From 1f5cd93c2d7acb79f16b9db699cf68cd5fb0026c Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 30 Nov 2023 15:07:17 -0600 Subject: [PATCH 01/24] Update and rename Tissue.yaml to SpecimenType.yaml --- modules/Sample/{Tissue.yaml => SpecimenType.yaml} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename modules/Sample/{Tissue.yaml => SpecimenType.yaml} (99%) diff --git a/modules/Sample/Tissue.yaml b/modules/Sample/SpecimenType.yaml similarity index 99% rename from modules/Sample/Tissue.yaml rename to modules/Sample/SpecimenType.yaml index b4e398bc..fad1d825 100644 --- a/modules/Sample/Tissue.yaml +++ b/modules/Sample/SpecimenType.yaml @@ -1,5 +1,5 @@ enums: - TissueEnum: + SpecimenTypeEnum: permissible_values: cerebral cortex: description: The outer layer of the cerebrum composed of neurons and unmyelinated nerve fibers. It is responsible for memory, attention, consciousness and other higher levels of mental function. From 1b055a21526b37705b844c5892766a101a9aa790 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 30 Nov 2023 15:09:06 -0600 Subject: [PATCH 02/24] change tissue to specimentype --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 3ec876fa..ea14354a 100644 --- a/README.md +++ b/README.md @@ -69,9 +69,9 @@ All slots are in the file `modules/props.yaml`. ``` slots: #...more above - tissue: + specimenType: description: Association with some tissue (a mereologically maximal collection of cells that together perform physiological function). - range: TissueEnum # Take a look at TissueEnum below + range: SpecimenTypeEnum # Take a look at SpecimenTypeEnum below required: false title: description: Title of a resource. @@ -91,11 +91,11 @@ Note: In situations where "the data meets the template", issues with a required An enumeration is a set of controlled values. Enums are most of the files `modules`, everything except for what's in `Templates` and `props.yaml`. -##### Example: Tissue enumeration +##### Example: SpecimenType enumeration ``` enums: - TissueEnum: + SpecimenTypeEnum: permissible_values: cerebral cortex: description: The outer layer of the cerebrum composed of neurons and unmyelinated nerve fibers. It is responsible for memory, attention, consciousness and other higher levels of mental function. From d6704a3723704709a59b7dab13d7403f26afdd54 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 30 Nov 2023 15:10:38 -0600 Subject: [PATCH 03/24] tissue -> specimentype --- docs/index.Rmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/index.Rmd b/docs/index.Rmd index fde7d4c5..ec489fe7 100644 --- a/docs/index.Rmd +++ b/docs/index.Rmd @@ -431,14 +431,14 @@ module_section("Data", "FileFormat", "FileFormatEnum") Sample typically refers to a **biosample**, but on some rare occasions can refer to an inorganic sample from which data are generated. For biosamples, there is a distinction between individual-level and specimen-level data. Data can be linked to individual-level sample information such as sex, species, diagnosis, and genotype. -Data can be linked to specimen-level information such as sample site (the organ or body part), specimen tissue or cell type, tumor class (if specimen is a tumor), and specimen state. +Data can be linked to specimen-level information such as sample site (the organ or body part), specimen type or cell type, tumor class (if specimen is a tumor), and specimen state. ::: -```{r sample_tissue, echo=FALSE, results='asis'} +```{r sample_specimenType, echo=FALSE, results='asis'} -module_section("Sample", "Tissue", "TissueEnum") +module_section("Sample", "SpecimenType", "SpecimenTypeEnum") ``` From fe327542f92c35b945a945cda6f42c2c049722d8 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 30 Nov 2023 15:12:19 -0600 Subject: [PATCH 04/24] tissue -> specimentype --- ext_classes.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ext_classes.csv b/ext_classes.csv index bddab73c..b9b1178e 100644 --- a/ext_classes.csv +++ b/ext_classes.csv @@ -28,5 +28,5 @@ Methods,Methods,Class,Class, NGS_Parameter,NGS_Parameter,Class,Class,Methods Unit,Unit,Class,Class, Time_Unit ,Time_Unit ,Class,Class,Unit -Tissue,Tissue,Class,Class, +SpecimenType,SpecimenType,Class,Class, Data,Data,Class,Class, From 90fe7249e8bf9e9da6cb85823c55699c1d7965b1 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 30 Nov 2023 15:15:24 -0600 Subject: [PATCH 05/24] Update props.yaml --- modules/props.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/props.yaml b/modules/props.yaml index 173236eb..b83b96dd 100644 --- a/modules/props.yaml +++ b/modules/props.yaml @@ -670,9 +670,9 @@ slots: description: For timed experiments this represents the unit of time measured range: TimeUnit required: false - tissue: + specimenType: description: A tissue is a mereologically maximal collection of cells that together perform physiological function. - range: TissueEnum + range: SpecimenTypeEnum required: false title: description: Title of a resource. From 3ff2d122e210cb81c1e16640e13e23625abecdcc Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 30 Nov 2023 15:17:25 -0600 Subject: [PATCH 06/24] Update props.yaml --- modules/props.yaml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/modules/props.yaml b/modules/props.yaml index b83b96dd..6e5575fd 100644 --- a/modules/props.yaml +++ b/modules/props.yaml @@ -65,7 +65,7 @@ slots: required: false bodySite: comments: - - Helpful to consider where tissue/cell samples came from, e.g. something like "schwannoma" gets put in `tumorType`, but `bodySite` gives us the original location of the tumor. + - Helpful to consider where /cell samples came from, e.g. something like "schwannoma" gets put in `tumorType`, but `bodySite` gives us the original location of the tumor. description: Sample location referring to a named area of the body, inclusive of gross anatomical structures and organ parts. range: BodyPartEnum required: false @@ -671,7 +671,8 @@ slots: range: TimeUnit required: false specimenType: - description: A tissue is a mereologically maximal collection of cells that together perform physiological function. + description: > + The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances. range: SpecimenTypeEnum required: false title: @@ -684,14 +685,14 @@ slots: validationRules: int required: false transplantationRecipientSpecies: - description: Species into which donor tissue was grown + description: Species into which donor was grown enum_range: - Human - Mouse required: false - transplantationRecipientTissue: - description: Tissue into which a xenograph sample is transplanted - range: Tissue + transplantationRecipient: + description: into which a xenograph sample is transplanted + range: required: false transplantationType: description: Type of transplantation involved in the experiment, derived from MESH From b5bdac0b07bc84ac5bafbe95865b1367a43834e7 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 30 Nov 2023 15:18:31 -0600 Subject: [PATCH 07/24] Update Data.yaml --- modules/Template/Data.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/Template/Data.yaml b/modules/Template/Data.yaml index 023b0243..3165f534 100644 --- a/modules/Template/Data.yaml +++ b/modules/Template/Data.yaml @@ -79,7 +79,7 @@ classes: is_a: GeneticsAssayTemplate description: General template for raw (level 1) RNA/DNA data, i.e. sequence data from a sequencing assay. slots: - - tissue + - specimenType - runType - libraryStrand - libraryPrep From e13cc14701343ff4c52c7304f54e5045c3dccc6c Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 30 Nov 2023 15:19:18 -0600 Subject: [PATCH 08/24] Update GenomicsAssayTemplate_1.csv --- tests/validate/GenomicsAssayTemplate_1.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/validate/GenomicsAssayTemplate_1.csv b/tests/validate/GenomicsAssayTemplate_1.csv index dc6e5677..0dd5b3c3 100644 --- a/tests/validate/GenomicsAssayTemplate_1.csv +++ b/tests/validate/GenomicsAssayTemplate_1.csv @@ -1,4 +1,4 @@ -Component,Filename,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,species,sex,age,ageUnit,diagnosis,nf1Genotype,nf2Genotype,modelSystemName,parentSpecimenID,specimenID,aliquotID,tumorType,platform,nucleicAcidSource,specimenPreparationMethod,tissue,runType,libraryStrand,libraryPrep,libraryPreparationMethod,readPair,readLength,readDepth,targetDepth,batchID +Component,Filename,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,species,sex,age,ageUnit,diagnosis,nf1Genotype,nf2Genotype,modelSystemName,parentSpecimenID,specimenID,aliquotID,tumorType,platform,nucleicAcidSource,specimenPreparationMethod,specimenType,runType,libraryStrand,libraryPrep,libraryPreparationMethod,readPair,readLength,readDepth,targetDepth,batchID GenomicsAssayTemplate,a,fastq,experimentalData,geneExpression,raw,RNA-seq,A,Homo sapiens,,,,,,,,,A1,,Malignant Peripheral Nerve Sheath Tumor,Illumina NovaSeq 6000,,RNAlater,,pairedEnd,FirstStranded,,TruSeq standard total RNA library kit,,,,, GenomicsAssayTemplate,b,fastq,experimentalData,geneExpression,raw,RNA-seq,B,Homo sapiens,,,,,,,,,B2,,Malignant Peripheral Nerve Sheath Tumor,Illumina NovaSeq 6000,,RNAlater,,pairedEnd,FirstStranded,,TruSeq standard total RNA library kit,,,,, GenomicsAssayTemplate,c1,fastq,experimentalData,geneExpression,raw,RNA-seq,C,Homo sapiens,,,,,,,NCC-MPNST1-C1,,C1,,Malignant Peripheral Nerve Sheath Tumor,Illumina NovaSeq 6000,,RNAlater,,pairedEnd,FirstStranded,,TruSeq standard total RNA library kit,,,,, From 1e74af18f888cabef3babe0238b478ed06079666 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 30 Nov 2023 15:19:42 -0600 Subject: [PATCH 09/24] Update GenomicsAssayTemplate_0.csv --- tests/validate/GenomicsAssayTemplate_0.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/validate/GenomicsAssayTemplate_0.csv b/tests/validate/GenomicsAssayTemplate_0.csv index 558b9c59..2fa15a7d 100644 --- a/tests/validate/GenomicsAssayTemplate_0.csv +++ b/tests/validate/GenomicsAssayTemplate_0.csv @@ -1,4 +1,4 @@ -Component,Filename,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,species,sex,age,ageUnit,diagnosis,nf1Genotype,nf2Genotype,modelSystemName,parentSpecimenID,specimenID,aliquotID,tumorType,platform,nucleicAcidSource,specimenPreparationMethod,tissue,runType,libraryStrand,libraryPrep,libraryPreparationMethod,readPair,readLength,readDepth,targetDepth,batchID +Component,Filename,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,species,sex,age,ageUnit,diagnosis,nf1Genotype,nf2Genotype,modelSystemName,parentSpecimenID,specimenID,aliquotID,tumorType,platform,nucleicAcidSource,specimenPreparationMethod,specimenType,runType,libraryStrand,libraryPrep,libraryPreparationMethod,readPair,readLength,readDepth,targetDepth,batchID GenomicsAssayTemplate,a,fastq,experimentalData,geneExpression,raw,RNA-seq,A,Homo sapiens,,,,,,,,,A1,,Not Applicable,Illumina NovaSeq 6000,,RNAlater,,pairedEnd,FirstStranded,,TruSeq standard total RNA library kit,,,,, GenomicsAssayTemplate,b,fastq,experimentalData,geneExpression,raw,RNA-seq,B,Homo sapiens,,,,,,,,,B2,,Not Applicable,Illumina NovaSeq 6000,,RNAlater,,pairedEnd,FirstStranded,,TruSeq standard total RNA library kit,,,,, GenomicsAssayTemplate,c,fastq,experimentalData,geneExpression,raw,RNA-seq,C,Homo sapiens,,,,,,,,,C3,,Not Applicable,Illumina NovaSeq 6000,,RNAlater,,pairedEnd,FirstStranded,,TruSeq standard total RNA library kit,,,,, From d40b0fc566fcaaba9064b4c438e0890bbce76643 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 30 Nov 2023 15:20:17 -0600 Subject: [PATCH 10/24] Update settings.json --- .vscode/settings.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index d7404041..a022f31b 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -6,7 +6,7 @@ "modules/Experiment/Method.yaml", "modules/Experiment/Unit.yaml", "modules/Sample/BodyPart.yaml", "modules/Sample/Genotype.yaml", "modules/Sample/Sex.yaml", "Tmodules/Sample/Tumor.yaml", "modules/Sample/CellLineModel.yaml", "modules/Sample/Material.yaml", "modules/Sample/Species.yaml", "modules/Sample/Cell.yaml", "modules/Sample/MouseModel.yaml", "modules/Sample/SpecimenProcessing.yaml", - "modules/Sample/Diagnosis.yaml", "modules/Sample/Tissue.yaml"], + "modules/Sample/Diagnosis.yaml", "modules/Sample/SpecimenType.yaml"], "./utils/schematic-flavored-linkml-slot.json": ["modules/*/props.yaml"] } } From 6a670553c53c3b58487e76cdfd83e0ffeb00f83f Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 30 Nov 2023 15:20:38 -0600 Subject: [PATCH 11/24] Update GenomicsAssayTemplate_2.csv --- tests/validate/GenomicsAssayTemplate_2.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/validate/GenomicsAssayTemplate_2.csv b/tests/validate/GenomicsAssayTemplate_2.csv index 09339b4f..7adf278b 100644 --- a/tests/validate/GenomicsAssayTemplate_2.csv +++ b/tests/validate/GenomicsAssayTemplate_2.csv @@ -1,4 +1,4 @@ -Component,Filename,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,species,sex,age,ageUnit,diagnosis,nf1Genotype,nf2Genotype,modelSystemName,parentSpecimenID,specimenID,aliquotID,tumorType,platform,nucleicAcidSource,specimenPreparationMethod,tissue,runType,libraryStrand,libraryPrep,libraryPreparationMethod,readPair,readLength,readDepth,targetDepth,batchID +Component,Filename,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,species,sex,age,ageUnit,diagnosis,nf1Genotype,nf2Genotype,modelSystemName,parentSpecimenID,specimenID,aliquotID,tumorType,platform,nucleicAcidSource,specimenPreparationMethod,specimenType,runType,libraryStrand,libraryPrep,libraryPreparationMethod,readPair,readLength,readDepth,targetDepth,batchID GenomicsAssayTemplate,a,fastq,experimentalData,geneExpression,raw,RNA-seq,A,Homo sapiens,,21,years,,,,,,A1,,Not Applicable,Illumina NovaSeq 6000,,RNAlater,,pairedEnd,FirstStranded,,TruSeq standard total RNA library kit,,,,, GenomicsAssayTemplate,b,fastq,experimentalData,geneExpression,raw,RNA-seq,B,Homo sapiens,,22,years,,,,,,B2,,Not Applicable,Illumina NovaSeq 6000,,RNAlater,,pairedEnd,FirstStranded,,TruSeq standard total RNA library kit,,,,, GenomicsAssayTemplate,c,fastq,experimentalData,geneExpression,raw,RNA-seq,C,Homo sapiens,,23,,,,,,,C3,,Not Applicable,Illumina NovaSeq 6000,,RNAlater,,pairedEnd,FirstStranded,,TruSeq standard total RNA library kit,,,,, From 3cded16d017997ed1f91b87f7c25403bc7b9d619 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 30 Nov 2023 21:22:41 +0000 Subject: [PATCH 12/24] Build jsonld --- NF.jsonld | 171 +++++++++++++++++++++++++++--------------------------- 1 file changed, 85 insertions(+), 86 deletions(-) diff --git a/NF.jsonld b/NF.jsonld index 151a3d6d..36e790e6 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -515,37 +515,37 @@ "sms:displayName" : "CuratedDataEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:TissueEnum", + "@id" : "bts:Institution", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "TissueEnum", + "rdfs:label" : "Institution", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TissueEnum", + "sms:displayName" : "Institution", "sms:required" : "sms:false" }, { - "@id" : "bts:Institution", + "@id" : "bts:ReadStrandOriginEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "Institution", + "rdfs:label" : "ReadStrandOriginEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Institution", + "sms:displayName" : "ReadStrandOriginEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:ReadStrandOriginEnum", + "@id" : "bts:SpecimenTypeEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "ReadStrandOriginEnum", + "rdfs:label" : "SpecimenTypeEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ReadStrandOriginEnum", + "sms:displayName" : "SpecimenTypeEnum", "sms:required" : "sms:false" }, { "@id" : "bts:GenePerturbationTechnologyEnum", @@ -1940,68 +1940,6 @@ "rdfs:comment" : "One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.\n", "@type" : "rdfs:Class", "sms:displayName" : "captureArea" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:tissue", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:cerebralcortex" - }, { - "@id" : "bts:bonemarrow" - }, { - "@id" : "bts:plasma" - }, { - "@id" : "bts:DorsalRootGanglion" - }, { - "@id" : "bts:opticnerve" - }, { - "@id" : "bts:tumor-adjacentnormal" - }, { - "@id" : "bts:serum" - }, { - "@id" : "bts:spheroid" - }, { - "@id" : "bts:sciaticnerve" - }, { - "@id" : "bts:meninges" - }, { - "@id" : "bts:nervetissue" - }, { - "@id" : "bts:BuccalMucosa" - }, { - "@id" : "bts:embryonictissue" - }, { - "@id" : "bts:wholebrain" - }, { - "@id" : "bts:microtissue" - }, { - "@id" : "bts:retina" - }, { - "@id" : "bts:CDXtissue" - }, { - "@id" : "bts:organoid" - }, { - "@id" : "bts:splenocyte" - }, { - "@id" : "bts:blood" - }, { - "@id" : "bts:connectivetissue" - }, { - "@id" : "bts:primarytumor" - }, { - "@id" : "bts:PDXtissue" - }, { - "@id" : "bts:BuffyCoat" - }, { - "@id" : "bts:normal" - } ], - "rdfs:label" : "tissue", - "rdfs:comment" : "A tissue is a mereologically maximal collection of cells that together perform physiological function.", - "@type" : "rdfs:Class", - "sms:displayName" : "tissue" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:experimentalFactor", @@ -2565,6 +2503,17 @@ }, "sms:displayName" : "fundingAgency", "sms:required" : "sms:false" + }, { + "@id" : "bts:transplantationRecipient", + "@type" : "rdfs:Class", + "rdfs:comment" : "into which a xenograph sample is transplanted", + "rdfs:label" : "transplantationRecipient", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "transplantationRecipient", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:nucleicAcidSource", @@ -3086,16 +3035,66 @@ "sms:displayName" : "concentrationNaClUnit" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:transplantationRecipientTissue", + "@id" : "bts:specimenType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "transplantationRecipientTissue", - "rdfs:comment" : "Tissue into which a xenograph sample is transplanted", + "schema:rangeIncludes" : [ { + "@id" : "bts:cerebralcortex" + }, { + "@id" : "bts:bonemarrow" + }, { + "@id" : "bts:plasma" + }, { + "@id" : "bts:DorsalRootGanglion" + }, { + "@id" : "bts:opticnerve" + }, { + "@id" : "bts:tumor-adjacentnormal" + }, { + "@id" : "bts:serum" + }, { + "@id" : "bts:spheroid" + }, { + "@id" : "bts:sciaticnerve" + }, { + "@id" : "bts:meninges" + }, { + "@id" : "bts:nervetissue" + }, { + "@id" : "bts:BuccalMucosa" + }, { + "@id" : "bts:embryonictissue" + }, { + "@id" : "bts:wholebrain" + }, { + "@id" : "bts:microtissue" + }, { + "@id" : "bts:retina" + }, { + "@id" : "bts:CDXtissue" + }, { + "@id" : "bts:organoid" + }, { + "@id" : "bts:splenocyte" + }, { + "@id" : "bts:blood" + }, { + "@id" : "bts:connectivetissue" + }, { + "@id" : "bts:primarytumor" + }, { + "@id" : "bts:PDXtissue" + }, { + "@id" : "bts:BuffyCoat" + }, { + "@id" : "bts:normal" + } ], + "rdfs:label" : "specimenType", + "rdfs:comment" : "The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances.\n", "@type" : "rdfs:Class", - "sms:displayName" : "transplantationRecipientTissue" + "sms:displayName" : "specimenType" }, { "@id" : "bts:datasetItemCount", "@type" : "rdfs:Class", @@ -4233,7 +4232,7 @@ "@id" : "bts:Mouse" } ], "rdfs:label" : "transplantationRecipientSpecies", - "rdfs:comment" : "Species into which donor tissue was grown", + "rdfs:comment" : "Species into which donor was grown", "@type" : "rdfs:Class", "sms:displayName" : "transplantationRecipientSpecies" }, { @@ -5703,7 +5702,7 @@ }, { "@id" : "bts:specimenPreparationMethod" }, { - "@id" : "bts:tissue" + "@id" : "bts:specimenType" }, { "@id" : "bts:runType" }, { @@ -5871,7 +5870,7 @@ }, { "@id" : "bts:specimenPreparationMethod" }, { - "@id" : "bts:tissue" + "@id" : "bts:specimenType" }, { "@id" : "bts:runType" }, { @@ -6033,7 +6032,7 @@ }, { "@id" : "bts:specimenPreparationMethod" }, { - "@id" : "bts:tissue" + "@id" : "bts:specimenType" }, { "@id" : "bts:runType" }, { @@ -6318,7 +6317,7 @@ }, { "@id" : "bts:specimenPreparationMethod" }, { - "@id" : "bts:tissue" + "@id" : "bts:specimenType" }, { "@id" : "bts:runType" }, { @@ -6596,7 +6595,7 @@ }, { "@id" : "bts:specimenPreparationMethod" }, { - "@id" : "bts:tissue" + "@id" : "bts:specimenType" }, { "@id" : "bts:runType" }, { @@ -6799,7 +6798,7 @@ }, { "@id" : "bts:specimenPreparationMethod" }, { - "@id" : "bts:tissue" + "@id" : "bts:specimenType" }, { "@id" : "bts:runType" }, { @@ -7071,7 +7070,7 @@ }, { "@id" : "bts:specimenPreparationMethod" }, { - "@id" : "bts:tissue" + "@id" : "bts:specimenType" }, { "@id" : "bts:runType" }, { @@ -7611,7 +7610,7 @@ }, { "@id" : "bts:specimenPreparationMethod" }, { - "@id" : "bts:tissue" + "@id" : "bts:specimenType" }, { "@id" : "bts:runType" }, { @@ -7727,7 +7726,7 @@ }, { "@id" : "bts:specimenPreparationMethod" }, { - "@id" : "bts:tissue" + "@id" : "bts:specimenType" }, { "@id" : "bts:runType" }, { From 551f5270172bc4e52a98895000cc1eed2f0c6fcd Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 30 Nov 2023 15:25:27 -0600 Subject: [PATCH 13/24] add saliva, remove 'normal' --- modules/Sample/SpecimenType.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/Sample/SpecimenType.yaml b/modules/Sample/SpecimenType.yaml index fad1d825..9a454c7c 100644 --- a/modules/Sample/SpecimenType.yaml +++ b/modules/Sample/SpecimenType.yaml @@ -71,6 +71,6 @@ enums: Buffy Coat: description: The middle layer of an anticoagulated blood specimen following separation by centrifugation. It contains most of the white blood cells and platelets. meaning: http://purl.obolibrary.org/obo/NCIT_C84507 - normal: - description: No pathological entity observable. - meaning: http://purl.obolibrary.org/obo/MPATH_458 + saliva: + description: The watery fluid in the mouth made by the salivary glands. Saliva moistens food to help digestion and it helps protect the mouth against infections. + meaning: http://purl.obolibrary.org/obo/NCIT_C13275 From 71d78b382e42efbfdfc1c58c715c08930b4dac8a Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 30 Nov 2023 21:25:39 +0000 Subject: [PATCH 14/24] Build jsonld --- NF.jsonld | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/NF.jsonld b/NF.jsonld index 36e790e6..4d4445cd 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -3089,7 +3089,7 @@ }, { "@id" : "bts:BuffyCoat" }, { - "@id" : "bts:normal" + "@id" : "bts:saliva" } ], "rdfs:label" : "specimenType", "rdfs:comment" : "The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances.\n", @@ -13058,17 +13058,6 @@ }, "sms:displayName" : "calcium retention capacity assay", "sms:required" : "sms:false" - }, { - "@id" : "bts:normal", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "normal", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "normal", - "sms:required" : "sms:false" }, { "@id" : "bts:HS-PSS", "@type" : "rdfs:Class", @@ -15115,6 +15104,17 @@ }, "sms:displayName" : "SZ-NF4", "sms:required" : "sms:false" + }, { + "@id" : "bts:saliva", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "saliva", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "saliva", + "sms:required" : "sms:false" }, { "@id" : "bts:sorbitoldehydrogenaseactivitylevelassay", "@type" : "rdfs:Class", From 021b2177005b25972a1c86b3480c56f4d746ea24 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 30 Nov 2023 15:37:59 -0600 Subject: [PATCH 15/24] Update Parameter.yaml --- modules/Assay/Parameter.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/modules/Assay/Parameter.yaml b/modules/Assay/Parameter.yaml index f86d960d..1d3d1fe3 100644 --- a/modules/Assay/Parameter.yaml +++ b/modules/Assay/Parameter.yaml @@ -102,6 +102,8 @@ enums: 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 + unknown: + description: information not provided MRISequenceEnum: permissible_values: PD-weighted: From 2914d8fb4f0466761b4916cff4a0865f02afe356 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 30 Nov 2023 21:38:14 +0000 Subject: [PATCH 16/24] Build jsonld --- NF.jsonld | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/NF.jsonld b/NF.jsonld index 4d4445cd..8d5c2bf2 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -1541,6 +1541,8 @@ "@id" : "bts:TruSeq" }, { "@id" : "bts:TruSeqstandardtotalRNAlibrarykit" + }, { + "@id" : "bts:unknown" } ], "rdfs:label" : "libraryPreparationMethod", "rdfs:comment" : "Method by which library was prepared", @@ -16831,6 +16833,17 @@ }, "sms:displayName" : "American University", "sms:required" : "sms:false" + }, { + "@id" : "bts:unknown", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "unknown", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "unknown", + "sms:required" : "sms:false" }, { "@id" : "bts:positronemissiontomography", "@type" : "rdfs:Class", From 73a8cde5a3a12414d15121a38682a85b170a0919 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 30 Nov 2023 15:54:25 -0600 Subject: [PATCH 17/24] Update Platform.yaml --- modules/Assay/Platform.yaml | 87 ++++++++++++++++++++----------------- 1 file changed, 46 insertions(+), 41 deletions(-) diff --git a/modules/Assay/Platform.yaml b/modules/Assay/Platform.yaml index 35e98c46..99217440 100644 --- a/modules/Assay/Platform.yaml +++ b/modules/Assay/Platform.yaml @@ -3,7 +3,7 @@ enums: permissible_values: Zeiss LSM 980: description: A Zeiss Confocal Microscope - meaning: https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwirj4XuwtXsAhVBrp4KHVZyARIQFjABegQIAhAC&url=https%3A%2F%2Fzeiss.ly%2Flsm980-info&usg=AOvVaw0rD50U0aMwfvt4bdfW0Yjd + source: https://pages.zeiss.com/rs/896-XMS-794/images/ZEISS-Microscopy_Product-Brochure_ZEISS-LSM-980.pdf Illumina NovaSeq 6000: description: A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. meaning: http://purl.obolibrary.org/obo/OBI_0002630 @@ -11,53 +11,53 @@ enums: description: '' Affymetrix Genome-Wide Human SNP 5.0 Array: description: Affymetrix Genome-Wide Human SNP 5.0 Array - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6804 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6804 Illumina HumanMethylation450: description: Illumina HumanMethylation450 BeadChip - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13534 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13534 Illumina HumanOmni1-Quadv1.0: description: '' - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL24663 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL24663 Vectra H1 3D Imaging System: description: (From vendor) Handheld imaging system for clinical-quality 3D imaging; applications for facial aesthetics and clinical documention. - meaning: https://www.canfieldsci.com/imaging-systems/vectra-h1-3d-imaging-system/ + source: https://www.canfieldsci.com/imaging-systems/vectra-h1-3d-imaging-system/ Illumina NextSeq 1000: description: Illumina NextSeq 1000 Illumina HiSeq X: description: Illumina HiSeq X Platform for whole-genome sequencing - meaning: https://www.illumina.com/systems/sequencing-platforms/hiseq-x.html + source: https://www.illumina.com/systems/sequencing-platforms/hiseq-x.html Chromium X: description: (From 10x Genomics) Single-cell platform that can analyze hundreds to hundreds of thousands of cells in single run for e.g. gene expression, chromatin accessibility, cell surface proteins, immune clonotype, antigen specificity, CRISPR perturbation screens). - meaning: https://www.10xgenomics.com/chromium-x + source: https://www.10xgenomics.com/chromium-x Orbitrap Fusion Lumos Tribrid: description: Thermo Scientific Orbitrap Fusion Lumos Tribrid Mass Spectrometer - meaning: https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-systems/orbitrap-lc-ms/orbitrap-tribrid-mass-spectrometers/orbitrap-fusion-lumos-mass-spectrometer.html + source: https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-systems/orbitrap-lc-ms/orbitrap-tribrid-mass-spectrometers/orbitrap-fusion-lumos-mass-spectrometer.html Illumina HiSeq 4000: description: Illumina HiSeq 4000 - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20301 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20301 EnVision 2103 Multiplate Reader: description: EnVision 2103 Multiplate Reader Affymetrix Human Gene 1.0 ST Array: description: Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] in situ oligonucleotide - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6244 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6244 Illumina MiSeq: description: Illumina MiSeq - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15520 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15520 Illumina WholeGenome DASL: description: Illumina Human Whole-Genome DASL HT - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13369 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13369 Illumina Genome Analyzer IIx: description: Illumina Genome Analyzer IIx - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16061 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16061 Illumina Infinium MethylationEPIC BeadChip v1.0 (850k): description: The version 1.0 Illumina beadchip array interrogates ~850,000 methylation sites per sample at single-nucleotide resolution. meaning: http://purl.obolibrary.org/obo/OBI_0002131 Illumina Human660W-Quad v1.0 BeadChip: description: '' - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL8888 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL8888 Spectramax M Series: description: A Spectramax M Series Microplate Reader - meaning: https://www.moleculardevices.com/products/microplate-readers/multi-mode-readers/spectramax-m-series-readers + source: https://www.moleculardevices.com/products/microplate-readers/multi-mode-readers/spectramax-m-series-readers Illumina NextSeq 2000: description: Illumina NextSeq 2000 Illumina 1M: @@ -67,31 +67,31 @@ enums: meaning: http://purl.obolibrary.org/obo/MS_10025223 Illumina NextSeq 550: description: Illumina NextSeq 550 - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21697 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21697 Affymetrix U133AB: description: '' Illumina HiSeq 3000: description: Illumina HiSeq 3000 - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21290 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21290 Illumina HiSeq 2500: description: Illumina HiSeq 2500 - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16791 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16791 Illumina MouseWG-6 v2.0 expression beadchip: description: Whole-genome expression profiling in the mouse - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6887 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6887 LTQ Orbitrap XL: description: LTQ Orbitrap XL Hybrid Ion Trap-Orbitrap Mass Spectrometer - meaning: https://www.thermofisher.com/order/catalog/product/IQLAAEGAAPFADBMAOK + source: https://www.thermofisher.com/order/catalog/product/IQLAAEGAAPFADBMAOK Illumina Infinium MethylationEPIC BeadChip v2.0 (935k): description: The version 2.0 Illumina beadchip array interrogates ~935,000 methylation sites per sample at single-nucleotide resolution. Illumina Omni5M: description: '' Affymetrix Genome-Wide Human SNP 6.0 Array: description: Affymetrix Genome-Wide Human SNP 6.0 Array - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6801 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6801 LifeViz Micro System: description: (From vendor) Portable 3D imaging system for skin microstructure analysis. - meaning: https://www.quantificare.com/3d-photography-systems_old/lifeviz-micro/ + source: https://www.quantificare.com/3d-photography-systems_old/lifeviz-micro/ 10x Visium Spatial Gene Expression: description: '10x Genomics product that includes special slides, reagents and technology to allow whole transcriptome profiling with morphological (spatial) context in FFPE or fresh-frozen tissues. Vendor ref: https://www.10xgenomics.com/products/spatial-gene-expression' meaning: http://www.ebi.ac.uk/efo/EFO_0010961 @@ -99,70 +99,70 @@ enums: description: NanostringGeoMx Illumina HumanHap300: description: '' - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6083 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6083 Vevo 3100 Imaging System: description: (From vendor) A micro-ultrasound imaging system for anatomical, hemodynamic, functional, and molecular data all in one platform. - meaning: https://www.visualsonics.com/product/imaging-systems/vevo-3100 + source: https://www.visualsonics.com/product/imaging-systems/vevo-3100 Illumina HumanOmniExpress-24 v1.0 BeadChip: description: '' - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21168 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21168 Illumina HiSeq 2000: description: Illumina HiSeq 2000 - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL11154 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL11154 PacBio Sequel IIe System: description: PacBio Sequel IIe System Illumina NextSeq 500: description: Illumina NextSeq 500 - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18573 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18573 Affymetrix Human Genome U133 Plus 2.0 Array: description: Affymetrix Human Genome U133 Plus 2.0 Array - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570 Perlegen 300Karray: description: '' Illumina HumanOmniExpress-24 v1.2 BeadChip: description: '' - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL31092 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL31092 Illumina Omni2pt5M: description: '' LI-COR Odyssey CLx: description: A LI-COR Odyssey CLx imaging system - meaning: https://www.licor.com/bio/odyssey-clx/ + source: https://www.licor.com/bio/odyssey-clx/ Cherry Imaging TRACE Platform: description: (From vendor) Full skin 3D imaging platform designed for research; uses a handheld scanner to capture thousands of images from multiple angles, which can be analyzed to create precise skin morphology model with a 100 micron accuracy to assess treatment results over time. - meaning: https://www.cherryimaging.com/home + source: https://www.cherryimaging.com/home Cherry Imaging FACE Platform: description: (From vendor) A micro-ultrasound imaging system for anatomical, hemodynamic, functional, and molecular data all in one platform. - meaning: https://www.cherryimaging.com/home + source: https://www.cherryimaging.com/home PacBio RS II: description: PacBio RS II - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21311 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21311 Infinium HumanOmniExpressExome: description: Infinium HumanOmniExpressExome BeadChip - meaning: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18224 + source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18224 LifeViz Infinity System: description: (From vendor) All-in-one 3D imaging system for face, body and breast. - meaning: https://www.quantificare.com/3d-photography-systems_old/lifeviz-infinity/ + source: https://www.quantificare.com/3d-photography-systems_old/lifeviz-infinity/ Olympus DP80: description: Dual-Sensor Monochrome and Color Camera - meaning: https://www.olympus-lifescience.com/en/camera/color/dp80/ + source: https://www.olympus-lifescience.com/en/camera/color/dp80/ Nanostring Counter: description: '' Illumina h650: description: '' BGISEQ-500: description: (From vendor) BGISEQ-500 is an industry leading high-throughput sequencing solution, powered by combinatorial Probe-Anchor Synthesis (cPAS) and improved DNA Nanoballs (DNB™) technology. - meaning: https://www.bgi.com/wp-content/uploads/sites/4/2017/05/GLOBAL_BGISEQ-500_WholeGenomeSeq_ServiceOverview_04-17.pdf + source: https://www.bgi.com/wp-content/uploads/sites/4/2017/05/GLOBAL_BGISEQ-500_WholeGenomeSeq_ServiceOverview_04-17.pdf PacBio Sequel II System: description: PacBio Sequel II System Promega GloMax Discover: description: (From vendor) Microplate reader with high-performance luminescence, fluorescence, UV-Visible absorbance, BRET and FRET, two-color filtered luminescence and kinetic measurement capabilities. - meaning: https://www.promega.com/products/microplate-readers-fluorometers-luminometers/microplate-readers/glomax-discover-system/?catNum=GM3000 + source: https://www.promega.com/products/microplate-readers-fluorometers-luminometers/microplate-readers/glomax-discover-system/?catNum=GM3000 Bionano Irys: description: Performs whole genome mapping in a nanoscale fluidic environment enabling the structure of the genome to be imaged and then analyzed at the single molecule level - meaning: https://bionanogenomics.com/products/irys/ + source: https://bionanogenomics.com/products/irys/ Leica Aperio AT2: description: (From vendor) The Aperio AT2 is the most compact, highest capacity, brightfield Digital Pathology scanner available. - meaning: https://www.leicabiosystems.com/sites/default/files/2020-10/Aperio_AT2_Brochure_USA.pdf + source: https://www.leicabiosystems.com/sites/default/files/2020-10/Aperio_AT2_Brochure_USA.pdf Leica S9 Stereomicroscope: description: '' Philips Achieva 3T: @@ -185,4 +185,9 @@ enums: meaning: http://snomed.info/id/44056008 TOOsonix System ONE-M: description: High intensity focused ultrasound (HIFU) technology which delivers highly accurate and non-invasive ultrasound energy to target areas within the human skin. - meaning: https://www.toosonix.com/ + source: https://www.toosonix.com/ + MGI T-series: + description: deep whole genome sequencing + source: https://en.mgi-tech.com/products/ + Not Applicable: + description: '' From 98fa3d524d449dcb60962bea0616f93b4b2c2470 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 30 Nov 2023 21:54:40 +0000 Subject: [PATCH 18/24] Build jsonld --- NF.jsonld | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/NF.jsonld b/NF.jsonld index 8d5c2bf2..a2a64a5d 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -5190,6 +5190,10 @@ "@id" : "bts:Caliper" }, { "@id" : "bts:TOOsonixSystemONE-M" + }, { + "@id" : "bts:MGIT-series" + }, { + "@id" : "bts:NotApplicable" } ], "rdfs:label" : "platform", "rdfs:comment" : "A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.", @@ -16459,6 +16463,17 @@ }, "sms:displayName" : "Texas Tech University of Health Sciences Center", "sms:required" : "sms:false" + }, { + "@id" : "bts:MGIT-series", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "MGIT-series", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "MGI T-series", + "sms:required" : "sms:false" }, { "@id" : "bts:InfiniumHumanOmniExpressExome", "@type" : "rdfs:Class", From eaf483c64ebec2c1620bddbe1cda05d77598bfa9 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu <32753274+anngvu@users.noreply.github.com> Date: Fri, 1 Dec 2023 14:40:00 -0700 Subject: [PATCH 19/24] Implement alternative strategy with better backwards compatibility (#373) --- modules/Sample/SpecimenType.yaml | 52 +++++++++++++++++++++----------- modules/props.yaml | 10 +++--- 2 files changed, 40 insertions(+), 22 deletions(-) diff --git a/modules/Sample/SpecimenType.yaml b/modules/Sample/SpecimenType.yaml index 9a454c7c..5eca4699 100644 --- a/modules/Sample/SpecimenType.yaml +++ b/modules/Sample/SpecimenType.yaml @@ -1,54 +1,55 @@ enums: - SpecimenTypeEnum: + Tissue: + description: Tissue is a group of cells that have similar structure and that function together as a unit. permissible_values: cerebral cortex: - description: The outer layer of the cerebrum composed of neurons and unmyelinated nerve fibers. It is responsible for memory, attention, consciousness and other higher levels of mental function. - meaning: http://purl.obolibrary.org/obo/NCIT_C12443 + description: The surface layer of gray matter of the cerebrum that functions chiefly in coordination of sensory and motor information. + meaning: http://purl.obolibrary.org/obo/BTO_0000233 bone marrow: description: The soft, fatty, vascular tissue that fills most bone cavities and is the source of red blood cells and many white blood cells. meaning: http://purl.obolibrary.org/obo/BTO_0000141 plasma: description: Plasma is the fluid (noncellular) portion of the circulating blood, as distinguished from the serum that is the fluid portion of the blood obtained by removal of the fibrin clot and blood cells after coagulation. - meaning: http://purl.obolibrary.org/obo/NCIT_C13356 + meaning: http://purl.obolibrary.org/obo/BTO_0000131 Dorsal Root Ganglion: description: Ganglion with sensory function within the vertebral column. meaning: http://purl.obolibrary.org/obo/NCIT_C12462 optic nerve: description: The nerve that carries messages from the retina to the brain. - meaning: http://purl.obolibrary.org/obo/NCIT_C12761 + meaning: http://purl.obolibrary.org/obo/BTO_0000966 tumor-adjacent normal: description: Tissue comprised of morphologically normal tissue collected from the area immediately surrounding a tumor. meaning: http://purl.obolibrary.org/obo/NCIT_C164032 serum: description: Liquid derived from blood plasma that has clotting factors removed. - meaning: https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0001977 + meaning: http://purl.obolibrary.org/obo/BTO_0001239 spheroid: description: Spheroids are 3D culture systems that can be used to model multicellular tumors; more broadly, spheroids can be defined as cell aggregates cultured on nonadherent substrates. meaning: https://www.nature.com/articles/s41378-020-00185-3 sciatic nerve: description: The longest single nerve that is formed by the merging of the ventral rami of the L4, L5, and S1 in the pelvis and passes down the lower limb where it divides into the common peroneal and tibial nerves - meaning: http://purl.obolibrary.org/obo/NCIT_C52810 + meaning: http://purl.obolibrary.org/obo/BTO_0001221 meninges: description: The three thin layers of tissue that cover and protect the brain and spinal cord. - meaning: https://www.ncbi.nlm.nih.gov/pubmedhealth/PMHT0024758/ + meaning: http://purl.obolibrary.org/obo/BTO_0000144 nerve tissue: description: Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. - meaning: https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0003714 + meaning: http://purl.obolibrary.org/obo/BTO_0000925 Buccal Mucosa: description: The mucosal membranes located on the inside of the cheek, in the buccal cavity.The inner lining of the cheeks. - meaning: http://purl.obolibrary.org/obo/NCIT_C12505 + meaning: http://purl.obolibrary.org/obo/BTO_0003833 embryonic tissue: description: A portion of tissue that is part of an embryo. - meaning: http://purl.obolibrary.org/obo/UBERON_0005291 + meaning: http://purl.obolibrary.org/obo/BTO_0000379 whole brain: description: Brain tissue not limited to a specific region. - meaning: Sage Bionetworks + meaning: http://purl.obolibrary.org/obo/BTO_0000142 microtissue: description: Microtissue usually refers to the microtissue formed by the aggregation of seed cells under the action of cell-cell or cell-extracellular matrix (ECM). Compared with traditional cell monolayer culture, cells are cultivated into a three-dimensional microstructure in a specific way. The microstructure characteristics of microtissue are similar to natural tissues and can promote cell proliferation and differentiation. meaning: https://doi.org/10.1089/ten.teb.2020.0370 retina: description: A light-sensitive membrane that lines the back wall of the eyeball. The retina is continuous with the optic nerve and this way transmits optical images to the brain. [ NCI ] - meaning: http://purl.obolibrary.org/obo/NCIT_C12343 + meaning: http://purl.obolibrary.org/obo/BTO_0001175 CDX tissue: description: Cell line derived xenograft tissue meaning: http://purl.obolibrary.org/obo/NCIT_C156443 @@ -57,20 +58,35 @@ enums: meaning: https://www.nature.com/articles/s41378-020-00185-3 splenocyte: description: Any leukocyte that is part of a spleen. - meaning: https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_2000074 + meaning: http://purl.obolibrary.org/obo/BTO_0001598 blood: description: A fluid that is composed of blood plasma and erythrocytes. - meaning: https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0000178 + meaning: http://purl.obolibrary.org/obo/BTO_0000089 connective tissue: - description: '' + description: Tissue which binds together and is the support of the various structures of the body. It is made up of fibroblasts, fibroglia, collagen fibrils, and elastic fibrils. + meaning: http://purl.obolibrary.org/obo/BTO_0000421 primary tumor: - description: A primary tumor is the tumor at the initial site of cancer, not where the cancer may have spread or metastasized, called the secondary tumor. + description: A primary tumor is the tumor at the initial site of cancer, not where the cancer may have spread or metastasized, called the secondary tumor. Use `tumorType` to further describe the primary tumor. meaning: https://cancergenome.nih.gov/cancersselected/biospeccriteria PDX tissue: description: Patient derived xenograft tissue Buffy Coat: description: The middle layer of an anticoagulated blood specimen following separation by centrifugation. It contains most of the white blood cells and platelets. - meaning: http://purl.obolibrary.org/obo/NCIT_C84507 + meaning: http://purl.obolibrary.org/obo/BTO_0006181 + + OrganismSubstance: + description: This preferred root in the UBERON ontology is meant to cover organism-produced substances (bodily secretions and excreta) commonly used as assay specimens. + meaning: http://purl.obolibrary.org/obo/UBERON_0000463 + permissible_values: saliva: description: The watery fluid in the mouth made by the salivary glands. Saliva moistens food to help digestion and it helps protect the mouth against infections. meaning: http://purl.obolibrary.org/obo/NCIT_C13275 + mucus: + description: A bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. + meaning: http://purl.obolibrary.org/obo/UBERON_0000912 + urine: + description: Excretion that is the output of a kidney. + meaning: http://purl.obolibrary.org/obo/UBERON_0001088 + stool: + description: Portion of semisolid bodily waste discharged through the anus. + meaning: http://purl.obolibrary.org/obo/UBERON_0001988 diff --git a/modules/props.yaml b/modules/props.yaml index 6e5575fd..a4023bf2 100644 --- a/modules/props.yaml +++ b/modules/props.yaml @@ -673,7 +673,9 @@ slots: specimenType: description: > The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances. - range: SpecimenTypeEnum + enum_range: + - Tissue + - OrganismSubstance required: false title: description: Title of a resource. @@ -690,9 +692,9 @@ slots: - Human - Mouse required: false - transplantationRecipient: - description: into which a xenograph sample is transplanted - range: + transplantationRecipientTissue: + description: Tissue into which a xenograph sample is transplanted + range: Tissue required: false transplantationType: description: Type of transplantation involved in the experiment, derived from MESH From be618581cad6931460265919c1a8d73d65d91cce Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Fri, 1 Dec 2023 21:40:18 +0000 Subject: [PATCH 20/24] Build jsonld --- NF.jsonld | 117 +++++++++++++++++++++++++++++++++++++++++++----------- 1 file changed, 93 insertions(+), 24 deletions(-) diff --git a/NF.jsonld b/NF.jsonld index a2a64a5d..4d0748d2 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -206,6 +206,17 @@ }, "sms:displayName" : "StrandednessEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:OrganismSubstance", + "@type" : "rdfs:Class", + "rdfs:comment" : "This preferred root in the UBERON ontology is meant to cover organism-produced substances (bodily secretions and excreta) commonly used as assay specimens.", + "rdfs:label" : "OrganismSubstance", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "OrganismSubstance", + "sms:required" : "sms:false" }, { "@id" : "bts:BiologicalProcess", "@type" : "rdfs:Class", @@ -294,6 +305,17 @@ }, "sms:displayName" : "LibraryPrepEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:Tissue", + "@type" : "rdfs:Class", + "rdfs:comment" : "Tissue is a group of cells that have similar structure and that function together as a unit.", + "rdfs:label" : "Tissue", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Tissue", + "sms:required" : "sms:false" }, { "@id" : "bts:DataSubtype", "@type" : "rdfs:Class", @@ -536,17 +558,6 @@ }, "sms:displayName" : "ReadStrandOriginEnum", "sms:required" : "sms:false" - }, { - "@id" : "bts:SpecimenTypeEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SpecimenTypeEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "SpecimenTypeEnum", - "sms:required" : "sms:false" }, { "@id" : "bts:GenePerturbationTechnologyEnum", "@type" : "rdfs:Class", @@ -2505,17 +2516,6 @@ }, "sms:displayName" : "fundingAgency", "sms:required" : "sms:false" - }, { - "@id" : "bts:transplantationRecipient", - "@type" : "rdfs:Class", - "rdfs:comment" : "into which a xenograph sample is transplanted", - "rdfs:label" : "transplantationRecipient", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "transplantationRecipient", - "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:nucleicAcidSource", @@ -3037,7 +3037,7 @@ "sms:displayName" : "concentrationNaClUnit" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:specimenType", + "@id" : "bts:transplantationRecipientTissue", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, @@ -3090,8 +3090,22 @@ "@id" : "bts:PDXtissue" }, { "@id" : "bts:BuffyCoat" + } ], + "rdfs:label" : "transplantationRecipientTissue", + "rdfs:comment" : "Tissue into which a xenograph sample is transplanted", + "@type" : "rdfs:Class", + "sms:displayName" : "transplantationRecipientTissue" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:specimenType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Tissue" }, { - "@id" : "bts:saliva" + "@id" : "bts:OrganismSubstance" } ], "rdfs:label" : "specimenType", "rdfs:comment" : "The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances.\n", @@ -10567,6 +10581,17 @@ }, "sms:displayName" : "Illinois Institute of Technology", "sms:required" : "sms:false" + }, { + "@id" : "bts:stool", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "stool", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "stool", + "sms:required" : "sms:false" }, { "@id" : "bts:Nf1-/-skin-derivedprecursorcells", "@type" : "rdfs:Class", @@ -11799,6 +11824,17 @@ }, "sms:displayName" : "Bowling Green State University", "sms:required" : "sms:false" + }, { + "@id" : "bts:urine", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "urine", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "urine", + "sms:required" : "sms:false" }, { "@id" : "bts:UniversityofToledo", "@type" : "rdfs:Class", @@ -12107,6 +12143,17 @@ }, "sms:displayName" : "University of Oklahoma", "sms:required" : "sms:false" + }, { + "@id" : "bts:OrganismSubstance", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "OrganismSubstance", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "OrganismSubstance", + "sms:required" : "sms:false" }, { "@id" : "bts:Schwanncelli28cNFNF1-/-(#14)", "@type" : "rdfs:Class", @@ -16232,6 +16279,17 @@ }, "sms:displayName" : "oxBS-seq", "sms:required" : "sms:false" + }, { + "@id" : "bts:mucus", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "mucus", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "mucus", + "sms:required" : "sms:false" }, { "@id" : "bts:Interview", "@type" : "rdfs:Class", @@ -20401,6 +20459,17 @@ }, "sms:displayName" : "University of Southern California", "sms:required" : "sms:false" + }, { + "@id" : "bts:Tissue", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Tissue", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Tissue", + "sms:required" : "sms:false" }, { "@id" : "bts:forearm", "@type" : "rdfs:Class", From aa41a8376433db39746d701e5c3b6daeab917cb6 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Fri, 1 Dec 2023 15:05:17 -0700 Subject: [PATCH 21/24] Resolve docs and add one more thing --- docs/index.Rmd | 10 ++++++++-- modules/Sample/SpecimenType.yaml | 3 +++ 2 files changed, 11 insertions(+), 2 deletions(-) diff --git a/docs/index.Rmd b/docs/index.Rmd index ec489fe7..b88e8055 100644 --- a/docs/index.Rmd +++ b/docs/index.Rmd @@ -436,9 +436,15 @@ Data can be linked to specimen-level information such as sample site (the organ ::: -```{r sample_specimenType, echo=FALSE, results='asis'} +```{r sample_specimenType_tissue, echo=FALSE, results='asis'} -module_section("Sample", "SpecimenType", "SpecimenTypeEnum") +module_section("Sample", "SpecimenType", "Tissue") + +``` + +```{r sample_specimenType_other, echo=FALSE, results='asis'} + +module_section("Sample", "SpecimenType", "OrganismSubstance") ``` diff --git a/modules/Sample/SpecimenType.yaml b/modules/Sample/SpecimenType.yaml index 5eca4699..e86c4ebc 100644 --- a/modules/Sample/SpecimenType.yaml +++ b/modules/Sample/SpecimenType.yaml @@ -90,3 +90,6 @@ enums: stool: description: Portion of semisolid bodily waste discharged through the anus. meaning: http://purl.obolibrary.org/obo/UBERON_0001988 + sweat: + description: Secretion produced by a sweat gland. + meaning: http://purl.obolibrary.org/obo/UBERON_0001089 From 2a7744213dbd7845c2d39acdeaacd7c982d5898c Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Fri, 1 Dec 2023 22:06:46 +0000 Subject: [PATCH 22/24] Build jsonld --- NF.jsonld | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/NF.jsonld b/NF.jsonld index 4d0748d2..78cc532b 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -12077,6 +12077,17 @@ }, "sms:displayName" : "shoulder", "sms:required" : "sms:false" + }, { + "@id" : "bts:sweat", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "sweat", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "sweat", + "sms:required" : "sms:false" }, { "@id" : "bts:yaml", "@type" : "rdfs:Class", From 2532f0a0df2ef55d53921a654531c8a247f55ad0 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Mon, 4 Dec 2023 10:00:41 -0700 Subject: [PATCH 23/24] Correct syntax --- modules/props.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/props.yaml b/modules/props.yaml index a4023bf2..9a0189fc 100644 --- a/modules/props.yaml +++ b/modules/props.yaml @@ -673,9 +673,9 @@ slots: specimenType: description: > The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances. - enum_range: - - Tissue - - OrganismSubstance + any_of: + - range: Tissue + - range: OrganismSubstance required: false title: description: Title of a resource. From 754c880729c4c3b9616583eb0ec2e43e170f2b2f Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Mon, 4 Dec 2023 17:00:59 +0000 Subject: [PATCH 24/24] Build jsonld --- NF.jsonld | 80 ++++++++++++++++++++++++++++++++++++++----------------- 1 file changed, 56 insertions(+), 24 deletions(-) diff --git a/NF.jsonld b/NF.jsonld index 78cc532b..473ebcaa 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -3103,9 +3103,63 @@ }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:Tissue" + "@id" : "bts:cerebralcortex" + }, { + "@id" : "bts:bonemarrow" + }, { + "@id" : "bts:plasma" + }, { + "@id" : "bts:DorsalRootGanglion" + }, { + "@id" : "bts:opticnerve" + }, { + "@id" : "bts:tumor-adjacentnormal" + }, { + "@id" : "bts:serum" + }, { + "@id" : "bts:spheroid" + }, { + "@id" : "bts:sciaticnerve" + }, { + "@id" : "bts:meninges" + }, { + "@id" : "bts:nervetissue" + }, { + "@id" : "bts:BuccalMucosa" + }, { + "@id" : "bts:embryonictissue" + }, { + "@id" : "bts:wholebrain" + }, { + "@id" : "bts:microtissue" + }, { + "@id" : "bts:retina" + }, { + "@id" : "bts:CDXtissue" + }, { + "@id" : "bts:organoid" + }, { + "@id" : "bts:splenocyte" }, { - "@id" : "bts:OrganismSubstance" + "@id" : "bts:blood" + }, { + "@id" : "bts:connectivetissue" + }, { + "@id" : "bts:primarytumor" + }, { + "@id" : "bts:PDXtissue" + }, { + "@id" : "bts:BuffyCoat" + }, { + "@id" : "bts:saliva" + }, { + "@id" : "bts:mucus" + }, { + "@id" : "bts:urine" + }, { + "@id" : "bts:stool" + }, { + "@id" : "bts:sweat" } ], "rdfs:label" : "specimenType", "rdfs:comment" : "The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances.\n", @@ -12154,17 +12208,6 @@ }, "sms:displayName" : "University of Oklahoma", "sms:required" : "sms:false" - }, { - "@id" : "bts:OrganismSubstance", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "OrganismSubstance", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "OrganismSubstance", - "sms:required" : "sms:false" }, { "@id" : "bts:Schwanncelli28cNFNF1-/-(#14)", "@type" : "rdfs:Class", @@ -20470,17 +20513,6 @@ }, "sms:displayName" : "University of Southern California", "sms:required" : "sms:false" - }, { - "@id" : "bts:Tissue", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Tissue", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Tissue", - "sms:required" : "sms:false" }, { "@id" : "bts:forearm", "@type" : "rdfs:Class",