diff --git a/modules/Template/Template.yaml b/modules/Template/Template.yaml index ca3b6b0c..0dd7175b 100644 --- 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 index 67ff334c..6120e995 100644 --- 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