Merge pull request #357 from ncihtan/355-move-precancerous-condition-…

…type-from-clinical-tier-2-to-clinical-tier-1-diagnosis

Move Precancerous Condition Type to Diagnosis

HTAN.model.csv

@@ -14,7 +14,7 @@ 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,,,
+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, 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,,,
@@ -31,7 +31,7 @@ Family History,Family cancer history,,"Component, HTAN Participant ID, Relative
 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,,,
 Follow Up,Follow up clinical visits,,"Component, HTAN Participant ID, Days to Follow Up, Adverse Event, Progression or Recurrence, Barretts Esophagus Goblet Cells Present, BMI, Cause of Response, Comorbidity, Comorbidity Method of Diagnosis, Days to Adverse Event, Days to Comorbidity, Diabetes Treatment Type, Disease Response, DLCO Ref Predictive Percent, ECOG Performance Status, FEV1 FVC Post Bronch Percent, FEV 1 FVC Pre Bronch Percent, FEV1 Ref Post Bronch Percent, FEV1 Ref Pre Bronch Percent, Height, Hepatitis Sustained Virological Response, HPV Positive Type, Karnofsky Performance Status, Menopause Status, Pancreatitis Onset Year,  Reflux Treatment Type, Risk Factor, Risk Factor Treatment, Viral Hepatitis Serologies, Weight, Adverse Event Grade, AIDS Risk Factors, Body Surface Area, CD4 Count, CDC HIV Risk Factors, Days to Imaging, Evidence of Recurrence Type, HAART Treatment Indicator, HIV Viral Load, Hormonal Contraceptive Use, Hysterectomy Margins Involved, Hysterectomy Type, Imaging Result, Imaging Type, Immunosuppressive Treatment Type, Nadir CD4 Count, Pregnancy Outcome, Recist Targeted Regions Number, Recist Targeted Regions Sum, Scan Tracer Used",,FALSE,Patient,,,
 Therapy,Clinical therapy or treatment,,"Component, HTAN Participant ID, Treatment or Therapy, Treatment Type, Treatment Effect, Treatment Outcome, Days to Treatment End, Treatment Anatomic Site, Days to Treatment Start, Initial Disease Status, Regimen or Line of Therapy, Therapeutic Agents, Treatment Intent Type, Chemo Concurrent to Radiation, Number of Cycles, Reason Treatment Ended, Treatment Arm, Treatment Dose, Treatment Dose Units, Treatment Effect Indicator, Treatment Frequency",,FALSE,Patient,,,
-Diagnosis,Disease diagnosis,,"Component, HTAN Participant ID, Age at Diagnosis, Year of Diagnosis, Primary Diagnosis, Site of Resection or Biopsy, Tissue or Organ of Origin, Morphology, Tumor Grade, Progression or Recurrence, Last Known Disease Status, Days to Last Follow up, Days to Last Known Disease Status,  Method of Diagnosis, Prior Malignancy, Prior Treatment, Metastasis at Diagnosis, Metastasis at Diagnosis Site, First Symptom Prior to Diagnosis, Days to Diagnosis, Percent Tumor Invasion, Residual Disease, Synchronous Malignancy, Tumor Confined to Organ of Origin, Tumor Focality, Tumor Largest Dimension Diameter, Gross Tumor Weight, Breslow Thickness, Vascular Invasion Present, Vascular Invasion Type, Anaplasia Present, Anaplasia Present Type, Laterality, Perineural Invasion Present, Lymphatic Invasion Present, Lymph Nodes Positive, Lymph Nodes Tested, Peritoneal Fluid Cytological Status, Classification of Tumor, Best Overall Response, Mitotic Count, AJCC Clinical M, AJCC Clinical N, AJCC Clinical Stage, AJCC Clinical T, AJCC Pathologic M, AJCC Pathologic N, AJCC Pathologic Stage, AJCC Pathologic T, AJCC Staging System Edition, Cog Neuroblastoma Risk Group, Cog Rhabdomyosarcoma Risk Group, Gleason Grade Group, Gleason Grade Tertiary, Gleason Patterns Percent, Greatest Tumor Dimension, IGCCCG Stage, INPC Grade, INPC Histologic Group, INRG Stage, INSS Stage, International Prognostic Index, IRS Group, IRS Stage, ISS Stage, Lymph Node Involved Site, Margin Distance, Margins Involved Site, Medulloblastoma Molecular Classification, Micropapillary Features, Mitosis Karyorrhexis Index, Non Nodal Regional Disease, Non Nodal Tumor Deposits, Ovarian Specimen Status, Ovarian Surface Involvement, Pregnant at Diagnosis, Primary Gleason Grade, Secondary Gleason Grade, Supratentorial Localization, Tumor Depth, WHO CNS Grade, WHO NTE Grade",,FALSE,Patient,,,
+Diagnosis,Disease diagnosis,,"Component, HTAN Participant ID, Age at Diagnosis, Year of Diagnosis, Primary Diagnosis, Precancerous Condition Type, Site of Resection or Biopsy, Tissue or Organ of Origin, Morphology, Tumor Grade, Progression or Recurrence, Last Known Disease Status, Days to Last Follow up, Days to Last Known Disease Status,  Method of Diagnosis, Prior Malignancy, Prior Treatment, Metastasis at Diagnosis, Metastasis at Diagnosis Site, First Symptom Prior to Diagnosis, Days to Diagnosis, Percent Tumor Invasion, Residual Disease, Synchronous Malignancy, Tumor Confined to Organ of Origin, Tumor Focality, Tumor Largest Dimension Diameter, Gross Tumor Weight, Breslow Thickness, Vascular Invasion Present, Vascular Invasion Type, Anaplasia Present, Anaplasia Present Type, Laterality, Perineural Invasion Present, Lymphatic Invasion Present, Lymph Nodes Positive, Lymph Nodes Tested, Peritoneal Fluid Cytological Status, Classification of Tumor, Best Overall Response, Mitotic Count, AJCC Clinical M, AJCC Clinical N, AJCC Clinical Stage, AJCC Clinical T, AJCC Pathologic M, AJCC Pathologic N, AJCC Pathologic Stage, AJCC Pathologic T, AJCC Staging System Edition, Cog Neuroblastoma Risk Group, Cog Rhabdomyosarcoma Risk Group, Gleason Grade Group, Gleason Grade Tertiary, Gleason Patterns Percent, Greatest Tumor Dimension, IGCCCG Stage, INPC Grade, INPC Histologic Group, INRG Stage, INSS Stage, International Prognostic Index, IRS Group, IRS Stage, ISS Stage, Lymph Node Involved Site, Margin Distance, Margins Involved Site, Medulloblastoma Molecular Classification, Micropapillary Features, Mitosis Karyorrhexis Index, Non Nodal Regional Disease, Non Nodal Tumor Deposits, Ovarian Specimen Status, Ovarian Surface Involvement, Pregnant at Diagnosis, Primary Gleason Grade, Secondary Gleason Grade, Supratentorial Localization, Tumor Depth, WHO CNS Grade, WHO NTE Grade",,FALSE,Patient,,,
 Molecular Test,Clinical molecular test data,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Gene Symbol, Molecular Analysis Method, Test Result, AA Change, Antigen, Clinical Biospecimen Type, Blood Test Normal Range Upper, Blood Test Normal Range Lower, Cell Count, Chromosome, Clonality, Copy Number, Cytoband, Exon, Histone Family, Histone Variant, Intron, Laboratory Test, Loci Abnormal Count, Loci Count, Locus, Mismatch Repair Mutation, Molecular Consequence, Pathogenicity, Ploidy, Second Exon, Second Gene Symbol, Specialized Molecular Test, Test Analyte Type, Test Units, Test Value, Transcript, Variant Origin, Variant Type, Zygosity",,FALSE,Patient,,,
 Biospecimen,"HTAN biological entity; this can be tissue, blood, analyte and subsamples of those",,"Component, HTAN Biospecimen ID, Source HTAN Biospecimen ID, HTAN Parent ID, Timepoint Label, Collection Days from Index, Adjacent Biospecimen IDs, Biospecimen Type, Acquisition Method Type, Fixative Type, Storage Method, Processing Days from Index, Protocol Link,  Site Data Source, Collection Media, Mounting Medium, Processing Location, Histology Assessment By, Histology Assessment Medium, Preinvasive Morphology, Tumor Infiltrating Lymphocytes, Degree of Dysplasia, Dysplasia Fraction, Number Proliferating Cells, Percent Eosinophil Infiltration, Percent Granulocyte Infiltration, Percent Inflam Infiltration, Percent Lymphocyte Infiltration, Percent Monocyte Infiltration, Percent Necrosis, Percent Neutrophil Infiltration, Percent Normal Cells, Percent Stromal Cells, Percent Tumor Cells, Percent Tumor Nuclei, Fiducial Marker, Slicing Method,  Lysis Buffer, Method of Nucleic Acid Isolation",,FALSE,Biosample,Patient,,
 SRRS Biospecimen,"SRRS-specific HTAN biological entity; this can be tissue, blood, analyte and subsamples of those, however it can be described via fewer attributes than a standard HTAN specimen",,"Component, HTAN Biospecimen ID, Source HTAN Biospecimen ID, HTAN Parent ID, Adjacent Biospecimen IDs, Biospecimen Type, Timepoint Label, Collection Days from Index, Acquisition Method Type, Ischemic Time, Ischemic Temperature, Collection Media, Topography Code, Additional Topography, Fixative Type, Storage Method, Preinvasive Morphology, Histologic Morphology Code, Preservation Method, Processing Days from Index, Protocol Link",,FALSE,Biosample,Patient,,