From f84d3eab5adb051a2ac524a7872f8b09b1882a31 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Mon, 4 Dec 2023 12:31:47 -0700 Subject: [PATCH 1/8] Add back assayTarget at top-level for now --- modules/Template/Data.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/modules/Template/Data.yaml b/modules/Template/Data.yaml index 3165f534..17d9e96c 100644 --- a/modules/Template/Data.yaml +++ b/modules/Template/Data.yaml @@ -470,6 +470,7 @@ classes: description: General template for describing imaging data. slots: - platform + - assayTarget - auxiliaryAsset annotations: requiresComponent: '' @@ -481,6 +482,7 @@ classes: - in vivo bioluminescence - gel filtration chromatography - laser speckle imaging + - photograph - positron emission tomography - spatial frequency domain imaging - western blot From 82e3571a51322a44d7b155139004974a3843a2d7 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Mon, 4 Dec 2023 12:40:40 -0700 Subject: [PATCH 2/8] Update library prep kits --- modules/Assay/Parameter.yaml | 69 +++++++++++++++++++----------------- 1 file changed, 36 insertions(+), 33 deletions(-) diff --git a/modules/Assay/Parameter.yaml b/modules/Assay/Parameter.yaml index 1d3d1fe3..65da4e25 100644 --- a/modules/Assay/Parameter.yaml +++ b/modules/Assay/Parameter.yaml @@ -3,33 +3,33 @@ enums: permissible_values: Cy3: description: Fluorescent dye used for the green channel on an array - meaning: http://purl.obolibrary.org/obo/FBbi_00000449 + source: http://purl.obolibrary.org/obo/FBbi_00000449 Cy5: description: Fluorescent dye used for the red channel on an array - meaning: http://purl.obolibrary.org/obo/FBbi_00000450 + source: http://purl.obolibrary.org/obo/FBbi_00000450 GenePerturbationEnum: permissible_values: knockdown: description: Gene knockdown refers to techniques by which the expression of one or more of an organism's genes is reduced, either through genetic modification (a change in the DNA of one of the organism's chromosomes) or by treatment with a reagent such as a short DNA or RNA oligonucleotide with a sequence complementary to either an mRNA transcript or a gene. - meaning: http://www.bioassayontology.org/bao#BAO_0002433 + source: http://www.bioassayontology.org/bao#BAO_0002433 knockout: description: A gene knockout is a genetic technique in which an organism is engineered to carry genes that have been made inoperative (have been 'knocked out' of the organism). - meaning: http://www.bioassayontology.org/bao#BAO_0002441 + source: http://www.bioassayontology.org/bao#BAO_0002441 non-targeting control: description: Use of a guide RNA that is designed to not target any gene in particular, used as a control for a targeting gRNA overexpression: description: Gene overexpression refers to genetic techniques in which an organism or cell line is engineered to express increased levels of a gene. - meaning: http://www.bioassayontology.org/bao#BAO_0002442 + source: http://www.bioassayontology.org/bao#BAO_0002442 GenePerturbationTechnologyEnum: permissible_values: CRE Recombinase: description: CRE Recombinase catalyses site-specific recombination between two 34 base pair loxp sites and maintains the phage genome as a monomeric unit-copy plasmid in the lysogenic state. - meaning: http://purl.obolibrary.org/obo/NCIT_C17285 + source: http://purl.obolibrary.org/obo/NCIT_C17285 CRISPR: description: '' RNAi: description: High throughput sample analysis of RNAi molecules for potential application in gene knockdown or gene silencing of target genes - meaning: http://purl.obolibrary.org/obo/ERO_0001688 + source: http://purl.obolibrary.org/obo/ERO_0001688 GenomicReferenceEnum: permissible_values: GRCh38: @@ -61,47 +61,50 @@ enums: permissible_values: 10x: description: 10x Genomics library preparation - meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json + source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json CEL-seq: description: CEL-Seq library preparation - meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json + source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json Drop-Seq: description: Drop-Seq library preparation - meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json + source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json GTAC@WUSTL in-house prep: description: Non-stranded library prep that uses a TruSeq-like (in-house) library design (includes cDNA generation, end-repair, A-tailing, ligation, and PCR amplification with unique dual indexing) IDT xGen Exome Research Panel: description: '' - meaning: https://www.idtdna.com/pages/products/next-generation-sequencing/targeted-sequencing/hybridization-capture/predesigned-panels/xgen-exome-research-panel-v2 + source: https://www.idtdna.com/pages/products/next-generation-sequencing/targeted-sequencing/hybridization-capture/predesigned-panels/xgen-exome-research-panel-v2 Illumina TruSeq DNA Nano: description: '' KAPA HyperPrep Kit PCR-free: description: KAPA HyperPrep Kits offer a streamlined library preparation protocol that combines several enzymatic steps and eliminates bead cleanups to significantly reduce library preparation time and improve consistency. - meaning: https://sequencing.roche.com/en/products-solutions/products/sample-preparation/dna-reagents/library-preparation/kapa-hyperprep/ordering.html + source: https://sequencing.roche.com/en/products-solutions/products/sample-preparation/dna-reagents/library-preparation/kapa-hyperprep/ordering.html KAPA RNA HyperPrep Kit with RiboErase (HMR): description: The KAPA RNA HyperPrep Kits utilize novel chemistry that enables the combination of enzymatic steps and fewer reaction purifications, resulting in a truly streamlined solution for the preparation of high-quality RNA-seq libraries. - meaning: https://rochesequencingstore.com/catalog/kapa-rna-hyperprep-kit-with-riboerase-hmr/ + source: https://rochesequencingstore.com/catalog/kapa-rna-hyperprep-kit-with-riboerase-hmr/ KAPA mRNA HyperPrep Kit: description: The KAPA mRNA HyperPrep Kit is a highly efficient library preparation kit designed for generating stranded RNA-seq libraries with low input amounts and reduced bias. - meaning: https://sequencing.roche.com/global/en/products/group/kapa-rna-hyperprep-kits.html + source: https://sequencing.roche.com/global/en/products/group/kapa-rna-hyperprep-kits.html NEBNext mRNA Library Prep Reagent Set for Illumina: description: NEBNext mRNA Library Prep Reagent Set for Illumina - meaning: https://www.neb.com/products/e6100-nebnext-mrna-library-prep-reagent-set-for-illumina + source: https://www.neb.com/products/e6100-nebnext-mrna-library-prep-reagent-set-for-illumina Omni-ATAC: description: Omni-ATAC-seq library preparation - meaning: https://protocolexchange.researchsquare.com/article/nprot-6107/v1 + source: https://protocolexchange.researchsquare.com/article/nprot-6107/v1 + QuantSeq FWD V2 with UDI: + description: Prep kit for next-gen sequencing with low-abundance samples. For analysis, note that this only provides gene-level counts, not transcript-level. + source: https://www.lexogen.com/quantseq-fwd-udi-v2/ Smart-seq2: description: Smart-seq 2 library preparation - meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json + source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json Smart-seq4: description: Smart-seq4 library preparation - meaning: https://www.takarabio.com/products/next-generation-sequencing/single-cell-rna-and-dna-seq/smart-seq-v4-for-mrna-seq + source: https://www.takarabio.com/products/next-generation-sequencing/single-cell-rna-and-dna-seq/smart-seq-v4-for-mrna-seq TruSeq: description: TruSeq library preparation - meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json + source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json TruSeq standard total RNA library kit: description: '' - meaning: https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-stranded-total-rna.html + source: https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-stranded-total-rna.html unknown: description: information not provided MRISequenceEnum: @@ -118,33 +121,33 @@ enums: permissible_values: bulk cell: description: All cells from bulk sample - meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json + source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json bulk nuclei: description: All nuclei from bulk sample - meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json + source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json mitochondria: description: Mitochondria only - meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json + source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json single cell: description: Single cell - meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json + source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json single nucleus: description: Single nuclei - meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json + source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json ProteinExtractSourceEnum: permissible_values: cell lysate: description: A material entity which is output of a cell lysis process - meaning: http://purl.obolibrary.org/obo/OBI_1000036 + source: http://purl.obolibrary.org/obo/OBI_1000036 cytoplasm: description: That portion of the cell contained within the plasma membrane but excluding the nucleus. - meaning: http://purl.obolibrary.org/obo/NCIT_C13226 + source: http://purl.obolibrary.org/obo/NCIT_C13226 mitochondria: description: Mitochondria only - meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json + source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json nuclear extract: description: Nuclear extracts contain proteins in nuclear compartment of the cell - meaning: http://purl.obolibrary.org/obo/NCIT_C19832 + source: http://purl.obolibrary.org/obo/NCIT_C19832 ReadPairOrientationEnum: permissible_values: fr-firststrand: @@ -159,18 +162,18 @@ enums: permissible_values: forward: description: Read 1 (or unpaired read) comes from the forward strand and read 2 (if applicable) comes from the reverse strand - meaning: 'FALSE' + source: 'FALSE' reverse: description: read 1 (or unpaired read) comes from the reverse strand and read 2 (if applicable) comes from the forward strand - meaning: 'FALSE' + source: 'FALSE' RunTypeEnum: permissible_values: pairedEnd: description: A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. - meaning: http://purl.obolibrary.org/obo/OBI_0001852 + source: http://purl.obolibrary.org/obo/OBI_0001852 singleEnd: description: A library preparation that results in the creation of a library of 5' ends of DNA. - meaning: Sage Bionetworks + source: Sage Bionetworks StrandednessEnum: permissible_values: FirstStranded: From 320f2425b30bbb298d6082684d780bdb4733ae9c Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Mon, 4 Dec 2023 12:45:03 -0700 Subject: [PATCH 3/8] Copy over templates config.json --- dca-template-config.json | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 dca-template-config.json diff --git a/dca-template-config.json b/dca-template-config.json new file mode 100644 index 00000000..2bb71611 --- /dev/null +++ b/dca-template-config.json @@ -0,0 +1,27 @@ +{ + "manifest_schemas": [ + {"display_name": "Whole Genome Sequencing Assay", "schema_name": "WGSTemplate", "type": "file"}, + {"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": "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"}, + {"display_name": "MRI Assay", "schema_name": "MRIAssayTemplate", "type": "file"}, + {"display_name": "Pharmacokinetics Assay", "schema_name": "PharmacokineticsAssayTemplate", "type": "file"}, + {"display_name": "Proteomics Assay", "schema_name": "ProteomicsAssayTemplate", "type": "file"}, + {"display_name": "Plate-Based Reporter Assay", "schema_name": "PlateBasedReporterAssayTemplate", "type": "file"}, + {"display_name": "Update Milestone Report", "schema_name": "UpdateMilestoneReport", "type": "file"}, + {"display_name": "Clinical Assay Template", "schema_name": "ClinicalAssayTemplate", "type": "file"}, + {"display_name": "Processed/Aligned Sequencing Reads", "schema_name": "ProcessedAlignedReadsTemplate", "type": "file"}, + {"display_name": "Processed Variant Calls", "schema_name": "ProcessedVariantCallsTemplate", "type": "file"}, + {"display_name": "Processed Expression Data", "schema_name": "ProcessedExpressionTemplate", "type": "file"}, + {"display_name": "FACS Template", "schema_name": "FlowCytometryTemplate", "type": "file"}, + {"display_name": "Light Scattering Assay", "schema_name": "LightScatteringAssayTemplate", "type": "file"}, + {"display_name": "Protocol Resource", "schema_name": "ProtocolTemplate", "type": "file"} + ], + "main_fileview" : "syn16858331", + "community" : "NF", + "schematic_service": "v1" +} From 399729d002bbfa771c1067cddfb8cbf26d73b4df Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Mon, 4 Dec 2023 14:45:55 -0700 Subject: [PATCH 4/8] Simplify test generate to use local templates config instead of remote config --- tests/generate/basic_templates.sh | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/tests/generate/basic_templates.sh b/tests/generate/basic_templates.sh index 517a6f0b..1176f650 100755 --- a/tests/generate/basic_templates.sh +++ b/tests/generate/basic_templates.sh @@ -1,8 +1,7 @@ #!/bin/bash # Test generate GoogleSheets templates -CONFIG=https://raw.githubusercontent.com/nf-osi/NF_data_curator/staging/www/config.json -TEST_CONFIG=config.json +TEST_CONFIG=../../dca-template-config.json CREDS=creds.json DATA_MODEL_PATH=../../NF.jsonld DATA_MODEL=NF.jsonld @@ -23,17 +22,10 @@ else exit 1 fi -# Setup config -if [ -f "$TEST_CONFIG" ]; then - echo "Local $TEST_CONFIG present, running test with this local config..." -else - echo "Getting $CONFIG to use as test config..." - wget $CONFIG -O $TEST_CONFIG -fi TEMPLATES=($(jq '.manifest_schemas[] | .schema_name' $TEST_CONFIG | tr -d '"')) #TITLES=($(jq '.manifest_schemas[] | .display_name' $TEST_CONFIG | tr -d '"')) -echo "✓ Retrieved config with ${#TEMPLATES[@]} templates..." +echo "✓ Using config with ${#TEMPLATES[@]} templates..." # Setup data model cp $DATA_MODEL_PATH $DATA_MODEL From 02290ec6f051ef5690000f31e586b0a58edc8834 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Mon, 4 Dec 2023 21:48:30 +0000 Subject: [PATCH 5/8] Build jsonld --- NF.jsonld | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/NF.jsonld b/NF.jsonld index 473ebcaa..c23f89cb 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -1544,6 +1544,8 @@ "@id" : "bts:NEBNextmRNALibraryPrepReagentSetforIllumina" }, { "@id" : "bts:Omni-ATAC" + }, { + "@id" : "bts:QuantSeqFWDV2withUDI" }, { "@id" : "bts:Smart-seq2" }, { @@ -5876,6 +5878,8 @@ "@id" : "bts:comments" }, { "@id" : "bts:platform" + }, { + "@id" : "bts:assayTarget" }, { "@id" : "bts:auxiliaryAsset" } ], @@ -7287,6 +7291,8 @@ "@id" : "bts:comments" }, { "@id" : "bts:platform" + }, { + "@id" : "bts:assayTarget" }, { "@id" : "bts:auxiliaryAsset" }, { @@ -7362,6 +7368,8 @@ "@id" : "bts:comments" }, { "@id" : "bts:platform" + }, { + "@id" : "bts:assayTarget" }, { "@id" : "bts:auxiliaryAsset" }, { @@ -7606,6 +7614,8 @@ "@id" : "bts:comments" }, { "@id" : "bts:platform" + }, { + "@id" : "bts:assayTarget" }, { "@id" : "bts:auxiliaryAsset" }, { @@ -20161,6 +20171,17 @@ }, "sms:displayName" : "10", "sms:required" : "sms:false" + }, { + "@id" : "bts:QuantSeqFWDV2withUDI", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "QuantSeqFWDV2withUDI", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "QuantSeq FWD V2 with UDI", + "sms:required" : "sms:false" }, { "@id" : "bts:B6.129(Cg)-Nf1tm1Par/J", "@type" : "rdfs:Class", From 61800d89b21de18aaf29d8bb09b7930da519387a Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Tue, 5 Dec 2023 09:39:29 -0700 Subject: [PATCH 6/8] Change a minority of refs back to source --- modules/Assay/Parameter.yaml | 24 +++++++++++------------- 1 file changed, 11 insertions(+), 13 deletions(-) diff --git a/modules/Assay/Parameter.yaml b/modules/Assay/Parameter.yaml index 65da4e25..fcf2ce91 100644 --- a/modules/Assay/Parameter.yaml +++ b/modules/Assay/Parameter.yaml @@ -3,33 +3,33 @@ enums: permissible_values: Cy3: description: Fluorescent dye used for the green channel on an array - source: http://purl.obolibrary.org/obo/FBbi_00000449 + meaning: http://purl.obolibrary.org/obo/FBbi_00000449 Cy5: description: Fluorescent dye used for the red channel on an array - source: http://purl.obolibrary.org/obo/FBbi_00000450 + meaning: http://purl.obolibrary.org/obo/FBbi_00000450 GenePerturbationEnum: permissible_values: knockdown: description: Gene knockdown refers to techniques by which the expression of one or more of an organism's genes is reduced, either through genetic modification (a change in the DNA of one of the organism's chromosomes) or by treatment with a reagent such as a short DNA or RNA oligonucleotide with a sequence complementary to either an mRNA transcript or a gene. - source: http://www.bioassayontology.org/bao#BAO_0002433 + meaning: http://www.bioassayontology.org/bao#BAO_0002433 knockout: description: A gene knockout is a genetic technique in which an organism is engineered to carry genes that have been made inoperative (have been 'knocked out' of the organism). - source: http://www.bioassayontology.org/bao#BAO_0002441 + meaning: http://www.bioassayontology.org/bao#BAO_0002441 non-targeting control: description: Use of a guide RNA that is designed to not target any gene in particular, used as a control for a targeting gRNA overexpression: description: Gene overexpression refers to genetic techniques in which an organism or cell line is engineered to express increased levels of a gene. - source: http://www.bioassayontology.org/bao#BAO_0002442 + meaning: http://www.bioassayontology.org/bao#BAO_0002442 GenePerturbationTechnologyEnum: permissible_values: CRE Recombinase: description: CRE Recombinase catalyses site-specific recombination between two 34 base pair loxp sites and maintains the phage genome as a monomeric unit-copy plasmid in the lysogenic state. - source: http://purl.obolibrary.org/obo/NCIT_C17285 + meaning: http://purl.obolibrary.org/obo/NCIT_C17285 CRISPR: description: '' RNAi: description: High throughput sample analysis of RNAi molecules for potential application in gene knockdown or gene silencing of target genes - source: http://purl.obolibrary.org/obo/ERO_0001688 + meaning: http://purl.obolibrary.org/obo/ERO_0001688 GenomicReferenceEnum: permissible_values: GRCh38: @@ -138,16 +138,16 @@ enums: permissible_values: cell lysate: description: A material entity which is output of a cell lysis process - source: http://purl.obolibrary.org/obo/OBI_1000036 + meaning: http://purl.obolibrary.org/obo/OBI_1000036 cytoplasm: description: That portion of the cell contained within the plasma membrane but excluding the nucleus. - source: http://purl.obolibrary.org/obo/NCIT_C13226 + meaning: http://purl.obolibrary.org/obo/NCIT_C13226 mitochondria: description: Mitochondria only source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json nuclear extract: description: Nuclear extracts contain proteins in nuclear compartment of the cell - source: http://purl.obolibrary.org/obo/NCIT_C19832 + meaning: http://purl.obolibrary.org/obo/NCIT_C19832 ReadPairOrientationEnum: permissible_values: fr-firststrand: @@ -162,15 +162,13 @@ enums: permissible_values: forward: description: Read 1 (or unpaired read) comes from the forward strand and read 2 (if applicable) comes from the reverse strand - source: 'FALSE' reverse: description: read 1 (or unpaired read) comes from the reverse strand and read 2 (if applicable) comes from the forward strand - source: 'FALSE' RunTypeEnum: permissible_values: pairedEnd: description: A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. - source: http://purl.obolibrary.org/obo/OBI_0001852 + meaning: http://purl.obolibrary.org/obo/OBI_0001852 singleEnd: description: A library preparation that results in the creation of a library of 5' ends of DNA. source: Sage Bionetworks From 4b8b43b45c5db85ce2e6142a82ed8f52742f82b3 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Tue, 5 Dec 2023 09:40:55 -0700 Subject: [PATCH 7/8] Update assayTarget def --- modules/props.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/props.yaml b/modules/props.yaml index 9a0189fc..d1637f20 100644 --- a/modules/props.yaml +++ b/modules/props.yaml @@ -38,7 +38,7 @@ slots: range: AssayEnum required: true assayTarget: - description: The HUGO gene symbol that represents the target assayed. + description: Target of the assay such as a HUGO gene symbol, cell type, or tissue region depending on the capabilities of the assay. required: false author: description: The author of the resource; preferably use an ORCID ID, GitHub profile link, etc., if available and a text name if not. From ee34dfb0b7175ca8b728d3508679ffe842fa96c3 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Tue, 5 Dec 2023 16:41:16 +0000 Subject: [PATCH 8/8] Build jsonld --- NF.jsonld | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NF.jsonld b/NF.jsonld index c23f89cb..94cf1ddc 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -1689,7 +1689,7 @@ }, { "@id" : "bts:assayTarget", "@type" : "rdfs:Class", - "rdfs:comment" : "The HUGO gene symbol that represents the target assayed.", + "rdfs:comment" : "Target of the assay such as a HUGO gene symbol, cell type, or tissue region depending on the capabilities of the assay.", "rdfs:label" : "assayTarget", "rdfs:subClassOf" : [ ], "schema:isPartOf" : {