From 957d1b28082206ffefc7e685db35055e19398ce6 Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 10 Sep 2025 11:59:18 +0100 Subject: [PATCH 01/14] Add PubMedForAI table query for Liverpool AI prototype MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Unifies PubMed references from curated sources and user comments - Outputs pubmed_id, pubmed_source, source_id, and project_id - Labels sources as 'Curated', 'User comments', or 'Curated & User comments' - Uses Oracle LISTAGG to handle duplicate PMIDs across sources - Includes comprehensive test parameters for all major projects 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- .../wdk/model/records/geneTableQueries.xml | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml index 81730ba16..1703b666f 100644 --- a/Model/lib/wdk/model/records/geneTableQueries.xml +++ b/Model/lib/wdk/model/records/geneTableQueries.xml @@ -3599,6 +3599,69 @@ GROUP BY + + + PF3D7_0523000 + + + TGME49_220400 + + + cgd3_1400 + + + GL50803_112048 + + + TVAG_386080 + + + Tb927.8.4640 + + + + + + + + + + + From 09a6360eaf6aca84766465594d5377d4268882ee Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 10 Sep 2025 12:14:53 +0100 Subject: [PATCH 02/14] Add PubMedLiverpoolLinks table for Liverpool AI prototype MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Creates new gene record table with AI summary link-outs - Links to Liverpool collaborators' AI summary service - Includes PubMed ID links and source attribution - Uses internal="false" for external Liverpool links - Adds ontology entry in Literature and Reference category 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- Model/lib/wdk/model/records/geneRecord.xml | 42 ++++++++++++++++++++++ Model/lib/wdk/ontology/individuals.txt | 1 + 2 files changed, 43 insertions(+) diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml index b4223f39a..7fe922826 100644 --- a/Model/lib/wdk/model/records/geneRecord.xml +++ b/Model/lib/wdk/model/records/geneRecord.xml @@ -2687,6 +2687,48 @@ name" internal="true"/> true + + + + + + PubMed references with AI summary links. The AI summary links open new tabs at our Liverpool collaborators' site.]]> + + + + + + + + + + + + + + + + + + + + +
+ diff --git a/Model/lib/wdk/ontology/individuals.txt b/Model/lib/wdk/ontology/individuals.txt index 454ceca4a..666c0825a 100644 --- a/Model/lib/wdk/ontology/individuals.txt +++ b/Model/lib/wdk/ontology/individuals.txt @@ -303,6 +303,7 @@ GeneRecordClasses.GeneRecordClass.MetabolicPathways http://edamontology.org/topi GeneRecordClasses.GeneRecordClass.Alias http://edamontology.org/topic_0219 Curation and Annotation GeneRecordClasses.GeneRecordClass table Alias transcript record download GeneRecordClasses.GeneRecordClass.strain http://edamontology.org/topic_3299 Evolutionary Biology GeneRecordClasses.GeneRecordClass attribute strain gene record-internal download GeneRecordClasses.GeneRecordClass.PubMed http://edamontology.org/topic_3068 Literature and Reference GeneRecordClasses.GeneRecordClass table PubMed transcript record download +GeneRecordClasses.GeneRecordClass.PubMedLiverpoolLinks http://edamontology.org/topic_3068 Literature and Reference GeneRecordClasses.GeneRecordClass table PubMedLiverpoolLinks transcript record download GeneRecordClasses.GeneRecordClass.Cellxgene http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table Cellxgene transcript record GeneRecordClasses.GeneRecordClass.GeneLinkouts http://edamontology.org/topic_3345 Data identity and mapping GeneRecordClasses.GeneRecordClass table GeneLinkouts transcript record download GeneRecordClasses.GeneRecordClass.3dPreds http://edamontology.org/topic_0081 Structure Analysis GeneRecordClasses.GeneRecordClass table 3dPreds transcript 2 record download From 35f277d1dfd6e72d7dd9e94b43a57137c89bba6e Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 10 Sep 2025 14:01:24 +0100 Subject: [PATCH 03/14] fix incompatible types in UNION --- Model/lib/wdk/model/records/geneTableQueries.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml index 1703b666f..faf187356 100644 --- a/Model/lib/wdk/model/records/geneTableQueries.xml +++ b/Model/lib/wdk/model/records/geneTableQueries.xml @@ -3639,13 +3639,13 @@ GROUP BY listagg(pubmed_source, ',') within group (order by pubmed_source) as pubmed_source_list FROM ( -- Curated PubMed references - SELECT gene_source_id as source_id, project_id, pubmed_id, 'Curated' as pubmed_source + SELECT gene_source_id as source_id, project_id, TO_CHAR(pubmed_id) as pubmed_id, 'Curated' as pubmed_source FROM ApidbTuning.GenePubmed UNION -- User comment PubMed references - SELECT c.stable_id as source_id, c.project_name as project_id, cr.source_id as pubmed_id, 'User comments' as pubmed_source + SELECT c.stable_id as source_id, c.project_name as project_id, TO_CHAR(cr.source_id) as pubmed_id, 'User comments' as pubmed_source FROM @COMMENT_SCHEMA@MappedComment@COMMENT_DBLINK@ c, @COMMENT_SCHEMA@CommentReference@COMMENT_DBLINK@ cr WHERE c.comment_id = cr.comment_id From 78facd7b2a95fdb305da95f115df77cfd7aaa2a9 Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 10 Sep 2025 14:31:40 +0100 Subject: [PATCH 04/14] fix data interpolation --- Model/lib/wdk/model/records/geneRecord.xml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml index 7fe922826..1e0c3d9bd 100644 --- a/Model/lib/wdk/model/records/geneRecord.xml +++ b/Model/lib/wdk/model/records/geneRecord.xml @@ -2696,7 +2696,12 @@ name" internal="true"/> inReportMaker="true" queryRef="GeneTables.PubMedForAI"> PubMed references with AI summary links. The AI summary links open new tabs at our Liverpool collaborators' site.]]> - + + + + + + @@ -2714,8 +2719,7 @@ name" internal="true"/> + displayName="AI Summary" > Date: Wed, 10 Sep 2025 14:37:22 +0100 Subject: [PATCH 05/14] reorder Literature items --- Model/lib/wdk/ontology/individuals.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/wdk/ontology/individuals.txt b/Model/lib/wdk/ontology/individuals.txt index 666c0825a..08c2b1a6f 100644 --- a/Model/lib/wdk/ontology/individuals.txt +++ b/Model/lib/wdk/ontology/individuals.txt @@ -302,8 +302,8 @@ GeneRecordClasses.GeneRecordClass.MetabolicPathwaysMPMP http://edamontology.org/ GeneRecordClasses.GeneRecordClass.MetabolicPathways http://edamontology.org/topic_0753 Metabolic Pathways GeneRecordClasses.GeneRecordClass table MetabolicPathways transcript 2 record download GeneRecordClasses.GeneRecordClass.Alias http://edamontology.org/topic_0219 Curation and Annotation GeneRecordClasses.GeneRecordClass table Alias transcript record download GeneRecordClasses.GeneRecordClass.strain http://edamontology.org/topic_3299 Evolutionary Biology GeneRecordClasses.GeneRecordClass attribute strain gene record-internal download -GeneRecordClasses.GeneRecordClass.PubMed http://edamontology.org/topic_3068 Literature and Reference GeneRecordClasses.GeneRecordClass table PubMed transcript record download -GeneRecordClasses.GeneRecordClass.PubMedLiverpoolLinks http://edamontology.org/topic_3068 Literature and Reference GeneRecordClasses.GeneRecordClass table PubMedLiverpoolLinks transcript record download +GeneRecordClasses.GeneRecordClass.PubMed http://edamontology.org/topic_3068 Literature and Reference GeneRecordClasses.GeneRecordClass table PubMed transcript 1 record download +GeneRecordClasses.GeneRecordClass.PubMedLiverpoolLinks http://edamontology.org/topic_3068 Literature and Reference GeneRecordClasses.GeneRecordClass table PubMedLiverpoolLinks transcript 2 record download GeneRecordClasses.GeneRecordClass.Cellxgene http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table Cellxgene transcript record GeneRecordClasses.GeneRecordClass.GeneLinkouts http://edamontology.org/topic_3345 Data identity and mapping GeneRecordClasses.GeneRecordClass table GeneLinkouts transcript record download GeneRecordClasses.GeneRecordClass.3dPreds http://edamontology.org/topic_0081 Structure Analysis GeneRecordClasses.GeneRecordClass table 3dPreds transcript 2 record download From c0ac07d007df2d3400e08bd3eb26e99659cf8e98 Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 10 Sep 2025 14:52:59 +0100 Subject: [PATCH 06/14] tweak description and title --- Model/lib/wdk/model/records/geneRecord.xml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml index 1e0c3d9bd..1adc26efb 100644 --- a/Model/lib/wdk/model/records/geneRecord.xml +++ b/Model/lib/wdk/model/records/geneRecord.xml @@ -2692,12 +2692,13 @@ name" internal="true"/> - PubMed references with AI summary links. The AI summary links open new tabs at our Liverpool collaborators' site.]]> + queryRef="GeneTables.PubMedForAI" + help="this is a test"> + Explore, evaluate and feed back on AI summaries for PubMed references sourced from either our curated database (see section above) or user-contributed comments. The AI summary links open new tabs at our Liverpool collaborators' site.]]> - + From 460437dc723c9bd6abb61bb2543ecc1203126c97 Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 10 Sep 2025 14:59:06 +0100 Subject: [PATCH 07/14] add title/headline column --- Model/lib/wdk/model/records/geneRecord.xml | 1 + .../wdk/model/records/geneTableQueries.xml | 23 ++++++++++++------- 2 files changed, 16 insertions(+), 8 deletions(-) diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml index 1adc26efb..68df97178 100644 --- a/Model/lib/wdk/model/records/geneRecord.xml +++ b/Model/lib/wdk/model/records/geneRecord.xml @@ -2718,6 +2718,7 @@ name" internal="true"/> + diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml index faf187356..c672d5a24 100644 --- a/Model/lib/wdk/model/records/geneTableQueries.xml +++ b/Model/lib/wdk/model/records/geneTableQueries.xml @@ -3623,29 +3623,36 @@ GROUP BY + Date: Wed, 10 Sep 2025 15:31:15 +0100 Subject: [PATCH 08/14] tweak verbiage and help --- Model/lib/wdk/model/records/geneRecord.xml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml index 68df97178..d2c352b15 100644 --- a/Model/lib/wdk/model/records/geneRecord.xml +++ b/Model/lib/wdk/model/records/geneRecord.xml @@ -2692,10 +2692,10 @@ name" internal="true"/>
+ help="An experimental feature harnessing AI to extract salient information about this gene from open access publications."> Explore, evaluate and feed back on AI summaries for PubMed references sourced from either our curated database (see section above) or user-contributed comments. The AI summary links open new tabs at our Liverpool collaborators' site.]]> @@ -2718,7 +2718,11 @@ name" internal="true"/> - + From 680a6ae661d129c65fa796b266d7fe3995cb32fa Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 10 Sep 2025 23:00:42 +0100 Subject: [PATCH 09/14] capitalization --- Model/lib/wdk/model/records/geneRecord.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml index d2c352b15..9dfcb4679 100644 --- a/Model/lib/wdk/model/records/geneRecord.xml +++ b/Model/lib/wdk/model/records/geneRecord.xml @@ -2692,7 +2692,7 @@ name" internal="true"/>
From 1096e72fe0fa7cfff574f2edf6c6aebfeca02e23 Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 10 Sep 2025 23:09:26 +0100 Subject: [PATCH 10/14] remove new table; add column to PubMed table --- Model/lib/wdk/model/records/geneRecord.xml | 49 +++---------- .../wdk/model/records/geneTableQueries.xml | 70 ------------------- Model/lib/wdk/ontology/individuals.txt | 1 - 3 files changed, 8 insertions(+), 112 deletions(-) diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml index 9dfcb4679..ad64a18fb 100644 --- a/Model/lib/wdk/model/records/geneRecord.xml +++ b/Model/lib/wdk/model/records/geneRecord.xml @@ -2653,6 +2653,8 @@ name" internal="true"/> Shown are references from the NCBI gene2pubmed database and from manual assignment by curators.]]> + + @@ -2684,48 +2686,11 @@ name" internal="true"/> - true -
- - - - - - - Explore, evaluate and feed back on AI summaries for PubMed references sourced from either our curated database (see section above) or user-contributed comments. The AI summary links open new tabs at our Liverpool collaborators' site.]]> - - - - - - - - - - - - - - - - - - + ]]> + + true
diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml index c672d5a24..81730ba16 100644 --- a/Model/lib/wdk/model/records/geneTableQueries.xml +++ b/Model/lib/wdk/model/records/geneTableQueries.xml @@ -3599,76 +3599,6 @@ GROUP BY - - - PF3D7_0523000 - - - TGME49_220400 - - - cgd3_1400 - - - GL50803_112048 - - - TVAG_386080 - - - Tb927.8.4640 - - - - - - - - - - - - diff --git a/Model/lib/wdk/ontology/individuals.txt b/Model/lib/wdk/ontology/individuals.txt index 08c2b1a6f..bf192d48f 100644 --- a/Model/lib/wdk/ontology/individuals.txt +++ b/Model/lib/wdk/ontology/individuals.txt @@ -303,7 +303,6 @@ GeneRecordClasses.GeneRecordClass.MetabolicPathways http://edamontology.org/topi GeneRecordClasses.GeneRecordClass.Alias http://edamontology.org/topic_0219 Curation and Annotation GeneRecordClasses.GeneRecordClass table Alias transcript record download GeneRecordClasses.GeneRecordClass.strain http://edamontology.org/topic_3299 Evolutionary Biology GeneRecordClasses.GeneRecordClass attribute strain gene record-internal download GeneRecordClasses.GeneRecordClass.PubMed http://edamontology.org/topic_3068 Literature and Reference GeneRecordClasses.GeneRecordClass table PubMed transcript 1 record download -GeneRecordClasses.GeneRecordClass.PubMedLiverpoolLinks http://edamontology.org/topic_3068 Literature and Reference GeneRecordClasses.GeneRecordClass table PubMedLiverpoolLinks transcript 2 record download GeneRecordClasses.GeneRecordClass.Cellxgene http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table Cellxgene transcript record GeneRecordClasses.GeneRecordClass.GeneLinkouts http://edamontology.org/topic_3345 Data identity and mapping GeneRecordClasses.GeneRecordClass table GeneLinkouts transcript record download GeneRecordClasses.GeneRecordClass.3dPreds http://edamontology.org/topic_0081 Structure Analysis GeneRecordClasses.GeneRecordClass table 3dPreds transcript 2 record download From 94384abcd780a011b7ed8173dbdab8e9e082c9e8 Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 10 Sep 2025 23:30:32 +0100 Subject: [PATCH 11/14] improve help --- Model/lib/wdk/model/records/geneRecord.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml index ad64a18fb..1f5531200 100644 --- a/Model/lib/wdk/model/records/geneRecord.xml +++ b/Model/lib/wdk/model/records/geneRecord.xml @@ -2690,7 +2690,7 @@ name" internal="true"/> + help="Experimental feature that aims to extract gene function summaries from publications. Links open in a new tab at our Liverpool colleagues' website." > Date: Wed, 10 Sep 2025 23:46:16 +0100 Subject: [PATCH 12/14] add comma-separated HTML links to user comments table --- .../wdk/model/records/commentTableQueries.xml | 17 +++++++++++------ Model/lib/wdk/model/records/geneRecord.xml | 4 ++++ 2 files changed, 15 insertions(+), 6 deletions(-) diff --git a/Model/lib/wdk/model/records/commentTableQueries.xml b/Model/lib/wdk/model/records/commentTableQueries.xml index e00e139b5..18b47656d 100644 --- a/Model/lib/wdk/model/records/commentTableQueries.xml +++ b/Model/lib/wdk/model/records/commentTableQueries.xml @@ -58,7 +58,7 @@ - + @@ -86,11 +86,16 @@ SELECT c.comment_target_id, c.project_name as project_id, c.comment_id, ga.source_id, c.stable_id, c.comment_date, c.headline, files.filecount, references.pmids, - CASE WHEN (references.pmids is null) THEN '' - WHEN REGEXP_LIKE(references.pmids , '^-?[[:digit:],.]*$') - THEN '' || references.pmids || '' - ELSE '' || references.pmids || '' - END AS pmids_link, + CASE WHEN (references.pmids is null) THEN '' + ELSE REPLACE( + REGEXP_REPLACE( + references.pmids, + '([0-9]+)', + '\1' + ), + ',', ', ' + ) + END AS liverpool_ai_links, gene_counts.geneCount, &&selectReviewed&& u.first_name || ' ' || u.last_name || ', ' || u.organization as user_name_org diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml index 1f5531200..13a96a3f9 100644 --- a/Model/lib/wdk/model/records/geneRecord.xml +++ b/Model/lib/wdk/model/records/geneRecord.xml @@ -1688,6 +1688,10 @@ name" internal="true"/> + + From 36e266317a5fde08ea0e78d56c41ad46c2edce0a Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 10 Sep 2025 23:55:50 +0100 Subject: [PATCH 13/14] simplify link text for single pmids --- Model/lib/wdk/model/records/commentTableQueries.xml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Model/lib/wdk/model/records/commentTableQueries.xml b/Model/lib/wdk/model/records/commentTableQueries.xml index 18b47656d..72f90141b 100644 --- a/Model/lib/wdk/model/records/commentTableQueries.xml +++ b/Model/lib/wdk/model/records/commentTableQueries.xml @@ -87,6 +87,8 @@ ga.source_id, c.stable_id, c.comment_date, c.headline, files.filecount, references.pmids, CASE WHEN (references.pmids is null) THEN '' + WHEN INSTR(references.pmids, ',') = 0 THEN + 'View AI Summary' ELSE REPLACE( REGEXP_REPLACE( references.pmids, From eb13f9bac18a3a114849b2e27fab5216e3fe777b Mon Sep 17 00:00:00 2001 From: Bob Date: Fri, 12 Sep 2025 18:09:58 +0100 Subject: [PATCH 14/14] use shorter URL alias --- Model/lib/wdk/model/records/commentTableQueries.xml | 4 ++-- Model/lib/wdk/model/records/geneRecord.xml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Model/lib/wdk/model/records/commentTableQueries.xml b/Model/lib/wdk/model/records/commentTableQueries.xml index 72f90141b..011ddd16d 100644 --- a/Model/lib/wdk/model/records/commentTableQueries.xml +++ b/Model/lib/wdk/model/records/commentTableQueries.xml @@ -88,12 +88,12 @@ files.filecount, references.pmids, CASE WHEN (references.pmids is null) THEN '' WHEN INSTR(references.pmids, ',') = 0 THEN - 'View AI Summary' + 'View AI Summary' ELSE REPLACE( REGEXP_REPLACE( references.pmids, '([0-9]+)', - '\1' + '\1' ), ',', ', ' ) diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml index 13a96a3f9..81816c43f 100644 --- a/Model/lib/wdk/model/records/geneRecord.xml +++ b/Model/lib/wdk/model/records/geneRecord.xml @@ -2702,7 +2702,7 @@ name" internal="true"/>