Antibody array WDK: EDA transcript columns and gene record graph tables#177
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Antibody array WDK: EDA transcript columns and gene record graph tables#177
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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
New templates appended to antibodyArray.dst: - antibodyArrayEdaAttributeQueriesNumeric: crosstab sqlQuery + meta sqlQuery pivoting on sample_stable_id for normalized intensities - antibodyArrayEdaAttributeRef: attributeQueryRef injection into transcriptRecord.xml - antibodyArrayEdaAttributeCategory: TSV ontology rows for individuals.txt - antibodyArrayEdaGeneTableSql: UNION clause linking gene ids via VEUPATHDB_GENE_ID - antibodyArrayDataTableGeneTableSql: UNION clause for full data table with all attributes Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…uery blocks Add two new gene record graph table queries for antibody array EDA datasets targeting PlasmoDB and UniDB. Follows the same pattern as existing EDA phenotype queries but without the tgonGT1 special case, using category 'Immunology' and assay_type 'Antibody Array'. Includes TEMPLATE_ANCHOR placeholders for both the gene table SQL and the data table SQL. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…nitions to geneRecord.xml
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…tegory anchors - Add antibodyArrayEdaAttributeQueriesNumericByDataset, antibodyArrayEdaAttributeRefByDataset, and antibodyArrayEdaAttributeCategoryByDataset DST templates for datasets split by sub-dataset - Add TEMPLATE_ANCHOR entries in transcriptAttributeQueries.xml and transcriptRecord.xml for ByDataset variants - Add TEMPLATE_ANCHOR antibodyArrayEdaAttributeCategory and antibodyArrayEdaAttributeCategoryByDataset to individuals.txt — these were missing, causing per-sample intensity columns to have no UI category - Fix column alignment in antibodyArrayEdaAttributeCategory individuals.txt template Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
EdaAntibodyArrayDatasetsandEdaAntibodyArrayGraphsDataTableSQL queries togeneTableQueries.xml— gene record graph table queries for EDA antibody array datasets, modeled on EDAPhenotype but without the tgonGT1 special case, filtering bycategory = 'Immunology'geneRecord.xmlantibodyArrayEdaAttributeQueriesNumericDST template toantibodyArray.dst— crosstab query pivoting onsample_stable_id(one column per sample) via the EDA ancestor table, producing normalized intensity columns on the transcript recordantibodyArrayEdaAttributeRef,antibodyArrayEdaAttributeCategory,antibodyArrayEdaGeneTableSql, andantibodyArrayDataTableGeneTableSqlDST templates<!-- TEMPLATE_ANCHOR antibodyArrayEdaAttributeRef -->totranscriptRecord.xmlContext
Antibody array EDA studies have two entity types:
Sample(parent) andAntbdyAr(child). TheAntbdyArentity has onlyVEUPATHDB_GENE_IDandNORMALIZED_INTENSITYattributes. The transcript column crosstab pivots onsample_stable_idfrom the ancestor table — not onattribute_stable_idas Phenotype/CellularLocalization do — producing one intensity column per sample per gene.Test Plan
Companion PR: VEuPathDB/EbrcModelCommon#antibody-array-wdk-2
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