diff --git a/HTAN.model.csv b/HTAN.model.csv index 6e422023..1aa016f8 100644 --- a/HTAN.model.csv +++ b/HTAN.model.csv @@ -14,18 +14,18 @@ HTAN Biospecimen ID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTAN Parent ID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,,,,TRUE,Biospecimen,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing, HTAN Parent Biospecimen ID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,,,,TRUE,Biospecimen,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing, HTAN Parent Data File ID,HTAN Data File Identifier indicating the file(s) from which these files were derived,,,,TRUE,File,,, -Clinical Data Tier 2,Tier 2 Cancer Data,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Sentinel Lymph Node Count, Sentinel Node Positive Assessment Count, Tumor Extranodal Extension Indicator, Satellite Metastasis Present Indicator, Other Biopsy Resection Site, Extent of Tumor Resection, Precancerous Condition Type, Prior Sites of Radiation, Immunosuppression, Concomitant Medication Received Type, Family Member Vital Status Indicator, COVID19 Occurrence Indicator, COVID19 Current Status, COVID19 Positive Lab Test Indicator, COVID19 Antibody Testing, COVID19 Complications Severity, COVID19 Cancer Treatment Followup, Ecig vape use, Ecig vape 30 day use num, Ecig vape times per day, Type of smoke exposure cumulative years, Chewing tobacco daily use count, Second hand smoke exposure years, Known Genetic Predisposition Mutation, Hereditary Cancer Predisposition Syndrome, Cancer Associated Gene Mutations, Mutational Signatures, Mismatch Repair System Status, Lab Tests for MMR Status, Mode of Cancer Detection, Education Level, Country of Birth, Medically Underserved Area, Rural vs Urban, Cancer Incidence, Cancer Incidence Location",,FALSE,Patient,Patient,, -SRRS Clinical Data Tier 2,Cancer related clinical data specific to SRRS,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Education Level, Country of Birth, Medically Underserved Area, Rural vs Urban, Cancer Incidence, Cancer Incidence Location, Ethnicity, Gender, Race, Vital Status, Age at Diagnosis, Days to Last Follow up, Days to Last Known Disease Status, Days to Recurrence, Last Known Disease Status, Morphology, Primary Diagnosis, Progression or Recurrence, Site of Resection or Biopsy, Tissue or Organ of Origin, NCI Atlas Cancer Site, Tumor Grade, Pack Years Smoked, Years Smoked, Days to Follow Up, Gene Symbol, Molecular Analysis Method, Test Result, Treatment Type, Tumor Largest Dimension Diameter",,FALSE,Patient,Patient,, -Lung Cancer Tier 3,Lung cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Lung Cancer Detection Method Type, Lung Cancer Participant Procedure History, Lung Adjacent Histology Type, Lung Tumor Location Anatomic Site, Lung Tumor Lobe Bronchial Location, Current Lung Cancer Symptoms, Lung Topography, Lung Cancer Harboring Genomic Aberrations",,FALSE,Patient,Patient,, -Colorectal Cancer Tier 3,Colorectal cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Colorectal Cancer Detection Method Type, History of Prior Colon Polyps, Family Colon Cancer History Indicator, Family Medical History Colorectal Polyp Diagnosis, Immediate Family History Endometrial Cancer, Immediate Family History Ovarian Cancer, Patient Inflammatory Bowel Disease Personal Medica History, Patient Colonoscopy Performed Indicator, Colorectal Cancer Tumor Border Configuration, MLH1 Promoter Methylation Status, Colorectal Cancer KRAS Indicator, Colon Polyp Occurence Indicator, Family History Colorectal Polyp, Colorectal Polyp New Indicator, Colorectal Polyp Shape, Size of Polyp Removed, Colorectal Polyp Count, Colorectal Polyp Type, Colorectal Polyp Adenoma Type",,FALSE,Patient,Patient,, -Breast Cancer Tier 3,Breast cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Breast Carcinoma Detection Method Type, Breast Carcinoma Histology Category, Invasive Lobular Breast Carcinoma Histologic Category, Invasive Ductal Breast Carcinoma Histologic Category, Breast Biopsy Procedure Finding Type, Breast Quadrant Site, Breast Cancer Assessment Tests, Breast Cancer Genomic Test Performed, Mammaprint Risk Group, Oncotype Risk Group, Breast Carcinoma Estrogen Receptor Status, Breast Carcinoma Progesteroner Receptor Status, Breast Cancer Allred Estrogen Receptor Score, Prior Invasive Breast Disease, Breast Carcinoma ER Status Percentage Value, Breast Carcinoma PR Status Percentage Value, HER2 Breast Carcinoma Copy Number Total, Breast Carcinoma Centromere 17 Copy Number, Breast Carcinoma HER2 Centromere17 Copynumber Total, Breast Carcinoma HER2 Chromosome17 Ratio, Breast Carcinoma Surgical Procedure Name, Breast Carcinoma HER2 Ratio Diagnosis, Breast Carcinoma HER2 Status, Hormone Therapy Breast Cancer Prevention Indicator, Breast Carcinoma ER Staining Intensity, Breast Carcinoma PR Staining Intensity, Oncotype Score, Breast Imaging Performed Type, Multifocal Breast Carcinoma Present Indicator, Multicentric Breast Carcinoma Present Indicator, BIRADS Mammography Breast Density Category",,FALSE,Patient,Patient,, -Neuroblastoma and Glioma Tier 3,Brain cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,CNS Tumor Primary Anatomic Site, Glioma Specific Metastasis Sites, Glioma Specific Radiation Field, Supra Tentorial Ependymoma Molecular Subgroup, Infra Tentorial Ependymoma Molecular Subgroup, Neuroblastoma MYCN Gene Amplification Status",,FALSE,Patient,Patient,, -Acute Lymphoblastic Leukemia Tier 3,Acute Lymphoblastic Leukemia attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Specimen Blast Count Percentage Value, NCI ALL Risk Group, MRD ALL Diagnostic Sensitivity, CNS Leukemia Status",,FALSE,Patient,Patient,, -Ovarian Cancer Tier 3,Ovarian cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Ovarian Cancer Histologic Subtype, Ovarian Cancer Surgical Outcome, Ovarian Cancer Platinum Status",,FALSE,Patient,Patient,, -Prostate Cancer Tier 3,Prostate cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Location Extent Extraprostatic Extension, Location Nature Positive Margins, Seminal Vesicle Invasion, Prostate Carcinoma Histologic Type, Prostate Cancer Local Extent, Additonal Findings Uninvolved Prostate, Prostate Cancer Cytologic Morphologic Subtypes",,FALSE,Patient,Patient,, -Sarcoma Tier 3,Sarcoma specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Sarcoma Subtype, Sarcoma Diagnosis Classification Category, Sarcoma Tumor Extension Type",,FALSE,Patient,Patient,, -Pancreatic Cancer Tier 3,Pancreatic cancer specific attributes in Clinical Tier Data 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Pancreas Precancer Histopathologic Grade, Pancreatic IPMN Pathology Epithelial Subtype, Pancreatic Duct Final Pathology Type",,FALSE,Patient,Patient,, -Melanoma Tier 3,Melanoma specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Cutaneous Melanoma Tumor Infiltrating Lymphocytes, Cutaneous Melanoma Tumor Regression Range, Melanoma Specimen Clark Level Value, Cutaneous Melanoma Surgical Margins, Melanoma Lesion Size, History of Atypical Nevi, Fitzpatrick Skin Tone, History of Chronic UV Exposure, History of Blistering Sunburn, History of Tanning Bed Use, Immediate Family History Melanoma, Melanoma Biopsy Resection Sites, Cutaneous Melanoma Ulceration, Cutaneous Melanoma Additional Findings",,FALSE,Patient,Patient,, +Clinical Data Tier 2,Tier 2 Cancer Data,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Sentinel Lymph Node Count, Sentinel Node Positive Assessment Count, Tumor Extranodal Extension Indicator, Satellite Metastasis Present Indicator, Other Biopsy Resection Site, Extent of Tumor Resection, Precancerous Condition Type, Prior Sites of Radiation, Immunosuppression, Concomitant Medication Received Type, Family Member Vital Status Indicator, COVID19 Occurrence Indicator, COVID19 Current Status, COVID19 Positive Lab Test Indicator, COVID19 Antibody Testing, COVID19 Complications Severity, COVID19 Cancer Treatment Followup, Ecig vape use, Ecig vape 30 day use num, Ecig vape times per day, Type of smoke exposure cumulative years, Chewing tobacco daily use count, Second hand smoke exposure years, Known Genetic Predisposition Mutation, Hereditary Cancer Predisposition Syndrome, Cancer Associated Gene Mutations, Mutational Signatures, Mismatch Repair System Status, Lab Tests for MMR Status, Mode of Cancer Detection, Education Level, Country of Birth, Medically Underserved Area, Rural vs Urban, Cancer Incidence, Cancer Incidence Location",,FALSE,Patient,,, +SRRS Clinical Data Tier 2,Cancer related clinical data specific to SRRS,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Education Level, Country of Birth, Medically Underserved Area, Rural vs Urban, Cancer Incidence, Cancer Incidence Location, Ethnicity, Gender, Race, Vital Status, Age at Diagnosis, Days to Last Follow up, Days to Last Known Disease Status, Days to Recurrence, Last Known Disease Status, Morphology, Primary Diagnosis, Progression or Recurrence, Site of Resection or Biopsy, Tissue or Organ of Origin, NCI Atlas Cancer Site, Tumor Grade, Pack Years Smoked, Years Smoked, Days to Follow Up, Gene Symbol, Molecular Analysis Method, Test Result, Treatment Type, Tumor Largest Dimension Diameter",,FALSE,Patient,,, +Lung Cancer Tier 3,Lung cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Lung Cancer Detection Method Type, Lung Cancer Participant Procedure History, Lung Adjacent Histology Type, Lung Tumor Location Anatomic Site, Lung Tumor Lobe Bronchial Location, Current Lung Cancer Symptoms, Lung Topography, Lung Cancer Harboring Genomic Aberrations",,FALSE,Patient,,, +Colorectal Cancer Tier 3,Colorectal cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Colorectal Cancer Detection Method Type, History of Prior Colon Polyps, Family Colon Cancer History Indicator, Family Medical History Colorectal Polyp Diagnosis, Immediate Family History Endometrial Cancer, Immediate Family History Ovarian Cancer, Patient Inflammatory Bowel Disease Personal Medica History, Patient Colonoscopy Performed Indicator, Colorectal Cancer Tumor Border Configuration, MLH1 Promoter Methylation Status, Colorectal Cancer KRAS Indicator, Colon Polyp Occurence Indicator, Family History Colorectal Polyp, Colorectal Polyp New Indicator, Colorectal Polyp Shape, Size of Polyp Removed, Colorectal Polyp Count, Colorectal Polyp Type, Colorectal Polyp Adenoma Type",,FALSE,Patient,,, +Breast Cancer Tier 3,Breast cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Breast Carcinoma Detection Method Type, Breast Carcinoma Histology Category, Invasive Lobular Breast Carcinoma Histologic Category, Invasive Ductal Breast Carcinoma Histologic Category, Breast Biopsy Procedure Finding Type, Breast Quadrant Site, Breast Cancer Assessment Tests, Breast Cancer Genomic Test Performed, Mammaprint Risk Group, Oncotype Risk Group, Breast Carcinoma Estrogen Receptor Status, Breast Carcinoma Progesteroner Receptor Status, Breast Cancer Allred Estrogen Receptor Score, Prior Invasive Breast Disease, Breast Carcinoma ER Status Percentage Value, Breast Carcinoma PR Status Percentage Value, HER2 Breast Carcinoma Copy Number Total, Breast Carcinoma Centromere 17 Copy Number, Breast Carcinoma HER2 Centromere17 Copynumber Total, Breast Carcinoma HER2 Chromosome17 Ratio, Breast Carcinoma Surgical Procedure Name, Breast Carcinoma HER2 Ratio Diagnosis, Breast Carcinoma HER2 Status, Hormone Therapy Breast Cancer Prevention Indicator, Breast Carcinoma ER Staining Intensity, Breast Carcinoma PR Staining Intensity, Oncotype Score, Breast Imaging Performed Type, Multifocal Breast Carcinoma Present Indicator, Multicentric Breast Carcinoma Present Indicator, BIRADS Mammography Breast Density Category",,FALSE,Patient,,, +Neuroblastoma and Glioma Tier 3,Brain cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,CNS Tumor Primary Anatomic Site, Glioma Specific Metastasis Sites, Glioma Specific Radiation Field, Supra Tentorial Ependymoma Molecular Subgroup, Infra Tentorial Ependymoma Molecular Subgroup, Neuroblastoma MYCN Gene Amplification Status",,FALSE,Patient,,, +Acute Lymphoblastic Leukemia Tier 3,Acute Lymphoblastic Leukemia attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Specimen Blast Count Percentage Value, NCI ALL Risk Group, MRD ALL Diagnostic Sensitivity, CNS Leukemia Status",,FALSE,Patient,,, +Ovarian Cancer Tier 3,Ovarian cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Ovarian Cancer Histologic Subtype, Ovarian Cancer Surgical Outcome, Ovarian Cancer Platinum Status",,FALSE,Patient,,, +Prostate Cancer Tier 3,Prostate cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Location Extent Extraprostatic Extension, Location Nature Positive Margins, Seminal Vesicle Invasion, Prostate Carcinoma Histologic Type, Prostate Cancer Local Extent, Additonal Findings Uninvolved Prostate, Prostate Cancer Cytologic Morphologic Subtypes",,FALSE,Patient,,, +Sarcoma Tier 3,Sarcoma specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Sarcoma Subtype, Sarcoma Diagnosis Classification Category, Sarcoma Tumor Extension Type",,FALSE,Patient,,, +Pancreatic Cancer Tier 3,Pancreatic cancer specific attributes in Clinical Tier Data 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Pancreas Precancer Histopathologic Grade, Pancreatic IPMN Pathology Epithelial Subtype, Pancreatic Duct Final Pathology Type",,FALSE,Patient,,, +Melanoma Tier 3,Melanoma specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Cutaneous Melanoma Tumor Infiltrating Lymphocytes, Cutaneous Melanoma Tumor Regression Range, Melanoma Specimen Clark Level Value, Cutaneous Melanoma Surgical Margins, Melanoma Lesion Size, History of Atypical Nevi, Fitzpatrick Skin Tone, History of Chronic UV Exposure, History of Blistering Sunburn, History of Tanning Bed Use, Immediate Family History Melanoma, Melanoma Biopsy Resection Sites, Cutaneous Melanoma Ulceration, Cutaneous Melanoma Additional Findings",,FALSE,Patient,,, Demographics,Demographic attributes,,"Component, HTAN Participant ID, Ethnicity, Gender, Race, Vital Status, Days to Birth, Country of Residence, Age Is Obfuscated, Year Of Birth, Occupation Duration Years, Premature At Birth, Weeks Gestation at Birth",,FALSE,Patient,,, Family History,Family cancer history,,"Component, HTAN Participant ID, Relative with Cancer History",,FALSE,Patient,,, Exposure,Exposure to carcinogens,,"Component, HTAN Participant ID, Start Days from Index, Smoking Exposure, Alcohol Exposure, Asbestos Exposure, Coal Dust Exposure, Environmental Tobacco Smoke Exposure, Radon Exposure, Respirable Crystalline Silica Exposure",,FALSE,Patient,,, @@ -161,7 +161,7 @@ Loop Calling,Tool used for identifying loop interactions,,,,TRUE,Sequencing,,, Imaging Level 4,Derived imaging data: Object-by-feature array,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Parent Channel Metadata ID, HTAN Data File ID, Parameter file, Software and Version, Commit SHA,Number of Objects, Number of Features,Imaging Object Class, Imaging Summary Statistic",,FALSE,Assay,Imaging Level 3 Channels,, SRRS Imaging Level 2,SRRS-specific HTAN raw and pre-processed image data,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Data File ID, Channel Metadata Filename, Imaging Assay Type, Protocol Link, Software and Version, Microscope, Objective, NominalMagnification, Pyramid, Zstack, Tseries, Passed QC, Frame Averaging, Image ID, DimensionOrder, PhysicalSizeX, PhysicalSizeXUnit, PhysicalSizeY, PhysicalSizeYUnit, Pixels BigEndian, PlaneCount, SizeC, SizeT, SizeX, SizeY, SizeZ, PixelType",,FALSE,Assay,Biospecimen,, RPPA Level 2,Array based protemics. Each dilution curve of spot intensities is fitted using the monotone increasing B-spline model in the SuperCurve R package. This fits a single curve using all the samples on a slide with the signal intensity as the response variable and the dilution steps as independent variables. The fitted curve is plotted with the signal intensities on the y-axis and the log2-concentration of proteins on the x-axis for diagnostic purposes.,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, HTAN RPPA Antibody Table, Assay Type, Protocol Link, Software and Version",,FALSE,Assay,Biospecimen,, -HTAN RPPA Antibody Table,A table containing antibody level metadata for RPPA,,"HTAN RPPA Antibody Table ID, Filename, File Format, Ab Name Reported on Dataset, GENCODE Gene Symbol Target, UNIPROT Protein ID Target, Phosphoprotein Flag, Vendor, Catalog Number, Internal Ab ID, Species, RPPA Dilution, Phospho Site, RPPA Validation Status, Clone, Clonality, Antibody Notes",,TRUE,RPPA Level 2,RPPA Level 2,, +HTAN RPPA Antibody Table,A table containing antibody level metadata for RPPA,,"HTAN RPPA Antibody Table ID, Filename, File Format, Ab Name Reported on Dataset, GENCODE Gene Symbol Target, UNIPROT Protein ID Target, Phosphoprotein Flag, Vendor, Catalog Number, Internal Ab ID, Species, RPPA Dilution, Phospho Site, RPPA Validation Status, Clone, Clonality, Antibody Notes",,TRUE,RPPA Level 2,,, RPPA Level 3,Level 3 Reverse Phase Protein Array (RPPA) data contains intra-batch normalized intensities.,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Assay Type, Software and Version, Normalization Method",,FALSE,Assay,Biospecimen,, RPPA Level 4,Level 4 Reverse Phase Protein Array (RPPA) data contains intra-batch corrected intensities.,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Assay Type, Batch Correction Method",,FALSE,Assay,RPPA Level 2,, Mass Spectrometry Level 1,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 1",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, MS Batch ID, MS-based Assay Type, Analyte Type, MS-based Targeted, MS Instrument Vendor and Model, MS Source, Polarity, Mass Range Low Value, Mass Range High Value, Data Collection Mode, MS Scan Mode, MS Labeling, Protocol Link, LC Instrument Vendor and Model, LC Column Vendor and Model, LC Resin, LC Length Value, LC Temp Value, LC ID Value, LC Flow Rate, LC Gradient, LC Mobile Phase A, LC Mobile Phase B, Software and Version, MS Instrument Metadata File",,FALSE,Assay,Biospecimen,, @@ -985,7 +985,7 @@ Proportion of Minimum CpG Coverage 10X,"Proportion of all reference bases for wh DMC Calling Tool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),"MethylKit, BSmooth, BiSeq, MethylSig, DSS, MOABS, DSS-single, metilene, MACAU, MethylDackel",,,TRUE,Bulk Methylation-seq Level 3,,, DMC Calling Workflow URL,Generic name for the workflow used to analyze a data set,,,,TRUE,Bulk Methylation-seq Level 3,,,url DMR Calling Tool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),"MethylKit, BSmooth, BiSeq, MethylSig, DSS, MOABS, DSS-single, metilene, MACAU",,,TRUE,Bulk Methylation-seq Level 3,,, -DMR Calling Workflow URL,Generic name for the workflow used to analyze a data set,"Github, Synapse",,,TRUE,Bulk Methylation-seq Level 3,,, +DMR Calling Workflow URL,Generic name for the workflow used to analyze a data set,,,,TRUE,Bulk Methylation-seq Level 3,,,url pUC19 methylation ratio,"Methylation ratio of mostly methylated pUC19 control, as a percentage",,,,TRUE,Bulk Methylation-seq Level 3,,, Lambda methylation ratio,"Methylation ratio of mostly unmethylated lambda control, as a percentage",,,,TRUE,Bulk Methylation-seq Level 3,,, DMC data file format,Format of the data files,"BED, bedGraph",,,TRUE,Bulk Methylation-seq Level 3,,, diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld index 87902bdc..9e71820b 100644 --- a/HTAN.model.jsonld +++ b/HTAN.model.jsonld @@ -3098,11 +3098,6 @@ }, "sms:displayName": "Clinical Data Tier 2", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Patient" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" @@ -6583,11 +6578,6 @@ }, "sms:displayName": "SRRS Clinical Data Tier 2", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Patient" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" @@ -11169,11 +11159,6 @@ }, "sms:displayName": "Lung Cancer Tier 3", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Patient" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" @@ -12017,11 +12002,6 @@ }, "sms:displayName": "Colorectal Cancer Tier 3", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Patient" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" @@ -12719,11 +12699,6 @@ }, "sms:displayName": "Breast Cancer Tier 3", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Patient" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" @@ -13904,11 +13879,6 @@ }, "sms:displayName": "Neuroblastoma and Glioma Tier 3", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Patient" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" @@ -14201,11 +14171,6 @@ }, "sms:displayName": "Acute Lymphoblastic Leukemia Tier 3", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Patient" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" @@ -14380,11 +14345,6 @@ }, "sms:displayName": "Ovarian Cancer Tier 3", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Patient" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" @@ -14551,11 +14511,6 @@ }, "sms:displayName": "Prostate Cancer Tier 3", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Patient" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" @@ -14996,11 +14951,6 @@ }, "sms:displayName": "Sarcoma Tier 3", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Patient" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" @@ -15167,11 +15117,6 @@ }, "sms:displayName": "Pancreatic Cancer Tier 3", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Patient" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" @@ -15347,11 +15292,6 @@ }, "sms:displayName": "Melanoma Tier 3", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Patient" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" @@ -37515,17 +37455,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Github" - }, - { - "@id": "bts:Synapse" - } - ], "sms:displayName": "DMR Calling Workflow URL", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "url" + ] }, { "@id": "bts:PUC19methylationratio", @@ -43292,11 +43226,6 @@ }, "sms:displayName": "HTAN RPPA Antibody Table", "sms:required": "sms:true", - "sms:requiresComponent": [ - { - "@id": "bts:RPPALevel2" - } - ], "sms:requiresDependency": [ { "@id": "bts:HTANRPPAAntibodyTableID" @@ -149489,40 +149418,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:Github", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Github", - "rdfs:subClassOf": [ - { - "@id": "bts:DMRCallingWorkflowURL" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Github", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Synapse", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Synapse", - "rdfs:subClassOf": [ - { - "@id": "bts:DMRCallingWorkflowURL" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Synapse", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:BED", "@type": "rdfs:Class",