From 233d2aeab52f5aac999291a54a8a0deadfdca7e1 Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Fri, 20 Mar 2026 12:24:44 -0400 Subject: [PATCH 01/18] First pass at antismash query --- .../lib/wdk/model/questions/geneQuestions.xml | 29 ++++++++ .../wdk/model/questions/params/geneParams.xml | 74 +++++++++++++++++++ .../model/questions/params/organismParams.xml | 40 ++++++++++ .../model/questions/queries/geneQueries.xml | 45 +++++++++++ 4 files changed, 188 insertions(+) diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index 7690d0569e..907692a2e3 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -931,6 +931,35 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " + + + + + + + + + + + + + + + + + + diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index 6be78fbb21..fdb9eed62c 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -5104,6 +5104,29 @@ products of your selected type (or types).

+ + + Select one or more secondary metabolite cluster categories. + + + + + Select an annotation. Options filter based on the selected category. + + + @@ -9729,6 +9752,57 @@ end as term + + + + + + + + + + + + + + + + + + + + + diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml index 5fb56512b6..f89f7de759 100644 --- a/Model/lib/wdk/model/questions/params/organismParams.xml +++ b/Model/lib/wdk/model/questions/params/organismParams.xml @@ -438,6 +438,21 @@ + + Select the organism(s) to search. + + pruneNodesWithSingleExtendingChild + showOnlyPreferredOrganisms + + + @@ -1170,6 +1185,31 @@ + + + + + + + + + diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index db008903c7..3280de878f 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -5773,6 +5773,51 @@ select distinct ta.gene_source_id + + + + + + + + + + + + + + + + + + + From 2eea907a7368523090109eacaa0e907f6c4f6eb7 Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Fri, 20 Mar 2026 13:49:55 -0400 Subject: [PATCH 02/18] Add attributes and summary --- Model/lib/wdk/model/questions/geneQuestions.xml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index 907692a2e3..2a7a1a95d4 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -948,9 +948,17 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " + + + + + + + + Date: Fri, 20 Mar 2026 13:50:41 -0400 Subject: [PATCH 03/18] Add default and fix depended params --- Model/lib/wdk/model/questions/params/geneParams.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index fdb9eed62c..75dc1ea326 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -5113,7 +5113,7 @@ products of your selected type (or types).

dependedParamRef="organismParams.antismash_organism" includeProjects="FungiDB,UniDB"> Select one or more secondary metabolite cluster categories. - +
prompt="Annotation" multiPick="true" quote="true" - dependedParamRef="geneParams.antismash_category" + dependedParamRef="geneParams.antismash_category, organismParams.antismash_organism" includeProjects="FungiDB,UniDB"> Select an annotation. Options filter based on the selected category. From e9b3a999ba7b0cb042773c8de0711989e4415043 Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Tue, 24 Mar 2026 11:55:17 -0400 Subject: [PATCH 04/18] Add quotes to project_id macro --- Model/lib/wdk/model/questions/params/organismParams.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml index f89f7de759..d3dae06639 100644 --- a/Model/lib/wdk/model/questions/params/organismParams.xml +++ b/Model/lib/wdk/model/questions/params/organismParams.xml @@ -1196,7 +1196,7 @@ FROM apidbtuning.geneattributes ga , apidb.antismashfeature af WHERE ga.na_feature_id = af.na_feature_id - AND (ga.project_id = @PROJECT_ID@ OR 'UniDB' = @PROJECT_ID@) + AND (ga.project_id = '@PROJECT_ID@' OR 'UniDB' = '@PROJECT_ID@') ) SELECT DISTINCT term , parentTerm From 01abc289a8b4eea16a00f9c149ffb4db73bbd802 Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Tue, 24 Mar 2026 11:56:29 -0400 Subject: [PATCH 05/18] Defaults and ordering --- .../lib/wdk/model/questions/params/geneParams.xml | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index 75dc1ea326..db7b828b44 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -5113,7 +5113,7 @@ products of your selected type (or types).

dependedParamRef="organismParams.antismash_organism" includeProjects="FungiDB,UniDB"> Select one or more secondary metabolite cluster categories. - +
dependedParamRef="geneParams.antismash_category, organismParams.antismash_organism" includeProjects="FungiDB,UniDB"> Select an annotation. Options filter based on the selected category. - + @@ -9785,6 +9787,11 @@ end as term From 46eda15dcd5ce013c7dc4fe132f8af4e6195a72d Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Tue, 24 Mar 2026 11:57:18 -0400 Subject: [PATCH 06/18] Multipick, so no option for any --- Model/lib/wdk/model/questions/queries/geneQueries.xml | 1 - 1 file changed, 1 deletion(-) diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index 3280de878f..876501d370 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -5812,7 +5812,6 @@ select distinct ta.gene_source_id AND (af.antismash_annotation IN ($$antismash_annotation$$) -- OR ($$antismash_annotation$$ = 'biosynthetic any' AND af.antismash_annotation like 'biosynthetic%') OR ($$antismash_annotation$$ = 'unknown' AND af.antismash_annotation IS NULL) - OR ($$antismash_annotation$$ = 'any') ) ]]> From 10e4ab9e8b9c0913d242b7d2c742e1f970775b00 Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Tue, 24 Mar 2026 13:09:09 -0400 Subject: [PATCH 07/18] Fix to handle genes that appear in more than one cluster --- .../model/questions/queries/geneQueries.xml | 66 ++++++++++++------- 1 file changed, 43 insertions(+), 23 deletions(-) diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index 876501d370..64f6f263c2 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -5787,32 +5787,52 @@ select distinct ta.gene_source_id + From 8edc28ec9827859674ec54163ee9e57ae1f13998 Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Tue, 24 Mar 2026 13:09:39 -0400 Subject: [PATCH 08/18] Add overlapping clusters column --- Model/lib/wdk/model/questions/geneQuestions.xml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index 2a7a1a95d4..b2b83232f3 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -948,7 +948,7 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " @@ -957,6 +957,7 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " + From f44de1cb89231d502cd5d8bbfe4699f0d0d634a8 Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Thu, 26 Mar 2026 11:00:41 -0400 Subject: [PATCH 09/18] Add JBrowse links in results --- .../lib/wdk/model/questions/geneQuestions.xml | 12 ++++- .../model/questions/queries/geneQueries.xml | 49 ++++++++++++------- 2 files changed, 43 insertions(+), 18 deletions(-) diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index b2b83232f3..d9b5e1ac1e 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -948,7 +948,7 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " @@ -957,7 +957,17 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " + + + + + + $$sequence_id$$:$$cluster_start$$-$$cluster_end$$ + ]]> + + diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index 64f6f263c2..93c7853797 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -5787,12 +5787,16 @@ select distinct ta.gene_source_id + + + ', + gc2.sequence_id, ':', gc2.cluster_start, '-', gc2.cluster_end, '' + ), + ', ' ORDER BY gc2.cluster_start + ) AS overlapping_clusters + FROM ranked r + JOIN gene_clusters gc2 + ON gc2.source_id = r.source_id + AND gc2.antismash_cluster_id != r.antismash_cluster_id + WHERE r.rn = 1 + GROUP BY r.source_id ) - SELECT source_id, gene_source_id, project_id, + SELECT r.source_id, r.gene_source_id, r.project_id, 10 AS wdk_weight, 'Y' AS matched_result, - category, antismash_annotation, cluster_start, cluster_end, sequence_id, - overlapping_clusters - FROM ranked - WHERE rn = 1 + r.category, r.antismash_annotation, r.cluster_start, r.cluster_end, r.sequence_id, + r.org_abbrev, + GREATEST(r.cluster_start - 1000, 1) AS cluster_context_start, + r.cluster_end + 1000 AS cluster_context_end, + COALESCE(go.overlapping_clusters, 'No') AS overlapping_clusters + FROM ranked r + LEFT JOIN gene_overlaps go ON go.source_id = r.source_id + WHERE r.rn = 1 ]]> From a90c4780fb3d7d20ecc442acdc8d882f4a45ebd9 Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Mon, 27 Apr 2026 13:16:49 -0400 Subject: [PATCH 10/18] Add help text --- .../lib/wdk/model/questions/geneQuestions.xml | 44 ++++++++++++++++--- .../wdk/model/questions/params/geneParams.xml | 4 +- 2 files changed, 39 insertions(+), 9 deletions(-) diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index d9b5e1ac1e..e291644f02 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -952,15 +952,14 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " sorting="gene_source_id asc"/> - - - + + - + - +
+ + In addition to primary metabolites essential for growth and survival, fungi, and some other microorganisms produce secondary metabolites. These often provide competitive advantages for the microorganism in its environment. Importantly, they are also an important source of natural products. These compounds are typically encoded by co-located and co-expressed groups of genes that function together to build, modify, and export the final molecule. This co-localised group is called a biosynthetic gene cluster (BGC). Well-known examples of secondary metabolites include antibiotics like penicillin and erythromycin, antifungals, and immunosuppressants like rapamycin.

+ + antiSMASH is a bioinformatics tool to identify and annotate biosynthetic gene clusters. It works by searching for signature biosynthetic genes whose sequences are well conserved across known clusters. When it detects one of these signature genes, it defines a genomic region around it, predicts the cluster boundaries, and annotates every gene within that region with a predicted function. It then compares the identified cluster against a database of known BGCs to predict what compound the cluster might produce.

+ + Cluster Category
+ The cluster category groups biosynthetic gene clusters (BGCs) into broad classes based on the type of natural product they produce. This is predicted based on the biochemical machinery represented in the cluster.

+ + Common categories you are likely to see include:
+
    +
  • PKS (Polyketide synthases): Clusters that synthesize secondary metabolites comprising complex chains of alternating ketone and methylene groups. These molecules often function as antibiotics, antifungals, or anticancer compounds. Examples include erythromycin and rapamycin.
    • +
  • NRPS (Nonribosomal peptide synthases): Clusters that synthesise secondary metabolites comprising amino acids, including non-proteinogenic amino acids, polymerized without using ribosomes. These molecules often functions as antibiotics or siderophores. Examples include penicillin and vancomycin.
    • +
  • Terpenes: Clusters that make terpenoids, a huge and diverse class of unsaturated hydrocarbons including sterols, pigments, and volatile compounds.
    • +
  • RiPP (Ribosomally synthesised and post-translationally modified peptides): These clusters create compounds from small peptides that are initially made by the ribosome and then heavily modified. Examples include lanthipeptides and bacteriocins.
    • +
  • Other: Clusters whose products cannot be categorized or that use a combination of structures from multiple categories.
    • +


+ + Annotation
+ The annotation describes what a specific gene or protein within the cluster is predicted to do based on sequence similarity to known proteins.

+ + Common annotations you are likely to see include:
+
    +
  • Biosynthetic: These are the signature biosynthetic genes that define a cluster and predict its function. These may be referred to as core or backbone genes.
    • +
  • Biosynthetic additional: These are additional biosynthetic genes that further modify the primary product of a cluster, sometimes called tailoring enzymes, or aiding production of the product by supplying cofactors or substrates.
    • +
  • Regulatory: These are transcription factors or other regulatory elements that control expression of this cluster.
    • +
  • Resistance: The products of these genes protect the organism from its own toxic products. Examples include efflux pumps or enzymes that modify the product futher.
    • +
  • Transport: The products of these genes transport the product to its final location
    • +
  • Other: This label is applied by antiSMASH when a gene has similarity to genes that appear in other BCGs but where the function is not understood.
    • +
  • Unknown: This category is used for genes that have not been annotated by antiSMASH.
    • +


+ +Read more about antismash here

]]> diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index db7b828b44..61fd2a9b1d 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -5112,7 +5112,7 @@ products of your selected type (or types).

quote="true" dependedParamRef="organismParams.antismash_organism" includeProjects="FungiDB,UniDB"> - Select one or more secondary metabolite cluster categories. + The cluster category describes what kind of molecule the cluster is likely to make based on the biochemical machinery represnted in the cluster. Select one or more secondary metabolite cluster categories to explore. @@ -5123,7 +5123,7 @@ products of your selected type (or types).

quote="true" dependedParamRef="geneParams.antismash_category, organismParams.antismash_organism" includeProjects="FungiDB,UniDB"> - Select an annotation. Options filter based on the selected category. + The annotation described the function of a specific gene within a biosynthetic cluster. Select one or more annotations to explore. From 449c5d872b3e51da47def88f4352bcd7cbe64029 Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Mon, 27 Apr 2026 13:26:42 -0400 Subject: [PATCH 11/18] Fix typo --- Model/lib/wdk/model/questions/params/geneParams.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index 61fd2a9b1d..b6f0a9054b 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -5123,7 +5123,7 @@ products of your selected type (or types).

quote="true" dependedParamRef="geneParams.antismash_category, organismParams.antismash_organism" includeProjects="FungiDB,UniDB"> - The annotation described the function of a specific gene within a biosynthetic cluster. Select one or more annotations to explore. + The annotation describes the function of a specific gene within a biosynthetic cluster. Select one or more annotations to explore. From 59b1b37b3adadfd886d6d0b34c79db0020fde862 Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Tue, 28 Apr 2026 11:48:39 -0400 Subject: [PATCH 12/18] Fixes to typos and grammar for Learn More text --- .../lib/wdk/model/questions/geneQuestions.xml | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index e291644f02..45f3f73e27 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -937,7 +937,7 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as "
- In addition to primary metabolites essential for growth and survival, fungi, and some other microorganisms produce secondary metabolites. These often provide competitive advantages for the microorganism in its environment. Importantly, they are also an important source of natural products. These compounds are typically encoded by co-located and co-expressed groups of genes that function together to build, modify, and export the final molecule. This co-localised group is called a biosynthetic gene cluster (BGC). Well-known examples of secondary metabolites include antibiotics like penicillin and erythromycin, antifungals, and immunosuppressants like rapamycin.

+ In addition to primary metabolites essential for growth and survival, fungi and some other microorganisms produce secondary metabolites. These often provide competitive advantages for the microorganism in its environment. They are also of interest as an important source of natural products. These compounds are typically encoded by co-located and co-expressed groups of genes that function together to build, modify, and export the final molecule. This co-located group is called a biosynthetic gene cluster (BGC). Well-known examples of secondary metabolites include antibiotics like penicillin and erythromycin, antifungals, and immunosuppressants like rapamycin.

- antiSMASH is a bioinformatics tool to identify and annotate biosynthetic gene clusters. It works by searching for signature biosynthetic genes whose sequences are well conserved across known clusters. When it detects one of these signature genes, it defines a genomic region around it, predicts the cluster boundaries, and annotates every gene within that region with a predicted function. It then compares the identified cluster against a database of known BGCs to predict what compound the cluster might produce.

+ antiSMASH is a bioinformatics tool to identify and annotate biosynthetic gene clusters. It works by searching for signature biosynthetic genes whose sequences are well conserved across known clusters. When it detects one of these signature genes, it defines a genomic region around it, predicts the cluster boundaries, and annotates every gene within that region with a predicted function. It then compares the identified cluster against a database of known BGCs to predict what compound the cluster might produce.

Cluster Category
The cluster category groups biosynthetic gene clusters (BGCs) into broad classes based on the type of natural product they produce. This is predicted based on the biochemical machinery represented in the cluster.

@@ -984,8 +984,8 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " Common categories you are likely to see include:
  • PKS (Polyketide synthases): Clusters that synthesize secondary metabolites comprising complex chains of alternating ketone and methylene groups. These molecules often function as antibiotics, antifungals, or anticancer compounds. Examples include erythromycin and rapamycin.
    • -
  • NRPS (Nonribosomal peptide synthases): Clusters that synthesise secondary metabolites comprising amino acids, including non-proteinogenic amino acids, polymerized without using ribosomes. These molecules often functions as antibiotics or siderophores. Examples include penicillin and vancomycin.
    • -
  • Terpenes: Clusters that make terpenoids, a huge and diverse class of unsaturated hydrocarbons including sterols, pigments, and volatile compounds.
    • +
  • NRPS (Nonribosomal peptide synthases): Clusters that synthesize secondary metabolites comprising amino acids, including non-proteinogenic amino acids, polymerized without using ribosomes. These molecules often function as antibiotics or siderophores. Examples include penicillin and vancomycin.
    • +
  • Terpenes: Clusters that make terpenoids, a huge and diverse class of compounds derived from isoprene units, including sterols, pigments, and volatile compounds.
  • RiPP (Ribosomally synthesised and post-translationally modified peptides): These clusters create compounds from small peptides that are initially made by the ribosome and then heavily modified. Examples include lanthipeptides and bacteriocins.
  • Other: Clusters whose products cannot be categorized or that use a combination of structures from multiple categories.


@@ -996,12 +996,12 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " Common annotations you are likely to see include:
  • Biosynthetic: These are the signature biosynthetic genes that define a cluster and predict its function. These may be referred to as core or backbone genes.
    • -
  • Biosynthetic additional: These are additional biosynthetic genes that further modify the primary product of a cluster, sometimes called tailoring enzymes, or aiding production of the product by supplying cofactors or substrates.
    • +
  • Biosynthetic additional: These are additional biosynthetic genes that further modify the primary product of a cluster (tailoring or decorating enzymes), or aid production of the product by supplying cofactors or substrates.
  • Regulatory: These are transcription factors or other regulatory elements that control expression of this cluster.
    • -
  • Resistance: The products of these genes protect the organism from its own toxic products. Examples include efflux pumps or enzymes that modify the product futher.
    • -
  • Transport: The products of these genes transport the product to its final location
    • -
  • Other: This label is applied by antiSMASH when a gene has similarity to genes that appear in other BCGs but where the function is not understood.
    • -
  • Unknown: This category is used for genes that have not been annotated by antiSMASH.
    • +
  • Resistance: These genes protect the organism from its own toxic products. Examples include efflux pumps or enzymes that modify the product futher to protect the host.
    • +
  • Transport: These genes transport the product to its final location.
    • +
  • Other: This label is applied by antiSMASH when a gene has similarity to genes that appear in other BCGs but where the role of the gene within the BCG is not understood.
    • +
  • Unknown: This category is used for genes with no detectable similarity to antiSMASH models, and which have therefore not been annotated by antiSMASH.


Read more about antismash here

From 0b138b8b477781dede89f4e66a5154be64fc8b4c Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Wed, 29 Apr 2026 07:00:12 -0400 Subject: [PATCH 13/18] Add ontology entry, tab separated this time! --- Model/lib/wdk/ontology/individuals.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/Model/lib/wdk/ontology/individuals.txt b/Model/lib/wdk/ontology/individuals.txt index 2fee398d65..efcb6f8792 100644 --- a/Model/lib/wdk/ontology/individuals.txt +++ b/Model/lib/wdk/ontology/individuals.txt @@ -75,6 +75,7 @@ TranscriptRecordClasses.TranscriptRecordClass.GeneQuestions.GenesByGeneType http TranscriptRecordClasses.TranscriptRecordClass.GeneQuestions.GenesByIntronJunctions http://edamontology.org/topic_0114 Gene Structure TranscriptRecordClasses.TranscriptRecordClass search GeneQuestions.GenesByIntronJunctions menu webservice TranscriptRecordClasses.TranscriptRecordClass.GeneQuestions.GenesByGeneModelChars http://edamontology.org/topic_0114 Gene Structure TranscriptRecordClasses.TranscriptRecordClass search GeneQuestions.GenesByGeneModelChars menu webservice TranscriptRecordClasses.TranscriptRecordClass.GeneQuestions.GenesByGoTerm http://edamontology.org/topic_1775 Function analysis TranscriptRecordClasses.TranscriptRecordClass search GeneQuestions.GenesByGoTerm menu webservice +TranscriptRecordClasses.TranscriptRecordClass.GeneQuestions.GenesBySecondaryMetabolites http://edamontology.org/topic_1775 Function analysis TranscriptRecordClasses.TranscriptRecordClass search GeneQuestions.GenesBySecondaryMetabolites menu webservice ## TEMPLATE_ANCHOR geneImageGoTermOntology TranscriptRecordClasses.TranscriptRecordClass.GeneQuestions.GenesByPhenotype_phenotype_QIAGEN_RSRC searchCategory-phenotype-curated phenotype TranscriptRecordClasses.TranscriptRecordClass search GeneQuestions.GenesByPhenotype_phenotype_QIAGEN_RSRC webservice TranscriptRecordClasses.TranscriptRecordClass.GeneQuestions.GenesByPhenotype_phenotype_DATA_RSRC searchCategory-phenotype-curated phenotype TranscriptRecordClasses.TranscriptRecordClass search GeneQuestions.GenesByPhenotype_phenotype_DATA_RSRC webservice From feb28248ed237d05fa75ee6c08ba9ba691cda583 Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Wed, 29 Apr 2026 09:34:26 -0400 Subject: [PATCH 14/18] Add gene page table for antismash --- Model/lib/wdk/model/records/geneRecord.xml | 12 +++++++ .../wdk/model/records/geneTableQueries.xml | 32 +++++++++++++++++++ 2 files changed, 44 insertions(+) diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml index af8f7b2164..a07850cea2 100644 --- a/Model/lib/wdk/model/records/geneRecord.xml +++ b/Model/lib/wdk/model/records/geneRecord.xml @@ -3174,6 +3174,18 @@ name" internal="true"/> + + + + + + +
+ diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml index 309b2a94b7..8017f7d51c 100644 --- a/Model/lib/wdk/model/records/geneTableQueries.xml +++ b/Model/lib/wdk/model/records/geneTableQueries.xml @@ -4849,5 +4849,37 @@ FROM webready.GeneAttributes_p ga, ( + + + + + + + + + + + + + From c29d54d6fd578cd2758bc16733c15b5b5770d92d Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Wed, 29 Apr 2026 09:35:00 -0400 Subject: [PATCH 15/18] Add ontology for antismash table --- Model/lib/wdk/ontology/individuals.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Model/lib/wdk/ontology/individuals.txt b/Model/lib/wdk/ontology/individuals.txt index efcb6f8792..b5c054403c 100644 --- a/Model/lib/wdk/ontology/individuals.txt +++ b/Model/lib/wdk/ontology/individuals.txt @@ -236,7 +236,8 @@ GeneRecordClasses.GeneRecordClass.specialJbrowseUrl http://edamontology.org/topi GeneRecordClasses.GeneRecordClass.ExpressionGraphsDataTable http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table ExpressionGraphsDataTable gene record-internal GeneRecordClasses.GeneRecordClass.UserDatasetsTranscriptomicsGraphsDataTable http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table UserDatasetsTranscriptomicsGraphsDataTable gene record-internal GeneRecordClasses.GeneRecordClass.FacetMetadata http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table FacetMetadata gene record-internal -GeneRecordClasses.GeneRecordClass.FungiVBOrgLinkoutsTable http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table FungiVBOrgLinkoutsTable gene record-internal +GeneRecordClasses.GeneRecordClass.FungiVBOrgLinkoutsTable http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table FungiVBOrgLinkoutsTable gene record-internal +GeneRecordClasses.GeneRecordClass.AntiSmashClusters http://edamontology.org/topic_0753 Metabolic Pathways GeneRecordClasses.GeneRecordClass table AntiSmashClusters gene record 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 From 6cb545e04ff5ce23350073ee4fd620a2519113d0 Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Wed, 29 Apr 2026 10:23:12 -0400 Subject: [PATCH 16/18] Change name to secondary metabolites to match search. Fixes to ontology --- Model/lib/wdk/model/records/geneRecord.xml | 4 ++-- Model/lib/wdk/model/records/geneTableQueries.xml | 2 +- Model/lib/wdk/ontology/individuals.txt | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml index a07850cea2..00d5e450ee 100644 --- a/Model/lib/wdk/model/records/geneRecord.xml +++ b/Model/lib/wdk/model/records/geneRecord.xml @@ -3174,11 +3174,11 @@ name" internal="true"/> - + queryRef="GeneTables.SecondaryMetaboliteClusters"> diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml index 8017f7d51c..8f8ac9d617 100644 --- a/Model/lib/wdk/model/records/geneTableQueries.xml +++ b/Model/lib/wdk/model/records/geneTableQueries.xml @@ -4849,7 +4849,7 @@ FROM webready.GeneAttributes_p ga, ( - + diff --git a/Model/lib/wdk/ontology/individuals.txt b/Model/lib/wdk/ontology/individuals.txt index b5c054403c..0f9987c0ce 100644 --- a/Model/lib/wdk/ontology/individuals.txt +++ b/Model/lib/wdk/ontology/individuals.txt @@ -237,7 +237,7 @@ GeneRecordClasses.GeneRecordClass.ExpressionGraphsDataTable http://edamontology. GeneRecordClasses.GeneRecordClass.UserDatasetsTranscriptomicsGraphsDataTable http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table UserDatasetsTranscriptomicsGraphsDataTable gene record-internal GeneRecordClasses.GeneRecordClass.FacetMetadata http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table FacetMetadata gene record-internal GeneRecordClasses.GeneRecordClass.FungiVBOrgLinkoutsTable http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table FungiVBOrgLinkoutsTable gene record-internal -GeneRecordClasses.GeneRecordClass.AntiSmashClusters http://edamontology.org/topic_0753 Metabolic Pathways GeneRecordClasses.GeneRecordClass table AntiSmashClusters gene record +GeneRecordClasses.GeneRecordClass.SecondaryMetaboliteClusters http://edamontology.org/topic_1775 Function analysis GeneRecordClasses.GeneRecordClass table SecondaryMetaboliteClusters transcript record download 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 From d11ba69611b887b388402ab93aeb23ee16c6c9ad Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Wed, 29 Apr 2026 13:35:56 -0400 Subject: [PATCH 17/18] Change ontology to gene scope --- Model/lib/wdk/ontology/individuals.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/wdk/ontology/individuals.txt b/Model/lib/wdk/ontology/individuals.txt index 0f9987c0ce..3240ffe622 100644 --- a/Model/lib/wdk/ontology/individuals.txt +++ b/Model/lib/wdk/ontology/individuals.txt @@ -237,7 +237,7 @@ GeneRecordClasses.GeneRecordClass.ExpressionGraphsDataTable http://edamontology. GeneRecordClasses.GeneRecordClass.UserDatasetsTranscriptomicsGraphsDataTable http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table UserDatasetsTranscriptomicsGraphsDataTable gene record-internal GeneRecordClasses.GeneRecordClass.FacetMetadata http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table FacetMetadata gene record-internal GeneRecordClasses.GeneRecordClass.FungiVBOrgLinkoutsTable http://edamontology.org/topic_3308 Transcriptomics GeneRecordClasses.GeneRecordClass table FungiVBOrgLinkoutsTable gene record-internal -GeneRecordClasses.GeneRecordClass.SecondaryMetaboliteClusters http://edamontology.org/topic_1775 Function analysis GeneRecordClasses.GeneRecordClass table SecondaryMetaboliteClusters transcript record download +GeneRecordClasses.GeneRecordClass.SecondaryMetaboliteClusters http://edamontology.org/topic_1775 Function analysis GeneRecordClasses.GeneRecordClass table SecondaryMetaboliteClusters gene record download 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 From 903f4a9465099cdcc9a4989c12f9fb25ed16b04b Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Thu, 30 Apr 2026 14:09:08 -0400 Subject: [PATCH 18/18] FungalGPIForm also for FungiDB only! duh!! --- .../apicommon/model/datasetInjector/AnnotatedGenome.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/AnnotatedGenome.java b/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/AnnotatedGenome.java index e7c2a06d5e..3ea86df2e6 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/AnnotatedGenome.java +++ b/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/AnnotatedGenome.java @@ -321,10 +321,10 @@ public void addModelReferences() { addWdkReference("GeneRecordClasses.GeneRecordClass", "attribute", "SyntenyGbrowseUrl"); } - // FungalGPIForm only for FungiDB - if (!(projectName.equals("FungiDB"))){ + // for FungiDB only + if (projectName.equals("FungiDB")){ addWdkReference("GeneRecordClasses.GeneRecordClass", "table", "FungalGPIForm"); - addWdkReference("GeneRecordClasses.GeneRecordClass", "table", "SecondaryMetaboliteClusters"); + addWdkReference("GeneRecordClasses.GeneRecordClass", "table", "SecondaryMetaboliteClusters"); } // CommunityExpComments for only GiardiaDB and FungiDB