From 60441452473d28a212463c48de52ac08ed3725a1 Mon Sep 17 00:00:00 2001
From: Bob MacCallum <uncoolbob@gmail.com>
Date: Wed, 19 Feb 2025 12:53:08 +0000
Subject: [PATCH 1/6] register new SingleGeneAiExpressionReporter as
 'aiExpression'

---
 Model/lib/wdk/model/records/geneRecord.xml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml
index a901e1d32..61d1231a8 100644
--- a/Model/lib/wdk/model/records/geneRecord.xml
+++ b/Model/lib/wdk/model/records/geneRecord.xml
@@ -153,6 +153,11 @@
          <reporter name="singleGene" displayName="Arbitrary information about a single gene (multiple formats provided)" scopes=""
                     implementation="org.apidb.apicommon.model.report.SingleGeneReporter">
           </reporter>
+
+	  <reporter name="aiExpression" displayName="AI summary of transcriptomics data for a single gene" scopes=""
+		    implementation="org.apidb.apicommon.model.report.ai.SingleGeneAiExpressionReporter">
+	  </reporter>
+
 <!--
           <reporter name="fullRecordDump" displayName="Text SLOW: choose from columns and/or tables"
                     

From 532d2654a088a7b0140855a520aa0c0ac87b480b Mon Sep 17 00:00:00 2001
From: Bob MacCallum <uncoolbob@gmail.com>
Date: Wed, 19 Feb 2025 18:34:50 +0000
Subject: [PATCH 2/6] added placeholder attribute and ontology

---
 Model/lib/wdk/model/records/geneRecord.xml | 7 +++++++
 Model/lib/wdk/ontology/individuals.txt     | 1 +
 2 files changed, 8 insertions(+)

diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml
index 61d1231a8..f0996810a 100644
--- a/Model/lib/wdk/model/records/geneRecord.xml
+++ b/Model/lib/wdk/model/records/geneRecord.xml
@@ -367,6 +367,13 @@
             <columnAttribute name="show_strains" displayName='HAH' />
             <columnAttribute name="location_text" displayName="Genomic Location" help="Contig/Chromosome:start-end(strand)" />
 
+            <textAttribute name="ai_expression" displayName="AI Expression Summary"
+               help="TO DO/optional" >
+               <display>YES</display>
+               <text>YES</text>
+            </textAttribute>
+
+	    
          </attributeQueryRef>
 
 
diff --git a/Model/lib/wdk/ontology/individuals.txt b/Model/lib/wdk/ontology/individuals.txt
index dabf11ce1..4d1980d41 100644
--- a/Model/lib/wdk/ontology/individuals.txt
+++ b/Model/lib/wdk/ontology/individuals.txt
@@ -249,6 +249,7 @@ GeneRecordClasses.GeneRecordClass.FacetMetadata	http://edamontology.org/topic_33
 GeneRecordClasses.GeneRecordClass.FungiVBOrgLinkoutsTable	http://edamontology.org/topic_3308	Transcriptomics	GeneRecordClasses.GeneRecordClass	table	FungiVBOrgLinkoutsTable				gene		record-internal		
 													
 GeneRecordClasses.GeneRecordClass.ContXAxisMetadata	http://edamontology.org/topic_3308	Transcriptomics	GeneRecordClasses.GeneRecordClass	table	ContXAxisMetadata				gene		record-internal		
+GeneRecordClasses.GeneRecordClass.ai_expression	http://edamontology.org/topic_3308	Transcriptomics	GeneRecordClasses.GeneRecordClass	attribute	ai_expression				gene	2	record		
 GeneRecordClasses.GeneRecordClass.TranscriptionSummary	http://edamontology.org/topic_3308	Transcriptomics	GeneRecordClasses.GeneRecordClass	table	TranscriptionSummary				gene	2	record		
 GeneRecordClasses.GeneRecordClass.ExpressionGraphs	http://edamontology.org/topic_3308	Transcriptomics	GeneRecordClasses.GeneRecordClass	table	ExpressionGraphs				gene	3	record		
 GeneRecordClasses.GeneRecordClass.UserDatasetsTranscriptomicsGraphs	http://edamontology.org/topic_3308	Transcriptomics	GeneRecordClasses.GeneRecordClass	table	UserDatasetsTranscriptomicsGraphs				gene	4	record		

From 389b82219362f53da836e8c7bc7b06d483a8a5d3 Mon Sep 17 00:00:00 2001
From: Bob MacCallum <uncoolbob@gmail.com>
Date: Wed, 19 Feb 2025 18:59:56 +0000
Subject: [PATCH 3/6] add 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 f0996810a..ddcb53b25 100644
--- a/Model/lib/wdk/model/records/geneRecord.xml
+++ b/Model/lib/wdk/model/records/geneRecord.xml
@@ -368,7 +368,7 @@
             <columnAttribute name="location_text" displayName="Genomic Location" help="Contig/Chromosome:start-end(strand)" />
 
             <textAttribute name="ai_expression" displayName="AI Expression Summary"
-               help="TO DO/optional" >
+               help="This experimental feature uses OpenAI's GPT-4o language model to summarise and organise all the expression data for this gene." >
                <display>YES</display>
                <text>YES</text>
             </textAttribute>

From 54f790b94f11e74dba77cf328132b7797c9a19e8 Mon Sep 17 00:00:00 2001
From: Bob MacCallum <uncoolbob@gmail.com>
Date: Mon, 24 Feb 2025 17:55:56 -0500
Subject: [PATCH 4/6] US spelling for attribute 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 fb173f2a5..afe7de8ae 100644
--- a/Model/lib/wdk/model/records/geneRecord.xml
+++ b/Model/lib/wdk/model/records/geneRecord.xml
@@ -368,7 +368,7 @@
             <columnAttribute name="location_text" displayName="Genomic Location" help="Contig/Chromosome:start-end(strand)" />
 
             <textAttribute name="ai_expression" displayName="AI Expression Summary"
-               help="This experimental feature uses OpenAI's GPT-4o language model to summarise and organise all the expression data for this gene." >
+               help="This experimental feature uses OpenAI's GPT-4o language model to summarize and organize all the expression data for this gene." >
                <display>YES</display>
                <text>YES</text>
             </textAttribute>

From 75b0bba2a0dca2fbee4dd245ef80cbca2cff1b0c Mon Sep 17 00:00:00 2001
From: aurreco-uga <aurreco@uga.edu>
Date: Sat, 1 Mar 2025 13:42:04 -0500
Subject: [PATCH 5/6] fix qa.veupathdb

---
 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 afe7de8ae..e9af1d042 100644
--- a/Model/lib/wdk/model/records/geneRecord.xml
+++ b/Model/lib/wdk/model/records/geneRecord.xml
@@ -385,7 +385,7 @@
           </attributeQueryRef>
 
 
-          <attributeQueryRef ref="GeneAttributes.AssayCounts">
+          <attributeQueryRef ref="GeneAttributes.AssayCounts" excludeProjects="EuPathDB">
             <columnAttribute displayName="# Microarray Datasets" name="microarray_dataset_count" inReportMaker="false"/>
             <columnAttribute displayName="# RNASeq Datasets" name="rnaseq_dataset_count" inReportMaker="false"/>
           </attributeQueryRef>

From e8d8ebd1a6b26bd5e3e4c5d5f715d6496b4d07fb Mon Sep 17 00:00:00 2001
From: Bob MacCallum <uncoolbob@gmail.com>
Date: Mon, 7 Apr 2025 10:09:19 +0100
Subject: [PATCH 6/6] improve help text for AI expr summaries

---
 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 e9af1d042..9d94c633b 100644
--- a/Model/lib/wdk/model/records/geneRecord.xml
+++ b/Model/lib/wdk/model/records/geneRecord.xml
@@ -368,7 +368,7 @@
             <columnAttribute name="location_text" displayName="Genomic Location" help="Contig/Chromosome:start-end(strand)" />
 
             <textAttribute name="ai_expression" displayName="AI Expression Summary"
-               help="This experimental feature uses OpenAI's GPT-4o language model to summarize and organize all the expression data for this gene." >
+               help="This experimental feature uses AI to help interpret the gene's expression data shown in the &quot;Transcript Expression&quot; section further down the page. First, the AI analyzes each individual experiment using its numeric data and metadata to generate a one-sentence summary and an estimated biological relevance score. Then, those per-experiment summaries are grouped into topics to highlight common expression patterns across experiments." >
                <display>YES</display>
                <text>YES</text>
             </textAttribute>