Update props

nf-osi · Jun 30, 2023 · 34f5cb3 · 34f5cb3
1 parent 8dd6a97
commit 34f5cb3
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diff --git a/modules/Template/Template.yaml b/modules/Template/Template.yaml
@@ -534,6 +534,7 @@ classes:
     - Component
     - Filename
     - resourceType
+    - title
     - author
     - citation
     - license
@@ -561,6 +562,37 @@ classes:
       requiresComponent: ''
       required: false
 
+#######################################
+# Other Artifacts           
+#######################################
+
+# DatasetTemplate:
+#   is_a: Template
+#   description: Template that specifies NF portal dataset properties should have for more consistent community-curated datasets.
+#   notes:
+#   - This is intended to be compiled to JSON schema and bound to dataset entities, NOT used in DCA.
+#   slots:
+#   - id # Synapse id used as accession for citation when no doi
+#   - doi
+#   - title
+#   - creator
+#   - contributor
+#   - currentVersion
+#   - description
+#   - license
+#   - dataType
+#   - studyName
+#   - studyId
+#   - manifestation
+#   - diseaseFocus
+#   - fundingAgency
+#   - series
+#   - publisher
+#   - yearProcessed
+#   - yearPublished
+#   - datasetItemCount
+#   - datasetSizeInBytes
+
 #######################################
 # PartialTemplate              
 #######################################

diff --git a/modules/props.yaml b/modules/props.yaml
@@ -161,6 +161,16 @@ slots:
     notes:
       - Currently no dependencies or validation rules.
     required: false
+  contributor:
+    description: An entity responsible for making contributions to the resource.
+    meaning: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#contributor
+    required: false
+  creator:
+    description: An entity responsible for making the resource.
+    notes:
+    - Recommended practice is to identify the creator with a URI. If this is not possible or feasible, a literal value that identifies the creator may be provided.
+    meaning: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#creator
+    required: true
   createdBy:
     description: Refers to the user who created the resource.
     in_subset:
@@ -177,6 +187,7 @@ slots:
     required: false
   currentVersion:
     description: (Versionable entities only) The current version number of the resource.
+    meaning: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_version
     in_subset:
       - Synapse
     notes:
@@ -204,12 +215,28 @@ slots:
     description: |
       A type of data -- experimental, clinical, or other. Most typically refers to a high-level data type that can be related to an assay type.  For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.
     required: false
+  datasetSizeInBytes:
+    description: Size of dataset entity in bytes. Auto-calculated by Synapse.
+    in_subset:
+      - Synapse
+    required: false
+  datasetItemCount:
+    description: Count of files in dataset. Auto-calculated by Synapse.
+    in_subset:
+      - Synapse
+    required: false
+  description:
+    description: Text describing a resource.
+    required: false
   diagnosis:
     description: A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.
     notes:
       - Currently no dependencies or validation rules.
     range: DiagnosisEnum
     required: false
+  diseaseFocus:
+    description: Disease that acts as the main topic.
+    required: false
   dissociationMethod:
     description: Procedure by which a biological specimen is dissociated into individual cells or a cell suspension
     notes:
@@ -221,6 +248,9 @@ slots:
     notes:
       - Currently no dependencies or validation rules.
     required: false
+  doi: 
+    description: Digital object identifier of the resource.
+    required: false
   drugScreenType:
     description: String describing general class of drug screen
     notes:
@@ -266,6 +296,18 @@ slots:
       - Currently no dependencies or validation rules.
     range: BooleanEnum
     required: false
+  fileCount:
+    description: Number of files in the resource collection.
+    notes:
+    - This is auto-generated by Synapse for datasets.
+    in_subset:
+      - Synapse
+    required: false
+  fileSize:
+    description: Size of file in bytes.
+    in_subset:
+      - Synapse
+    required: false
   fileFormat:
     description: Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software
     notes:
@@ -387,6 +429,9 @@ slots:
     notes:
       - Currently no dependencies or validation rules.
     required: false
+  manifestation:
+    description: An associated phenotype characteristic.
+    required: false
   materialType:
     description: Type of material in the characterization
     enum_range:
@@ -532,9 +577,15 @@ slots:
   protocolAssay:
     description: >
       Main assay type that this protocol is related to, e.g. this is a prep protocol for single-cell RNA-seq assay. This is especially helpful for newly-developed or in-house assays.
-    range: Assay
+    range: AssayEnum
+    required: false
   protocolPurpose:
-    description: Brief description of the protocol purpose.  
+    description: Brief description of the protocol purpose.
+    required: false
+  publisher:
+    description: An entity responsible for making the resource available.
+    meaning: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/publisher
+    required: false
   readDepth:
     description: If available, the coverage statistic as output from bedtools coverage or samtools stats.
     notes:
@@ -629,6 +680,10 @@ slots:
     notes:
       - Currently no dependencies or validation rules.
     required: false
+  series:
+    description: Which series this resource belongs to, can be a name or link.
+    meaning: http://www.w3.org/ns/dcat#inSeries
+    required: false
   species:
     description: The name of a species (typically a taxonomic group) of organism.
     notes:
@@ -651,6 +706,12 @@ slots:
       - Currently no dependencies or validation rules.
     range: SpecimenPreparationMethodEnum
     required: false
+  studyId:
+    description: Id of study.
+    required: true
+  studyName:
+    description: Name of a study.
+    required: true
   targetCaptureKitID:
     description: A unique identifier for the kit used to construct a genomic library using target capture-based techniques, which should be composed of the vendor name, kit name and kit version.
     notes:
@@ -673,6 +734,10 @@ slots:
       - Currently no dependencies or validation rules.
     range: TissueEnum
     required: false
+  title:
+    description: Title of a resource.
+    meaning: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_title
+    required: true
   totalReads:
     description: If available, the total number of reads collected from samtools.
     notes:
@@ -711,6 +776,12 @@ slots:
     notes:
       - Currently no dependencies or validation rules.
     required: false
+  yearProcessed:
+    description: Year in which the resource was processed/derived.
+    required: false
+  yearPublished:
+    description: Year in which the resource was published.
+    required: false
   workflow:
     annotations:
       requiresDependency: workflowLink