Feat/meth array template (#408)

* Add optional methylation array data props defined by GDC * Add MethylationArrayTemplate * Update channel prop * Add template to menu * Update throttle param * Rebuild NF.jsonld, json * Add data type values * Lint * Rebuild NF.jsonld, json --------- Co-authored-by: nf-osi[bot] <[email protected]>
nf-osi · Mar 20, 2024 · 9dd7d7a · 9dd7d7a
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commit 9dd7d7a
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diff --git a/NF.jsonld b/NF.jsonld
@@ -220,7 +220,7 @@
   }, {
     "@id" : "bts:Data",
     "@type" : "rdfs:Class",
-    "rdfs:comment" : "TBD",
+    "rdfs:comment" : "What the data (file) contains.",
     "rdfs:label" : "Data",
     "rdfs:subClassOf" : [ ],
     "schema:isPartOf" : {
@@ -2732,6 +2732,81 @@
       "@id" : "bts:progressReportNumber"
     } ],
     "sms:displayName" : "UpdateMilestoneReport"
+  }, {
+    "rdfs:subClassOf" : [ {
+      "@id" : "bts:GenomicsArrayTemplate"
+    } ],
+    "@id" : "bts:MethylationArrayTemplate",
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:required" : "sms:false",
+    "sms:requiresComponent" : "",
+    "rdfs:label" : "MethylationArrayTemplate",
+    "rdfs:comment" : "Template for raw data files (idat) from DNA methylation arrays.",
+    "@type" : "rdfs:Class",
+    "sms:requiresDependency" : [ {
+      "@id" : "bts:Component"
+    }, {
+      "@id" : "bts:Filename"
+    }, {
+      "@id" : "bts:fileFormat"
+    }, {
+      "@id" : "bts:resourceType"
+    }, {
+      "@id" : "bts:dataType"
+    }, {
+      "@id" : "bts:dataSubtype"
+    }, {
+      "@id" : "bts:assay"
+    }, {
+      "@id" : "bts:individualID"
+    }, {
+      "@id" : "bts:species"
+    }, {
+      "@id" : "bts:sex"
+    }, {
+      "@id" : "bts:age"
+    }, {
+      "@id" : "bts:ageUnit"
+    }, {
+      "@id" : "bts:diagnosis"
+    }, {
+      "@id" : "bts:nf1Genotype"
+    }, {
+      "@id" : "bts:nf2Genotype"
+    }, {
+      "@id" : "bts:tumorType"
+    }, {
+      "@id" : "bts:modelSystemName"
+    }, {
+      "@id" : "bts:organ"
+    }, {
+      "@id" : "bts:comments"
+    }, {
+      "@id" : "bts:parentSpecimenID"
+    }, {
+      "@id" : "bts:specimenID"
+    }, {
+      "@id" : "bts:aliquotID"
+    }, {
+      "@id" : "bts:platform"
+    }, {
+      "@id" : "bts:nucleicAcidSource"
+    }, {
+      "@id" : "bts:specimenPreparationMethod"
+    }, {
+      "@id" : "bts:channel"
+    }, {
+      "@id" : "bts:chipID"
+    }, {
+      "@id" : "bts:chipPosition"
+    }, {
+      "@id" : "bts:plateName"
+    }, {
+      "@id" : "bts:plateWell"
+    } ],
+    "sms:displayName" : "MethylationArrayTemplate"
   }, {
     "rdfs:subClassOf" : [ {
       "@id" : "bts:BiologicalAssayDataTemplate"
@@ -5523,6 +5598,17 @@
     "rdfs:comment" : "(Legacy/deprecated annotation) Whether or not is paired-end sequencing (Yes; No).",
     "@type" : "rdfs:Class",
     "sms:displayName" : "isPairedEnd"
+  }, {
+    "@id" : "bts:plateName",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "User-specified identifier of the plate used to prepare the sample for analysis.",
+    "rdfs:label" : "plateName",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "plateName",
+    "sms:required" : "sms:false"
   }, {
     "rdfs:subClassOf" : [ ],
     "@id" : "bts:numberOfSchwannomas",
@@ -6129,6 +6215,22 @@
     },
     "sms:displayName" : "meanCoverage",
     "sms:required" : "sms:false"
+  }, {
+    "rdfs:subClassOf" : [ ],
+    "@id" : "bts:channel",
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:required" : "sms:true",
+    "schema:rangeIncludes" : [ {
+      "@id" : "bts:Cy3"
+    }, {
+      "@id" : "bts:Cy5"
+    } ],
+    "rdfs:label" : "channel",
+    "rdfs:comment" : "Color channel used to generate data file.",
+    "@type" : "rdfs:Class",
+    "sms:displayName" : "channel"
   }, {
     "@id" : "bts:genePerturbed",
     "@type" : "rdfs:Class",
@@ -7015,6 +7117,10 @@
       "@id" : "bts:genomicVariants"
     }, {
       "@id" : "bts:rawcounts"
+    }, {
+      "@id" : "bts:RawIntensities"
+    }, {
+      "@id" : "bts:NormalizedIntensities"
     }, {
       "@id" : "bts:PharmacokineticStudy"
     }, {
@@ -7675,6 +7781,28 @@
     "rdfs:comment" : "Characterization of the manifestation of Dermal neurofibromas.",
     "@type" : "rdfs:Class",
     "sms:displayName" : "dermalNeurofibromas"
+  }, {
+    "@id" : "bts:plateWell",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "User-specified identifier for the specific well of the plate used to prepare the sample for analysis.",
+    "rdfs:label" : "plateWell",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "plateWell",
+    "sms:required" : "sms:false"
+  }, {
+    "@id" : "bts:chipID",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "User-specified identifier for the chip used to perform the methylation microarray.",
+    "rdfs:label" : "chipID",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "chipID",
+    "sms:required" : "sms:false"
   }, {
     "rdfs:subClassOf" : [ ],
     "@id" : "bts:proteinExtractSource",
@@ -8890,6 +9018,17 @@
     },
     "sms:displayName" : "bisulfiteConversionKitID",
     "sms:required" : "sms:false"
+  }, {
+    "@id" : "bts:chipPosition",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "User-specified identifier for the specific position on the chip that the sample was loaded into to perform the methylation microarray.",
+    "rdfs:label" : "chipPosition",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "chipPosition",
+    "sms:required" : "sms:false"
   }, {
     "rdfs:subClassOf" : [ ],
     "@id" : "bts:assay",
@@ -21150,6 +21289,17 @@
     },
     "sms:displayName" : "University of Washington, Seattle",
     "sms:required" : "sms:false"
+  }, {
+    "@id" : "bts:NormalizedIntensities",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "TBD",
+    "rdfs:label" : "NormalizedIntensities",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "NormalizedIntensities",
+    "sms:required" : "sms:false"
   }, {
     "@id" : "bts:LTQOrbitrapXL",
     "@type" : "rdfs:Class",
@@ -21722,6 +21872,17 @@
     },
     "sms:displayName" : "bed gappedPeak",
     "sms:required" : "sms:false"
+  }, {
+    "@id" : "bts:RawIntensities",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "TBD",
+    "rdfs:label" : "RawIntensities",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "RawIntensities",
+    "sms:required" : "sms:false"
   }, {
     "@id" : "bts:AnnotatedSomaticVariants",
     "@type" : "rdfs:Class",

diff --git a/dca-template-config.json b/dca-template-config.json
@@ -4,7 +4,8 @@
       {"display_name": "Whole Exome Sequencing Assay", "schema_name": "WESTemplate", "type": "file"},
       {"display_name": "RNA Sequencing Assay", "schema_name": "RNASeqTemplate", "type": "file"},
       {"display_name": "Single-cell RNA Sequencing Assay", "schema_name": "ScRNASeqTemplate", "type": "file"},
-      {"display_name": "Epigenetics Assay", "schema_name": "EpigeneticsAssayTemplate", "type": "file"},
+      {"display_name": "Epigenetics Sequencing Assay", "schema_name": "EpigeneticsAssayTemplate", "type": "file"},
+      {"display_name": "Methylation Array", "schema_name": "MethylationArrayTemplate", "type": "file"},
       {"display_name": "Other Genomics Assay", "schema_name": "GenomicsAssayTemplate", "type": "file"},
       {"display_name": "Extended Genomics Assay", "schema_name": "GenomicsAssayTemplateExtended", "type": "file"},
       {"display_name": "Imaging Assay", "schema_name": "ImagingAssayTemplate", "type": "file"},

diff --git a/modules/Data/Data.yaml b/modules/Data/Data.yaml
@@ -1,5 +1,6 @@
 enums:
   Data:
+    description: What the data (file) contains.
     permissible_values:
       immunoassay:
         description: Laboratory test involving interaction of antigens with specific antibodies.
@@ -60,6 +61,10 @@ enums:
       raw counts:
         description: The number or amount of something.
         meaning: http://purl.obolibrary.org/obo/NCIT_C25463
+      RawIntensities:
+        description: Raw intensity values from the instrument.
+      NormalizedIntensities:
+        description: Normalized intensity values from the instrument/machine.
       Pharmacokinetic Study:
         description: A study of the process by which a drug is absorbed, distributed, metabolized, and eliminated by the body.
         meaning: http://purl.obolibrary.org/obo/NCIT_C49663
@@ -71,7 +76,7 @@ enums:
         meaning: https://en.wikipedia.org/wiki/Chromatin_remodeling
       StructuralVariants:
         description: Genomic variants data that covers deletions, duplications, CNVs, insertions, inversions, and translocations, which may be derived from specialized variant calling workflows.
-        source: hhttps://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=structural_variation
+        source: https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=structural_variation
       GermlineVariants:
         description: Called germline variants
         meaning: https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=simple_germline_variation

diff --git a/modules/Template/Data.yaml b/modules/Template/Data.yaml
@@ -285,6 +285,23 @@ classes:
         dataType:
         - geneExpression
 
+  MethylationArrayTemplate:
+    is_a: GenomicsArrayTemplate
+    description: Template for raw data files (idat) from DNA methylation arrays.
+    source: https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=raw_methylation_array
+    slots:
+    - chipID
+    - chipPosition
+    - plateName
+    - plateWell
+    annotations:
+      requiresComponent: ''
+      required: false
+      match:
+        assay: 
+        - methylation array
+
+
   #########################################################
   # Biological Assay Data  / Sequencing / Processed            
   #########################################################

diff --git a/modules/props.yaml b/modules/props.yaml
@@ -172,6 +172,20 @@ slots:
     description: A cell type is a distinct morphological or functional form of cell.
     range: Cell
     required: false
+  channel:
+    description: Color channel used to generate data file.
+    required: true
+    range: ChannelEnum
+    source: Genomic Data Commons
+  chipID:
+    description: User-specified identifier for the chip used to perform the methylation microarray.
+    required: false
+    source: Genomic Data Commons
+  chipPosition:
+    description: User-specified identifier for the specific position on the chip that 
+      the sample was loaded into to perform the methylation microarray.
+    required: false
+    source: Genomic Data Commons
   citation:
     description: Citation (e.g. doi) that usage of data or resource should be cited with.
     required: false
@@ -751,6 +765,14 @@ slots:
     range: PresenceEnum
     required: false
     title: Pheochromocytoma
+  plateName:
+    description: User-specified identifier of the plate used to prepare the sample for analysis.
+    required: false
+    source: Genomic Data Commons
+  plateWell:
+    description: User-specified identifier for the specific well of the plate used to prepare the sample for analysis.
+    required: false
+    source: Genomic Data Commons
   platform:
     description: A sequencing platform, microscope, spectroscope/plate reader, or
       other platform for collecting data.

diff --git a/registered-json-schemas/PortalDataset.json b/registered-json-schemas/PortalDataset.json
@@ -196,7 +196,7 @@
       },
       "dataType": {
         "items": {
-          "description": "",
+          "description": "What the data (file) contains.",
           "enum": [
             "immunoassay",
             "behavior process",
@@ -217,6 +217,8 @@
             "genomicFeatures",
             "genomicVariants",
             "raw counts",
+            "RawIntensities",
+            "NormalizedIntensities",
             "Pharmacokinetic Study",
             "mask image",
             "chromatinActivity",

diff --git a/registered-json-schemas/PortalStudy.json b/registered-json-schemas/PortalStudy.json
@@ -24,7 +24,7 @@
       },
       "dataType": {
         "items": {
-          "description": "",
+          "description": "What the data (file) contains.",
           "enum": [
             "immunoassay",
             "behavior process",
@@ -45,6 +45,8 @@
             "genomicFeatures",
             "genomicVariants",
             "raw counts",
+            "RawIntensities",
+            "NormalizedIntensities",
             "Pharmacokinetic Study",
             "mask image",
             "chromatinActivity",

diff --git a/tests/generate/basic_templates.sh b/tests/generate/basic_templates.sh
@@ -6,7 +6,7 @@ CREDS=creds.json
 DATA_MODEL_PATH=../../NF.jsonld
 DATA_MODEL=NF.jsonld
 LOG_DIR=logs
-SLEEP_THROTTLE=17 # API rate-limiting, need to better figure out dynamically based on # of templates
+SLEEP_THROTTLE=20 # API rate-limiting, need to better figure out dynamically based on # of templates
 
 # Setup for creds
 # If testing locally, it might already be in folder;