From 722666cb730a8ce1327b0b8ef5bc6a7e9f0ebaa0 Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Mon, 3 Jul 2023 20:17:45 -0400 Subject: [PATCH] Patch/cohort (#47) * patch-scRNAseqlvl4 * edit cohort core * add quotations * add quotes * edit biospecimen error * add validation rule blank * edit biospecimen * Update scRNA-seq_Level_4.csv * Build csv, jsonld * edit cohort * Build csv, jsonld * add RAD51C mutation * Build csv, jsonld * removed collection center from sample core * Build csv, jsonld * change to atlas participant id * Build csv, jsonld --------- Co-authored-by: github-actions --- .vscode/settings.json | 12 + GF.csv | 11 +- GF.jsonld | 324 ++++++++++++------ .../scRNA-seq/scRNA-seq_Level_4.csv | 2 + modules/Biospecimen/Biospecimen.csv | 2 +- modules/Patient/Core.csv | 6 +- modules/Patient/Family_History.csv | 2 +- 7 files changed, 239 insertions(+), 120 deletions(-) create mode 100644 .vscode/settings.json create mode 100644 modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_4.csv diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..2fff7ef --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,12 @@ +{ + "yaml.customTags": [ + "!upload scalar", + "!remove scalar", + "!keep scalar", + "!erase scalar", + "!jwt scalar" + ], + "yaml.schemas": { + "https://raw.githubusercontent.com/doanthuanthanh88/testapi6/main/schema.json": "*.yaml" + } +} \ No newline at end of file diff --git a/GF.csv b/GF.csv index 09953a0..509be41 100644 --- a/GF.csv +++ b/GF.csv @@ -94,7 +94,8 @@ scRNA-seq Level 3,Gene and Isoform expression files,,"Component, Filename, File Cell Median Number Reads,Median number of reads per cell. Number,"","","",TRUE,scRNA-seq Level 3,"","","" Cell Median Number Genes,Median number of genes detected per cell. Number,"","","",TRUE,scRNA-seq Level 3,"","","" Cell Total,Number of sequenced cells. Applies to raw counts matrix only.,"","","",TRUE,scRNA-seq Level 3,"","","" -Biospecimen,"Biological entity; this can be tissue, blood, analyte and subsamples of those",,"Biospecimen ID, Parent ID, Parent Biospecimen ID, Adjacent Biospecimen IDs,Biospecimen Type,Timepoint Label,Specimen Laterality",,FALSE,,Patient,, +scRNA-seq Level 4,"Gene and Isoform expression files",,"Component, Filename, File Format, Data Category, Matrix Type, Linked Matrices, Cell Median Number Reads, Cell Median Number Genes, Cell Total, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Link, Workflow Version",,FALSE,Single_Cell_Sequencing,,, +Biospecimen,"Biological entity; this can be tissue, blood, analyte and subsamples of those","","Biospecimen ID, Parent ID, Parent Biospecimen ID, Adjacent Biospecimen IDs,Biospecimen Type,Timepoint Label,Specimen Laterality","",FALSE,Patient,"","","" Biospecimen ID, ID associated with a biosample based on ID SOP (eg x_yyy_zzz),"","","",TRUE,Biospecimen,"",https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,"" Parent ID, 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,"" Parent Biospecimen ID, Biospecimen Identifier (eg x_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,"" @@ -194,10 +195,8 @@ Multifocal Breast Carcinoma Present Indicator,A response to indicate if there is Multicentric Breast Carcinoma Present Indicator,A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from different clones and usually located in different quadrants of the breast.,"Yes, No, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" BIRADS Mammography Breast Density Category,The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines.,"Predominantly fatty, Scattered fibroglandular densities, Heterogeneously dense, Extremely dense, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" BIRADS Score,Score within the BI-RADS system to characterize abnormal findings,"0,1,2,3,4,4A,4B,4C,5,6","","",FALSE,Breast Cancer Tier 3,"","","" -Cohort Core,"Minimal required set of individual-level clinical data across different cohort collections in practice","","Lab ID,Sex,Race,Ethnicity,Age,BMI,Age at Menarche,Genetic Alteration,Menopause Status,Gravidity,Parity,Menopause Status","",FALSE,Patient,,"","" -Cohort Core RFC,"More idealized, RFC-proposed set of individual-level clinical data that extends Cohort Core","","Class BRCA1,Class BRCA2,Menopause Cycle Stage,Primary Diagnosis,Previous Diagnosis,Tobacco Use,Pack Years Smoked,Alcohol Use,Drinks Per Week,Antibiotic Use","",FALSE,Patient,"Cohort Core","","" -Cohort Core Portal,"Portal-specific augmented set of individual-level clinical data that extends Cohort Core","","Participant ID,Atlas Group","",FALSE,Patient,"Cohort Core","","" -Sample Core,Minimal required set of sample-level clinical data,"","Sample ID, Sample Collection Center, Sample Site, Tumor Grade, Status ER, Status PR, Status HER2","",FALSE,Sample,Sample,"","" +Cohort Core,Set of individual-level clinical data across different cohort collections,"","Atlas Participant ID,Age,Sex,BMI,Race,Ethnicity,Vital Status,Height,Weight,Gravidity,Parity,Age At Menarche,Menstrual Cycle Phase,Menopause Status,Primary Diagnosis,Age at Diagnosis,Diagnosis Status Type,Class BRCA1,Class BRCA2,Tobacco Use,Pack Years Smoked,Alcohol Use,Number of Drinks Per Week,Antibiotic Use,Sample Collection Center,Sample Collection Year,ER Status, PR Status, HER2 Status","",FALSE,Patient,,"","" +Sample Core,Minimal required set of sample-level clinical data,"","Sample ID,Atlas Participant ID, Sample Site, Tumor Grade, Status ER, Status PR, Status HER2","",FALSE,Sample,Sample,"","" Ethnicity,"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.","hispanic or latino, not hispanic or latino, unknown, Not Reported, not allowed to collect","","",TRUE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2192217&version=2.0,"" Gender,"Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]","female, male, unknown, unspecified, Not Reported","","",TRUE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2200604&version=3.0,"" Race,"An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.","white, american indian or alaska native, black or african american, asian, native hawaiian or other pacific islander, other, unknown, Not Reported, not allowed to collect","","",TRUE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2192199&version=1.0,"" @@ -399,7 +398,7 @@ Yes - Cancer History Relative,Individual has a relative with cancer history,""," Family Member Vital Status Indicator,The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1),"Vital Status Alive, Vital Status Dead, unknown, Not Reported","","",FALSE,Family History,"","","" Known Genetic Predisposition Mutation,A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.,"Yes, No, unknown","","",FALSE,Family History,"","","" Hereditary Cancer Predisposition Syndrome,History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.,"Alpha-1 antitrypsin,Attenuated familial adenomatous polyposis,BAP1 mutant disease,Beckwith-Wiedemann,Biliary disorder,Birt-Hogg-Dube syndrome,Carney complex,Cirrhosis unknown etiology,Constitutional mismatch repair deficiency,Familial adenomatous polyposis,Familial gastrointestinal stromal tumor,Familial pancreatic cancer,Familial prostate cancer,Familial renal cancer,Fanconi anemia,Glycogen Storage Disease,Gorlin syndrome,Hereditary breast–ovarian cancer syndrome,Hereditary diffuse gastric cancer ,Hereditary leiomyoma-renal cell carcinoma,Hereditary melanoma,Hereditary mixed polyposis syndrome,Hereditary papillary RCC ,Hereditary papillary renal cell carcinoma,Hereditary paraganglioma–pheochromocytoma syndrome,Hereditary renal oncocytoma,Hereditary retinoblastoma ,Juvenile polyposis syndrome,Li-Fraumeni syndrome,Lynch syndrome,Melanoma–astrocytoma syndrome,Multiple endocrine neoplasia type I,Multiple endocrine neoplasia type II,MUTYH-associated polyposis,Nevoid basal cell carcinoma syndrome ,Not Applicable ,Not Reported,Peutz–Jeghers syndrome,Cowden syndrome,Rhabdoid tumor predisposition syndrome type I,Rhabdoid tumor predisposition syndrome type II,Rubinstein-Taybi syndrome,SDH associated renal cancer,Serrated polyposis syndrome,Tuberous sclerosis complex ,Turcot syndrome,Tyrosinemia,unknown,von Hippel-Lindau Syndrome","","",FALSE,Family History,"","","" -Cancer Associated Gene Mutations,Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history,"APC mutation,ALK mutation,ARF mutation,ATM mutation,ATRX mutation,ACVR1 mutation,BAP1 mutation,BMPR1A mutation,BLM mutation,BRCA1 mutation,BRCA1 and 2 mutation,BRCA2 mutation,BRAF mutation,CDH1 mutation,CDKN2A mutation,CDKN2A and p14ARF mutation,CHK mutation,ETV6 mutation, EGFR mutation, FH mutation,FLCN mutation,GREM1 mutation,HOXB13 mutation,H3K27M mutation,H3G34R/V mutation,IKZF1 mutation,KIT mutation, KRAS mutation, MAX mutation,MEN1 mutation,MET mutation,MLH1 mutation,MSH2 mutation,MSH6 mutation,MUTYH mutation,NF1 mutation,NF2 mutation,Not Applicable,Not Reported,p14ARF mutation,PALB2 mutation,PAX5 mutation,PDGFRA mutation,PHOX2B mutation,PMS2 mutation,PolD mutation,PolE mutation,POT1 mutation,PRKAR1A mutation,PTCH mutation,PTEN mutation,ROS1 mutation,RB1 mutation,RET mutation,SDHAF2 mutation,SDHB mutation,SDHC mutation,SDHD mutation,SETD2 mutation,SMAD4 mutation,SMARCA4 mutation,SMARCB1 mutation,STK11 mutation,TMEM127 mutation,TP53 mutation,TSC1 mutation,TSC2 mutation,unknown,VHL mutation","","",FALSE,Family History,"","","" +Cancer Associated Gene Mutations,Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history,"APC mutation,ALK mutation,ARF mutation,ATM mutation,ATRX mutation,ACVR1 mutation,BAP1 mutation,BMPR1A mutation,BLM mutation,BRCA1 mutation,BRCA1 and 2 mutation,BRCA2 mutation,BRAF mutation,CDH1 mutation,CDKN2A mutation,CDKN2A and p14ARF mutation,CHK mutation,ETV6 mutation, EGFR mutation, FH mutation,FLCN mutation,GREM1 mutation,HOXB13 mutation,H3K27M mutation,H3G34R/V mutation,IKZF1 mutation,KIT mutation, KRAS mutation, MAX mutation,MEN1 mutation,MET mutation,MLH1 mutation,MSH2 mutation,MSH6 mutation,MUTYH mutation,NF1 mutation,NF2 mutation,Not Applicable,Not Reported,p14ARF mutation,PALB2 mutation,PAX5 mutation,PDGFRA mutation,PHOX2B mutation,PMS2 mutation,PolD mutation,PolE mutation,POT1 mutation,PRKAR1A mutation,PTCH mutation,PTEN mutation,RAD51C mutation,ROS1 mutation,RB1 mutation,RET mutation,SDHAF2 mutation,SDHB mutation,SDHC mutation,SDHD mutation,SETD2 mutation,SMAD4 mutation,SMARCA4 mutation,SMARCB1 mutation,STK11 mutation,TMEM127 mutation,TP53 mutation,TSC1 mutation,TSC2 mutation,unknown,VHL mutation","","",FALSE,Family History,"","","" Days to Follow Up,Number of days between the date used for index and the date of the patient's last follow-up appointment or contact.,"","","",TRUE,Follow Up,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154727&version=1.0,"" Adverse Event,Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.,"Abdominal Distension, Abdominal Infection,Abdominal Pain,Abdominal Soft Tissue Necrosis,Abducens Nerve Disorder,Accessory Nerve Disorder,Acidosis,Acoustic Nerve Disorder NOS,Activated Partial Thromboplastin Time Prolonged,Acute Coronary Syndrome,Acute Kidney Injury,Adrenal Insufficiency,Adult Respiratory Distress Syndrome, Agitation, Akathisia, Alanine Aminotransferase Increased,Alcohol Intolerance,Alkaline Phosphatase Increased,Alkalosis,Allergic Reaction,Allergic Rhinitis, Alopecia, Amnesia,Anal Fistula,Anal Hemorrhage,Anal Mucositis, Anal Necrosis,Anal Pain,Anal Stenosis,Anal Ulcer,Anaphylaxis,Anemia,Ankle Fracture,Anorectal Infection,Anorexia,Anorgasmia,Anxiety,Aortic Injury,Aortic Valve Disease,Aphonia,Apnea,Appendicitis,Appendicitis Perforated,Arachnoiditis,Arterial Injury,Arteritis Infective,Arthralgia,Arthritis,Ascites,Aspartate Aminotransferase Increased,Aspiration,Asystole,Ataxia,Atelectasis,Atrial Fibrillation,Atrial Flutter,Atrioventricular Block Complete,Atrioventricular Block First Degree,Autoimmune Disorder,Avascular Necrosis,Azoospermia,Back Pain,Bile Duct Stenosis,Biliary Anastomotic Leak,Biliary Fistula,Biliary Tract Infection,Bladder Anastomotic Leak,Bladder Infection,Bladder Perforation,Bladder Spasm,Bloating,Blood and Lymphatic System Disorders Other,Blood Antidiuretic Hormone Abnormal,Blood Bilirubin Increased,Blood Corticotrophin Decreased,Blood Gonadotrophin Abnormal,Blood Prolactin Abnormal,Blurred Vision,Body Odor,Bone Infection,Bone Marrow Hypocellular,Bone Pain,Brachial Plexopathy,Breast Atrophy,Breast Infection,Breast Pain,Bronchial Fistula,Bronchial Infection,Bronchial Obstruction,Bronchial Stricture,Bronchopleural Fistula,Bronchopulmonary Hemorrhage,Bronchospasm,Bruising,Bullous Dermatitis,Burn,Buttock Pain,Capillary Leak Syndrome,Carbon Monoxide Diffusing Capacity Decreased,Cardiac Arrest,Cardiac Disorders Other,Cardiac Troponin I Increased,Cardiac Troponin T Increased,Cataract,Catheter Related Infection,CD4 Lymphocytes Decreased,Cecal Hemorrhage,Cecal Infection,Central Nervous System Necrosis,Cerebrospinal Fluid Leakage,Cervicitis Infection,Cheilitis,Chest Pain Cardiac,Chest Wall Pain,Chills,Cholecystitis,Cholesterol High,Chronic Kidney Disease,Chylothorax,Cognitive Disturbance,Colitis,Colonic Fistula,Colonic Hemorrhage,Colonic Obstruction,Colonic Perforation,Colonic Stenosis,Colonic Ulcer,Concentration Impairment,Conduction Disorder,Confusion,Congenital, Familial and Genetic Disorders Other,Conjunctivitis,Conjunctivitis Infective,Constipation,Constrictive Pericarditis,Corneal Infection,Corneal Ulcer,Cough,CPK Increased,Cranial Nerve Infection,Creatinine Increased,Cushingoid,Cystitis Noninfective,Cytokine Release Syndrome,Death Neonatal,Death NOS,Dehydration,Delayed Orgasm,Delayed Puberty,Delirium,Delusions,Dental Caries,Depressed Level of Consciousness,Depression,Dermatitis Radiation,Device Related Infection,Diarrhea,Disseminated Intravascular Coagulation,Dizziness,Dry Eye,Dry Mouth,Dry Skin,Duodenal Fistula,Duodenal Hemorrhage,Duodenal Infection,Duodenal Obstruction,Duodenal Perforation,Duodenal Stenosis,Duodenal Ulcer,Dysarthria,Dysesthesia,Dysgeusia,Dysmenorrhea,Dyspareunia,Dyspepsia,Dysphagia,Dysphasia,Dyspnea,Ear and Labyrinth Disorders Other,Ear Pain,Edema Cerebral,Edema Face,Edema Limbs,Edema Trunk,Ejaculation Disorder,Ejection Fraction Decreased,Electrocardiogram QT Corrected Interval Prolonged,Encephalitis Infection,Encephalomyelitis Infection,Encephalopathy,Endocarditis Infective,Endocrine Disorders Other,Endophthalmitis,Enterocolitis,Enterocolitis Infectious,Enterovesical Fistula,Epistaxis,Erectile Dysfunction,Erythema Multiforme,Erythroderma,Esophageal Anastomotic Leak,Esophageal Fistula,Esophageal Hemorrhage,Esophageal Infection,Esophageal Necrosis,Esophageal Obstruction,Esophageal Pain,Esophageal Perforation,Esophageal Stenosis,Esophageal Ulcer,Esophageal Varices Hemorrhage,Esophagitis,Euphoria,Exostosis,External Ear Inflammation,External Ear Pain,Extraocular Muscle Paresis,Extrapyramidal Disorder,Eye Disorders Other,Eye Infection,Eye Pain,Eyelid Function Disorder,Facial Muscle Weakness,Facial Nerve Disorder,Facial Pain,Fall,Fallopian Tube Anastomotic Leak,Fallopian Tube Obstruction,Fallopian Tube Perforation,Fallopian Tube Stenosis,Fat Atrophy,Fatigue,Febrile Neutropenia,Fecal Incontinence,Female Genital Tract Fistula,Feminization Acquired,Fetal Death,Fetal Growth Retardation,Fever,Fibrinogen Decreased,Fibrosis Deep Connective Tissue,Flank Pain,Flashing Lights,Flatulence,Floaters,Flu Like Symptoms,Flushing,Forced Expiratory Volume Decreased,Fracture,Gait Disturbance,Gallbladder Fistula,Gallbladder Infection,Gallbladder Necrosis,Gallbladder Obstruction,Gallbladder Pain,Gallbladder Perforation,Gastric Anastomotic Leak,Gastric Fistula,Gastric Hemorrhage,Gastric Necrosis,Gastric Perforation,Gastric Stenosis,Gastric Ulcer,Gastritis,Gastroesophageal Reflux Disease,Gastrointestinal Anastomotic Leak,Gastrointestinal Disorders Other,Gastrointestinal Fistula,Gastrointestinal Pain,Gastrointestinal Stoma Necrosis,Gastroparesis,General Disorders and Administration Site Conditions Other,Generalized Muscle Weakness,Genital Edema,GGT Increased,Gingival Pain,Glaucoma,Glossopharyngeal Nerve Disorder,Glucose Intolerance,Growth Accelerated,Growth Hormone Abnormal,Growth Suppression,Gum Infection,Gynecomastia,Hallucinations,Haptoglobin Decreased,Head Soft Tissue Necrosis,Headache,Hearing Impaired,Heart Failure,Hematoma,Hematosalpinx,Hematuria,Hemoglobin Increased,Hemoglobinuria,Hemolysis,Hemolytic Uremic Syndrome,Hemorrhoidal Hemorrhage,Hemorrhoids,Hepatic Failure,Hepatic Hemorrhage,Hepatic Infection,Hepatic Necrosis,Hepatic Pain,Hepatitis Viral,Hepatobiliary Disorders Other,Hiccups,Hip Fracture,Hirsutism,Hoarseness,Hot Flashes,Hydrocephalus,Hypercalcemia,Hyperglycemia,Hyperhidrosis,Hyperkalemia,Hypermagnesemia,Hypernatremia,Hyperparathyroidism,Hypersomnia,Hypertension,Hyperthyroidism,Hypertrichosis,Hypertriglyceridemia,Hyperuricemia,Hypoalbuminemia,Hypocalcemia,Hypoglossal Nerve Disorder,Hypoglycemia,Hypohidrosis,Hypokalemia,Hypomagnesemia,Hyponatremia,Hypoparathyroidism,Hypophosphatemia,Hypotension,Hypothermia,Hypothyroidism,Hypoxia,Ileal Fistula,Ileal Hemorrhage,Ileal Obstruction,Ileal Perforation,Ileal Stenosis,Ileal Ulcer,Ileus,Immune System Disorders Other,Infections and Infestations Other,Infective Myositis,Infusion Related Reaction,Infusion Site Extravasation,Injection Site Reaction,Injury to Carotid Artery,Injury to Inferior Vena Cava,Injury to Jugular Vein,Injury to Superior Vena Cava,Injury, Poisoning and Procedural Complications Other,INR Increased,Insomnia,Intestinal Stoma Leak,Intestinal Stoma Obstruction,Intestinal Stoma Site Bleeding,Intra-Abdominal Hemorrhage,Intracranial Hemorrhage,Intraoperative Arterial Injury,Intraoperative Breast Injury,Intraoperative Cardiac Injury,Intraoperative Ear Injury,Intraoperative Endocrine Injury,Intraoperative Gastrointestinal Injury,Intraoperative Head and Neck Injury,Intraoperative Hemorrhage,Intraoperative Hepatobiliary Injury,Intraoperative Musculoskeletal Injury,Intraoperative Neurological Injury,Intraoperative Ocular Injury,Intraoperative Renal Injury,Intraoperative Reproductive Tract Injury,Intraoperative Respiratory Injury,Intraoperative Skin Injury,Intraoperative Splenic Injury,Intraoperative Urinary Injury,Intraoperative Venous Injury,Investigations Other,Iron Overload,Irregular Menstruation,Irritability,Ischemia Cerebrovascular,IVth Nerve Disorder,Jejunal Fistula,Jejunal Hemorrhage,Jejunal Obstruction,Jejunal Perforation,Jejunal Stenosis,Jejunal Ulcer,Joint Effusion,Joint Infection,Joint Range of Motion Decreased,Joint Range of Motion Decreased Cervical Spine,Joint Range of Motion Decreased Lumbar Spine,Keratitis,Kidney Anastomotic Leak,Kidney Infection,Kyphosis,Lactation Disorder,Large Intestinal Anastomotic Leak,Laryngeal Edema,Laryngeal Fistula,Laryngeal Hemorrhage,Laryngeal Inflammation,Laryngeal Mucositis,Laryngeal Obstruction,Laryngeal Stenosis,Laryngitis,Laryngopharyngeal Dysesthesia,Laryngospasm,Left Ventricular Systolic Dysfunction,Lethargy,Leukemia Secondary to Oncology Chemotherapy,Leukocytosis,Leukoencephalopathy,Libido Decreased,Libido Increased,Lip Infection,Lip Pain,Lipase Increased,Lipohypertrophy,Localized Edema,Lordosis,Lower Gastrointestinal Hemorrhage,Lung Infection,Lymph Gland Infection,Lymph Leakage,Lymph Node Pain,Lymphedema,Lymphocele,Lymphocyte Count Decreased,Lymphocyte Count Increased,Malabsorption,Malaise,Mania,Mediastinal Hemorrhage,Mediastinal Infection,Memory Impairment,Meningismus,Meningitis,Menopause,Menorrhagia,Metabolism and Nutrition Disorders Other,Middle Ear Inflammation,Mitral Valve Disease,Mobitz (Type) II Atrioventricular Block,Mobitz Type I,Movements Involuntary,Mucosal Infection,Mucositis Oral,Multi-Organ Failure,Muscle Weakness Left-Sided,Muscle Weakness Lower Limb,Muscle Weakness Right-Sided,Muscle Weakness Trunk,Muscle Weakness Upper Limb,Musculoskeletal and Connective Tissue Disorders Other,Musculoskeletal Deformity,Myalgia,Myelitis,Myelodysplastic Syndrome,Myocardial Infarction,Myocarditis,Myositis,Nail Discoloration,Nail Infection,Nail Loss,Nail Ridging,Nasal Congestion,Nausea,Neck Edema,Neck Pain,Neck Soft Tissue Necrosis,Neoplasms Benign, Malignant and Unspecified (Incl Cysts and Polyps) Other,Nervous System Disorders Other,Neuralgia,Neutrophil Count Decreased,Night Blindness,Nipple Deformity,Non-Cardiac Chest Pain,Nystagmus,Obesity,Obstruction Gastric,Oculomotor Nerve Disorder,Olfactory Nerve Disorder,Oligospermia,Optic Nerve Disorder,Oral Cavity Fistula,Oral Dysesthesia,Oral Hemorrhage,Oral Pain,Osteonecrosis of Jaw,Osteoporosis,Otitis Externa,Otitis Media,Ovarian Hemorrhage,Ovarian Infection,Ovarian Rupture,Ovulation Pain,Pain,Pain in Extremity,Pain of Skin,Palmar-Plantar Erythrodysesthesia Syndrome,Palpitations,Pancreas Infection,Pancreatic Anastomotic Leak,Pancreatic Duct Stenosis,Pancreatic Enzymes Decreased,Pancreatic Fistula,Pancreatic Hemorrhage,Pancreatic Necrosis,Pancreatitis,Papilledema,Papulopustular Rash,Paresthesia,Paronychia,Paroxysmal Atrial Tachycardia,Pelvic Floor Muscle Weakness,Pelvic Infection,Pelvic Pain,Pelvic Soft Tissue Necrosis,Penile Infection,Penile Pain,Perforation Bile Duct,Pericardial Effusion,Pericardial Tamponade,Pericarditis,Perineal Pain,Periodontal Disease,Periorbital Edema,Periorbital Infection,Peripheral Ischemia,Peripheral Motor Neuropathy,Peripheral Nerve Infection,Peripheral Sensory Neuropathy,Peritoneal Infection,Peritoneal Necrosis,Personality Change,Phantom Pain,Pharyngeal Anastomotic Leak,Pharyngeal Fistula,Pharyngeal Hemorrhage,Pharyngeal Mucositis,Pharyngeal Necrosis,Pharyngeal Stenosis,Pharyngitis,Pharyngolaryngeal Pain,Phlebitis,Phlebitis Infective,Photophobia,Photosensitivity,Platelet Count Decreased,Pleural Effusion,Pleural Hemorrhage,Pleural Infection,Pleuritic Pain,Pneumonitis,Pneumothorax,Portal Hypertension,Portal Vein Thrombosis,Postnasal Drip,Postoperative Hemorrhage,Postoperative Thoracic Procedure Complication,Precocious Puberty,Pregnancy, Puerperium and Perinatal Conditions Other,Premature Delivery,Premature Menopause,Presyncope,Proctitis,Productive Cough,Prolapse of Intestinal Stoma,Prolapse of Urostomy,Prostate Infection,Prostatic Hemorrhage,Prostatic Obstruction,Prostatic Pain,Proteinuria,Pruritus,Psychiatric Disorders Other,Psychosis,Pulmonary Edema,Pulmonary Fibrosis,Pulmonary Fistula,Pulmonary Hypertension,Pulmonary Valve Disease,Purpura,Pyramidal Tract Syndrome,Radiation Recall Reaction (Dermatologic),Radiculitis,Rash Acneiform,Rash Maculo-Papular,Rash Pustular,Rectal Anastomotic Leak,Rectal Fistula,Rectal Hemorrhage,Rectal Mucositis,Rectal Necrosis,Rectal Obstruction,Rectal Pain,Rectal Perforation,Rectal Stenosis,Rectal Ulcer,Recurrent Laryngeal Nerve Palsy,Renal and Urinary Disorders Other,Renal Calculi,Renal Colic,Renal Hemorrhage,Reproductive System and Breast Disorders Other,Respiratory Failure,Respiratory, Thoracic and Mediastinal Disorders Other,Restlessness,Restrictive Cardiomyopathy,Retinal Detachment,Retinal Tear,Retinal Vascular Disorder,Retinoic Acid Syndrome,Retinopathy,Retroperitoneal Hemorrhage,Reversible Posterior Leukoencephalopathy Syndrome,Rhinitis Infective,Right Ventricular Dysfunction,Salivary Duct Inflammation,Salivary Gland Fistula,Salivary Gland Infection,Scalp Pain,Scleral Disorder,Scoliosis,Scrotal Infection,Scrotal Pain,Seizure,Sepsis,Seroma,Serum Amylase Increased,Serum Sickness,Sick Sinus Syndrome,Sinus Bradycardia,Sinus Disorder,Sinus Pain,Sinus Tachycardia,Sinusitis,Skin and Subcutaneous Tissue Disorders Other,Skin Atrophy,Skin Hyperpigmentation,Skin Hypopigmentation,Skin Induration,Skin Infection,Skin Ulceration,Sleep Apnea,Small Intestinal Anastomotic Leak,Small Intestinal Mucositis,Small Intestinal Obstruction,Small Intestinal Perforation,Small Intestinal Stenosis,Small Intestine Infection,Small Intestine Ulcer,Sneezing,Social Circumstances Other,Soft Tissue Infection,Soft Tissue Necrosis Lower Limb,Soft Tissue Necrosis Upper Limb,Somnolence,Sore Throat,Spasticity,Spermatic Cord Anastomotic Leak,Spermatic Cord Hemorrhage,Spermatic Cord Obstruction,Spinal Fracture,Spleen Disorder,Splenic Infection,Stenosis of Gastrointestinal Stoma,Stevens-Johnson Syndrome,Stoma Site Infection,Stomach Pain,Stomal Ulcer,Stridor,Stroke,Sudden Death NOS,Suicidal Ideation,Suicide Attempt,Superficial Soft Tissue Fibrosis,Superficial Thrombophlebitis,Superior Vena Cava Syndrome,Supraventricular Tachycardia,Surgical and Medical Procedures Other,Syncope,Telangiectasia,Testicular Disorder,Testicular Hemorrhage,Testicular Pain,Thromboembolic Event,Thrombotic Thrombocytopenic Purpura,Tinnitus,Tooth Development Disorder,Tooth Discoloration,Tooth Infection,Toothache,Toxic Epidermal Necrolysis,Tracheal Fistula,Tracheal Hemorrhage,Tracheal Mucositis,Tracheal Obstruction,Tracheal Stenosis,Tracheitis,Tracheostomy Site Bleeding,Transient Ischemic Attacks,Treatment Related Secondary Malignancy,Tremor,Tricuspid Valve Disease,Trigeminal Nerve Disorder,Trismus,Tumor Lysis Syndrome,Tumor Pain,Typhlitis,Unequal Limb Length,Unintended Pregnancy,Upper Gastrointestinal Hemorrhage,Upper Respiratory Infection,Ureteric Anastomotic Leak,Urethral Anastomotic Leak,Urethral Infection,Urinary Fistula,Urinary Frequency,Urinary Incontinence,Urinary Retention,Urinary Tract Infection,Urinary Tract Obstruction,Urinary Tract Pain,Urinary Urgency,Urine Discoloration,Urine Output Decreased,Urostomy Leak,Urostomy Obstruction,Urostomy Site Bleeding,Urostomy Stenosis,Urticaria,Uterine Anastomotic Leak,Uterine Fistula,Uterine Hemorrhage,Uterine Infection,Uterine Obstruction,Uterine Pain,Uterine Perforation,Uveitis,Vaginal Anastomotic Leak,Vaginal Discharge,Vaginal Dryness,Vaginal Fistula,Vaginal Hemorrhage,Vaginal Infection,Vaginal Inflammation,Vaginal Obstruction,Vaginal Pain,Vaginal Perforation,Vaginal Stricture,Vaginismus,Vagus Nerve Disorder,Vas Deferens Anastomotic Leak,Vascular Access Complication,Vascular Disorders Other,Vasculitis,Vasovagal Reaction,Venous Injury,Ventricular Arrhythmia,Ventricular Fibrillation,Ventricular Tachycardia,Vertigo,Vestibular Disorder,Virilization,Visceral Arterial Ischemia,Vital Capacity Abnormal,Vitreous Hemorrhage,Voice Alteration,Vomiting,Vulval Infection,Watering Eyes,Weight Gain,Weight Loss,Wheezing,White Blood Cell Decreased,Wolff-Parkinson-White Syndrome,Wound Complication,Wound Dehiscence,Wound Infection,Wrist Fracture","","",FALSE,Follow Up,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3125302&version=1.1,"" BMI,A calculated numerical quantity that represents an individual's weight to height ratio.,"","","",FALSE,Follow Up,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2006410&version=3.0,"" diff --git a/GF.jsonld b/GF.jsonld index c1d10c0..6651253 100644 --- a/GF.jsonld +++ b/GF.jsonld @@ -5099,25 +5099,78 @@ "sms:validationRules": [] }, { - "@id": "bts:Biospecimen", + "@id": "bts:ScRNA-seqLevel4", "@type": "rdfs:Class", - "rdfs:comment": "Biological entity; this can be tissue, blood, analyte and subsamples of those", - "rdfs:label": "Biospecimen", + "rdfs:comment": "Gene and Isoform expression files", + "rdfs:label": "ScRNA-seqLevel4", "rdfs:subClassOf": [ { - "@id": "bts:Thing" + "@id": "bts:SingleCellSequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Biospecimen", + "sms:displayName": "scRNA-seq Level 4", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:DataCategory" + }, + { + "@id": "bts:MatrixType" + }, + { + "@id": "bts:LinkedMatrices" + }, + { + "@id": "bts:CellMedianNumberReads" + }, + { + "@id": "bts:CellMedianNumberGenes" + }, + { + "@id": "bts:CellTotal" + }, + { + "@id": "bts:ScRNAseqWorkflowType" + }, + { + "@id": "bts:ScRNAseqWorkflowParametersDescription" + }, + { + "@id": "bts:WorkflowLink" + }, + { + "@id": "bts:WorkflowVersion" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:Biospecimen", + "@type": "rdfs:Class", + "rdfs:comment": "Biological entity; this can be tissue, blood, analyte and subsamples of those", + "rdfs:label": "Biospecimen", + "rdfs:subClassOf": [ { "@id": "bts:Patient" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Biospecimen", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:BiospecimenID" @@ -8267,7 +8320,7 @@ { "@id": "bts:CohortCore", "@type": "rdfs:Class", - "rdfs:comment": "Minimal required set of individual-level clinical data across different cohort collections in practice", + "rdfs:comment": "Set of individual-level clinical data across different cohort collections", "rdfs:label": "CohortCore", "rdfs:subClassOf": [ { @@ -8281,31 +8334,31 @@ "sms:required": "sms:false", "sms:requiresDependency": [ { - "@id": "bts:LabID" + "@id": "bts:AtlasParticipantID" }, { - "@id": "bts:Sex" + "@id": "bts:Age" }, { - "@id": "bts:Race" + "@id": "bts:Sex" }, { - "@id": "bts:Ethnicity" + "@id": "bts:BMI" }, { - "@id": "bts:Age" + "@id": "bts:Race" }, { - "@id": "bts:BMI" + "@id": "bts:Ethnicity" }, { - "@id": "bts:AgeatMenarche" + "@id": "bts:VitalStatus" }, { - "@id": "bts:GeneticAlteration" + "@id": "bts:Height" }, { - "@id": "bts:MenopauseStatus" + "@id": "bts:Weight" }, { "@id": "bts:Gravidity" @@ -8314,46 +8367,28 @@ "@id": "bts:Parity" }, { - "@id": "bts:MenopauseStatus" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:CohortCoreRFC", - "@type": "rdfs:Class", - "rdfs:comment": "More idealized, RFC-proposed set of individual-level clinical data that extends Cohort Core", - "rdfs:label": "CohortCoreRFC", - "rdfs:subClassOf": [ + "@id": "bts:AgeAtMenarche" + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cohort Core RFC", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:MenstrualCyclePhase" + }, { - "@id": "bts:CohortCore" - } - ], - "sms:requiresDependency": [ + "@id": "bts:MenopauseStatus" + }, { - "@id": "bts:ClassBRCA1" + "@id": "bts:PrimaryDiagnosis" }, { - "@id": "bts:ClassBRCA2" + "@id": "bts:AgeatDiagnosis" }, { - "@id": "bts:MenopauseCycleStage" + "@id": "bts:DiagnosisStatusType" }, { - "@id": "bts:PrimaryDiagnosis" + "@id": "bts:ClassBRCA1" }, { - "@id": "bts:PreviousDiagnosis" + "@id": "bts:ClassBRCA2" }, { "@id": "bts:TobaccoUse" @@ -8365,40 +8400,25 @@ "@id": "bts:AlcoholUse" }, { - "@id": "bts:DrinksPerWeek" + "@id": "bts:NumberofDrinksPerWeek" }, { "@id": "bts:AntibioticUse" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:CohortCorePortal", - "@type": "rdfs:Class", - "rdfs:comment": "Portal-specific augmented set of individual-level clinical data that extends Cohort Core", - "rdfs:label": "CohortCorePortal", - "rdfs:subClassOf": [ + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cohort Core Portal", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:SampleCollectionCenter" + }, { - "@id": "bts:CohortCore" - } - ], - "sms:requiresDependency": [ + "@id": "bts:SampleCollectionYear" + }, { - "@id": "bts:ParticipantID" + "@id": "bts:ERStatus" }, { - "@id": "bts:AtlasGroup" + "@id": "bts:PRStatus" + }, + { + "@id": "bts:HER2Status" } ], "sms:validationRules": [] @@ -8428,7 +8448,7 @@ "@id": "bts:SampleID" }, { - "@id": "bts:SampleCollectionCenter" + "@id": "bts:AtlasParticipantID" }, { "@id": "bts:SampleSite" @@ -19556,6 +19576,9 @@ { "@id": "bts:PTENmutation" }, + { + "@id": "bts:RAD51Cmutation" + }, { "@id": "bts:ROS1mutation" }, @@ -39693,10 +39716,10 @@ "sms:validationRules": [] }, { - "@id": "bts:GeneticAlteration", + "@id": "bts:AtlasParticipantID", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "GeneticAlteration", + "rdfs:label": "AtlasParticipantID", "rdfs:subClassOf": [ { "@id": "bts:CohortCore" @@ -39705,75 +39728,92 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genetic Alteration", + "sms:displayName": "Atlas Participant ID", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ClassBRCA1", + "@id": "bts:AgeAtMenarche", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "ClassBRCA1", + "rdfs:label": "AgeAtMenarche", "rdfs:subClassOf": [ { - "@id": "bts:CohortCoreRFC" + "@id": "bts:CohortCore" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Class BRCA1", + "sms:displayName": "Age At Menarche", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ClassBRCA2", + "@id": "bts:MenstrualCyclePhase", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "ClassBRCA2", + "rdfs:label": "MenstrualCyclePhase", "rdfs:subClassOf": [ { - "@id": "bts:CohortCoreRFC" + "@id": "bts:CohortCore" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Class BRCA2", + "sms:displayName": "Menstrual Cycle Phase", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DiagnosisStatusType", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "DiagnosisStatusType", + "rdfs:subClassOf": [ + { + "@id": "bts:CohortCore" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Diagnosis Status Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MenopauseCycleStage", + "@id": "bts:ClassBRCA1", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "MenopauseCycleStage", + "rdfs:label": "ClassBRCA1", "rdfs:subClassOf": [ { - "@id": "bts:CohortCoreRFC" + "@id": "bts:CohortCore" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Menopause Cycle Stage", + "sms:displayName": "Class BRCA1", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PreviousDiagnosis", + "@id": "bts:ClassBRCA2", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "PreviousDiagnosis", + "rdfs:label": "ClassBRCA2", "rdfs:subClassOf": [ { - "@id": "bts:CohortCoreRFC" + "@id": "bts:CohortCore" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Previous Diagnosis", + "sms:displayName": "Class BRCA2", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -39784,7 +39824,7 @@ "rdfs:label": "TobaccoUse", "rdfs:subClassOf": [ { - "@id": "bts:CohortCoreRFC" + "@id": "bts:CohortCore" } ], "schema:isPartOf": { @@ -39801,7 +39841,7 @@ "rdfs:label": "AlcoholUse", "rdfs:subClassOf": [ { - "@id": "bts:CohortCoreRFC" + "@id": "bts:CohortCore" } ], "schema:isPartOf": { @@ -39812,61 +39852,112 @@ "sms:validationRules": [] }, { - "@id": "bts:DrinksPerWeek", + "@id": "bts:NumberofDrinksPerWeek", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "DrinksPerWeek", + "rdfs:label": "NumberofDrinksPerWeek", "rdfs:subClassOf": [ { - "@id": "bts:CohortCoreRFC" + "@id": "bts:CohortCore" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Drinks Per Week", + "sms:displayName": "Number of Drinks Per Week", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AtlasGroup", + "@id": "bts:SampleCollectionCenter", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "AtlasGroup", + "rdfs:label": "SampleCollectionCenter", "rdfs:subClassOf": [ { - "@id": "bts:CohortCorePortal" + "@id": "bts:CohortCore" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Atlas Group", + "sms:displayName": "Sample Collection Center", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SampleID", + "@id": "bts:SampleCollectionYear", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "SampleID", + "rdfs:label": "SampleCollectionYear", "rdfs:subClassOf": [ { - "@id": "bts:SampleCore" + "@id": "bts:CohortCore" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sample ID", + "sms:displayName": "Sample Collection Year", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SampleCollectionCenter", + "@id": "bts:ERStatus", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "SampleCollectionCenter", + "rdfs:label": "ERStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:CohortCore" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "ER Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PRStatus", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "PRStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:CohortCore" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "PR Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HER2Status", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "HER2Status", + "rdfs:subClassOf": [ + { + "@id": "bts:CohortCore" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HER2 Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SampleID", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "SampleID", "rdfs:subClassOf": [ { "@id": "bts:SampleCore" @@ -39875,7 +39966,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sample Collection Center", + "sms:displayName": "Sample ID", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -71176,6 +71267,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:RAD51Cmutation", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "RAD51Cmutation", + "rdfs:subClassOf": [ + { + "@id": "bts:CancerAssociatedGeneMutations" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "RAD51C mutation", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:ROS1mutation", "@type": "rdfs:Class", diff --git a/modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_4.csv b/modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_4.csv new file mode 100644 index 0000000..7b392f7 --- /dev/null +++ b/modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_4.csv @@ -0,0 +1,2 @@ +Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules +scRNA-seq Level 4,"Gene and Isoform expression files",,"Component, Filename, File Format, Data Category, Matrix Type, Linked Matrices, Cell Median Number Reads, Cell Median Number Genes, Cell Total, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Link, Workflow Version",,FALSE,Single_Cell_Sequencing,,, diff --git a/modules/Biospecimen/Biospecimen.csv b/modules/Biospecimen/Biospecimen.csv index 1527fd1..7b1720c 100644 --- a/modules/Biospecimen/Biospecimen.csv +++ b/modules/Biospecimen/Biospecimen.csv @@ -1,5 +1,5 @@ Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Biospecimen,"Biological entity; this can be tissue, blood, analyte and subsamples of those",,"Biospecimen ID, Parent ID, Parent Biospecimen ID, Adjacent Biospecimen IDs,Biospecimen Type,Timepoint Label,Specimen Laterality",,FALSE,,Patient,, +Biospecimen,"Biological entity; this can be tissue, blood, analyte and subsamples of those","","Biospecimen ID, Parent ID, Parent Biospecimen ID, Adjacent Biospecimen IDs,Biospecimen Type,Timepoint Label,Specimen Laterality","",FALSE,Patient,"","","" Biospecimen ID, ID associated with a biosample based on ID SOP (eg x_yyy_zzz),"","","",TRUE,Biospecimen,"",https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,"" Parent ID, 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,"" Parent Biospecimen ID, Biospecimen Identifier (eg x_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,"" diff --git a/modules/Patient/Core.csv b/modules/Patient/Core.csv index 5a6ebbb..d68fc60 100644 --- a/modules/Patient/Core.csv +++ b/modules/Patient/Core.csv @@ -1,5 +1,3 @@ Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Cohort Core,"Minimal required set of individual-level clinical data across different cohort collections in practice","","Lab ID,Sex,Race,Ethnicity,Age,BMI,Age at Menarche,Genetic Alteration,Menopause Status,Gravidity,Parity,Menopause Status","",FALSE,Patient,,"","" -Cohort Core RFC,"More idealized, RFC-proposed set of individual-level clinical data that extends Cohort Core","","Class BRCA1,Class BRCA2,Menopause Cycle Stage,Primary Diagnosis,Previous Diagnosis,Tobacco Use,Pack Years Smoked,Alcohol Use,Drinks Per Week,Antibiotic Use","",FALSE,Patient,"Cohort Core","","" -Cohort Core Portal,"Portal-specific augmented set of individual-level clinical data that extends Cohort Core","","Participant ID,Atlas Group","",FALSE,Patient,"Cohort Core","","" -Sample Core,Minimal required set of sample-level clinical data,"","Sample ID, Sample Collection Center, Sample Site, Tumor Grade, Status ER, Status PR, Status HER2","",FALSE,Sample,Sample,"","" +Cohort Core,Set of individual-level clinical data across different cohort collections,"","Atlas Participant ID,Age,Sex,BMI,Race,Ethnicity,Vital Status,Height,Weight,Gravidity,Parity,Age At Menarche,Menstrual Cycle Phase,Menopause Status,Primary Diagnosis,Age at Diagnosis,Diagnosis Status Type,Class BRCA1,Class BRCA2,Tobacco Use,Pack Years Smoked,Alcohol Use,Number of Drinks Per Week,Antibiotic Use,Sample Collection Center,Sample Collection Year,ER Status, PR Status, HER2 Status","",FALSE,Patient,,"","" +Sample Core,Minimal required set of sample-level clinical data,"","Sample ID,Atlas Participant ID, Sample Site, Tumor Grade, Status ER, Status PR, Status HER2","",FALSE,Sample,Sample,"","" diff --git a/modules/Patient/Family_History.csv b/modules/Patient/Family_History.csv index 2cc8d19..3f1d50e 100644 --- a/modules/Patient/Family_History.csv +++ b/modules/Patient/Family_History.csv @@ -13,4 +13,4 @@ Yes - Cancer History Relative,Individual has a relative with cancer history,""," Family Member Vital Status Indicator,The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1),"Vital Status Alive, Vital Status Dead, unknown, Not Reported","","",FALSE,Family History,"","","" Known Genetic Predisposition Mutation,A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.,"Yes, No, unknown","","",FALSE,Family History,"","","" Hereditary Cancer Predisposition Syndrome,History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.,"Alpha-1 antitrypsin,Attenuated familial adenomatous polyposis,BAP1 mutant disease,Beckwith-Wiedemann,Biliary disorder,Birt-Hogg-Dube syndrome,Carney complex,Cirrhosis unknown etiology,Constitutional mismatch repair deficiency,Familial adenomatous polyposis,Familial gastrointestinal stromal tumor,Familial pancreatic cancer,Familial prostate cancer,Familial renal cancer,Fanconi anemia,Glycogen Storage Disease,Gorlin syndrome,Hereditary breast–ovarian cancer syndrome,Hereditary diffuse gastric cancer ,Hereditary leiomyoma-renal cell carcinoma,Hereditary melanoma,Hereditary mixed polyposis syndrome,Hereditary papillary RCC ,Hereditary papillary renal cell carcinoma,Hereditary paraganglioma–pheochromocytoma syndrome,Hereditary renal oncocytoma,Hereditary retinoblastoma ,Juvenile polyposis syndrome,Li-Fraumeni syndrome,Lynch syndrome,Melanoma–astrocytoma syndrome,Multiple endocrine neoplasia type I,Multiple endocrine neoplasia type II,MUTYH-associated polyposis,Nevoid basal cell carcinoma syndrome ,Not Applicable ,Not Reported,Peutz–Jeghers syndrome,Cowden syndrome,Rhabdoid tumor predisposition syndrome type I,Rhabdoid tumor predisposition syndrome type II,Rubinstein-Taybi syndrome,SDH associated renal cancer,Serrated polyposis syndrome,Tuberous sclerosis complex ,Turcot syndrome,Tyrosinemia,unknown,von Hippel-Lindau Syndrome","","",FALSE,Family History,"","","" -Cancer Associated Gene Mutations,Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history,"APC mutation,ALK mutation,ARF mutation,ATM mutation,ATRX mutation,ACVR1 mutation,BAP1 mutation,BMPR1A mutation,BLM mutation,BRCA1 mutation,BRCA1 and 2 mutation,BRCA2 mutation,BRAF mutation,CDH1 mutation,CDKN2A mutation,CDKN2A and p14ARF mutation,CHK mutation,ETV6 mutation, EGFR mutation, FH mutation,FLCN mutation,GREM1 mutation,HOXB13 mutation,H3K27M mutation,H3G34R/V mutation,IKZF1 mutation,KIT mutation, KRAS mutation, MAX mutation,MEN1 mutation,MET mutation,MLH1 mutation,MSH2 mutation,MSH6 mutation,MUTYH mutation,NF1 mutation,NF2 mutation,Not Applicable,Not Reported,p14ARF mutation,PALB2 mutation,PAX5 mutation,PDGFRA mutation,PHOX2B mutation,PMS2 mutation,PolD mutation,PolE mutation,POT1 mutation,PRKAR1A mutation,PTCH mutation,PTEN mutation,ROS1 mutation,RB1 mutation,RET mutation,SDHAF2 mutation,SDHB mutation,SDHC mutation,SDHD mutation,SETD2 mutation,SMAD4 mutation,SMARCA4 mutation,SMARCB1 mutation,STK11 mutation,TMEM127 mutation,TP53 mutation,TSC1 mutation,TSC2 mutation,unknown,VHL mutation","","",FALSE,Family History,"","","" +Cancer Associated Gene Mutations,Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history,"APC mutation,ALK mutation,ARF mutation,ATM mutation,ATRX mutation,ACVR1 mutation,BAP1 mutation,BMPR1A mutation,BLM mutation,BRCA1 mutation,BRCA1 and 2 mutation,BRCA2 mutation,BRAF mutation,CDH1 mutation,CDKN2A mutation,CDKN2A and p14ARF mutation,CHK mutation,ETV6 mutation, EGFR mutation, FH mutation,FLCN mutation,GREM1 mutation,HOXB13 mutation,H3K27M mutation,H3G34R/V mutation,IKZF1 mutation,KIT mutation, KRAS mutation, MAX mutation,MEN1 mutation,MET mutation,MLH1 mutation,MSH2 mutation,MSH6 mutation,MUTYH mutation,NF1 mutation,NF2 mutation,Not Applicable,Not Reported,p14ARF mutation,PALB2 mutation,PAX5 mutation,PDGFRA mutation,PHOX2B mutation,PMS2 mutation,PolD mutation,PolE mutation,POT1 mutation,PRKAR1A mutation,PTCH mutation,PTEN mutation,RAD51C mutation,ROS1 mutation,RB1 mutation,RET mutation,SDHAF2 mutation,SDHB mutation,SDHC mutation,SDHD mutation,SETD2 mutation,SMAD4 mutation,SMARCA4 mutation,SMARCB1 mutation,STK11 mutation,TMEM127 mutation,TP53 mutation,TSC1 mutation,TSC2 mutation,unknown,VHL mutation","","",FALSE,Family History,"","",""