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AI expression summaries for gene pages #58

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AI expression summaries for gene pages #58

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6044145
register new SingleGeneAiExpressionReporter as 'aiExpression'
bobular Feb 19, 2025
532d265
added placeholder attribute and ontology
bobular Feb 19, 2025
389b822
add help
bobular Feb 19, 2025
fb00aef
Merge remote-tracking branch 'origin/master' into ai-expression
bobular Feb 24, 2025
54f790b
US spelling for attribute help
bobular Feb 24, 2025
75b0bba
fix qa.veupathdb
aurreco-uga Mar 1, 2025
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14 changes: 13 additions & 1 deletion Model/lib/wdk/model/records/geneRecord.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"

Expand Down Expand Up @@ -362,6 +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="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>


</attributeQueryRef>


Expand All @@ -373,7 +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>
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1 change: 1 addition & 0 deletions Model/lib/wdk/ontology/individuals.txt
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Expand Up @@ -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
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