015, 'chemical' # 015, phenotypeTerm.acc_txt # 015, phenotypeTerm.nm # 015, 'phenotype' # 015 from pub2.PHENOTYPE_TERM_REFERENCE ptr # 015, pub2.TERM chemTerm # 015, pub2.TERM phenotypeTerm # 015 where ptr.phenotype_id = phenotypeTerm.id # 015 and ptr.term_id = chemTerm.id # 015 and (ptr.term_id IN ( SELECT id FROM term WHERE nm IN ( -- TOP_CURATED_CHEMICALS 'Valproic Acid', 'Tetrachlorodibenzodioxin', 'bisphenol A', 'Benzo(a)pyrene', '(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine', '4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide', 'Acetaminophen', 'Dexamethasone', 'pirinixic acid', 'Estradiol', 'Lipopolysaccharides', 'Cisplatin' -- TOP_CURATED_GENES 'NOG', 'INS', 'TNF', 'CASP3', 'IL1B', 'PPARA', 'AHR', 'CYP1A1', 'IL6', 'MAPK1', 'PTGS2', 'MAPK3', -- TOP_CURATED_DISEASES 'Hypertension', 'Chemical and Drug Induced Liver Injury', 'Hypotension', 'Pain', 'Kidney Diseases', 'Breast Neoplasms', 'Acute Kidney Injury', 'Necrosis', 'Cocaine-Related Disorders', 'Drug-Related Side Effects and Adverse Reactions', 'Substance Withdrawal Syndrome', -- GO: 'cell proliferation', 'cell death', 'lipid oxidation', 'regulation of blood pressure', 'lipid catabolic process', 'positive regulation of cell death', 'positive regulation of apoptotic process', 'glutathione metabolic process', 'reactive oxygen species biosynthetic process', 'positive regulation of reactive oxygen species biosynthetic process', 'vasoconstriction')) or ptr.phenotype_id IN ( SELECT id FROM term WHERE nm IN ( -- TOP_CURATED_CHEMICALS 'Valproic Acid', 'Tetrachlorodibenzodioxin', 'bisphenol A', 'Benzo(a)pyrene', '(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine', '4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide', 'Acetaminophen', 'Dexamethasone', 'pirinixic acid', 'Estradiol', 'Lipopolysaccharides', 'Cisplatin' -- TOP_CURATED_GENES 'NOG', 'INS', 'TNF', 'CASP3', 'IL1B', 'PPARA', 'AHR', 'CYP1A1', 'IL6', 'MAPK1', 'PTGS2', 'MAPK3', -- TOP_CURATED_DISEASES 'Hypertension', 'Chemical and Drug Induced Liver Injury', 'Hypotension', 'Pain', 'Kidney Diseases', 'Breast Neoplasms', 'Acute Kidney Injury', 'Necrosis', 'Cocaine-Related Disorders', 'Drug-Related Side Effects and Adverse Reactions', 'Substance Withdrawal Syndrome', -- GO: 'cell proliferation', 'cell death', 'lipid oxidation', 'regulation of blood pressure', 'lipid catabolic process', 'positive regulation of cell death', 'positive regulation of apoptotic process', 'glutathione metabolic process', 'reactive oxygen species biosynthetic process', 'positive regulation of reactive oxygen species biosynthetic process', 'vasoconstriction'))) # 015 and (ptr.term_id, ptr.phenotype_id) in ( select chem_id, phenotype_id from tetramer) # 015 and source_cd = 'C' # 015 and term_object_type_id = 2 --chemical #015 LIMIT 200 # 015;

Date: 2025-01-14 15:20:09
Duration: 3s857ms
Database: ctddev51
User: pub2
Bind query: yes

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Times Reported Time consuming queries #10

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SELECT /* AdvancedIxnQueryDAO.getData */ g.nm geneSymbol, g.id geneId, g.acc_txt geneAcc, g.acc_db_cd geneAccDbCd, c.nm chemNm, c.nm_html chemNmhtml, c.acc_txt chemAcc, c.secondary_nm casRN, c.id chemId, i.id ixnId, i.ixn_prose_txt ixnProse, i.ixn_prose_html ixnProseHtml, i.actions_txt ixnActions, COUNT(DISTINCT gcr.reference_id) refCount, COUNT(DISTINCT gcr.taxon_id) taxonCount, COUNT(*) OVER () fullRowCount FROM gene_chem_reference gcr INNER JOIN ixn i ON gcr.ixn_id = i.id INNER JOIN term g ON gcr.gene_id = g.id INNER JOIN term c ON gcr.chem_id = c.id WHERE /* CIQH.getIxnWhereCore */ gcr.gene_id = ANY (ARRAY (( SELECT /* IQH.getMasterPathwayWhereEquals.Name */ tp.term_id FROM term_pathway tp WHERE UPPER(tp.pathway_nm) LIKE 'METABOLISM' AND tp.object_type_id = 4))) AND gcr.id IN ( SELECT gcra.gene_chem_reference_id FROM gene_chem_reference_axn gcra WHERE (gcra.action_degree_type_nm = 'increases')) GROUP BY g.nm, g.nm_sort, g.acc_txt, g.acc_db_cd, g.id, c.nm, c.nm_html, c.nm_sort, c.acc_txt, c.secondary_nm, c.id, i.ixn_prose_txt, i.ixn_prose_html, i.sort_txt, i.actions_txt, i.id ORDER BY g.nm_sort, c.nm_sort, i.sort_txt LIMIT 50;

Date: 2025-01-14 05:47:33
Duration: 3s584ms
Bind query: yes