VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:51:29 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:51:29 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:51:29 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:51:29 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:51:29 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:51:29 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:51:29 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:51:29 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:51:29 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:51:30 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:51:30 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:51:30 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:51:30 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:51:30 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:51:30 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:53:23 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:53:23 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:53:23 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:53:23 ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:53:23 ]

select pub2.maint_term_derive_data ();

[ Date: 2025-08-27 06:05:18 - Bind query: yes ]

select pub2.maint_gene_chem_ref_gene_form_refresh ();

[ Date: 2025-08-27 01:56:14 - Bind query: yes ]

SELECT maint_term_derive_nm_fts ();

[ Date: 2025-08-27 03:01:06 - Bind query: yes ]

VACUUM FULL ANALYZE;

[ Date: 2025-08-27 03:55:44 - Bind query: yes ]

SELECT /* AllGDRelationsDAO */ g.nm "GeneSymbol", g.acc_txt "GeneID", d.nm "DiseaseName", d.acc_db_cd || ':' || d.acc_txt "DiseaseID", CASE WHEN gdr.via_chem_id IS NULL THEN ( SELECT STRING_AGG(a.action_type_nm, '|' ORDER BY a.action_type_nm) FROM gene_disease_axn a WHERE a.gene_id = gdr.gene_id AND a.disease_id = gdr.disease_id) ELSE NULL END "DirectEvidence", c.nm "InferenceChemicalName", gdr.network_score "InferenceScore", STRING_AGG(gdr.source_acc_txt, '|' ORDER BY gdr.source_acc_txt) "OmimIDs", STRING_AGG(r.acc_txt, '|' ORDER BY r.acc_txt) "PubMedIDs" FROM gene_disease_reference gdr INNER JOIN term g ON gdr.gene_id = g.id INNER JOIN term d ON gdr.disease_id = d.id LEFT OUTER JOIN reference r ON gdr.reference_id = r.id LEFT OUTER JOIN term c ON gdr.via_chem_id = c.id GROUP BY g.nm, g.acc_txt, d.nm, d.acc_db_cd || ':' || d.acc_txt, CASE WHEN gdr.via_chem_id IS NULL THEN ( SELECT STRING_AGG(a.action_type_nm, '|' ORDER BY a.action_type_nm) FROM gene_disease_axn a WHERE a.gene_id = gdr.gene_id AND a.disease_id = gdr.disease_id) ELSE NULL END, c.nm, gdr.network_score ORDER BY g.nm, d.nm;

[ Date: 2025-08-27 15:00:30 - Database: ctdprd51 - User: qaeu - Bind query: yes ]

select pub2.maint_cached_value_refresh_data_metrics ();

[ Date: 2025-08-27 06:48:13 - Bind query: yes ]

update pub2.GENE_DISEASE gd set exposure_reference_qty = ( select count(distinct reference_id) from pub2.GENE_DISEASE_REFERENCE gdr where gd.gene_id = gdr.gene_id and gd.disease_id = gdr.disease_id and reference_id in ( select id from pub2.REFERENCE r where has_exposures = true));

[ Date: 2025-08-27 00:00:49 - Bind query: yes ]

/* * Run daily to prune LOG_QUERY, archive old queries to LOG_QUERY_ARCHIVE * and vacuum/analyze the tables. * * $Id: archive_query_logs.sql 10832 2012-03-19 15:27:11Z mcr $ */ SELECT maint_query_logs_archive ();

[ Date: 2025-08-27 00:09:35 ]

select pub2.maint_phenotype_term_derive_data ();

[ Date: 2025-08-27 06:15:16 - Bind query: yes ]

INSERT INTO pub2.TERM_REFERENCE (term_id, object_type_id, reference_id, ixn_type_id) SELECT DISTINCT term_id, object_type_id, reference_id, ixn_type_id FROM ( SELECT gene_id as term_id, ( SELECT object_type_id FROM pub2.TERM WHERE id = gene_id), reference_id, ( SELECT id FROM edit.IXN_TYPE WHERE nm = 'CHEMICAL-GENE') as ixn_type_id FROM pub2.GENE_CHEM_REFERENCE UNION SELECT chem_id as term_id, ( SELECT object_type_id FROM pub2.TERM WHERE id = chem_id), reference_id, ( SELECT id FROM edit.IXN_TYPE WHERE nm = 'CHEMICAL-GENE') as ixn_type_id FROM pub2.GENE_CHEM_REFERENCE UNION SELECT taxon_id as term_id, ( SELECT object_type_id FROM pub2.TERM WHERE id = taxon_id), reference_id, ( SELECT id FROM edit.IXN_TYPE WHERE nm = 'CHEMICAL-GENE') as ixn_type_id FROM pub2.GENE_CHEM_REFERENCE WHERE taxon_id IS NOT NULL UNION SELECT chem_id as term_id, ( SELECT object_type_id FROM pub2.TERM WHERE id = chem_id), reference_id, ( SELECT id FROM edit.IXN_TYPE WHERE nm = 'CHEMICAL-DISEASE') as ixn_type_id FROM pub2.CHEM_DISEASE_REFERENCE WHERE source_cd = 'C' UNION SELECT disease_id as term_id, ( SELECT object_type_id FROM pub2.TERM WHERE id = disease_id), reference_id, ( SELECT id FROM edit.IXN_TYPE WHERE nm = 'CHEMICAL-DISEASE') as ixn_type_id FROM pub2.CHEM_DISEASE_REFERENCE WHERE source_cd = 'C' UNION SELECT gene_id as term_id, ( SELECT object_type_id FROM pub2.TERM WHERE id = gene_id), reference_id, ( SELECT id FROM edit.IXN_TYPE WHERE nm = 'GENE-DISEASE') as ixn_type_id FROM pub2.GENE_DISEASE_REFERENCE WHERE source_cd = 'C' UNION SELECT disease_id as term_id, ( SELECT object_type_id FROM pub2.TERM WHERE id = disease_id), reference_id, ( SELECT id FROM edit.IXN_TYPE WHERE nm = 'GENE-DISEASE') as ixn_type_id FROM pub2.GENE_DISEASE_REFERENCE WHERE source_cd = 'C' UNION SELECT ee.exp_marker_term_id as term_id, ( SELECT object_type_id FROM term WHERE id = exp_marker_term_id), e.reference_id, ( SELECT id FROM edit.ixn_type WHERE nm = 'EXPOSURE') as ixn_type_id FROM pub2.EXPOSURE e, pub2.EXP_EVENT ee WHERE e.exp_event_id = ee.id AND exp_marker_term_id IS NOT NULL UNION SELECT er.term_id, ( SELECT object_type_id FROM term WHERE id = er.term_id), e.reference_id, ( SELECT id FROM edit.ixn_type WHERE nm = 'EXPOSURE') as ixn_type_id FROM pub2.EXPOSURE e, pub2.EXP_RECEPTOR er WHERE e.exp_receptor_id = er.id AND er.term_id IS NOT NULL UNION SELECT chem_id as term_id, ( SELECT object_type_id FROM term WHERE id = chem_id), e.reference_id, ( SELECT id FROM edit.ixn_type WHERE nm = 'EXPOSURE') as ixn_type_id FROM pub2.EXPOSURE e, pub2.EXP_STRESSOR es WHERE e.exp_stressor_id = es.id AND chem_id IS NOT NULL UNION SELECT phenotype_id as term_id, ( SELECT object_type_id FROM term WHERE id = phenotype_id), e.reference_id, ( SELECT id FROM edit.ixn_type WHERE nm = 'EXPOSURE') as ixn_type_id FROM pub2.EXPOSURE e, pub2.EXP_OUTCOME eo WHERE e.exp_outcome_id = eo.id AND phenotype_id IS NOT NULL UNION SELECT disease_id as term_id, ( SELECT object_type_id FROM term WHERE id = disease_id), e.reference_id, ( SELECT id FROM edit.ixn_type WHERE nm = 'EXPOSURE') as ixn_type_id FROM pub2.EXPOSURE e, pub2.EXP_OUTCOME eo WHERE e.exp_outcome_id = eo.id AND disease_id IS NOT NULL UNION SELECT phenotype_id as term_id, ( SELECT object_type_id FROM pub2.TERM WHERE id = phenotype_id), reference_id, ( SELECT id FROM edit.IXN_TYPE WHERE nm = 'PHENOTYPE') as ixn_type_id FROM pub2.PHENOTYPE_TERM_REFERENCE WHERE source_cd = 'C' UNION SELECT term_id, ( SELECT object_type_id FROM pub2.TERM WHERE id = term_id), reference_id, ( SELECT id FROM edit.IXN_TYPE WHERE nm = 'PHENOTYPE') as ixn_type_id FROM pub2.PHENOTYPE_TERM_REFERENCE WHERE source_cd = 'C' UNION SELECT taxon_id as term_id, ( SELECT object_type_id FROM pub2.TERM WHERE id = taxon_id), reference_id, ( SELECT id FROM edit.IXN_TYPE WHERE nm = 'PHENOTYPE') as ixn_type_id FROM pub2.PHENOTYPE_TERM_REFERENCE WHERE source_cd = 'C' AND taxon_id IS NOT NULL UNION SELECT from_gene_id as term_id, ( SELECT object_type_id FROM pub2.TERM WHERE id = from_gene_id), reference_id, ( SELECT id FROM edit.IXN_TYPE WHERE nm = 'GENE-GENE') as ixn_type_id FROM pub2.GENE_GENE_REFERENCE UNION SELECT to_gene_id as term_id, ( SELECT object_type_id FROM pub2.TERM WHERE id = to_gene_id), reference_id, ( SELECT id FROM edit.IXN_TYPE WHERE nm = 'GENE-GENE') as ixn_type_id FROM pub2.GENE_GENE_REFERENCE UNION SELECT from_taxon_id as term_id, ( SELECT object_type_id FROM pub2.TERM WHERE id = from_taxon_id), reference_id, ( SELECT id FROM edit.IXN_TYPE WHERE nm = 'GENE-GENE') as ixn_type_id FROM pub2.GENE_GENE_REFERENCE UNION SELECT to_taxon_id as term_id, ( SELECT object_type_id FROM pub2.TERM WHERE id = to_taxon_id), reference_id, ( SELECT id FROM edit.IXN_TYPE WHERE nm = 'GENE-GENE') as ixn_type_id FROM pub2.GENE_GENE_REFERENCE UNION SELECT DISTINCT t.id as taxon_id, t.object_type_id as taxon_object_id, r.id as reference_id, i.ixn_type_id as ixn_type_id FROM edit.REFERENCE_IXN ri, pub2.TERM t, edit.IXN i, pub2.REFERENCE r WHERE ri.taxon_acc_txt = t.acc_txt AND t.object_type_id = ( SELECT id FROM pub2.OBJECT_TYPE WHERE cd = 'taxon') AND ri.ixn_id = i.root_id AND i.ixn_type_id in ( SELECT id FROM edit.IXN_TYPE WHERE nm in ('CHEMICAL-DISEASE', 'GENE-DISEASE')) AND ri.reference_acc_txt = r.acc_txt AND ri.taxon_acc_txt IS NOT NULL AND ri.taxon_acc_txt <> '') as test UNION select ea.anatomy_id as term_id, ( select id from object_type where cd = 'anatomy') as object_type_id, r.id as reference_id, ( select id from ixn_type where nm = 'EXPOSURE') as ixn_type_id from pub2.EXP_ANATOMY ea, pub2.EXP_OUTCOME eo, pub2.EXPOSURE e, pub2.REFERENCE r where ea.exp_outcome_id = eo.id and eo.id = e.exp_outcome_id and e.reference_acc_txt = r.acc_txt UNION select anatomy_id as term_id, ( select id from object_type where cd = 'anatomy') as object_type_id, r.id as reference_id, ( select id from ixn_type where nm = 'PHENOTYPE') as ixn_type_id from pub2.IXN i, pub2.IXN_ANATOMY ia, edit.REFERENCE_IXN ri, pub2.REFERENCE r where i.id = ri.ixn_id and ri.reference_acc_txt = r.acc_txt and i.id = ia.ixn_id UNION select medium_term_id as term_id, ( select id from object_type where cd = 'anatomy') as object_type_id, r.id, ( select id from ixn_type where nm = 'EXPOSURE') as ixn_type_id from pub2.EXP_EVENT ee, pub2.EXPOSURE e, pub2.REFERENCE r where ee.id = e.exp_event_id and e.reference_acc_txt = r.acc_txt and medium_term_id is not null;

[ Date: 2025-08-27 01:59:03 - Bind query: yes ]

update pub2.PHENOTYPE_TERM pt set exposure_reference_qty = ( select count(distinct reference_id) from pub2.PHENOTYPE_TERM_REFERENCE ptr where pt.phenotype_id = ptr.phenotype_id and pt.term_id = ptr.term_id and reference_id in ( select id from pub2.REFERENCE r where has_exposures = true));

[ Date: 2025-08-27 00:03:20 - Bind query: yes ]

SELECT maint_term_label_derive_nm_fts ();

[ Date: 2025-08-27 03:03:46 - Bind query: yes ]

SELECT /* PhenotypeDiseasesDAO */ phenotypeTerm.nm "GOName", phenotypeTerm.acc_txt "GOID", diseaseTerm.nm "DiseaseName", diseaseTerm.acc_db_cd || ':' || diseaseTerm.acc_txt "DiseaseID", pt.via_chem_qty "InferenceChemicalQty", ( SELECT STRING_AGG(DISTINCT chemTermNetwork.nm, '|')) "InferenceChemicalNames", pt.via_gene_qty "InferenceGeneQty", ( SELECT STRING_AGG(DISTINCT geneTermNetwork.nm, '|')) "InferenceGeneSymbols" FROM phenotype_term_reference ptr INNER JOIN phenotype_term pt on ptr.phenotype_id = pt.phenotype_id AND ptr.term_id = pt.term_id INNER JOIN term phenotypeTerm on ptr.phenotype_id = phenotypeTerm.id INNER JOIN term diseaseTerm on ptr.term_id = diseaseTerm.id AND diseaseTerm.object_type_id = ( select id from object_type where cd = 'disease') LEFT OUTER JOIN term geneTermNetwork on ptr.via_term_id = geneTermNetwork.id AND geneTermNetwork.object_type_id = ( select id from object_type where cd = 'gene') LEFT OUTER JOIN term chemTermNetwork on ptr.via_term_id = chemTermNetwork.id AND chemTermNetwork.object_type_id = ( select id from object_type where cd = 'chem') WHERE phenotypeTerm.id IN ( SELECT dp.descendant_dag_node_id FROM dag_path dp WHERE dp.ancestor_object_id = ( select id from term where nm = 'biological_process')) AND ptr.source_cd = 'I' AND ptr.phenotype_id = phenotypeTerm.id AND ptr.term_id = diseaseTerm.id GROUP BY phenotypeTerm.nm, phenotypeTerm.acc_txt, diseaseTerm.nm, diseaseTerm.acc_db_cd || ':' || diseaseTerm.acc_txt, pt.via_chem_qty, pt.via_gene_qty;

[ Date: 2025-08-27 16:12:28 - Database: ctdprd51 - User: qaeu - Bind query: yes ]

SELECT /* AllCuratedChemPhenoIxnsDAO */ chemTerm.nm ChemicalName, chemTerm.acc_txt ChemicalID, chemTerm.secondary_nm CasRN, phenoTerm.nm PhenotypeName, phenoTerm.acc_txt PhenotypeID, ( SELECT STRING_AGG(distinct coMentionTerm.nm || '^' || coMentionTerm.acc_txt || '^' || coMentionTerm.acc_db_cd, '|')) as coMentionedTerms, taxonTerm.nm Organism, taxonTerm.acc_txt OrganismID, i.ixn_prose_txt Interaction, i.actions_txt InteractionActions, ( SELECT STRING_AGG(distinct ia.level_seq + 1 || '^' || anatomyTerm.nm || '^' || anatomyTerm.acc_txt, '|' ORDER BY ia.level_seq + 1 || '^' || anatomyTerm.nm || '^' || anatomyTerm.acc_txt)) as anatomyTerms, STRING_AGG(distinct inferredTerm.nm || '^' || inferredTerm.acc_txt || '^' || inferredTerm.acc_db_cd, '|' ORDER BY inferredTerm.nm || '^' || inferredTerm.acc_txt || '^' || inferredTerm.acc_db_cd) InferenceGeneSymbols, STRING_AGG(distinct r.acc_txt, '|' ORDER BY r.acc_txt) PubMedIDs, ptr.ixn_id ignorecolumnIxnId FROM phenotype_term_reference ptr LEFT OUTER JOIN term taxonTerm ON ptr.taxon_id = taxonTerm.id INNER JOIN ixn i ON ptr.ixn_id = i.id INNER JOIN term phenoTerm ON ptr.phenotype_id = phenoTerm.id INNER JOIN reference r ON ptr.reference_id = r.id INNER JOIN term chemTerm ON ptr.term_id = chemTerm.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 LEFT OUTER JOIN phenotype_term_reference ptr2 ON ptr.ixn_id = ptr2.ixn_id and (ptr.term_id <> ptr2.term_id or ptr.phenotype_id <> ptr2.phenotype_id) LEFT OUTER JOIN phenotype_term_reference ptr3 ON ptr.term_id = ptr3.term_id and (ptr.phenotype_id = ptr3.phenotype_id and ptr3.source_cd = 'I') LEFT OUTER JOIN term coMentionTerm ON coMentionTerm.id = ptr2.term_id LEFT OUTER JOIN term inferredTerm ON inferredTerm.id = ptr3.via_term_id WHERE ptr.source_cd = 'C' AND ptr.term_object_type_id = ( SELECT ot.id FROM object_type ot WHERE ot.cd = 'chem') GROUP BY chemTerm.nm, chemTerm.acc_txt, chemTerm.secondary_nm, phenoTerm.nm, phenoTerm.acc_txt, taxonTerm.nm, taxonTerm.acc_txt, i.ixn_prose_txt, i.actions_txt, ptr.ixn_id ORDER BY chemTerm.nm, phenoTerm.nm;

[ Date: 2025-08-27 16:09:18 - Database: ctdprd51 - User: qaeu - Bind query: yes ]

SELECT /* AllCDRelationsDAO */ c.nm "ChemicalName", c.acc_txt "ChemicalID", c.secondary_nm "CasRN", d.nm "DiseaseName", d.acc_db_cd || ':' || d.acc_txt "DiseaseID", a.action_type_nm "DirectEvidence", g.nm "InferenceGeneSymbol", cdr.network_score "InferenceScore", STRING_AGG(cdr.source_acc_txt, '|' ORDER BY cdr.source_acc_txt) "OmimIDs", STRING_AGG(r.acc_txt, '|' ORDER BY r.acc_txt) "PubMedIDs" FROM chem_disease_reference cdr INNER JOIN term d ON cdr.disease_id = d.id INNER JOIN term c ON cdr.chem_id = c.id LEFT OUTER JOIN chem_disease_reference_axn a ON cdr.id = a.chem_disease_reference_id LEFT OUTER JOIN reference r ON cdr.reference_id = r.id LEFT OUTER JOIN term g ON cdr.via_gene_id = g.id GROUP BY c.nm, c.nm_sort, c.acc_txt, c.secondary_nm, d.nm, d.acc_db_cd || ':' || d.acc_txt, a.action_type_nm, g.nm, cdr.network_score ORDER BY c.nm_sort, d.nm;

[ Date: 2025-08-27 14:18:09 - Database: ctdprd51 - User: qaeu - Bind query: yes ]

update pub2.IXN set ixn_xml = replace(ixn_xml, '''', '"');

[ Date: 2025-08-27 00:06:18 - Bind query: yes ]

INSERT INTO pub2.GENE_GENE_REFERENCE (id, from_gene_id, to_gene_id, reference_id, from_taxon_id, to_taxon_id, src_db_id, experimental_sys_nm, experimental_sys_type) select ggr. id, ggr.from_gene_id, ggr.to_gene_id, l.object_id, ggr.from_taxon_id, ggr.to_taxon_id, ggr.src_db_id, ggr.experimental_sys_nm, ggr.experimental_sys_type from load.GENE_GENE_REFERENCE ggr, edit.DB_LINK l where ggr.reference_acc_txt = l.acc_txt and l.object_type_id = 7 and l.db_id = 16;

[ Date: 2025-08-27 00:04:43 - Bind query: yes ]

CLUSTER pub2.TERM;

[ Date: 2025-08-27 03:06:13 - Bind query: yes ]

SELECT /* GoGenesDAO */ sq.*, COUNT(*) OVER () fullRowCount FROM ( SELECT DISTINCT gt.nm gonm, gt.nm_html gonmhtml, gt.nm_sort gonmsort, gt.acc_txt goacc, gt.object_id goid, g.nm genesymbol, g.nm_sort genesymbolsort, g.acc_txt geneacc, g.acc_db_cd geneaccdbcd, g.id geneid FROM dag_node gt INNER JOIN gene_go_annot gga ON gt.object_id = gga.go_term_id INNER JOIN term g ON gga.gene_id = g.id WHERE gt.id IN ( SELECT p.descendant_dag_node_id FROM dag_path p WHERE p.ancestor_object_id = '1239590') AND gga.is_not = false) sq ORDER BY sq.gonmsort, sq.genesymbolsort LIMIT 50;

[ Date: 2025-08-27 04:27:09 - Database: ctdprd51 - User: pubeu - Bind query: yes ]

SELECT /* NCBILinkOutDAO */ CAST(XMLELEMENT(name "Link", XMLELEMENT(name "LinkId", g.acc_txt), XMLELEMENT(name "ProviderId", '7845'), XMLELEMENT(name "ObjectSelector", XMLELEMENT(name "Database", 'Gene'), XMLELEMENT(name "ObjectList", ( SELECT XMLAGG(XMLFOREST(l.acc_txt AS "ObjId")) FROM db_link l WHERE l.object_type_id = g.object_type_id AND l.object_id = g.id AND l.type_cd = 'A'))), XMLELEMENT(name "ObjectUrl", XMLELEMENT(name "Base", 'http://ctdbase.org/detail.go?'), XMLELEMENT(name "Rule", 'type=gene&acc=' || g.acc_txt), XMLELEMENT(name "UrlName", 'CTD: Comparative Toxicogenomics Database - ' || g.nm))) AS TEXT) linkxml FROM term g WHERE g.object_type_id = get_object_type_id ('gene') ORDER BY g.acc_txt::int;

[ Date: 2025-08-27 14:06:38 - Database: ctdprd51 - User: qaeu - Bind query: yes ]