diff --git a/.gitignore b/.gitignore
index a56646eb23..3c07ee7fb6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -40,3 +40,4 @@ target
# JBrowse
/Model/lib/jbrowse/auto_generated/
+.worktrees
diff --git a/Model/lib/dst/antibodyArray.dst b/Model/lib/dst/antibodyArray.dst
index a8284edd88..55340f10e9 100644
--- a/Model/lib/dst/antibodyArray.dst
+++ b/Model/lib/dst/antibodyArray.dst
@@ -5,15 +5,15 @@ prop=datasetName
prop=projectName
>templateTextStart<
-
-
-
-
-
-
+
+
+
+
+
+
>templateTextEnd<
@@ -40,70 +40,70 @@ prop=includeProjectsExcludeEuPathDB
>templateTextStart<
+ displayName="${organismAbbrevDisplay} ${datasetDisplayName} Antibody Array (p-value)"
+ shortDisplayName="${datasetShortDisplayName} (p-val)"
+ searchCategory="Host Response"
+ queryRef="GeneId.GenesByTTestWithMetadata"
+ recordClassRef="TranscriptRecordClasses.TranscriptRecordClass">
-
+
'${function}'
+ sorting="p_value asc" />
-
-
-
-
-
-
-
- ${optionalQuestionDescription}
- ]]>
-
-
-
-
- Display the histogram of the values of this attribute
- float
-
+ summary="organism,gene_product,p_value, avg_group_two,avg_group_one"
+ sorting="p_value asc"
+ />
+
+
+
+
+
+
+
+ ${optionalQuestionDescription}
+ ]]>
+
+
+
+
+ Display the histogram of the values of this attribute
+ float
+
-
-
- Display the histogram of the values of this attribute
- int
-
+
+
+ Display the histogram of the values of this attribute
+ int
+
-
-
- Display the histogram of the values of this attribute
- int
-
+
+
+ Display the histogram of the values of this attribute
+ int
+
-
-
-
- ]]>
-
-
-
+
+
+
+ ]]>
+
+
+
@@ -123,11 +123,11 @@ prop=includeProjectsExcludeEuPathDB
displayName="${datasetShortDisplayName} - Intensity Graph"
inReportMaker="false" truncateTo="100000" sortable="false"
includeProjects="${includeProjectsExcludeEuPathDB}">
-
-
- ]]>
-
+
+
+ ]]>
+
>templateTextEnd<
@@ -137,7 +137,7 @@ anchorFile=ApiCommonModel/Model/lib/wdk/model/questions/categories.xml
prop=datasetName
prop=includeProjects
>templateTextStart<
- GeneQuestions.GenesByAntibodyArray${datasetName}
+ GeneQuestions.GenesByAntibodyArray${datasetName}
>templateTextEnd<
[templateStart]
@@ -152,27 +152,27 @@ prop=includeProjects
prop=antibodyArrayWdkAttributes
>templateTextStart<
+ displayName="${datasetDisplayName} Antibody Array"
+ shortDisplayName="${datasetShortDisplayName} (QAA)"
+ queryRef="GeneId.GenesByEdaVizWithCompute"
+ recordClassRef="TranscriptRecordClasses.TranscriptRecordClass">
-
-
+
+
-
- antibodyArrayNotebook
-
+
+ antibodyArrayNotebook
+
-
+
-
+ Find genes with differential expression in antibody array data based on EDA analysis.
+ ]]>
+
Removing outliers: If the PCA plot reveals samples that cluster away from the rest (potential outliers or contaminated arrays), you can exclude them using the Select Samples step at the top of the notebook.
Apply a filter on the sample identifier or a metadata variable to remove those samples before running Limma.
Note that changing the sample subset will reset any group assignments you have already made in the Limma step, so it is best to check the PCA first before defining your groups.
- ]]>
-
-
-
-
- Display the histogram of the values of this attribute
- float
-
-
-
-
- Display the histogram of the values of this attribute
- float
-
-
-
+ ]]>
+
+
+
+
+ Display the histogram of the values of this attribute
+ float
+
+
+
+
+ Display the histogram of the values of this attribute
+ float
+
+
+
>templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayEdaAttributeQueriesNumeric
+anchorFile=ApiCommonModel/Model/lib/wdk/model/records/transcriptAttributeQueries.xml
+prop=datasetName
+prop=edaStudyStableId
+prop=edaEntityAbbrev
+prop=includeProjects
+>templateTextStart<
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+>templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayEdaAttributeRef
+anchorFile=ApiCommonModel/Model/lib/wdk/model/records/transcriptRecord.xml
+prop=datasetName
+prop=includeProjects
+>templateTextStart<
+
+
+>templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayEdaAttributeQueriesNumericByDataset
+anchorFile=ApiCommonModel/Model/lib/wdk/model/records/transcriptAttributeQueries.xml
+prop=datasetName
+prop=edaStudyStableId
+prop=edaEntityAbbrev
+prop=includeProjects
+prop=subDatasetSuffix
+prop=subDatasetFilterValue
+prop=subDatasetAttributeStableId
+>templateTextStart<
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+>templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayEdaAttributeCategory
+anchorFile=ApiCommonModel/Model/lib/wdk/ontology/individuals.txt
+prop=datasetName
+prop=datasetDisplayName
+>templateTextStart<
+AntibodyArrayDataset_${datasetName} http://edamontology.org/topic_3360 Immunology DatasetRecordClasses.DatasetRecordClass dataset ${datasetName} ${datasetDisplayName} results
+TranscriptAttributes.MetaAntibodyArrayIntensities${datasetName} AntibodyArrayDataset_${datasetName} TranscriptRecordClasses.TranscriptRecordClass attributeMetaQuery MetaAntibodyArrayIntensities${datasetName} gene results download
+>templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayEdaAttributeRefByDataset
+anchorFile=ApiCommonModel/Model/lib/wdk/model/records/transcriptRecord.xml
+prop=datasetName
+prop=subDatasetSuffix
+prop=includeProjects
+>templateTextStart<
+
+
+>templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayEdaAttributeCategoryByDataset
+anchorFile=ApiCommonModel/Model/lib/wdk/ontology/individuals.txt
+prop=datasetName
+prop=datasetDisplayName
+prop=subDatasetSuffix
+>templateTextStart<
+AntibodyArrayDataset_${datasetName}_${subDatasetSuffix} http://edamontology.org/topic_3360 Immunology DatasetRecordClasses.DatasetRecordClass dataset ${datasetName} ${datasetDisplayName} (${subDatasetSuffix}) results
+TranscriptAttributes.MetaAntibodyArrayIntensities${datasetName}_${subDatasetSuffix} AntibodyArrayDataset_${datasetName}_${subDatasetSuffix} TranscriptRecordClasses.TranscriptRecordClass attributeMetaQuery MetaAntibodyArrayIntensities${datasetName}_${subDatasetSuffix} gene results download
+>templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayEdaGeneTableSql
+anchorFile=ApiCommonModel/Model/lib/wdk/model/records/geneTableQueries.xml
+prop=datasetName
+prop=edaStudyStableId
+prop=edaEntityAbbrev
+>templateTextStart<
+ UNION
+ SELECT '${datasetName}' AS dataset_name , string_value AS source_id
+ FROM eda.ATTRIBUTEvalue_${edaStudyStableId}_${edaEntityAbbrev} av
+ WHERE av.attribute_stable_id = 'VEUPATHDB_GENE_ID'
+>templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayDataTableGeneTableSql
+anchorFile=ApiCommonModel/Model/lib/wdk/model/records/geneTableQueries.xml
+prop=datasetName
+prop=edaStudyStableId
+prop=edaEntityAbbrev
+>templateTextStart<
+UNION
+SELECT genes.string_value AS gene,
+ ag.display_name AS variable,
+ av.string_value,
+ av.number_value,
+ av.date_value,
+ '${datasetName}' AS dataset_id
+FROM eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av,
+ eda.attributegraph_${edaStudyStableId}_${edaEntityAbbrev} ag,
+ (SELECT av.${edaEntityAbbrev}_stable_id, MIN(gi.gene) as string_value
+ FROM eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av
+ JOIN apidbtuning.GeneId gi ON gi.id = av.string_value
+ WHERE av.attribute_stable_id = 'VEUPATHDB_GENE_ID'
+ GROUP BY av.${edaEntityAbbrev}_stable_id) genes
+WHERE av.attribute_stable_id = ag.stable_id
+ AND av.${edaEntityAbbrev}_stable_id = genes.${edaEntityAbbrev}_stable_id
+ AND av.attribute_stable_id != 'VEUPATHDB_GENE_ID'
+>templateTextEnd<
diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml
index af8f7b2164..1ad349dcac 100644
--- a/Model/lib/wdk/model/records/geneRecord.xml
+++ b/Model/lib/wdk/model/records/geneRecord.xml
@@ -1343,6 +1343,46 @@ name" internal="true"/>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ true
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml
index 869b3d98f2..a761760a2d 100644
--- a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml
+++ b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml
@@ -192,6 +192,10 @@
+
+
+
+
diff --git a/Model/lib/wdk/model/records/transcriptRecord.xml b/Model/lib/wdk/model/records/transcriptRecord.xml
index 946385a18a..2bbcd47269 100644
--- a/Model/lib/wdk/model/records/transcriptRecord.xml
+++ b/Model/lib/wdk/model/records/transcriptRecord.xml
@@ -733,6 +733,10 @@
+
+
+
+
diff --git a/Model/lib/wdk/ontology/individuals.txt b/Model/lib/wdk/ontology/individuals.txt
index 8d3a2aa605..916ea2d34d 100644
--- a/Model/lib/wdk/ontology/individuals.txt
+++ b/Model/lib/wdk/ontology/individuals.txt
@@ -916,6 +916,8 @@ derisi_timeseries_pie http://purl.obolibrary.org/obo/OBI_0001985 PathwayRecordC
## TEMPLATE_ANCHOR profileMinMaxAttributesRnaAntisenseCategory
## TEMPLATE_ANCHOR phenotypeEdaAttributeCategory
## TEMPLATE_ANCHOR cellularLocalizationEdaAttributeCategory
+## TEMPLATE_ANCHOR antibodyArrayEdaAttributeCategory
+## TEMPLATE_ANCHOR antibodyArrayEdaAttributeCategoryByDataset
## TEMPLATE_ANCHOR metaboliteGraphTextAttributeCategory
## TEMPLATE_ANCHOR graphTextAttributeCategoryPathwayRecord