Patch validation typo (#137)

* Patch validation typo * Add changes * Add kapa hyperprep w riboerase * Add quotes * Add changes * Update annotationProperty.csv * Add changes * Add GTAC@WUSTL in-house prep * Add changes * Update annotationProperty.csv * Add changes Co-authored-by: nf-osi[bot] <[email protected]>
nf-osi · Apr 22, 2022 · 263c90c · 263c90c
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commit 263c90c
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Showing 5 changed files with 49 additions and 7 deletions.
diff --git a/NF.csv b/NF.csv
@@ -112,6 +112,8 @@ NEBNext mRNA Library Prep Reagent Set for Illumina,NEBNext mRNA Library Prep Rea
 IDT xGen Exome Research Panel,"","","",FALSE,https://www.idtdna.com/pages/products/next-generation-sequencing/targeted-sequencing/hybridization-capture/predesigned-panels/xgen-exome-research-panel-v2,libraryPreparationMethod,,"","",IDT_xGen_Exome_Research_Panel,Class,Assay,Assay_Parameter,Library_Prep,"","",""
 Illumina TruSeq DNA Nano,"","","",FALSE,Sage Bionetworks,libraryPreparationMethod,,"","",Illumina_TruSeq_DNA_Nano,Class,Assay,Assay_Parameter,Library_Prep,"","",""
 KAPA HyperPrep Kit PCR-free,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.,"","",FALSE,https://sequencing.roche.com/en/products-solutions/products/sample-preparation/dna-reagents/library-preparation/kapa-hyperprep/ordering.html,libraryPreparationMethod,,"","",KAPA HyperPrep Kit PCR-free,Class,Assay,Assay_Parameter,Library_Prep,"","",""
+KAPA RNA HyperPrep Kit with RiboErase (HMR),"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.","","",FALSE,https://rochesequencingstore.com/catalog/kapa-rna-hyperprep-kit-with-riboerase-hmr/,libraryPreparationMethod,,"","",KAPA RNA HyperPrep Kit with RiboErase (HMR),Class,Assay,Assay_Parameter,Library_Prep,"","",""
+GTAC@WUSTL in-house prep,"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)","","",FALSE,WUSTL,libraryPreparationMethod,,"","",GTAC@WUSTL in-house prep,Class,Assay,Assay_Parameter,Library_Prep,"","",""
 bulk cell,All cells from bulk sample,"","",FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,nucleicAcidSource,,"","",bulk_cell,Class,Assay,Assay_Parameter,Nucleic_Acid_Source,"","",""
 single cell,Single cell,"","",FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,nucleicAcidSource,,"","",single_cell,Class,Assay,Assay_Parameter,Nucleic_Acid_Source,"","",""
 bulk nuclei,All nuclei from bulk sample,"","",FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,nucleicAcidSource,,"","",bulk_nuclei,Class,Assay,Assay_Parameter,Nucleic_Acid_Source,"","",""
@@ -199,7 +201,7 @@ isStranded,Whether or not the library is stranded. (Note: TRUE = Yes; FALSE = No
 readPairOrientation,The relative orientation of the reads in a paired-end protocol,"inward, outward, matching, fr-firststrand",,FALSE,,ngs,,,,readPairOrientation,Property,Assay,annotationProperty,ngsParameter,Read_Pair_Orientation,,
 readStrandOrigin,The strand from which the read originates in a strand-specific protocol,"forward, reverse",,FALSE,,ngs,,,,readStrandOrigin,Property,Assay,annotationProperty,ngsParameter,Read_Strand_Origin,,
 libraryPrep,The general strategy by which the library was prepared,"rRNAdepletion, polyAselection, lncRNAenrichment, miRNAenrichment","libraryPreparationMethod,nucleicAcidSource,dissociationMethod",FALSE,,ngs,,,,libraryPrep,Property,Assay,annotationProperty,ngsParameter,Library_Prep,,
-libraryPreparationMethod,Method by which library was prepared,"10x, CEL-seq, Drop-Seq, Smart-seq2, TruSeq, Smart-seq4, Omni-ATAC, NEBNext mRNA Library Prep Reagent Set for Illumina, IDT xGen Exome Research Panel, TruSeq standard total RNA library kit, Illumina TruSeq DNA Nano, KAPA HyperPrep Kit PCR-free",,FALSE,,ngs,,,,libraryPreparationMethod,Property,Assay,annotationProperty,ngsParameter,Library_Preparation_Method,,
+libraryPreparationMethod,Method by which library was prepared,"10x, CEL-seq, Drop-Seq, Smart-seq2, TruSeq, Smart-seq4, Omni-ATAC, NEBNext mRNA Library Prep Reagent Set for Illumina, IDT xGen Exome Research Panel, TruSeq standard total RNA library kit, Illumina TruSeq DNA Nano, KAPA HyperPrep Kit PCR-free,KAPA RNA HyperPrep Kit with RiboErase (HMR),GTAC@WUSTL in-house prep",,FALSE,,ngs,,,,libraryPreparationMethod,Property,Assay,annotationProperty,ngsParameter,Library_Preparation_Method,,
 nucleicAcidSource,Source of the extracted nucleic acid used in the experiment,"bulk cell, single cell, bulk nuclei, single nucleus, mitochondria",,FALSE,Sage Bionetworks,ngs,,,,nucleicAcidSource,Property,Assay,annotationProperty,ngsParameter,Nucleic_Acid_Source,,
 dissociationMethod,Procedure by which a biological specimen is dissociated into individual cells or a cell suspension,"10x_v2, FACS, Fluidigm C1, drop-seq, inDrop, mouth pipette, bulk, enzymatic, mechanical, none",,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0009088,ngs,,,,dissociationMethod,Property,Assay,annotationProperty,ngsParameter,Dissociation_Method,,
 readLength,Number of base pairs (bp) sequenced for a read,,,FALSE,,ngs,,,,readLength,DataProperty,Assay,annotationProperty,ngsParameter,,,
@@ -471,7 +473,7 @@ tumor,"General term for tumor sample – use when it is unknown when a more spec
 metastatic tumor,"For neoplasms, a non-infiltrating and non-metastasizing neoplastic process that is characterized by the absence of morphologic features associated with malignancy (e.g., severe atypia, nuclear pleomorphism, tumor cell necrosis, and abnormal mitoses).","","",FALSE,http://purl.obolibrary.org/obo/NCIT_C14172,tissue,,"","",Metastatic_Tumor,Class,Biosample,Tumor,"","","",""
 metastatic/recurrent tumor,A tumor with metastatic/recurrent characteristic.,"","",FALSE,"",tissue,,"","",Metastatic_Recurrent_Tumor,Class,Biosample,Tumor,"","","",""
 recurrent tumor,A tumor described with recurrent characteristic.,"","",FALSE,http://purl.obolibrary.org/obo/NCIT_C4798,tissue,,"","",Recurrent_Tumor,Class,Biosample,Tumor,"","","",""
-tumorType,The type of tumor that the biospecimen used to generate the data were collected from.,"Teratoma, Cutaneous Neurofibroma, Subcutaneous Neurofibroma, Plexiform Neurofibroma, Atypical Neurofibroma, Malignant Peripheral Nerve Sheath Tumor, Glioma, Low-Grade Glioma NOS, Pilocytic Astrocytoma, Pilomyxoid Astrocytoma, Diffuse Astrocytoma, Glioblastoma Multiforme, Anaplastic Pilocytic Astrocytoma, Pleomorphic Xanthoastrocytoma, Oligoastrocytoma, High-Grade Glioma NOS, Unknown, Anaplastic Astrocytoma, Glioblastoma, Schwannoma, Meningioma, Massive Soft Tissue Neurofibroma, Diffuse Infiltrating Neurofibroma, Localized Neurofibroma, Neurofibroma with Degenerative Atypia, Neurofibroma, Anaplastic Pleomorphic Xanthoastrocytoma, Ganglioglioma, Anaplastic Ganglioglioma, Optic Pathway Glioma, Not Applicable,Colorectal Carcinoma,Recurrent MPNST,Juvenile Myelomonocytic Leukemia,Sarcoma,Fibromatosis,Fibrosarcoma,Necrotic Neoplasm,Hemorrhagic Neoplasm,NF1-Associated Tumor,NF2-Associated Tumor",,FALSE,Sage Bionetworks,cancer,,,a6,tumorType,Property,Biosample,annotationProperty,biosampleAnnotation,Tumor,,
+tumorType,The type of tumor that the biospecimen used to generate the data were collected from.,"Teratoma, Cutaneous Neurofibroma, Subcutaneous Neurofibroma, Plexiform Neurofibroma, Atypical Neurofibroma, Malignant Peripheral Nerve Sheath Tumor, Glioma, Low-Grade Glioma NOS, Pilocytic Astrocytoma, Pilomyxoid Astrocytoma, Diffuse Astrocytoma, Glioblastoma Multiforme, Anaplastic Pilocytic Astrocytoma, Pleomorphic Xanthoastrocytoma, Oligoastrocytoma, High-Grade Glioma NOS, Unknown, Anaplastic Astrocytoma, Glioblastoma, Schwannoma, Meningioma, Massive Soft Tissue Neurofibroma, Diffuse Infiltrating Neurofibroma, Localized Neurofibroma, Neurofibroma with Degenerative Atypia, Neurofibroma, Anaplastic Pleomorphic Xanthoastrocytoma, Ganglioglioma, Anaplastic Ganglioglioma, Optic Pathway Glioma, Not Applicable,Colorectal Carcinoma,Recurrent MPNST,Juvenile Myelomonocytic Leukemia,Sarcoma,Fibromatosis,Fibrosarcoma,Necrotic Neoplasm,Hemorrhagic Neoplasm,NF1-Associated Tumor,NF2-Associated Tumor",,FALSE,Sage Bionetworks,cancer,,,,tumorType,Property,Biosample,annotationProperty,biosampleAnnotation,Tumor,,
 diagnosis,A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.,"Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, Unknown, Not Applicable, Sporadic Schwannoma",,FALSE,,experimentalData,,,,diagnosis,Property,Biosample,annotationProperty,,Diagnosis,one,Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities.
 bodyPart,"Sample location referring to a named area of the body, inclusive of gross anatomical structures and organ parts. ","head, neck, scalp, leg, pelvis, mesentery, axilla, acetabulum, forearm, muscle, finger, thoracic spine, groin, back, iliac spine, spine, shoulder, scapula, lymph node, kidney, skin, mammary gland, nerves, brain, blood, breast, colon, lung, liver, prostate, pancreas, ovary, spleen, bone marrow, Bursa Of Fabricius, nose",,FALSE,,experimentalData,,,,bodyPart,Property,Biosample,annotationProperty,,Body_Part,,
 organ,A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.,"lymph node, kidney, skin, mammary gland, nerves, brain, blood, breast, colon, lung, liver, prostate, pancreas, ovary, spleen, bone marrow, Bursa Of Fabricius, nose",,FALSE,,experimentalData,,,,organ,Property,Biosample,annotationProperty,,Organ,,

diff --git a/NF.jsonld b/NF.jsonld
@@ -3920,6 +3920,40 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:KAPARNAHyperPrepKitwithRiboErase(HMR)",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "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.",
+            "rdfs:label": "KAPARNAHyperPrepKitwithRiboErase(HMR)",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:LibraryPreparationMethod"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "KAPA RNA HyperPrep Kit with RiboErase (HMR)",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:GTAC@WUSTLin-houseprep",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "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)",
+            "rdfs:label": "GTAC@WUSTLin-houseprep",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:LibraryPreparationMethod"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "GTAC@WUSTL in-house prep",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Bulkcell",
             "@type": "rdfs:Class",
@@ -5934,6 +5968,12 @@
                 },
                 {
                     "@id": "bts:KAPAHyperPrepKitPCR-free"
+                },
+                {
+                    "@id": "bts:KAPARNAHyperPrepKitwithRiboErase(HMR)"
+                },
+                {
+                    "@id": "bts:GTAC@WUSTLin-houseprep"
                 }
             ],
             "sms:displayName": "libraryPreparationMethod",
@@ -10776,9 +10816,7 @@
             ],
             "sms:displayName": "tumorType",
             "sms:required": "sms:false",
-            "sms:validationRules": [
-                "a6"
-            ]
+            "sms:validationRules": []
         },
         {
             "@id": "bts:Diagnosis",

diff --git a/modules/Assay/Assay_Parameter.csv b/modules/Assay/Assay_Parameter.csv
@@ -24,6 +24,8 @@ NEBNext mRNA Library Prep Reagent Set for Illumina,NEBNext mRNA Library Prep Rea
 IDT xGen Exome Research Panel,"","","",FALSE,https://www.idtdna.com/pages/products/next-generation-sequencing/targeted-sequencing/hybridization-capture/predesigned-panels/xgen-exome-research-panel-v2,libraryPreparationMethod,,"","",IDT_xGen_Exome_Research_Panel,Class,Assay,Assay_Parameter,Library_Prep,"","",""
 Illumina TruSeq DNA Nano,"","","",FALSE,Sage Bionetworks,libraryPreparationMethod,,"","",Illumina_TruSeq_DNA_Nano,Class,Assay,Assay_Parameter,Library_Prep,"","",""
 KAPA HyperPrep Kit PCR-free,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.,"","",FALSE,https://sequencing.roche.com/en/products-solutions/products/sample-preparation/dna-reagents/library-preparation/kapa-hyperprep/ordering.html,libraryPreparationMethod,,"","",KAPA HyperPrep Kit PCR-free,Class,Assay,Assay_Parameter,Library_Prep,"","",""
+KAPA RNA HyperPrep Kit with RiboErase (HMR),"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.","","",FALSE,https://rochesequencingstore.com/catalog/kapa-rna-hyperprep-kit-with-riboerase-hmr/,libraryPreparationMethod,,"","",KAPA RNA HyperPrep Kit with RiboErase (HMR),Class,Assay,Assay_Parameter,Library_Prep,"","",""
+GTAC@WUSTL in-house prep,"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)","","",FALSE,WUSTL,libraryPreparationMethod,,"","",GTAC@WUSTL in-house prep,Class,Assay,Assay_Parameter,Library_Prep,"","",""
 bulk cell,All cells from bulk sample,"","",FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,nucleicAcidSource,,"","",bulk_cell,Class,Assay,Assay_Parameter,Nucleic_Acid_Source,"","",""
 single cell,Single cell,"","",FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,nucleicAcidSource,,"","",single_cell,Class,Assay,Assay_Parameter,Nucleic_Acid_Source,"","",""
 bulk nuclei,All nuclei from bulk sample,"","",FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,nucleicAcidSource,,"","",bulk_nuclei,Class,Assay,Assay_Parameter,Nucleic_Acid_Source,"","",""

diff --git a/modules/Assay/annotationProperty.csv b/modules/Assay/annotationProperty.csv
@@ -14,7 +14,7 @@ isStranded,Whether or not the library is stranded. (Note: TRUE = Yes; FALSE = No
 readPairOrientation,The relative orientation of the reads in a paired-end protocol,"inward, outward, matching, fr-firststrand",,FALSE,,ngs,,,,readPairOrientation,Property,Assay,annotationProperty,ngsParameter,Read_Pair_Orientation,,
 readStrandOrigin,The strand from which the read originates in a strand-specific protocol,"forward, reverse",,FALSE,,ngs,,,,readStrandOrigin,Property,Assay,annotationProperty,ngsParameter,Read_Strand_Origin,,
 libraryPrep,The general strategy by which the library was prepared,"rRNAdepletion, polyAselection, lncRNAenrichment, miRNAenrichment","libraryPreparationMethod,nucleicAcidSource,dissociationMethod",FALSE,,ngs,,,,libraryPrep,Property,Assay,annotationProperty,ngsParameter,Library_Prep,,
-libraryPreparationMethod,Method by which library was prepared,"10x, CEL-seq, Drop-Seq, Smart-seq2, TruSeq, Smart-seq4, Omni-ATAC, NEBNext mRNA Library Prep Reagent Set for Illumina, IDT xGen Exome Research Panel, TruSeq standard total RNA library kit, Illumina TruSeq DNA Nano, KAPA HyperPrep Kit PCR-free",,FALSE,,ngs,,,,libraryPreparationMethod,Property,Assay,annotationProperty,ngsParameter,Library_Preparation_Method,,
+libraryPreparationMethod,Method by which library was prepared,"10x, CEL-seq, Drop-Seq, Smart-seq2, TruSeq, Smart-seq4, Omni-ATAC, NEBNext mRNA Library Prep Reagent Set for Illumina, IDT xGen Exome Research Panel, TruSeq standard total RNA library kit, Illumina TruSeq DNA Nano, KAPA HyperPrep Kit PCR-free,KAPA RNA HyperPrep Kit with RiboErase (HMR),GTAC@WUSTL in-house prep",,FALSE,,ngs,,,,libraryPreparationMethod,Property,Assay,annotationProperty,ngsParameter,Library_Preparation_Method,,
 nucleicAcidSource,Source of the extracted nucleic acid used in the experiment,"bulk cell, single cell, bulk nuclei, single nucleus, mitochondria",,FALSE,Sage Bionetworks,ngs,,,,nucleicAcidSource,Property,Assay,annotationProperty,ngsParameter,Nucleic_Acid_Source,,
 dissociationMethod,Procedure by which a biological specimen is dissociated into individual cells or a cell suspension,"10x_v2, FACS, Fluidigm C1, drop-seq, inDrop, mouth pipette, bulk, enzymatic, mechanical, none",,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0009088,ngs,,,,dissociationMethod,Property,Assay,annotationProperty,ngsParameter,Dissociation_Method,,
 readLength,Number of base pairs (bp) sequenced for a read,,,FALSE,,ngs,,,,readLength,DataProperty,Assay,annotationProperty,ngsParameter,,,