From 9bcbe7540ee0934ff3df7e0bd787b28893c663a1 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Fri, 10 May 2024 20:01:10 -0400 Subject: [PATCH] no-element-uri-quotes --- src/schema/annotation.yaml | 10 +++++----- src/schema/attribute_values.yaml | 14 ++++++------- src/schema/basic_classes.yaml | 12 +++++------ src/schema/core.yaml | 20 +++++++++---------- src/schema/nmdc.yaml | 2 +- src/schema/workflow_execution_activity.yaml | 22 ++++++++++----------- 6 files changed, 40 insertions(+), 40 deletions(-) diff --git a/src/schema/annotation.yaml b/src/schema/annotation.yaml index d0695ca098..d50f3f9c51 100644 --- a/src/schema/annotation.yaml +++ b/src/schema/annotation.yaml @@ -35,7 +35,7 @@ default_range: string classes: GenomeFeature: - class_uri: "nmdc:GenomeFeature" + class_uri: nmdc:GenomeFeature description: >- A feature localized to an interval along a genome comments: @@ -61,7 +61,7 @@ classes: required: true FunctionalAnnotationTerm: - class_uri: "nmdc:FunctionalAnnotationTerm" + class_uri: nmdc:FunctionalAnnotationTerm aliases: - function - FunctionalAnnotation @@ -74,7 +74,7 @@ classes: - Retaining this even after removing Reaction. See todos on the Pathway and OrthologyGroup subclasses. Pathway: - class_uri: "nmdc:Pathway" + class_uri: nmdc:Pathway aliases: - biological process - metabolic pathway @@ -92,7 +92,7 @@ classes: - is Pathway instantiated in an MongoDB collection? Aren't Pathways searchable in the Data Portal? OrthologyGroup: - class_uri: "nmdc:OrthologyGroup" + class_uri: nmdc:OrthologyGroup is_a: FunctionalAnnotationTerm description: >- A set of genes or gene products in which all members are orthologous @@ -112,7 +112,7 @@ classes: - is OrthologyGroup instantiated in an MongoDB collection? Aren't Pathways searchable in the Data Portal? FunctionalAnnotation: - class_uri: "nmdc:FunctionalAnnotation" + class_uri: nmdc:FunctionalAnnotation description: >- An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. diff --git a/src/schema/attribute_values.yaml b/src/schema/attribute_values.yaml index 838383902e..16b2a93204 100644 --- a/src/schema/attribute_values.yaml +++ b/src/schema/attribute_values.yaml @@ -21,7 +21,7 @@ classes: - type QuantityValue: - class_uri: "nmdc:QuantityValue" + class_uri: nmdc:QuantityValue is_a: AttributeValue description: A simple quantity, e.g. 2cm slots: @@ -41,7 +41,7 @@ classes: - schema:QuantityValue ImageValue: - class_uri: "nmdc:ImageValue" + class_uri: nmdc:ImageValue is_a: AttributeValue description: An attribute value representing an image. slots: @@ -50,7 +50,7 @@ classes: - display_order PersonValue: - class_uri: "nmdc:PersonValue" + class_uri: nmdc:PersonValue is_a: AttributeValue description: An attribute value representing a person slots: @@ -80,19 +80,19 @@ classes: annotations: display_hint: First name, middle initial, and last name of this person. TextValue: - class_uri: "nmdc:TextValue" + class_uri: nmdc:TextValue is_a: AttributeValue description: A basic string value slots: - language # UrlValue: - # class_uri: "nmdc:UrlValue" + # class_uri: nmdc:UrlValue # is_a: AttributeValue # description: A value that is a string that conforms to URL syntax TimestampValue: - class_uri: "nmdc:TimestampValue" + class_uri: nmdc:TimestampValue is_a: AttributeValue description: A value that is a timestamp. The range should be ISO-8601 notes: @@ -132,7 +132,7 @@ classes: required: true GeolocationValue: - class_uri: "nmdc:GeolocationValue" + class_uri: nmdc:GeolocationValue is_a: AttributeValue description: A normalized value for a location on the earth's surface slots: diff --git a/src/schema/basic_classes.yaml b/src/schema/basic_classes.yaml index cadeaa2cf1..62f4708743 100644 --- a/src/schema/basic_classes.yaml +++ b/src/schema/basic_classes.yaml @@ -16,7 +16,7 @@ imports: classes: NamedThing: - class_uri: "nmdc:NamedThing" + class_uri: nmdc:NamedThing description: "a databased entity or concept/class" abstract: true slots: @@ -26,7 +26,7 @@ classes: - alternative_identifiers - type OntologyClass: - class_uri: "nmdc:OntologyClass" + class_uri: nmdc:OntologyClass is_a: NamedThing notes: - The identifiers for terms from external ontologies can't have their ids constrained to the nmdc namespace @@ -42,7 +42,7 @@ classes: - type MaterialEntity: - class_uri: "nmdc:MaterialEntity" + class_uri: nmdc:MaterialEntity abstract: true aliases: - Material @@ -105,7 +105,7 @@ classes: see_also: - https://casrai.org/credit/ Doi: - class_uri: "nmdc:Doi" + class_uri: nmdc:Doi aliases: - DOIs - digital object identifiers @@ -341,7 +341,7 @@ classes: - OBI:0000070 - ISA:Assay WorkflowChain: - class_uri: "nmdc:WorkflowChain" + class_uri: nmdc:WorkflowChain is_a: PlannedProcess description: >- A workflow chain is a collection of Workflow Execution(s) that @@ -372,7 +372,7 @@ classes: output data and the metadata of the Data Generation. WorkflowExecution: - class_uri: "nmdc:WorkflowExecution" + class_uri: nmdc:WorkflowExecution is_a: PlannedProcess aliases: - analysis diff --git a/src/schema/core.yaml b/src/schema/core.yaml index f99ac5803a..920331d340 100644 --- a/src/schema/core.yaml +++ b/src/schema/core.yaml @@ -146,7 +146,7 @@ classes: interpolated: true MetagenomeAnnotation: - class_uri: "nmdc:MetagenomeAnnotation" + class_uri: nmdc:MetagenomeAnnotation description: A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs is_a: WorkflowExecution slots: @@ -1202,7 +1202,7 @@ classes: - OBI:0000094 PortionOfSubstance: - class_uri: "nmdc:PortionOfSubstance" + class_uri: nmdc:PortionOfSubstance title: Portion of a Substance mappings: - schema:Substance @@ -1218,7 +1218,7 @@ classes: - volume ProcessedSample: - class_uri: "nmdc:ProcessedSample" + class_uri: nmdc:ProcessedSample is_a: MaterialEntity title: Processed Sample slots: @@ -1235,7 +1235,7 @@ classes: interpolated: true Site: - class_uri: "nmdc:Site" + class_uri: nmdc:Site abstract: true is_a: MaterialEntity title: Site @@ -1253,7 +1253,7 @@ classes: class_uri: 'nmdc:EnvironmentalMaterialTerm' MagBin: - class_uri: "nmdc:MagBin" + class_uri: nmdc:MagBin slots: - bin_name - bin_quality @@ -1277,7 +1277,7 @@ classes: - type MetaboliteIdentification: - class_uri: "nmdc:MetaboliteIdentification" + class_uri: nmdc:MetaboliteIdentification description: This is used to link a metabolomics analysis workflow to a specific metabolite slots: - alternative_identifiers @@ -1286,7 +1286,7 @@ classes: - type PeptideQuantification: - class_uri: "nmdc:PeptideQuantification" + class_uri: nmdc:PeptideQuantification description: This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information slots: - type @@ -1298,7 +1298,7 @@ classes: - peptide_sum_masic_abundance ProteinQuantification: - class_uri: "nmdc:ProteinQuantification" + class_uri: nmdc:ProteinQuantification description: This is used to link a metaproteomics analysis workflow to a specific protein slots: - all_proteins @@ -1314,7 +1314,7 @@ classes: description: the grouped list of protein identifiers associated with the peptide sequences that were grouped to a best protein ChemicalEntity: - class_uri: "nmdc:ChemicalEntity" + class_uri: nmdc:ChemicalEntity aliases: - metabolite - chemical substance @@ -1348,7 +1348,7 @@ classes: - biolink:ChemicalSubstance GeneProduct: - class_uri: "nmdc:GeneProduct" + class_uri: nmdc:GeneProduct is_a: NamedThing description: A molecule encoded by a gene that has an evolved function notes: diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 9e8a1534cf..5e1b3636bf 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -169,7 +169,7 @@ classes: interpolated: true FunctionalAnnotationAggMember: - class_uri: "nmdc:FunctionalAnnotationAggMember" + class_uri: nmdc:FunctionalAnnotationAggMember slots: - metagenome_annotation_id - gene_function_id diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index e9a28d2221..ebe7ba256f 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -16,7 +16,7 @@ default_range: string classes: MetagenomeAssembly: - class_uri: "nmdc:MetagenomeAssembly" + class_uri: nmdc:MetagenomeAssembly description: A workflow execution activity that converts sequencing reads into an assembled metagenome. comments: - instances of this class may use a de novo assembly strategy in most or all cases relevant to NMDC @@ -60,7 +60,7 @@ classes: interpolated: true MetatranscriptomeAssembly: - class_uri: "nmdc:MetatranscriptomeAssembly" + class_uri: nmdc:MetatranscriptomeAssembly is_a: WorkflowExecution in_subset: - workflow subset @@ -102,7 +102,7 @@ classes: MetatranscriptomeAnnotation: - class_uri: "nmdc:MetatranscriptomeAnnotation" + class_uri: nmdc:MetatranscriptomeAnnotation is_a: WorkflowExecution slots: - img_identifiers @@ -118,7 +118,7 @@ classes: maximum_cardinality: 1 MetatranscriptomeAnalysis: - class_uri: "nmdc:MetatranscriptomeAnalysis" + class_uri: nmdc:MetatranscriptomeAnalysis is_a: WorkflowExecution description: >- A metatranscriptome activity that e.g. pools assembly and annotation activity. @@ -137,7 +137,7 @@ classes: MagsAnalysis: - class_uri: "nmdc:MagsAnalysis" + class_uri: nmdc:MagsAnalysis description: A workflow execution activity that uses computational binning tools to group assembled contigs into genomes title: Metagenome-Assembled Genome analysis activity is_a: WorkflowExecution @@ -162,7 +162,7 @@ classes: MetagenomeSequencing: - class_uri: "nmdc:MetagenomeSequencing" + class_uri: nmdc:MetagenomeSequencing description: Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data. title: Metagenome sequencing activity is_a: WorkflowExecution @@ -177,7 +177,7 @@ classes: ReadQcAnalysis: - class_uri: "nmdc:ReadQcAnalysis" + class_uri: nmdc:ReadQcAnalysis description: A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal title: Read quality control analysis activity is_a: WorkflowExecution @@ -198,7 +198,7 @@ classes: interpolated: true ReadBasedTaxonomyAnalysis: - class_uri: "nmdc:ReadBasedTaxonomyAnalysis" + class_uri: nmdc:ReadBasedTaxonomyAnalysis description: A workflow execution activity that performs taxonomy classification using sequencing reads title: Read based analysis activity is_a: WorkflowExecution @@ -213,7 +213,7 @@ classes: MetabolomicsAnalysis: - class_uri: "nmdc:MetabolomicsAnalysis" + class_uri: nmdc:MetabolomicsAnalysis is_a: WorkflowExecution in_subset: - workflow subset @@ -228,7 +228,7 @@ classes: interpolated: true MetaproteomicsAnalysis: - class_uri: "nmdc:MetaproteomicsAnalysis" + class_uri: nmdc:MetaproteomicsAnalysis is_a: WorkflowExecution in_subset: - workflow subset @@ -242,7 +242,7 @@ classes: interpolated: true NomAnalysis: - class_uri: "nmdc:NomAnalysis" + class_uri: nmdc:NomAnalysis is_a: WorkflowExecution in_subset: - workflow subset