HTAN.dependencies.csv

Unnamed: 0,Attribute,Label,Description,Required,Cond_Req,Valid Values,Conditional Requirements,Component
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Patient
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Patient
Vital Status,Vital Status,VitalStatus,The survival state of the person registered on the protocol.,True,,"['Dead', 'Not Reported', 'Alive', 'unknown']",,Demographics
Race,Race,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.",True,,"['not allowed to collect', 'american indian or alaska native', 'black or african american', 'native hawaiian or other pacific islander', 'white', 'unknown', 'Other', 'asian', 'Not Reported']",,Demographics
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Demographics
Occupation Duration Years,Occupation Duration Years,OccupationDurationYears,The number of years a patient worked in a specific occupation.,False,,,,Demographics
Weeks Gestation at Birth,Weeks Gestation at Birth,WeeksGestationatBirth,Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.,False,,,,Demographics
Gender,Gender,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.]",True,,"['Female', 'Unspecified', 'unknown', 'Male', 'Not Reported']",,Demographics
Age Is Obfuscated,Age Is Obfuscated,AgeIsObfuscated,The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.,False,,"['false', 'true', '']",,Demographics
Country of Residence,Country of Residence,CountryofResidence,Country of Residence at enrollment,False,,"['Saudi Arabia', 'Tunisia', 'Israel', 'Indonesia', 'Lesotho', 'Malta', 'India', 'Puerto Rico', 'Ethiopia', 'Guam', 'Serbia', 'Bosnia and Herzegovina', 'Lithuania', 'Ukraine', 'Burkina Faso', 'Guatemala', 'Yemen', 'Dominican Republic', 'Cambodia', 'State of Palestine', 'Cayman Islands', 'Maldives', 'Taiwan', 'Iraq', 'Saint Vincent and the Grenadines', 'Benin', 'Chad', 'Virgin Islands U.S.', 'Liechtenstein', 'Palau', 'Solomon Islands', 'Azerbaijan', 'Saint Kitts and Nevis', 'Mayotte', 'Aruba', 'Federated States of Micronesia', 'Brazil', 'Western Sahara', 'Ghana', 'Thailand', 'Sao Tome and Principe', 'Virgin Islands British', 'Panama', 'Bangladesh', 'Armenia', 'Saint Pierre and Miquelon', 'Libya', 'Holy See', 'Qatar', 'Turkey', 'Bermuda', 'Antigua and Barbuda', 'Germany', 'Isle of Man', 'Vietnam', 'Hong Kong', 'Trinidad and Tobago', 'Saint Lucia', 'Poland', 'Gabon', 'Nepal', 'Vanuatu', 'El Salvador', 'Portugal', 'Sri Lanka', 'Botswana', 'Mauritius', 'Timor-Leste', 'Peru', 'Argentina', 'Czech Republic (Czechia)', 'Northern Mariana Islands', 'Namibia', 'Uganda', 'Venezuela', 'Chile', 'Tajikistan', 'Svalbard & Jan Mayen Islands', 'Martinique', 'Papua New Guinea', 'Malaysia', 'Russia', 'United Arab Emirates', 'Senegal', 'Comoros', 'Anguilla', 'Finland', 'Moldova', 'Iceland', 'Gambia', 'Seychelles', 'Iran', 'Cameroon', 'Somalia', 'Italy', 'Belgium', 'Kuwait', 'Mozambique', 'Grenada', 'Bahamas', 'Guinea', 'Paraguay', 'Tuvalu', 'Suriname', 'Bahrain', 'Cook Islands', 'South Sudan', 'Burundi', 'Montenegro', 'Denmark', 'Singapore', 'Djibouti', 'Myanmar', 'Zimbabwe', 'Costa Rica', 'Barbados', 'United Kingdom', 'Bulgaria', 'Japan', 'Lebanon', 'Mongolia', 'French Guiana', 'Montserrat', 'Guyana', 'Oman', 'Georgia', 'Nauru', 'North Macedonia', 'Laos', 'Jamaica', 'South Korea', 'United States', 'Bhutan', 'San Marino', 'Hungary', 'Madagascar', 'Curacao', 'Latvia', 'Jordan', 'Ireland', 'Syria', 'Uruguay', 'Cuba', 'Mauritania', 'Mexico', 'Rwanda', 'Sierra Leone', 'North Korea', 'France', 'Tanzania', 'Saint Helena Ascension and Tristan da Cunha', 'Jersey', 'Mali', ""Cote d'Ivoire"", 'Nigeria', 'Slovenia', 'Equatorial Guinea', 'Nicaragua', 'Niue', 'Sweden', 'Belarus', 'Haiti', 'Eritrea', 'Zambia', 'Algeria', 'Congo', 'Uzbekistan', 'Democratic Republic of the Congo', 'Cyprus', 'Greece', 'Liberia', 'Kosovo', 'China', 'Reunion', 'Spain', 'Gibraltar', 'Honduras', 'Malawi', 'Netherlands', 'Kenya', 'Macau', 'Niger', 'Estonia', 'Australia', 'Dominica', 'French Polynesia', 'Guadeloupe', 'South Africa', 'Central African Republic', 'Canada', 'Kiribati', 'Romania', 'Greenland', 'Morocco', 'Switzerland', 'Tonga', 'Sudan', 'Monaco', 'Egypt', 'Afghanistan', 'Austria', 'Belize', 'Guernsey', 'New Zealand', 'New Caledonia', 'Angola', 'Albania', 'Ecuador', 'Wallis and Futuna', 'Colombia', 'Philippines', 'Andorra', 'Kyrgyzstan', 'Brunei', 'Faroe Islands', 'Falkland Islands (Malvinas)', 'Fiji', 'Kazakhstan', 'Tokelau', 'Turkmenistan', 'Eswatini', 'Luxembourg', 'Croatia', 'Norway', 'Pakistan', 'Cape Verde', 'Marshall Islands', 'Slovakia', 'Bolivia', 'Samoa', 'Guinea-Bissau', 'Togo', '']",,Demographics
Year Of Birth,Year Of Birth,YearOfBirth,Numeric value to represent the calendar year in which an individual was born.,False,,,,Demographics
Ethnicity,Ethnicity,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.",True,,"['not allowed to collect', 'hispanic or latino', 'unknown', 'not hispanic or latino', 'Not Reported']",,Demographics
Days to Birth,Days to Birth,DaystoBirth,Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days. If not applicable please enter 'Not Applicable',False,,,,Demographics
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Demographics
Premature At Birth,Premature At Birth,PrematureAtBirth,The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Demographics
Days to Death,Days to Death,DaystoDeath,Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days. If not applicable please enter 'Not Applicable',False,True,,"['Vital Status is ""Dead""']",Demographics
Cause of Death Source,Cause of Death Source,CauseofDeathSource,The text term used to describe the source used to determine the patient's cause of death.,False,True,"['Social Security Death Index', 'Death Certificate', 'Obituary', 'unknown', 'Autopsy', 'Medical Record', 'Not Reported', '']","['Vital Status is ""Dead""']",Demographics
Year of Death,Year of Death,YearofDeath,Numeric value to represent the year of the death of an individual.,False,True,,"['Vital Status is ""Dead""']",Demographics
Cause of Death,Cause of Death,CauseofDeath,The cause of death,False,True,"['Spinal Muscular Atrophy', 'Cancer Related', 'Surgical Complications', 'Infection', 'unknown', 'Not Cancer Related', 'Toxicity', 'Cardiovascular Disorder NOS', 'Not Applicable', 'Not Reported', 'Renal Disorder NOS', 'End-stage Renal Disease', '']","['Vital Status is ""Dead""']",Demographics
Days to Vital Status Reference,Days to Vital Status Reference,DaystoVitalStatusReference,Number of days between the date used for index and the reference date for designation of vital status,False,True,,"['Vital Status is ""Alive""']",Demographics
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,FamilyHistory
Relative with Cancer History,Relative with Cancer History,RelativewithCancerHistory,The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.,False,,"['Yes - Cancer History Relative', 'Not Reported', 'None', 'unknown', '']",,FamilyHistory
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,FamilyHistory
Relatives with Cancer History Count,Relatives with Cancer History Count,RelativeswithCancerHistoryCount,The number of relatives the patient has with a known history of cancer.,False,True,,"['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory
Relationship Type,Relationship Type,RelationshipType,The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.,False,True,"['Brother-in-law', 'Foster Son', 'Paternal Grandparent', 'Stepfather', 'Niece Second Degree Relative', 'Paternal Great Grandparent', 'Adoptive Father', 'Natural Grandchild', 'Paternal Half Sibling', 'Unrelated', 'Half Sibling', 'Brother', 'Natural Parent', 'Maternal Half Brother', 'Legal Guardian', 'Mother-in-law', 'Natural Daughter', 'Maternal First Cousin', 'Grandchild', 'Twin Sibling', 'Grand Nephew', 'Parent', 'Paternal First Cousin', 'Spouse', 'Granddaughter', 'Maternal Half Sibling', 'Paternal Uncle', 'Natural Grandparent', 'Father-in-law', 'Grandson', 'Refused', 'Stepson', 'Adopted Daughter', 'Maternal Grandfather', 'Foster Brother', 'Father', 'Daughter-in-law', 'Stepdaughter', 'Adoptive Sister', 'Adopted Son', 'Maternal Great Aunt', 'Uncle', 'Domestic Partner', 'Paternal Half Sister', 'Sister-in-law', 'Female Cousin', 'Paternal Great Uncle', 'Wife', 'Natural Grandfather', 'Step Sibling', 'Stepbrother', 'Maternal Great Grandparent', 'Not Reported', 'Grandmother', 'Great Grandchild', 'Paternal Grandfather', 'First Cousin Once Removed', 'Half Brother', 'Grandparent', 'Half Sister', 'Son-in-law', 'Grandfather', 'Male Cousin', 'Fraternal Twin Sister', 'Maternal Grandparent', 'Cousin', 'Full Brother', 'Natural Child', 'Fraternal Twin Sibling', 'Sibling', 'Niece', 'Step Child', 'Natural Son', 'Nephew', 'Paternal Half Brother', 'Adoptive Mother', 'Identical Twin Sibling', 'Maternal Half Sister', 'Natural Brother', 'unknown', 'Sister', 'Stepmother', 'Stepsister', 'Full Sister', 'Mother', 'Foster Sister', 'Child', 'Fraternal Twin Brother', 'Adoptive Brother', 'Identical Twin Brother', 'Maternal Aunt', 'Maternal Uncle', 'Natural Mother', 'Husband', 'Paternal Great Aunt', 'Paternal Aunt', 'Maternal First Cousin Once Removed', 'Aunt', 'Daughter', 'Foster Daughter', 'Paternal First Cousin Once Removed', 'Natural Sibling', 'Natural Father', 'Ward', 'Other', 'Natural Sister', 'First Cousin', 'Grand Niece', 'Maternal Great Uncle', 'Paternal Grandmother', 'Identical Twin Sister', 'Son', 'Foster Father', 'Natural Grandmother', 'Maternal Grandmother', 'Foster Mother', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory
Relationship Primary Diagnosis,Relationship Primary Diagnosis,RelationshipPrimaryDiagnosis,The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.,False,True,"['Throat Cancer', 'Gastric Cancer', 'Osteosarcoma', 'Colorectal Cancer', 'Pancreas Cancer', 'Lymph Node Cancer', 'Wilms Tumor', 'Basal Cell Cancer', 'Gallbladder Cancer', 'Breast Cancer', 'Rectal Cancer', 'Rhabdomyosarcoma', 'Hematologic Cancer', 'Uterine Cancer', 'CNS Cancer', 'Multiple Myeloma', 'Kidney Cancer', 'Ewing Sarcoma', 'Neuroblastoma', 'Bile Duct Cancer', 'Sarcoma', 'Spleen Cancer', 'Esophageal Cancer', 'Tonsillar Cancer', 'Gynecologic Cancer', 'Thyroid Cancer', 'Bone Cancer', 'Brain Cancer', 'Lung Cancer', 'Liver Cancer', 'Blood Cancer', 'Prostate Cancer', 'Kaposi Sarcoma', 'Melanoma', 'Leukemia', 'Cancer', 'unknown', 'Mesothelioma', 'Tongue Cancer', 'Glioblastoma', 'Chondrosarcoma', 'Head and Neck Cancer', 'Not Reported', 'Skin Cancer', 'Testicular Cancer', 'Lymphoma', 'Laryngeal Cancer', 'Ovarian Cancer', 'Bladder Cancer', 'Cervical Cancer', 'Adrenal Gland Cancer', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory
Relationship Gender,Relationship Gender,RelationshipGender,The text term used to describe the gender of the patient's relative with a history of cancer.,False,True,"['Female', 'Unspecified', 'unknown', 'Male', 'Not Reported', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory
Relationship Age at Diagnosis,Relationship Age at Diagnosis,RelationshipAgeatDiagnosis,The age (in years) when the patient's relative was first diagnosed.,False,True,,"['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory
Alcohol Exposure,Alcohol Exposure,AlcoholExposure,Indicate if individual has alcohol exposure,True,,"['Not Reported', 'Yes - Alcohol Exposure', 'No - Alcohol Exposure']",,Exposure
Asbestos Exposure,Asbestos Exposure,AsbestosExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Exposure
Respirable Crystalline Silica Exposure,Respirable Crystalline Silica Exposure,RespirableCrystallineSilicaExposure,"The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.",False,,"['yes', 'no', 'unknown', '']",,Exposure
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Exposure
Coal Dust Exposure,Coal Dust Exposure,CoalDustExposure,The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.,False,,"['yes', 'no', 'unknown', '']",,Exposure
Smoking Exposure,Smoking Exposure,SmokingExposure,Indicate if individual has smoking exposure,True,,"['No - Smoking Exposure', 'Not Reported', 'Yes - Smoking Exposure']",,Exposure
Radon Exposure,Radon Exposure,RadonExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to radon.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Exposure
Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,Exposure
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Exposure
Environmental Tobacco Smoke Exposure,Environmental Tobacco Smoke Exposure,EnvironmentalTobaccoSmokeExposure,"The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.",False,,"['yes', 'no', 'unknown', '']",,Exposure
Alcohol Drinks Per Day,Alcohol Drinks Per Day,AlcoholDrinksPerDay,Numeric value used to describe the average number of alcoholic beverages a person consumes per day.,False,True,,"['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure
Alcohol Days Per Week,Alcohol Days Per Week,AlcoholDaysPerWeek,Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.,False,True,,"['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure
Alcohol History,Alcohol History,AlcoholHistory,A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.,False,True,"['Not Reported', 'yes', 'no', 'unknown', '']","['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure
Alcohol Type,Alcohol Type,AlcoholType,Type of alcohol use,False,True,"['Wine', 'unknown', 'Liquor', 'Other', 'Beer', 'Not Reported', '']","['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure
Alcohol Intensity,Alcohol Intensity,AlcoholIntensity,Category to describe the patient's current level of alcohol use as self-reported by the patient.,False,True,"['Non-Drinker', 'Lifelong Non-Drinker', 'Heavy Drinker', 'unknown', 'Drinker', 'Occasional Drinker', 'Not Reported', '']","['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure
Secondhand Smoke as Child,Secondhand Smoke as Child,SecondhandSmokeasChild,The text term used to indicate whether the patient was exposed to secondhand smoke as a child.,False,True,"['Not Reported', 'yes', 'no', 'unknown', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure
Smoke Exposure Duration,Smoke Exposure Duration,SmokeExposureDuration,Text term used to describe the length of time the patient was exposed to an environmental factor.,False,True,"['Not Reported', 'Six Weeks or More', 'unknown', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure
Type of Smoke Exposure,Type of Smoke Exposure,TypeofSmokeExposure,The text term used to describe the patient's specific type of smoke exposure.,False,True,"['Workrelated smoke fire fighting', 'Furnace or boiler smoke', 'Workrelated smoke plumbing', 'No Smoke Exposure', 'Oil burning smoke NOS', 'Accidental vehicle fire smoke', 'Gas burning smoke propane', 'Tobacco smoke pipe', 'Tobacco smoke cigarettes', 'Environmental tobacco smoke', 'Workrelated smoke NOS', 'Electrical fire smoke', 'Workrelated smoke artificial smoke machines', 'Workrelated smoke foundry', 'Accidental forest fire smoke', 'Electronic cigarette smoke NOS', 'Wood burning smoke factory', 'Tobacco smoke cigar', 'Smoke exposure NOS', 'Factory smokestack smoke', 'Grease fire smoke', 'Coal smoke NOS', 'Machine smoke', 'Accidental grass fire smoke', 'Accidental building fire smoke', 'Workrelated smoke plastics factory', 'Workrelated smoke generators', 'Field burning smoke', 'Indoor wood burning stove or fireplace smoke', 'Workrelated smoke military', 'Indoor coal burning stove or fireplace smoke', 'Cooking related smoke NOS', 'Fire smoke NOS', 'Hashish smoke', 'unknown', 'Marijuana smoke', 'Workrelated smoke paint baking', 'Aircraft smoke', 'Indoor stove or fireplace smoke NOS', 'Recreational fire smoke', 'Smokehouse smoke', 'Waste burning smoke', 'Accidental fire smoke NOS', 'Wood burning smoke NOS', 'Workrelated smoke soldering/welding', 'Grilling smoke', 'Burning tree smoke', 'Volcanic smoke', 'Oil burning smoke Kerosene', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure
Smokeless Tobacco Quit Age,Smokeless Tobacco Quit Age,SmokelessTobaccoQuitAge,Smokeless tobacco quit age,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure
Pack Years Smoked,Pack Years Smoked,PackYearsSmoked,Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure
Tobacco Smoking Status,Tobacco Smoking Status,TobaccoSmokingStatus,Category describing current smoking status and smoking history as self-reported by a patient,False,True,"['Smoking history not documented', 'Current Reformed Smoker for < or = 15 yrs', 'Duration Not Specified', 'unknown', 'Current Reformed Smoker for > 15 yrs', 'Current Smoker', 'Not Reported', 'Lifelong Non-Smoker', 'Current Reformed Smoker', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure
Type of Tobacco Used,Type of Tobacco Used,TypeofTobaccoUsed,The text term used to describe the specific type of tobacco used by the patient.,False,True,"['Marijuana', 'Smokeless Tobacco', 'Pipe', 'Electronic Cigarette', 'unknown', 'Other', 'Not Reported', 'Cigarettes', 'Cigar', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure
Tobacco Smoking Quit Year,Tobacco Smoking Quit Year,TobaccoSmokingQuitYear,The year in which the participant quit smoking.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure
Tobacco Smoking Onset Year,Tobacco Smoking Onset Year,TobaccoSmokingOnsetYear,The year in which the participant began smoking.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure
Smoking Frequency,Smoking Frequency,SmokingFrequency,The text term used to generally decribe how often the patient smokes.,False,True,"['Some days', 'Every day', 'unknown', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure
Cigarettes per Day,Cigarettes per Day,CigarettesperDay,The average number of cigarettes smoked per day.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure
Tobacco Use per Day,Tobacco Use per Day,TobaccoUseperDay,Numeric value that represents the number of times the patient uses tobacco each day.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure
Time between Waking and First Smoke,Time between Waking and First Smoke,TimebetweenWakingandFirstSmoke,The text term used to describe the approximate amount of time elapsed between the time the patient wakes up in the morning to the time they smoke their first cigarette.,False,True,"['Within 5 Minutes', '31-60 Minutes', 'unknown', 'After 60 Minutes', '6-30 Minutes', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure
Years Smoked,Years Smoked,YearsSmoked,Numeric value (or unknown) to represent the number of years a person has been smoking.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure
Marijuana Use Per Week,Marijuana Use Per Week,MarijuanaUsePerWeek,Numeric value that represents the number of times the patient uses marijuana each day.,False,True,,"['Type is ""Marijuana smoke""']",Exposure
Body Surface Area,Body Surface Area,BodySurfaceArea,Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.,False,,,,FollowUp
ECOG Performance Status,ECOG Performance Status,ECOGPerformanceStatus,The ECOG functional performance status of the patient/participant.,False,,"['""3""', '""2""', '""1""', '""4""', '""5.0""', '""4.0""', '""0""', 'unknown', '""1.0""', '""2.0""', '""0.0""', 'Not Reported', '""3.0""', '""5""', '']",,FollowUp
Diabetes Treatment Type,Diabetes Treatment Type,DiabetesTreatmentType,Text term used to describe the types of treatment used to manage diabetes.,False,,"['Alpha-Glucosidase Inhibitor', 'Insulin', 'Biguanide', 'Oral Hypoglycemic', 'unknown', 'Other', 'Diet', 'Injected Insulin', 'Sulfonylurea', 'Thiazolidinedione', 'Not Reported', '']",,FollowUp
Reflux Treatment Type,Reflux Treatment Type,RefluxTreatmentType,Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).,False,,"['No Treatment', 'Surgically Treated', 'Medically Treated', 'Proton Pump Inhibitors', 'H2 Blockers', 'unknown', 'Antacids', 'Not Applicable', 'Not Reported', '']",,FollowUp
FEV 1 FVC Pre Bronch Percent,FEV 1 FVC Pre Bronch Percent,FEV1FVCPreBronchPercent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.,False,,,,FollowUp
Karnofsky Performance Status,Karnofsky Performance Status,KarnofskyPerformanceStatus,Text term used to describe the classification used of the functional capabilities of a person.,False,,"['""10""', '""80""', '""40""', '""70""', '""0""', '""100""', 'unknown', '""30""', '""60""', '""50""', 'Not Reported', '""20""', '""90""', '']",,FollowUp
Adverse Event Grade,Adverse Event Grade,AdverseEventGrade,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.",False,,"['Grade 3', 'Grade 1', 'Grade 5', 'Grade 2', 'Grade 4', '']",,FollowUp
Viral Hepatitis Serologies,Viral Hepatitis Serologies,ViralHepatitisSerologies,Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.,False,,"['HBV Surface Antibody', 'Hepatitis C Virus RNA', 'HBV Genotype', 'HBV Core Antibody', 'unknown', 'HCV Genotype', 'HBV DNA', 'Hepatitis B Surface Antigen', 'Not Reported', 'Hepatitis C Antibody', '']",,FollowUp
Days to Adverse Event,Days to Adverse Event,DaystoAdverseEvent,Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable',False,,,,FollowUp
FEV1 Ref Pre Bronch Percent,FEV1 Ref Pre Bronch Percent,FEV1RefPreBronchPercent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.,False,,,,FollowUp
Imaging Result,Imaging Result,ImagingResult,The text term used to describe the result of the imaging or scan performed on the patient.,False,,"['Not Performed', 'positive', 'Indeterminate', 'unknown', 'negative', 'Not Reported', '']",,FollowUp
Hysterectomy Type,Hysterectomy Type,HysterectomyType,The text term used to describe the type of hysterectomy the patient had.,False,,"['Simple Hysterectomy', 'Not performed', 'Hysterectomy NOS', 'unknown', 'Not Reported', 'Radical Hysterectomy', '']",,FollowUp
CDC HIV Risk Factors,CDC HIV Risk Factors,CDCHIVRiskFactors,"The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.",False,,"['None', 'unknown', 'Intravenous Drug User', 'Heterosexual Contact', 'Not Reported', 'Hemophiliac', 'Transfusion Recipient', 'Homosexual Contact', '']",,FollowUp
BMI,BMI,BMI,A calculated numerical quantity that represents an individual's weight to height ratio.,False,,,,FollowUp
Height,Height,Height,The height of the patient in centimeters.,False,,,,FollowUp
Days to Comorbidity,Days to Comorbidity,DaystoComorbidity,Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable',False,,,,FollowUp
Risk Factor,Risk Factor,RiskFactor,The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.,False,,"[""Behcet's Disease"", 'Parasitic Disease of Biliary Tract', 'Tobacco NOS', 'Endosalpingiosis', 'Oral Contraceptives', 'Hepatitis B Infection', 'Li-Fraumeni Syndrome', 'Diet', 'Fanconi Anemia', 'Diabetes NOS', 'Headache', 'Allergy Wasp', 'Lynch Syndrome', 'Autoimmune Atrophic Chronic Gastritis', 'Sarcoidosis', 'Diabetes Type II', 'Allergy Mold or Dust', 'Beckwith-Wiedemann', 'Nonalcoholic Steatohepatitis', 'Intestinal Metaplasia', 'Allergy Cat', 'Hepatitis C Infection', 'Alpha-1 Antitrypsin Deficiency', 'Fibrosis', 'Vision Changes', 'Low Grade Dysplasia', 'Human Papillomavirus Infection', 'Diverticulitis', ""Hashimoto's Thyroiditis"", 'Steatosis', 'Cholelithiasis', 'Thyroid Nodular Hyperplasia', 'Hematologic Disorder NOS', 'Helicobacter Pylori-Associated Gastritis', 'Alcohol Consumption', 'Chronic Hepatitis', 'Hepatic Encephalopathy', 'Not Reported', 'Turcot Syndrome', 'Denys-Drash Syndrome', 'Cirrhosis', 'Allergy Fruit', 'Hemochromatosis', 'Colon Polyps', 'Allergy Processed Foods', 'Tobacco Smoking', 'Allergy Seafood', 'Gorlin Syndrome', 'Recurrent Pyogenic Cholangitis', 'Sensory Changes', 'Obesity', 'Tobacco Smokeless', 'Nonalcoholic Fatty Liver Disease', 'Allergy Ant', 'Common variable immune deficiency (CVID)', 'Hypospadias', 'HIV', 'Allergy Bee', 'unknown', 'Allergy Meat', 'Pancreatitis', 'Epstein-Barr Virus', 'High Grade Dysplasia', 'Iron Overload', 'Primary Sclerosing Cholangitis', 'Familial Adenomatous Polyposis', 'Allergy Food NOS', 'Hay Fever', 'Allergy Dairy or Lactose', 'Hepatitis NOS', 'Myasthenia Gravis', 'Gastric Polyp(s)', 'Allergy Eggs', 'Seizure', ""Barrett's Esophagus"", 'Hemihypertrophy', 'Allergy Nuts', 'Serous tubal intraepithelial carcinoma (STIC)', 'Endometriosis', 'Alcoholic Liver Disease', 'Reflux Disease', 'Cancer', 'Undescended Testis', 'Rubinstein-Taybi Syndrome', 'Tattoo', 'Allergy Animal NOS', ""Gilbert's Syndrome"", 'Allergy Dog', 'Eczema', 'Wagr Syndrome', 'Rheumatoid Arthritis', 'Diabetes Type I', 'Lymphocytic Thyroiditis', '']",,FollowUp
Cause of Response,Cause of Response,CauseofResponse,The text term used to describe the suspected cause or reason for the patient disease response.,False,,,,FollowUp
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,FollowUp
HIV Viral Load,HIV Viral Load,HIVViralLoad,"Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.",False,,,,FollowUp
Barretts Esophagus Goblet Cells Present,Barretts Esophagus Goblet Cells Present,BarrettsEsophagusGobletCellsPresent,Presence or absennce of Barretts esophagus goblet cells.,False,,"['yes', 'no', '']",,FollowUp
Comorbidity Method of Diagnosis,Comorbidity Method of Diagnosis,ComorbidityMethodofDiagnosis,The text term used to describe the method used to diagnose the patient's comorbidity disease.,False,,"['Pathology', 'Histology', 'unknown', 'Radiology', 'Not Reported', '']",,FollowUp
Menopause Status,Menopause Status,MenopauseStatus,Text term used to describe the patient's menopause status.,False,,"['Postmenopausal', 'Premenopausal', 'unknown', 'Perimenopausal', 'Not Reported', '']",,FollowUp
HAART Treatment Indicator,HAART Treatment Indicator,HAARTTreatmentIndicator,The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,FollowUp
CD4 Count,CD4 Count,CD4Count,The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.,False,,,,FollowUp
Days to Imaging,Days to Imaging,DaystoImaging,Number of days between the date used for index and the date the imaging or scan was performed on the patient. If not applicable please enter 'Not Applicable',False,,,,FollowUp
Scan Tracer Used,Scan Tracer Used,ScanTracerUsed,The text term used to describe the type of tracer used during the imaging or scan of the patient.,False,,"['Acetate', 'Choline', 'PSMA', 'Axumin', 'Sodium Fluoride', '']",,FollowUp
DLCO Ref Predictive Percent,DLCO Ref Predictive Percent,DLCORefPredictivePercent,"The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.",False,,,,FollowUp
Disease Response,Disease Response,DiseaseResponse,Code assigned to describe the patient's response or outcome to the disease.,False,,"['CPD-Clinical Progression', 'IPD-Immunoprogression', 'MX-Mixed Response', 'DU-Disease Unchanged', 'RD-Responsive Disease', 'CR-Complete Response', 'BED-Biochemical Evidence of Disease', 'AJ-Adjuvant Therapy', 'PDM-Persistent Distant Metastasis', 'PPD-Pseudoprogression', 'PSR-Pseudoresponse', 'TF-Tumor Free', 'PD-Progressive Disease', 'sCR-Stringent Complete Response', 'SPD-Surgical Progression', 'NR-No Response', 'TE-Too Early', 'unknown', 'NPB-No Palliative Benefit', 'PR-Partial Response', 'PLD-Persistent Locoregional Disease', 'Not Reported', 'RPD-Radiographic Progressive Disease', 'PB-Palliative Benefit', 'SD-Stable Disease', 'VGPR-Very Good Partial Response', 'PA-Palliative Therapy', 'WT-With Tumor', 'MR-Minimal/Marginal response', 'Non-CR/Non-PD-Non-CR/Non-PD', 'CRU-Complete Response Unconfirmed', 'RP-Response', 'IMR-Immunoresponse', '']",,FollowUp
FEV1 FVC Post Bronch Percent,FEV1 FVC Post Bronch Percent,FEV1FVCPostBronchPercent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.,False,,,,FollowUp
Weight,Weight,Weight,The weight of the patient measured in kilograms.,False,,,,FollowUp
Evidence of Recurrence Type,Evidence of Recurrence Type,EvidenceofRecurrenceType,The text term used to describe the type of evidence used to determine whether the patient's disease recurred,False,,"['Biopsy with Histologic Confirmation', 'Positive Biomarkers', 'Convincing Image Source', '']",,FollowUp
Recist Targeted Regions Number,Recist Targeted Regions Number,RecistTargetedRegionsNumber,"Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria",False,,,,FollowUp
HPV Positive Type,HPV Positive Type,HPVPositiveType,Text classification to represent the strain or type of human papillomavirus identified in an individual.,False,,"['""58""', '""52""', '""33""', '""16""', '""26""', '""56""', 'Other', '""31""', '""59""', '""66""', '""39""', '""68""', '""82""', '""45""', '""70""', '""18""', '""73""', 'unknown', '""53""', '""63""', 'Not Reported', '""35""', '""51""', '']",,FollowUp
Pancreatitis Onset Year,Pancreatitis Onset Year,PancreatitisOnsetYear,Date of onset of pancreatitis.,False,,,,FollowUp
Nadir CD4 Count,Nadir CD4 Count,NadirCD4Count,Numeric value that represents the lowest point to which the CD4 count has dropped (nadir).,False,,,,FollowUp
Hysterectomy Margins Involved,Hysterectomy Margins Involved,HysterectomyMarginsInvolved,The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.,False,,"['Vagina', 'None', 'Microscopic Parametrium', 'unknown', 'Bladder', 'Not Reported', 'Macroscopic Parametrium', '']",,FollowUp
Comorbidity,Comorbidity,Comorbidity,"The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.",False,,"['Other Cancer Within 5 Years', 'Diabetes', 'Pulmonary Fibrosis', ""Behcet's Disease"", 'Ischemic Heart Disease', 'Cerebrovascular Disease', 'Anxiety', 'Organ transplant (site)', 'Lupus', 'Hepatitis B Infection', 'Li-Fraumeni Syndrome', 'High Grade Liver Dysplastic Nodule', 'Ulcerative Colitis', 'Fanconi Anemia', 'HIV / AIDS', 'Insulin Controlled Diabetes', 'Headache', 'Alpha-1 Antitrypsin', 'Epilepsy', 'Lynch Syndrome', 'Interstitial Pneumontis or ARDS', 'Peptic Ulcer (Ulcer)', 'Peripheral Neuropathy', 'Osteoarthritis', 'Sarcoidosis', 'Arrhythmia', 'Psoriasis', 'Peutz-Jeghers Disease', 'Beckwith-Wiedemann', 'Liver Toxicity (Non-Infectious)', 'Hypothyroidism', 'Nonalcoholic Steatohepatitis', 'Arthritis', 'Hepatitis C Infection', 'MAI', 'Coronary Artery Disease', 'Hereditary Non-polyposis Colon Cancer', 'Adenocarcinoma', 'Fibrosis', 'Human Papillomavirus Infection', 'Avascular Necrosis', 'Bronchitis', 'Liver Cirrhosis (Liver Disease)', 'Cataracts', 'Kidney Disease', 'Other Pulmonary Complications', 'Diverticulitis', 'Celiac Disease', 'Renal Dialysis', ""Hashimoto's Thyroiditis"", 'Hypercholesterolemia', 'Steatosis', 'Asthma', 'Adrenocortical Insufficiency', 'Cholelithiasis', 'Glaucoma', 'Intraductal Papillary Mucinous Neoplasm', 'Sleep apnea', 'Hyperglycemia', 'Type II', 'Chronic Hepatitis', 'Blood Clots', 'Not Reported', 'H. pylori Infection', 'Dyslipidemia', 'Low Grade Liver Dysplastic Nodule', 'Calcium Channel Blockers', 'Turcot Syndrome', 'Denys-Drash Syndrome', 'Cirrhosis', 'COPD', 'Inflammatory Bowel Disease', 'Colon Polyps', 'ITP', 'Stroke', 'Common Variable Immunodeficiency', 'Pain (Various)', 'Peripheral Vascular Disease', 'Tyrosinemia', 'Gorlin Syndrome', 'Allergies', 'Obesity', 'Neuroendocrine Tumor', 'Depression', 'Other Nonmalignant Systemic Disease', 'Heart Disease', 'Hepatitis A Infection', 'Pulmonary Hemorrhage', 'Deep Vein Thrombosis / Thromboembolism', 'HUS/TTP', 'Gonadal Dysfunction', 'Hypospadias', 'Acute Renal Failure', 'Chronic Renal Failure', 'Atrial Fibrillation', 'Tuberculosis', 'Rheumatologic Disease', 'Transient Ischemic Attack', 'GERD', 'unknown', 'Hyperlipidemia', 'Hypertension', 'Gout', 'Pancreatitis', 'Epstein-Barr Virus', 'Iron Overload', 'Hepatitis', 'Primary Sclerosing Cholangitis', 'Hemorrhagic Cystitis', 'Congestive Heart Failure (CHF)', 'Diet Controlled Diabetes', 'Familial Adenomatous Polyposis', 'Smoking', 'Glycogen Storage Disease', 'DVT/PE', 'Renal Failure (Requiring Dialysis)', 'Hypercalcemia', 'Myasthenia Gravis', 'Biliary Disorder', 'Myocardial Infarction', 'Seizure', 'Pregnancy in Patient or Partner', ""Barrett's Esophagus"", 'Other', 'Diabetic Neuropathy', 'Connective Tissue Disorder', 'Hemihypertrophy', ""Crohn's Disease"", 'Basal Cell Carcinoma', 'Cancer', 'Anemia', 'Rubinstein-Taybi Syndrome', 'Bone Fracture(s)', 'Cryptogenic Organizing Pneumonia', 'Osteoporosis or Osteopenia', 'Eczema', 'Joint Replacement', 'Herpes', 'Adenomatous Polyposis Coli', 'Wagr Syndrome', 'Rheumatoid Arthritis', 'Renal Insufficiency', 'Gastroesophageal Reflux Disease', 'unknown Etiology', '']",,FollowUp
Days to Follow Up,Days to Follow Up,DaystoFollowUp,Number of days between the date used for index and the date of the patient's last follow-up appointment or contact. If not applicable please enter 'Not Applicable',True,,,,FollowUp
Adverse Event,Adverse Event,AdverseEvent,Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.,False,,"['Pulmonary Fibrosis', 'Fallopian Tube Stenosis', 'Thromboembolic Event', 'Tricuspid Valve Disease', 'Anxiety', 'Colonic Hemorrhage', 'Lymphocyte Count Decreased', 'Gastric Perforation', 'Cytokine Release Syndrome', 'Prolapse of Intestinal Stoma', 'Genital Edema', 'Vaginal Anastomotic Leak', 'Wolff-Parkinson-White Syndrome', 'Anorectal Infection', 'Vaginal Infection', 'Duodenal Hemorrhage', 'Hip Fracture', 'Psychosis', 'Sinus Pain', 'Neck Pain', 'Headache', 'Urinary Tract Infection', 'Paronychia', 'Hallucinations', 'Gastric Hemorrhage', 'Hyperhidrosis', 'Meningismus', 'Scalp Pain', 'Arachnoiditis', 'Urinary Tract Pain', 'Hoarseness', 'Duodenal Ulcer', 'Uterine Fistula', 'Growth Hormone Abnormal', 'Cecal Infection', 'Mucositis Oral', 'Colonic Obstruction', 'Optic Nerve Disorder', 'Pancreatic Necrosis', 'Urinary Incontinence', 'Perforation Bile Duct', 'Urostomy Obstruction', 'Retroperitoneal Hemorrhage', 'Avascular Necrosis', 'Sore Throat', 'Osteonecrosis of Jaw', 'Cerebrospinal Fluid Leakage', 'Hepatic Necrosis', 'Reproductive System and Breast Disorders Other', 'Myocarditis', 'Gastrointestinal Anastomotic Leak', 'Jejunal Ulcer', 'Esophageal Perforation', 'Duodenal Fistula', 'Salivary Gland Infection', 'Injection Site Reaction', 'Proteinuria', 'Corneal Ulcer', 'Familial and Genetic Disorders Other', 'Abdominal Infection', 'Puerperium and Perinatal Conditions Other', 'Scoliosis', 'Neuralgia', 'Oligospermia', 'Pleural Effusion', 'Hyperthyroidism', 'Pharyngeal Necrosis', 'Uterine Hemorrhage', 'Voice Alteration', 'Dysphasia', 'Pruritus', 'Skin Ulceration', 'Pulmonary Valve Disease', 'Spinal Fracture', 'Adrenal Insufficiency', 'Urostomy Leak', 'Retinopathy', 'Gastrointestinal Stoma Necrosis', 'Duodenal Stenosis', 'Sinus Tachycardia', 'Small Intestinal Perforation', 'Aortic Valve Disease', 'Retinal Tear', 'Reversible Posterior Leukoencephalopathy Syndrome', 'Brachial Plexopathy', 'Acidosis', 'Cecal Hemorrhage', 'Jejunal Perforation', 'Tracheal Obstruction', 'Muscle Weakness Trunk', 'Injury to Jugular Vein', 'Prostate Infection', 'Body Odor', 'Lymph Gland Infection', 'Supraventricular Tachycardia', 'Intestinal Stoma Site Bleeding', 'Malignant and Unspecified (Incl Cysts and Polyps) Other', 'Pancreatic Enzymes Decreased', 'Radiation Recall Reaction (Dermatologic)', 'Dysmenorrhea', 'Hot Flashes', 'Skin Induration', 'Toothache', 'Facial Pain', 'Atrial Fibrillation', 'Breast Pain', 'Movements Involuntary', 'Vaginal Discharge', 'Ovarian Rupture', 'Catheter Related Infection', 'Vertigo', 'Intraoperative Renal Injury', 'Glossopharyngeal Nerve Disorder', 'Hemorrhoids', 'Lordosis', 'Rhinitis Infective', 'Fracture', 'Hypoglossal Nerve Disorder', 'Hypoparathyroidism', 'Pancreatitis', 'Pulmonary Edema', 'Venous Injury', 'Renal and Urinary Disorders Other', 'Injury', 'Lactation Disorder', 'Wound Complication', 'Laryngeal Hemorrhage', 'Retinal Vascular Disorder', 'Poisoning and Procedural Complications Other', 'Gallbladder Obstruction', 'Laryngeal Fistula', 'Fallopian Tube Perforation', 'Ileal Stenosis', 'Mobitz (Type) II Atrioventricular Block', 'Large Intestinal Anastomotic Leak', 'Rash Acneiform', 'Pharyngeal Anastomotic Leak', 'Head Soft Tissue Necrosis', 'Tooth Infection', 'Lymphedema', 'Intestinal Stoma Obstruction', 'Flushing', 'Urticaria', 'Hyperparathyroidism', 'Erythroderma', 'Hyperuricemia', 'Retinal Detachment', 'Intraoperative Cardiac Injury', 'Fibrinogen Decreased', 'Hydrocephalus', 'Skin and Subcutaneous Tissue Disorders Other', 'Insomnia', 'Salivary Duct Inflammation', 'Pneumonitis', 'Night Blindness', 'Sleep Apnea', 'Urostomy Site Bleeding', 'Malaise', 'Tracheal Fistula', 'Intraoperative Urinary Injury', 'Hypocalcemia', 'Anemia', 'Pain', 'External Ear Pain', 'Stridor', 'Transient Ischemic Attacks', 'Cheilitis', 'Mitral Valve Disease', 'Delusions', 'Palpitations', 'Joint Infection', 'Ileal Fistula', 'Portal Vein Thrombosis', 'Radiculitis', 'Respiratory Failure', 'Gastroesophageal Reflux Disease', 'Intraoperative Gastrointestinal Injury', 'Skin Atrophy', 'Superficial Soft Tissue Fibrosis', 'Pleural Infection', 'Vas Deferens Anastomotic Leak', 'Renal Calculi', 'Tracheal Hemorrhage', 'Psychiatric Disorders Other', 'Stomal Ulcer', 'Death Neonatal', 'Alkaline Phosphatase Increased', 'Neck Soft Tissue Necrosis', 'Sepsis', 'Pelvic Infection', 'Left Ventricular Systolic Dysfunction', 'Trigeminal Nerve Disorder', 'Eye Pain', 'Ileal Hemorrhage', 'Bile Duct Stenosis', 'Aspartate Aminotransferase Increased', 'Ear Pain', 'Growth Accelerated', 'Irregular Menstruation', 'Aspiration', 'Anorgasmia', 'Perineal Pain', 'Fall', 'Intraoperative Arterial Injury', 'Myositis', 'Vascular Disorders Other', 'Heart Failure', 'Ovarian Hemorrhage', 'Gallbladder Fistula', 'Esophageal Obstruction', 'Intraoperative Musculoskeletal Injury', 'Hypersomnia', 'Ileus', 'INR Increased', 'Toxic Epidermal Necrolysis', 'Chest Pain Cardiac', 'Paroxysmal Atrial Tachycardia', 'Abducens Nerve Disorder', 'Chest Wall Pain', 'Muscle Weakness Right-Sided', 'Watering Eyes', 'Arteritis Infective', 'Gastrointestinal Pain', 'Dehydration', 'Fallopian Tube Obstruction', 'Hypothyroidism', 'Pharyngolaryngeal Pain', 'Urinary Tract Obstruction', 'Arthritis', 'Weight Loss', 'Intraoperative Skin Injury', 'Fever', 'Phlebitis Infective', 'Rectal Obstruction', 'Retinoic Acid Syndrome', 'Superficial Thrombophlebitis', 'Urine Output Decreased', 'Pharyngeal Hemorrhage', 'Rectal Pain', 'Testicular Hemorrhage', 'Intraoperative Breast Injury', 'Hemolysis', 'Visceral Arterial Ischemia', 'Biliary Tract Infection', 'Hypohidrosis', 'GGT Increased', 'Intra-Abdominal Hemorrhage', 'Peripheral Nerve Infection', 'Esophagitis', 'Vasovagal Reaction', 'Memory Impairment', 'Corneal Infection', 'Biliary Anastomotic Leak', 'Vaginal Pain', 'Cholesterol High', 'Concentration Impairment', 'Infective Myositis', 'Rash Maculo-Papular', 'Tracheitis', 'Libido Decreased', 'Pericardial Tamponade', 'Photosensitivity', 'Creatinine Increased', 'Blood Corticotrophin Decreased', 'Irritability', 'Apnea', 'Soft Tissue Necrosis Upper Limb', 'Alopecia', 'Flu Like Symptoms', 'Lipase Increased', 'Hypoxia', 'Dry Eye', 'Gingival Pain', 'Unequal Limb Length', 'Kyphosis', 'Unintended Pregnancy', 'Hypertrichosis', 'Bloating', 'Tracheal Mucositis', 'Edema Cerebral', 'Anal Ulcer', 'Restlessness', 'Scleral Disorder', 'Eyelid Function Disorder', 'Laryngitis', 'Trismus', 'Enterocolitis', 'Diarrhea', 'Hepatic Failure', 'IVth Nerve Disorder', 'Fallopian Tube Anastomotic Leak', 'Hypoalbuminemia', 'Obesity', 'Pericarditis', 'Pulmonary Fistula', 'Wound Dehiscence', 'Alcohol Intolerance', 'Intraoperative Hepatobiliary Injury', 'Death NOS', 'Anal Stenosis', 'Pancreatic Duct Stenosis', 'Capillary Leak Syndrome', 'Menorrhagia', 'Periorbital Edema', 'Stevens-Johnson Syndrome', 'Central Nervous System Necrosis', 'Malabsorption', 'Endocarditis Infective', 'Uveitis', 'Ventricular Arrhythmia', 'Bladder Spasm', 'Lymphocyte Count Increased', 'Hypertension', 'Pancreatic Anastomotic Leak', 'Vital Capacity Abnormal', 'Joint Effusion', 'Hearing Impaired', 'Injury to Carotid Artery', 'Duodenal Infection', 'Penile Pain', 'Social Circumstances Other', 'wheezing', 'Conduction Disorder', 'Iron Overload', 'Abdominal Distension', 'Intraoperative Reproductive Tract Injury', 'Oral Pain', 'Leukocytosis', 'Cholecystitis', 'Investigations Other', 'Abdominal Pain', 'Oculomotor Nerve Disorder', 'Neutrophil Count Decreased', 'Hypomagnesemia', 'Nail Discoloration', 'Agitation', 'Hypercalcemia', 'Esophageal Stenosis', 'Nasal Congestion', 'Kidney Infection', 'Eye Infection', 'Delayed Puberty', 'Vascular Access Complication', 'Joint Range of Motion Decreased', 'Acute Kidney Injury', 'Lymph Leakage', 'Hypokalemia', 'Nystagmus', 'Pain of Skin', 'Delayed Orgasm', 'Duodenal Obstruction', 'Seizure', 'Adult Respiratory Distress Syndrome', 'Intracranial Hemorrhage', 'Bronchopleural Fistula', 'Alkalosis', 'Back Pain', 'Pyramidal Tract Syndrome', 'Bone Infection', 'Bladder Anastomotic Leak', 'Presyncope', 'Stoma Site Infection', 'Laryngeal Obstruction', 'Confusion', 'Anal Hemorrhage', 'Gastric Anastomotic Leak', 'Acoustic Nerve Disorder NOS', 'Esophageal Fistula', 'White Blood Cell Decreased', 'Nail Ridging', 'Spleen Disorder', 'Gastrointestinal Fistula', 'Alanine Aminotransferase Increased', 'Uterine Pain', 'Rectal Anastomotic Leak', 'Vaginal Obstruction', 'Vaginal Perforation', 'Rectal Necrosis', 'Papilledema', 'Fecal Incontinence', 'Small Intestinal Stenosis', 'Vitreous Hemorrhage', 'Fatigue', 'Vaginismus', 'Uterine Perforation', 'Bruising', 'Cardiac Arrest', 'Esophageal Infection', 'Bronchopulmonary Hemorrhage', 'Surgical and Medical Procedures Other', 'Sinus Bradycardia', 'Oral Cavity Fistula', 'Bladder Infection', 'Appendicitis Perforated', 'Accessory Nerve Disorder', 'Dermatitis Radiation', 'Papulopustular Rash', 'Intraoperative Splenic Injury', 'Postnasal Drip', 'Azoospermia', 'Spermatic Cord Obstruction', 'Dental Caries', 'Injury to Inferior Vena Cava', 'Delirium', 'Precocious Puberty', 'Sneezing', 'Encephalitis Infection', 'Constipation', 'Ureteric Anastomotic Leak', 'Musculoskeletal Deformity', 'Joint Range of Motion Decreased Cervical Spine', 'Restrictive Cardiomyopathy', 'Blood Prolactin Abnormal', 'External Ear Inflammation', 'Cervicitis Infection', 'Nervous System Disorders Other', 'Paresthesia', 'Peritoneal Necrosis', 'Respiratory', 'Renal Hemorrhage', 'Skin Hyperpigmentation', 'Testicular Disorder', 'Cardiac Troponin I Increased', 'Gait Disturbance', 'Jejunal Obstruction', 'Ventricular Fibrillation', 'Sudden Death NOS', 'Hematosalpinx', 'Osteoporosis', 'Autoimmune Disorder', 'Hypotension', 'Hyponatremia', 'Hypernatremia', 'Allergic Reaction', 'Lung Infection', 'Colitis', 'Mediastinal Hemorrhage', 'Atrial Flutter', 'Fibrosis Deep Connective Tissue', 'Gallbladder Infection', 'Pleural Hemorrhage', 'Bladder Perforation', 'Periodontal Disease', 'Pharyngitis', 'Esophageal Necrosis', 'Jejunal Hemorrhage', 'Otitis Externa', 'Bronchial Stricture', 'Ankle Fracture', 'Infusion Site Extravasation', 'Rectal Hemorrhage', 'Soft Tissue Necrosis Lower Limb', 'Glucose Intolerance', 'Immune System Disorders Other', 'Peripheral Motor Neuropathy', 'Neoplasms Benign', 'Recurrent Laryngeal Nerve Palsy', 'Infusion Related Reaction', 'Cognitive Disturbance', 'Hepatic Hemorrhage', 'Colonic Stenosis', 'Small Intestinal Anastomotic Leak', 'Hyperkalemia', 'Jejunal Stenosis', 'Urinary Urgency', 'Carbon Monoxide Diffusing Capacity Decreased', 'Middle Ear Inflammation', 'Stroke', 'Menopause', 'Gastroparesis', 'Sinusitis', 'Small Intestinal Mucositis', 'Tracheal Stenosis', 'Abdominal Soft Tissue Necrosis', 'Dry Mouth', 'Soft Tissue Infection', 'Urostomy Stenosis', 'Depression', 'Somnolence', 'Lip Pain', 'Bronchial Infection', 'Esophageal Anastomotic Leak', 'Lower Gastrointestinal Hemorrhage', 'Constrictive Pericarditis', 'Mucosal Infection', 'Urinary Frequency', 'Telangiectasia', 'Ovarian Infection', 'Ileal Obstruction', 'Tinnitus', 'Gastritis', 'Dysarthria', 'Hypothermia', 'Lymphocele', 'Vaginal Stricture', 'Upper Respiratory Infection', 'Leukoencephalopathy', 'Typhlitis', 'Tumor Lysis Syndrome', 'Vulval Infection', 'Atelectasis', 'Aphonia', 'Lymph Node Pain', 'Flatulence', 'Dysesthesia', 'Scrotal Pain', 'Cushingoid', 'Aortic Injury', 'Muscle Weakness Lower Limb', 'Periorbital Infection', 'Gallbladder Necrosis', 'Hemolytic Uremic Syndrome', 'Jejunal Fistula', 'Splenic Infection', 'Muscle Weakness Left-Sided', 'Allergic Rhinitis', 'Wrist Fracture', 'Superior Vena Cava Syndrome', 'Prostatic Obstruction', 'Rash Pustular', 'Facial Muscle Weakness', 'Localized Edema', 'Facial Nerve Disorder', 'Fetal Death', 'Personality Change', 'Pharyngeal Mucositis', 'Scrotal Infection', 'Peritoneal Infection', 'Erythema Multiforme', 'Urethral Infection', 'Uterine Infection', 'CD4 Lymphocytes Decreased', 'Amnesia', 'Flank Pain', 'Chylothorax', 'Myelitis', 'Phantom Pain', 'Rectal Fistula', 'Myocardial Infarction', 'Hematoma', 'Intraoperative Ear Injury', 'Spermatic Cord Hemorrhage', 'Colonic Ulcer', 'Epistaxis', 'Febrile Neutropenia', 'Upper Gastrointestinal Hemorrhage', 'Ventricular Tachycardia', 'Feminization Acquired', 'Generalized Muscle Weakness', 'Extraocular Muscle Paresis', 'Joint Range of Motion Decreased Lumbar Spine', 'Device Related Infection', 'Gastrointestinal Disorders Other', 'Salivary Gland Fistula', 'Spermatic Cord Anastomotic Leak', 'Productive Cough', 'Small Intestine Infection', 'Tooth Discoloration', 'Bone Pain', 'Urine Discoloration', 'Meningitis', 'Forced Expiratory Volume Decreased', 'Burn', 'Blood and Lymphatic System Disorders Other', 'Chronic Kidney Disease', 'Weight Gain', 'Encephalomyelitis Infection', 'Floaters', 'Metabolism and Nutrition Disorders Other', 'Conjunctivitis Infective', 'Nail Loss', 'Dizziness', 'Acute Coronary Syndrome', 'Anal Fistula', 'Vomiting', 'Sick Sinus Syndrome', 'Laryngeal Mucositis', 'Oral Dysesthesia', 'Pelvic Pain', 'Cranial Nerve Infection', 'Cough', 'Pleuritic Pain', 'Small Intestinal Obstruction', 'Anorexia', 'Vestibular Disorder', 'Esophageal Hemorrhage', 'Electrocardiogram QT Corrected Interval Prolonged', 'Hemoglobin Increased', 'Breast Atrophy', 'Intraoperative Head and Neck Injury', 'Suicidal Ideation', 'Pancreatic Fistula', 'Laryngeal Edema', 'Stenosis of Gastrointestinal Stoma', 'Buttock Pain', 'Growth Suppression', 'Hepatobiliary Disorders Other', 'Mania', 'Peripheral Ischemia', 'Edema Face', 'Dry Skin', 'Vasculitis', 'Appendicitis', 'Intraoperative Ocular Injury', 'Tracheostomy Site Bleeding', 'Treatment Related Secondary Malignancy', 'Tremor', 'Conjunctivitis', 'Endophthalmitis', 'Cataract', 'Nipple Deformity', 'Erectile Dysfunction', 'Oral Hemorrhage', 'Gastric Necrosis', 'Edema Limbs', 'General Disorders and Administration Site Conditions Other', 'Pericardial Effusion', 'Hepatic Infection', 'Intraoperative Venous Injury', 'Urinary Retention', 'Peripheral Sensory Neuropathy', 'Hepatitis Viral', 'Stomach Pain', 'Disseminated Intravascular Coagulation', 'Prolapse of Urostomy', 'Encephalopathy', 'Fetal Growth Retardation', 'Vaginal Inflammation', 'Proctitis', 'Vaginal Hemorrhage', 'Gallbladder Perforation', 'Esophageal Ulcer', 'Skin Hypopigmentation', 'Blood Bilirubin Increased', 'Female Genital Tract Fistula', 'Hiccups', 'Injury to Superior Vena Cava', 'Rectal Stenosis', 'Ejection Fraction Decreased', 'Glaucoma', 'Palmar-Plantar Erythrodysesthesia Syndrome', 'Uterine Anastomotic Leak', 'Postoperative Thoracic Procedure Complication', 'Laryngeal Inflammation', 'Laryngospasm', 'Gastric Fistula', 'Hypophosphatemia', 'Testicular Pain', 'Pelvic Floor Muscle Weakness', 'Pain in Extremity', 'Myelodysplastic Syndrome', 'Seroma', 'Hyperglycemia', 'Portal Hypertension', 'Arterial Injury', 'Thoracic and Mediastinal Disorders Other', 'Pharyngeal Stenosis', 'Small Intestine Ulcer', 'Breast Infection', 'Gallbladder Pain', 'Muscle Weakness Upper Limb', 'Akathisia', 'Esophageal Varices Hemorrhage', 'Hepatic Pain', 'Leukemia Secondary to Oncology Chemotherapy', 'Biliary Fistula', 'Ileal Ulcer', 'Urethral Anastomotic Leak', 'Congenital', 'Ischemia Cerebrovascular', 'Anal Necrosis', 'Penile Infection', 'Hypertriglyceridemia', 'Rectal Mucositis', 'Anal Pain', 'Hematuria', 'Ear and Labyrinth Disorders Other', 'Bone Marrow Hypocellular', 'Pulmonary Hypertension', 'Bullous Dermatitis', 'Euphoria', 'Non-Cardiac Chest Pain', 'Vaginal Dryness', 'Pelvic Soft Tissue Necrosis', 'Mobitz Type I', 'Ascites', 'Spasticity', 'Laryngopharyngeal Dysesthesia', 'Prostatic Hemorrhage', 'Suicide Attempt', 'Vagus Nerve Disorder', 'Fat Atrophy', 'Tooth Development Disorder', 'Bronchospasm', 'Depressed Level of Consciousness', 'Hemorrhoidal Hemorrhage', 'Intraoperative Neurological Injury', 'Premature Menopause', 'Infections and Infestations Other', 'Hirsutism', 'Rectal Ulcer', 'Extrapyramidal Disorder', 'Ovulation Pain', 'Chills', 'Premature Delivery', 'Blurred Vision', 'Anaphylaxis', 'CPK Increased', 'Ileal Perforation', 'Pneumothorax', 'Renal Colic', 'Right Ventricular Dysfunction', 'Dyspareunia', 'Duodenal Perforation', 'dyspnea', 'Flashing Lights', 'Tumor Pain', 'Hypoglycemia', 'Gastric Ulcer', 'Colonic Fistula', 'Atrioventricular Block First Degree', 'Intraoperative Hemorrhage', 'Urinary Fistula', 'Keratitis', 'Postoperative Hemorrhage', 'Myalgia', 'Gastric Stenosis', 'Obstruction Gastric', 'Purpura', 'Lethargy', 'Colonic Perforation', 'Rectal Perforation', 'Blood Gonadotrophin Abnormal', 'Musculoskeletal and Connective Tissue Disorders Other', 'Serum Sickness', 'Activated Partial Thromboplastin Time Prolonged', 'Pancreatic Hemorrhage', 'dysphagia', 'Nail Infection', 'Virilization', 'Haptoglobin Decreased', 'Sinus Disorder', 'Eye Disorders Other', 'Intraoperative Respiratory Injury', 'Phlebitis', 'Anal Mucositis', 'Multi-Organ Failure', 'Esophageal Pain', 'Bronchial Obstruction', 'Gynecomastia', 'Hypermagnesemia', 'Gum Infection', 'Cardiac Disorders Other', 'Laryngeal Stenosis', 'Intraoperative Endocrine Injury', 'Vaginal Fistula', 'Kidney Anastomotic Leak', 'Mediastinal Infection', 'Ataxia', 'Wound Infection', 'Nausea', 'Asystole', 'Skin Infection', 'Libido Increased', 'Edema Trunk', 'Serum Amylase Increased', 'Pancreas Infection', 'Arthralgia', 'Cystitis Noninfective', 'Lipohypertrophy', 'Cardiac Troponin T Increased', 'Ejaculation Disorder', 'Exostosis', 'Syncope', 'Pharyngeal Fistula', 'Olfactory Nerve Disorder', 'Thrombotic Thrombocytopenic Purpura', 'Prostatic Pain', 'Blood Antidiuretic Hormone Abnormal', 'Atrioventricular Block Complete', 'Endocrine Disorders Other', 'Intestinal Stoma Leak', 'Enterovesical Fistula', 'Platelet Count Decreased', 'Photophobia', 'Neck Edema', 'Lip Infection', 'Otitis Media', 'Dyspepsia', 'Uterine Obstruction', 'Enterocolitis Infectious', 'Dysgeusia', 'Pregnancy', 'Bronchial Fistula', 'Hemoglobinuria', '']",,FollowUp
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,FollowUp
Pregnancy Outcome,Pregnancy Outcome,PregnancyOutcome,The text term used to describe the type of pregnancy the patient had,False,,"['Miscarriage', 'Ectopic Pregnancy', 'Live Birth', 'unknown', 'Stillbirth', 'Not Reported', 'Induced Abortion', '']",,FollowUp
AIDS Risk Factors,AIDS Risk Factors,AIDSRiskFactors,The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.,False,,"['Encephalopathy', 'Cytomegalovirus', 'Herpes Simplex Virus', 'Pneumocystis Pneumonia', 'Mycobacterium tuberculosis', 'Isosporiasis', 'NOS', 'Toxoplasmosis', 'Nocardiosis', 'Mycobacterium avium Complex', 'Cryptococcosis', 'Salmonella Septicemia', 'Candidiasis', 'pneumonia', 'Progressive Multifocal Leukoencephalopathy', 'Mycobacterium', 'Wasting Syndrome', 'Coccidioidomycosis', 'Histoplasmosis', '']",,FollowUp
Hepatitis Sustained Virological Response,Hepatitis Sustained Virological Response,HepatitisSustainedVirologicalResponse,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,FollowUp
Immunosuppressive Treatment Type,Immunosuppressive Treatment Type,ImmunosuppressiveTreatmentType,The text term used to describe the type of immunosuppresive treatment the patient received.,False,,"['None', 'Azathioprine', 'Cyclophosphamide', 'Methotrexate', 'Anti-TNFTherapy', 'unknown', 'Other', 'Not Reported', '']",,FollowUp
Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['Not Reported', 'Yes - Progression or Recurrence', 'no', 'unknown']",,FollowUp
Recist Targeted Regions Sum,Recist Targeted Regions Sum,RecistTargetedRegionsSum,"Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.",False,,,,FollowUp
Risk Factor Treatment,Risk Factor Treatment,RiskFactorTreatment,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,FollowUp
FEV1 Ref Post Bronch Percent,FEV1 Ref Post Bronch Percent,FEV1RefPostBronchPercent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.,False,,,,FollowUp
Hormonal Contraceptive Use,Hormonal Contraceptive Use,HormonalContraceptiveUse,The text term used to indicate whether the patient used hormonal contraceptives.,False,,"['Former User', 'Current User', 'unknown', 'Never Used', 'Not Reported', '']",,FollowUp
Imaging Type,Imaging Type,ImagingType,The text term used to describe the type of imaging or scan performed on the patient.,False,,"['CT Scan', 'PET', 'MRI', '99mTc Bone Scintigraphy', '']",,FollowUp
Days to Progression Free,Days to Progression Free,DaystoProgressionFree,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp
Days to Progression,Days to Progression,DaystoProgression,Number of days between the date used for index and the date the patient's disease progressed. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp
Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Distant', 'Local', 'Regional', 'unknown', 'Biochemical', 'Not Reported', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp
Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Appendix', 'Parametrium', 'Aortic body and other paraganglia', 'Trachea', 'Transverse colon', 'Lateral floor of mouth', 'Cerebellum NOS', 'Paraurethral gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Cloacogenic zone', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Overlapping lesion of bladder', 'Overlapping lesion of retroperitoneum and peritoneum', 'Uterine adnexa', 'Vertebral column', 'Upper lobe lung', 'Overlapping lesion of floor of mouth', 'Spinal meninges', 'Labium minus', 'Hard palate', 'Spleen', 'Breast NOS', 'Middle third of esophagus', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Duodenum', 'Spinal cord', 'Anterior wall of nasopharynx', 'Body of pancreas', 'Fundus uteri', 'Upper third of esophagus', 'Short bones of upper limb and associated joints', 'Overlapping lesion of cervix uteri', 'Lateral wall of bladder', 'Nervous system NOS', 'Upper-outer quadrant of breast', 'Nipple', 'Labium majus', 'Exocervix', 'Vulva NOS', 'Gum NOS', 'Mediastinum NOS', 'Urinary system NOS', 'Medulla of adrenal gland', 'Tongue NOS', 'Overlapping lesion of eye and adnexa', 'Bone marrow', 'Reticuloendothelial system NOS', 'Renal pelvis', 'Brain stem', 'Ureter', 'Overlapping lesion of small intestine', 'unknown primary site', 'Intestinal tract NOS', 'Laryngeal cartilage', 'Scrotum NOS', 'Upper respiratory tract NOS', 'Rectosigmoid junction', 'Overlapping lesion of stomach', 'Sphenoid sinus', 'Lymph nodes of inguinal region or leg', 'Pancreas NOS', 'Kidney NOS', 'Branchial cleft', 'Pharynx NOS', 'Tonsillar pillar', 'Islets of Langerhans', 'Optic nerve', 'Lymph nodes of multiple regions', 'Overlapping lesion of tonsil', 'Posterior wall of hypopharynx', 'Intrahepatic bile duct', 'Lacrimal gland', 'Orbit NOS', 'Bone NOS', 'Submandibular gland', 'Endocervix', 'Corpus uteri', 'Skin of trunk', 'Retina', 'Overlapping lesion of endocrine glands and related structures', 'Ciliary body', 'Overlapping lesion of larynx', 'Anterior mediastinum', 'Lower limb NOS', 'Frontal sinus', 'Superior wall of nasopharynx', 'Prepuce', 'Major salivary gland NOS', 'Stomach NOS', 'Overlapping lesion of rectum anus and anal canal', 'Olfactory nerve', 'Peripheral nerves and autonomic nervous system of thorax', 'Testis NOS', 'Cheek mucosa', 'Abdomen NOS', 'Waldeyer ring', 'Bone of limb NOS', 'Cervical esophagus', 'Intrathoracic lymph nodes', 'Overlapping lesion of digestive system', 'Axillary tail of breast', 'Lower-outer quadrant of breast', 'Overlapping lesion of brain and central nervous system', 'Lymph node NOS', 'Adrenal gland NOS', 'Soft palate NOS', 'Overlapping lesion of pancreas', 'Autonomic nervous system NOS', 'Border of tongue', 'Posterior wall of oropharynx', 'Meninges NOS', 'Colon NOS', 'Lateral wall of oropharynx', 'Supraglottis', 'Overlapping lesion of vulva', 'Fallopian tube', 'Extrahepatic bile duct', 'Posterior wall of nasopharynx', 'External ear', 'skin of upper limb and shoulder', 'Craniopharyngeal duct', 'Specified parts of peritoneum', 'Lingual tonsil', 'Maxillary sinus', 'Lower gum', 'Female genital tract NOS', 'Central portion of breast', 'Overlapping lesion of male genital organs', 'Overlapping lesion of colon', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Mucosa of lower lip', 'Tonsillar fossa', 'Other specified parts of pancreas', 'Anterior wall of bladder', 'Overlapping lesion of esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Connective subcutaneous and other soft tissues of thorax', 'Conjunctiva', 'Nasopharynx NOS', 'Mandible', 'Lung NOS', 'Overlapping lesions of oropharynx', 'External upper lip', 'Vagina NOS', 'Short bones of lower limb and associated joints', 'Placenta', 'Ileum', 'Overlapping lesion of lung', 'Broad ligament', 'Lower third of esophagus', 'Abdominal esophagus', 'External lip NOS', 'Other specified parts of male genital organs', 'Lateral wall of nasopharynx', 'Other specified parts of female genital organs', 'Bones of skull and face and associated joints', 'Palate NOS', 'Retromolar area', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of heart mediastinum and pleura', 'Oropharynx NOS', 'Bladder neck', 'Anal canal', 'Lymph nodes of head face and neck', 'Middle ear', 'Brain NOS', 'Ascending colon', 'Isthmus uteri', 'Ill-defined sites within respiratory system', 'Eye NOS', 'Hematopoietic system NOS', 'Accessory sinus NOS', 'Gastric antrum', 'Trigone of bladder', 'Head face or neck NOS', 'Pylorus', 'Cornea NOS', 'Pelvic lymph nodes', 'Occipital lobe', 'Meckel diverticulum', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Base of tongue NOS', 'Cranial nerve NOS', 'Overlapping lesion of hypopharynx', 'Greater curvature of stomach NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Commissure of lip', 'Overlapping lesion of penis', 'Ovary', 'Cervix uteri', 'Vestibule of mouth', 'Hypopharyngeal aspect of aryepiglottic fold', 'Prostate gland', 'Dome of bladder', 'Parotid gland', 'Pelvis NOS', 'Lower-inner quadrant of breast', 'Connective subcutaneous and other soft tissues of abdomen', 'Pineal gland', 'Fundus of stomach', 'Endocrine gland NOS', 'Cerebrum', 'Splenic flexure of colon', 'Floor of mouth NOS', 'External lower lip', 'Eyelid', 'Carotid body', 'Choroid', 'Overlapping lesion of major salivary glands', 'Mucosa of lip NOS', 'Not Reported', 'Urachus', 'Liver', 'skin of lower limb and hip', 'Overlapping lesion of brain', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Thyroid gland', 'Thoracic esophagus', 'Biliary tract NOS', 'Other ill-defined sites', 'Overlapping lesion of palate', 'Heart', 'Larynx NOS', 'Clitoris', 'Middle lobe lung', 'Peripheral nerves and autonomic nervous system of abdomen', 'Upper gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Parathyroid gland', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lesser curvature of stomach NOS', 'Anterior 2/3 of tongue NOS', 'Thymus', 'Frontal lobe', 'Blood', 'Descending colon', 'Gallbladder', 'Pelvic bones sacrum coccyx and associated joints', 'Lymph nodes of axilla or arm', 'Male genital organs NOS', 'Acoustic nerve', 'Thorax NOS', 'Urethra', 'Connective subcutaneous and other soft tissues of pelvis', 'Body of penis', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Rib sternum clavicle and associated joints', 'Cortex of adrenal gland', 'Jejunum', 'Temporal lobe', 'Overlapping lesion of skin', 'Upper-inner quadrant of breast', 'Bladder NOS', 'Ventral surface of tongue NOS', 'Uterus NOS', 'Anus NOS', 'Overlapping lesion of accessory sinuses', 'Rectum NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Cardia NOS', 'Anterior surface of epiglottis', 'Overlapping lesion of urinary organs', 'Skin of other and unspecified parts of face', 'Skin of scalp and neck', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Lip NOS', 'Posterior mediastinum', 'Sigmoid colon', 'Main bronchus', 'Anterior floor of mouth', 'Overlapping lesion of ill-defined sites', 'Hepatic flexure of colon', 'Overlapping lesion of biliary tract', 'Connective subcutaneous and other soft tissues NOS', 'Tonsil NOS', 'Long bones of upper limb scapula and associated joints', 'Lower lobe lung', 'Myometrium', 'Posterior wall of bladder', 'Hypopharynx NOS', 'Skin of lip NOS', 'Cauda equina', 'Pleura NOS', 'Esophagus NOS', 'Overlapping lesion of breast', 'Cerebral meninges', 'Sublingual gland', 'Penis NOS', 'Overlapping lesion of lip', 'Descended testis', 'Glottis', 'Upper limb NOS', 'Nasal cavity', 'Ethmoid sinus', 'Ampulla of Vater', 'Vallecula', 'Overlapping lesion of tongue', 'skin NOS', 'Epididymis', 'Undescended testis', 'Ventricle NOS', 'Pancreatic duct', 'Body of stomach', 'Endometrium', 'Long bones of lower limb and associated joints', 'Dorsal surface of tongue NOS', 'unknown', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Head of pancreas', 'Gastrointestinal tract NOS', 'Glans penis', 'Postcricoid region', 'Mucosa of upper lip', 'Intra-abdominal lymph nodes', 'Pyriform sinus', 'Round ligament', 'Ureteric orifice', 'Cecum', 'Peritoneum NOS', 'Parietal lobe', 'Subglottis', 'Mouth NOS', 'Small intestine NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of corpus uteri', 'Uvula', 'Spermatic cord', 'Retroperitoneum', 'Tail of pancreas', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp
Days to Recurrence,Days to Recurrence,DaystoRecurrence,Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp
Days to Diagnosis,Days to Diagnosis,DaystoDiagnosis,Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable',False,,,,Diagnosis
Gleason Grade Tertiary,Gleason Grade Tertiary,GleasonGradeTertiary,The text term used to describe the tertiary pattern as described by the Gleason Grading System.,False,,"['Pattern 5', 'Pattern 4', '']",,Diagnosis
Best Overall Response,Best Overall Response,BestOverallResponse,The best improvement achieved throughout the entire course of protocol treatment.,False,,"['CPD-Clinical Progression', 'IPD-Immunoprogression', 'MX-Mixed Response', 'DU-Disease Unchanged', 'RD-Responsive Disease', 'CR-Complete Response', 'PPD-Pseudoprogression', 'AJ-Adjuvant Therapy', 'PSR-Pseudoresponse', 'MR-Minimal/Marginal Response', 'PD-Progressive Disease', 'sCR-Stringent Complete Response', 'SPD-Surgical Progression', 'NR-No Response', 'TE-Too Early', 'NPB-No Palliative Benefit', 'PR-Partial Response', 'RPD-Radiographic Progressive Disease', 'PB-Palliative Benefit', 'SD-Stable Disease', 'VGPR-Very Good Partial Response', 'PA-Palliative Therapy', 'Non-CR/Non-PD-Non-CR/Non-PD', 'CRU-Complete Response Unconfirmed', 'RP-Response', 'IMR-Immunoresponse', '']",,Diagnosis
Medulloblastoma Molecular Classification,Medulloblastoma Molecular Classification,MedulloblastomaMolecularClassification,The text term used to describe the classification of medulloblastoma tumors based on molecular features.,False,,"['Non-WNT/non-SHH Activated', 'WNT-Activated', 'unknown', 'Not Reported', 'SHH-Activated', 'Not Determined', '']",,Diagnosis
INSS Stage,INSS Stage,INSSStage,"Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).",False,,"['Stage 2A', 'Stage 4S', 'unknown', 'Stage 4', 'Stage 1', 'Stage 3', 'Stage 2B', 'Not Reported', '']",,Diagnosis
Cog Rhabdomyosarcoma Risk Group,Cog Rhabdomyosarcoma Risk Group,CogRhabdomyosarcomaRiskGroup,"Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).",False,,"['Intermediate Risk', 'unknown', 'Low Risk', 'Not Reported', 'High Risk', '']",,Diagnosis
ISS Stage,ISS Stage,ISSStage,The multiple myeloma disease stage at diagnosis.,False,,"['II', 'I', 'unknown', 'III', 'Not Reported', '']",,Diagnosis
Pregnant at Diagnosis,Pregnant at Diagnosis,PregnantatDiagnosis,The text term used to indicate whether the patient was pregnant at the time they were diagnosed.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Diagnosis
Last Known Disease Status,Last Known Disease Status,LastKnownDiseaseStatus,Text term that describes the last known state or condition of an individual's neoplasm.,True,,"['Tumor free', 'Not Allowed To Collect', 'Loco-regional recurrence/progression', 'Distant met recurrence/progression', 'With tumor', 'Biochemical evidence of disease without structural correlate', 'Not Applicable', 'Not Reported', 'unknown tumor status']",,Diagnosis
Residual Disease,Residual Disease,ResidualDisease,Text terms to describe the status of a tissue margin following surgical resection.,False,,"['R2', 'RX', 'R1', 'R0', 'unknown', 'Not Reported', '']",,Diagnosis
INPC Histologic Group,INPC Histologic Group,INPCHistologicGroup,"The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.",False,,"['Not Reported', 'Unfavorable', 'Favorable', 'unknown', '']",,Diagnosis
Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['Not Reported', 'Yes - Progression or Recurrence', 'no', 'unknown']",,Diagnosis
Mitosis Karyorrhexis Index,Mitosis Karyorrhexis Index,MitosisKaryorrhexisIndex,Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).,False,,"['High', 'unknown', 'Intermediate', 'Low', 'Not Reported', '']",,Diagnosis
Micropapillary Features,Micropapillary Features,MicropapillaryFeatures,The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.,False,,"['Not Reported', 'Absent', 'Present', 'unknown', '']",,Diagnosis
INPC Grade,INPC Grade,INPCGrade,"Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).",False,,"['unknown', 'Differentiating', 'Poorly Differentiated', 'Undifferentiated', 'Not Reported', '']",,Diagnosis
AJCC Pathologic N,AJCC Pathologic N,AJCCPathologicN,The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.,False,,"['N2b', 'N1b', 'N0', 'N1c', 'N1', 'N1bI', 'N1bIV', 'NX', 'N2', 'N3', 'N2a', 'N0 (mol+)', 'N3b', 'N3c', 'N0 (mol-)', 'N1a', 'N1bII', 'unknown', 'N4', 'N0 (i+)', 'N2c', 'Not Reported', 'N3a', 'N1bIII', 'N0 (i-)', 'N1mi', '']",,Diagnosis
Tumor Depth,Tumor Depth,TumorDepth,"Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).",False,,,,Diagnosis
Metastasis at Diagnosis Site,Metastasis at Diagnosis Site,MetastasisatDiagnosisSite,Text term to identify an anatomic site in which metastatic disease involvement is found.,False,,"['Soft Tissue', 'Cerebrospinal Fluid', 'Brain', 'Mediastinum', 'Ascites', 'Scalp', 'Lymph Node NOS', 'Abdomen', 'Peritoneum', 'Skin', 'Bone Marrow', 'Omentum', 'Pleura', 'Pelvis', 'Colon', 'Adrenal Gland', 'Small Intestine', 'Spinal Cord', 'Ovary', 'Central Nervous System', 'Lung', 'Distant Nodes', 'Bone', 'unknown', 'Peritoneal Cavity', 'Not Reported', 'Inguinal', 'Distant Organ', 'Kidney', 'Groin', 'Lymph Node', 'Axillary', 'Liver', '']",,Diagnosis
AJCC Clinical M,AJCC Clinical M,AJCCClinicalM,Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['M1c', 'M1a', 'M1b', 'M0', 'unknown', 'MX', 'Not Reported', 'M1', 'cM0 (i+)', '']",,Diagnosis
Perineural Invasion Present,Perineural Invasion Present,PerineuralInvasionPresent,A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Diagnosis
AJCC Pathologic Stage,AJCC Pathologic Stage,AJCCPathologicStage,"The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.",False,,"['Stage IIA1', 'Stage IVA', 'Stage IIB', 'Stage IB1', 'Stage X', 'Stage IIA2', 'Stage IS', 'Stage 0is', 'Stage IC', 'Stage IV', 'Stage Tis', 'Stage 0', 'Stage IIIB', 'Stage IVB', 'Stage IIIC1', 'Stage IA', 'Stage 0a', 'Stage IB', 'Stage IIA', 'Stage IIIC2', 'Stage IIIC', 'unknown', 'Not Reported', 'Stage IIC1', 'Stage I', 'Stage IA2', 'Stage IB2', 'Stage IIC', 'Stage II', 'Stage IIIA', 'Stage IA1', 'Stage III', 'Stage IVC', '']",,Diagnosis
Lymphatic Invasion Present,Lymphatic Invasion Present,LymphaticInvasionPresent,"A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement",False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Diagnosis
Breslow Thickness,Breslow Thickness,BreslowThickness,"The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.",False,,,,Diagnosis
Prior Malignancy,Prior Malignancy,PriorMalignancy,The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.,False,,"['Not Allowed To Collect', 'no', 'unknown', 'Not Reported', 'yes', '']",,Diagnosis
AJCC Clinical Stage,AJCC Clinical Stage,AJCCClinicalStage,"Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.",False,,"['Stage IIA1', 'Stage IVA', 'Stage IIB', 'Stage IB1', 'Stage X', 'Stage IIA2', 'Stage IS', 'Stage 0is', 'Stage IC', 'Stage IV', 'Stage Tis', 'Stage 0', 'Stage IIIB', 'Stage IVB', 'Stage IIIC1', 'Stage IA', 'Stage 0a', 'Stage IB', 'Stage IIA', 'Stage IIIC2', 'Stage IIIC', 'unknown', 'Not Reported', 'Stage IIC1', 'Stage I', 'Stage IA2', 'Stage IB2', 'Stage IIC', 'Stage II', 'Stage IIIA', 'Stage IA1', 'Stage III', 'Stage IVC', '']",,Diagnosis
Primary Diagnosis,Primary Diagnosis,PrimaryDiagnosis,"Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Bile duct adenocarcinoma', 'Classical Hodgkin lymphoma lymphocyte depletion reticular', 'Gastrin cell tumor malignant', 'Pagetoid reticulosis', 'Mixed pineal tumor', 'Squamous cell carcinoma clear cell type', 'Pancreatic endocrine tumor malignant', 'Carcinoma undifferentiated NOS', 'Bronchiolo-alveolar carcinoma Clara cell and goblet cell type', 'Tumor NOS', 'Malignant lymphoma large B-cell NOS', 'Pituitary carcinoma NOS', 'c-ALL', 'Secondary carcinoma', 'Splenic diffuse red pulp small B-cell lymphoma', 'Carcinoma in situ in a polyp NOS', 'Malignant lymphoma lymphocytic diffuse NOS', 'Medullary osteosarcoma', 'Capillary lymphangioma', 'Malignant melanoma in congenital melanocytic nevus', 'Combined large cell neuroendocrine carcinoma', 'Osteoblastoma malignant', 'Basal cell adenocarcinoma', 'Hodgkin lymphoma nodular sclerosis NOS', 'Transitional carcinoma', 'Renal carcinoma collecting duct type', 'Papillary adenocarcinoma NOS', 'Bile duct adenoma', 'Lobular carcinoma in situ NOS', 'Nevus NOS', 'Classical Hodgkin lymphoma nodular sclerosis grade 1', 'Papillary carcinoma NOS', 'Glioma NOS', 'Mixed adenocarcinoma and epidermoid carcinoma', 'Malignant lymphoma large B-cell diffuse NOS', 'T-cell lymphoma NOS', 'Hepatocarcinoma', 'Pigmented basal cell carcinoma', 'Classical Hodgkin lymphoma lymphocyte-rich', 'Diffuse astrocytoma IDH-mutant', 'Paraganglioma benign', 'Tumor metastatic', 'Liver cell adenoma', 'Renal medullary carcinoma', 'Cervical intraepithelial neoplasia low grade', 'Neoplasm malignant uncertain whether primary or metastatic', 'Neurofibromatosis NOS', 'Unclassified tumor uncertain whether benign or malignant', 'Acute myelomonocytic leukemia', 'Classical Hodgkin lymphoma nodular sclerosis cellular phase', 'Papilloma NOS', 'Familial adenomatous polyposis', 'Malignant lymphoma immunoblastic NOS', 'Intraductal and lobular carcinoma', 'Adenocarcinoma NOS', 'Undifferentiated pleomorphic sarcoma', 'Hodgkin sarcoma', 'Malignant lymphoma NOS', 'Melanoma in situ', 'Rodent ulcer', 'Cervical intraepithelial neoplasia grade III', 'Endometrioid carcinoma NOS', 'Ewing sarcoma', 'Malignant melanoma in Hutchinson melanotic freckle', 'Infiltrating basal cell carcinoma NOS', 'Ependymoma NOS', 'Combined small cell-large carcinoma', 'Papillomatosis NOS', 'Chronic myelomonocytic leukemia Type 1', 'Epithelial tumor malignant', 'Nephroblastoma NOS', 'Adenocarcinoma in situ NOS', 'Adult rhabdomyoma', 'Papillary microcarcinoma', 'Carcinoma in situ NOS', 'Papillary squamous cell carcinoma', 'Epidermoid carcinoma NOS', 'Interstitial cell tumor NOS', 'Melanotic psammomatous MPNST', 'Capillary hemangioma', 'Tubular adenocarcinoma', 'Combined small cell carcinoma', 'Classical Hodgkin lymphoma nodular sclerosis grade 2', 'Adenocarcinoma in situ mucinous', 'Paget disease and infiltrating duct carcinoma of breast', 'Intraductal carcinoma solid type', 'Esophageal squamous intraepithelial neoplasia (dysplasia) low grade', 'Precursor B-cell lymphoblastic leukemia', 'Papillary adenoma NOS', 'Diffuse large B-cell lymphoma NOS', 'Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL)', 'Adenocarcinoma in situ in tubular adenoma', 'Central neurocytoma', 'Tubulopapillary adenocarcinoma', 'Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive', 'Small cell sarcoma', 'Malignant melanoma NOS', 'Lymphoma NOS', 'Chronic myelomonocytic leukemia Type II', 'Melanoameloblastoma', 'Carcinoma in situ in adenomatous polyp', 'Rhabdoid tumor NOS', 'Bronchiolo-alveolar carcinoma non-mucinous', 'Liposarcoma NOS', 'Combined hepatocellular carcinoma and cholangiocarcinoma', 'Carcinoma NOS', 'Eosinophilic leukemia', 'Intraductal carcinoma clinging', 'Non-Hodgkin lymphoma NOS', 'Neurofibroma NOS', 'Bronchiolo-alveolar carcinoma indeterminate type', 'Mixed small cell carcinoma', 'Acute lymphoblastic leukemia precursor cell type', 'Adenocarcinoma in polypoid adenoma', 'Endometrioid adenocarcinoma NOS', 'Intravascular B-cell lymphoma', 'Myeloma NOS', 'Malignant lymphoma small B lymphocytic NOS', 'Hepatocellular adenoma', 'Pro-B ALL', 'Chronic lymphatic leukemia', 'B lymphoblastic leukemia/lymphoma with hyperdiploidy', 'Pigmented nevus NOS', 'Acute myeloid leukemia minimal differentiation', 'Adenocarcinoma of anal ducts', 'Bronchio-alveolar carcinoma mixed mucinous and non-mucinous', 'Dermal nevus', 'Glioma malignant', 'Intraductal tubular-papillary neoplasm low grade', 'Eosinophil adenoma', 'Tubular carcinoma', 'Mixed pancreatic endocrine and exocrine tumor malignant', 'Hodgkin lymphoma NOS', 'Tubulovillous adenoma NOS', 'Malignant melanoma in precancerous melanosis', 'Precursor T-cell lymphoblastic lymphoma', 'Adenocarcinoma intestinal type', 'Sclerosing hepatic carcinoma', 'Adenocarcinoma metastatic NOS', 'Therapy related myeloid neoplasm', 'Malignant lymphoma non-Hodgkin NOS', 'Mixed squamous cell and glandular papilloma', 'Epithelial tumor benign', 'Rhabdosarcoma', 'Composite Hodgkin and non-Hodgkin lymphoma', 'Hodgkin paragranuloma NOS', 'Paget disease and intraductal carcinoma of breast', 'Interstitial cell tumor benign', 'Pancreatobiliary neoplasm non-invasive', 'Carcinoma in a polyp NOS', 'Hepatoid adenocarcinoma', 'Basal cell tumor', 'Pancreatoblastoma', 'Chronic myeloproliferative disease NOS', 'Lymphoblastoma', 'Tumor embolus', 'Tumor benign', 'Inflammatory carcinoma', 'Small cell neuroendocrine carcinoma', 'High-grade serous carcinoma', 'Papillary squamous cell carcinoma in situ', 'B lymphoblastic leukemia/lymphoma NOS', 'Papillary cystadenoma NOS', 'Malignant lymphoma nodular NOS', 'T lymphoblastic leukemia/lymphoma', 'Acute promyelocytic leukemia NOS', 'Precursor B-cell lymphoblastic lymphoma', 'Adenocarcinoma in tubular adenoma', 'Skin appendage carcinoma', 'Eosinophil adenocarcinoma', 'Pancreatobiliary-type carcinoma', 'Acute myeloid leukemia MLL', 'Basal cell carcinoma NOS', 'Adenocarcinoma in situ in adenomatous polyp', 'Gastrin cell tumor', 'Malignant melanoma regressing', 'B cell lymphoma NOS', 'Cementoma NOS', 'Astrocytoma low grade', 'Astrocytoma NOS', 'Intraductal micropapillary carcinoma', 'Hepatocholangiocarcinoma', 'Renal cell carcinoma spindle cell', 'Neoplasm metastatic', 'Basophil adenoma', 'Papillary glioneuronal tumor', 'Endometrioid adenoma NOS', 'Monocytic leukemia NOS', 'Papillary adenocarcinoma follicular variant', 'Prostatic intraepithelial neoplasia grade III', 'B-ALL', 'Glioblastoma', 'B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL)', 'Splenic marginal zone lymphoma NOS', 'Hodgkin disease NOS', 'Classical Hodgkin lymphoma nodular sclerosis NOS', 'Intraductal adenocarcinoma noninfiltrating NOS', 'Melanocytoma NOS', 'Precursor cell lymphoblastic leukemia NOS', 'Non-invasive low grade serous carcinoma', 'Intraductal carcinoma NOS', 'Kaposi sarcoma', 'Malignant lymphoma mixed cell type nodular', 'Malignant lymphoma Hodgkin', 'Small congenital nevus', 'Tumor cells NOS', 'Renal cell carcinoma unclassified', 'Ductal carcinoma in situ NOS', 'Medullary carcinoma NOS', 'Astrocytoma anaplastic', 'Esophageal glandular dysplasia (intraepithelial neoplasia) low grade', 'Adenocarcinoma combined with other types of carcinoma', 'Rhabdomyosarcoma NOS', 'Adenocarcinoma in situ non-mucinous', 'Teratoma NOS', 'Classical Hodgkin lymphoma lymphocyte depletion NOS', 'Adenocarcinoma in a polyp NOS', 'Meningioma malignant', 'Neuroendocrine carcinoma NOS', 'Meningeal melanocytoma', 'Adenocarcinoma of anal glands', 'Neoplasm uncertain whether benign or malignant', 'Acute basophilic leukaemia', 'Undifferentiated uterine sarcoma', 'Gastrinoma malignant', 'Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis', 'B-cell lymphocytic leukemia/small lymphocytic lymphoma', 'Hepatoid carcinoma', 'Typical carcinoid', 'Papillary and follicular carcinoma', 'Rhabdomyoma NOS', 'Melanotic neurofibroma', 'Tubular androblastoma NOS', 'Undifferentiated spindle cell sarcoma', 'Adenocarcinoma diffuse type', 'Combined small cell-adenocarcinoma', 'Non-lymphocytic leukemia NOS', 'Undifferentiated epithelioid sarcoma', 'Papillary carcinoma in situ', 'Intraductal papillary carcinoma', 'Papillary meningioma', 'Carcinoma diffuse type', 'Bronchial adenoma carcinoid', 'Bronchiolar carcinoma', 'Duct cell carcinoma', 'Spindle cell melanoma NOS', 'Infiltrating duct and colloid carcinoma', 'Diffuse astrocytoma IDH-wildtype', 'Myelocytic leukemia NOS', 'Chronic myeloid leukemia NOS', 'Tubulo-papillary adenoma', 'Intraepidermal carcinoma NOS', 'Bile duct cystadenocarcinoma', 'Melanocytoma eyeball', 'Chronic neutrophilic leukemia', 'Mixed tumor NOS', 'Papillotubular adenoma', 'Tumor malignant NOS', 'Gastrinoma NOS', 'Diffuse astrocytoma low grade', 'Undifferentiated high-grade pleomorphic sarcoma', 'Preleukemia', 'Chronic granulocytic leukemia BCR/ABL', 'Duct carcinoma desmoplastic type', 'Duct adenocarcinoma NOS', 'Meningioma anaplastic', 'Undifferentiated sarcoma', 'Ductal carcinoma NOS', 'Lobular adenocarcinoma', 'Paraganglioma NOS', 'Adenocarcinoma pancreatobiliary type', 'Pituitary adenoma NOS', 'Tumorlet benign', 'Epidermoid carcinoma in situ NOS', 'Neoplasm secondary', 'Pleomorphic lobular carcinoma in situ', 'Teratoma malignant NOS', 'Chondrosarcoma grade 2/3', 'Duct carcinoma NOS', 'Malignant melanoma in giant pigmented nevus', 'Rhabdoid sarcoma', 'Malignant melanoma in junctional nevus', 'Endometrioid adenofibroma NOS', 'Tumor cells benign', 'Pleomorphic carcinoma', 'Unclassified tumor malignant uncertain whether primary or metastatic', 'Bronchial adenoma NOS', 'Hodgkin granuloma', 'Acute lymphoblastic leukemia mature B-cell type', 'Neoplasm benign', 'Infiltrating duct and cribriform carcinoma', 'Intraductal tubular-papillary neoplasm high grade', 'Melanotic MPNST', 'Pulmonary adenomatosis', 'Transitional cell carcinoma in situ', 'Malignant lymphoma mixed cell type diffuse', 'Central neuroblastoma', 'Rhabdomyosarcoma with ganglionic differentiation', 'Meningeal melanoma', 'Preleukemic syndrome', 'Pancreatic endocrine tumor nonfunctioning', 'Intraductal tubulopapillary neoplasm', 'Primary amyloidosis', 'Eosinophilic granuloma', 'Not Reported', 'Sarcoma NOS', 'Haemangioblastoma', 'Adenocarcinoma in villous adenoma', 'Precancerous melanosis NOS', 'Myeloid leukemia NOS', 'Adenocarcinoid tumor', 'Squamous cell carcinoma adenoid', 'Large cell carcinoma NOS', 'Malignant lymphoma lymphoblastic NOS', 'Pleomorphic liposarcoma', 'Mixed medullary-follicular carcinoma', 'Gastrointestinal stromal tumor malignant', 'Pancreatic endocrine tumor benign', 'Papillary serous cystadenoma NOS', 'Transitional cell carcinoma', 'Diffuse melanocytosis', 'Carcinoma metastatic NOS', 'Neoplasm malignant', 'Melanotic progonoma', 'Lobular carcinoma NOS', 'Carcinoma in pleomorphic adenoma', 'Esophageal glandular dysplasia (intraepithelial neoplasia) high grade', 'Non-small cell carcinoma', 'Burkitt tumor', 'Basal cell epithelioma', 'Bronchial adenoma cylindroid', 'Secretory carcinoma of breast', 'Chronic monocytic leukemia', 'Melanoma malignant of soft parts', 'Papillotubular adenocarcinoma', 'Chronic lymphocytic leukemia', 'Esophageal intraepithelial neoplasia high grade', 'Undifferentiated leukaemia', 'Adenocarcinoma in situ in a polyp NOS', 'Paget disease mammary', 'Intradermal nevus', 'Tubular androblastoma with lipid storage', 'Papilloma of bladder', 'Liposarcoma well differentiated', 'Acute lymphatic leukemia', 'Acute lymphoid leukemia', 'Unclassified tumor malignant', 'Carcinosarcoma NOS', 'Adenocarcinoma endocervical type', 'Mucous adenocarcinoma', 'Pancreatic microadenoma', 'Papillary transitional cell carcinoma', 'Papillary tumor of the pineal region', 'Serous surface papillary carcinoma', 'Spindle cell carcinoma NOS', 'Meningioma NOS', 'Tubular adenoma NOS', 'Cancer', 'Renal cell adenocarcinoma', 'Bile duct carcinoma', 'Cerebellar liponeurocytoma', 'Classical Hodgkin lymphoma mixed cellularity NOS', 'Paget disease of breast', 'Adenocarcinoma in adenomatous polyp', 'Acute leukemia NOS', 'Pigmented adenoma', 'Medulloblastoma NOS', 'Papillary serous adenocarcinoma', 'Neuroblastoma NOS', 'Hepatocellular carcinoma NOS', 'Bronchiolar adenocarcinoma', 'Bronchiolo-alveolar carcinoma Clara cell', 'Malignant lymphoma lymphocytic NOS', 'Inflammatory adenocarcinoma', 'Micropapillary carcinoma NOS', 'Juvenile myelomonocytic leukemia', 'Multiple myeloma', 'Pancreatic endocrine tumor NOS', 'Intracystic papilloma', 'Intraductal carcinoma and lobular carcinoma in situ', 'Lobular carcinoma noninfiltrating', 'Burkitt-like lymphoma', 'Carcinoma intestinal type', 'Squamous cell carcinoma NOS', 'Tumor cells malignant', 'Chronic myelogenous leukemia BCR-ABL positive', 'Melanotic schwannoma', 'Renal cell carcinoma chromophobe type', 'Bronchiolo-alveolar adenocarcinoma NOS', 'Bronchiolo-alveolar carcinoma goblet cell type', 'Carcinoma anaplastic NOS', 'Splenic lymphoma with villous lymphocytes', 'Melanotic medulloblastoma', 'Splenic B-cell lymphoma/leukemia unclassifiable', 'Chronic myelomonocytic leukemia in transformation', 'Liposarcoma differentiated', 'Splenic marginal zone B-cell lymphoma', 'Acute myeloid leukemia NOS', 'Hodgkin lymphoma mixed cellularity NOS', 'Endometrial sarcoma NOS', 'Acinar cell carcinoma', 'Bile duct cystadenoma', 'Cerebellar sarcoma NOS', 'Tubulocystic renal cell carcinoma', 'Liver cell carcinoma', 'Chronic myeloproliferative disorder', 'Unclassified tumor benign', 'Duct adenoma NOS', 'Pleomorphic lipoma', 'Neurosarcoma', 'Osteosarcoma NOS', 'Papillomatosis glandular', 'Medullary adenocarcinoma', 'Melanotic neuroectodermal tumor', 'Tumor cells uncertain whether benign or malignant', 'Peripheral T-cell lymphoma NOS', 'Acute lymphocytic leukemia', 'Papillary renal cell carcinoma', 'Acute lymphoblastic leukemia-lymphoma NOS', 'Papillary urothelial carcinoma', 'Tumor secondary', 'Pleomorphic lobular carcinoma', 'Lymphocytic leukemia NOS', 'Esophageal squamous intraepithelial neoplasia (dysplasia) high grade', 'Small cell carcinoma NOS', 'Basal cell adenoma', 'Neurofibrosarcoma', 'Paraganglioma malignant', 'Malignant lymphoma diffuse NOS', 'Mixed medullary-papillary carcinoma', 'Myoepithelioma', 'Bronchiolo-alveolar carcinoma NOS', 'Papillary epidermoid carcinoma', 'Malignancy', 'Intraepidermal squamous cell carcinoma Bowen type', 'Chronic myelocytic leukemia NOS', 'Paget disease extramammary', 'Bronchio-alveolar carcinoma mucinous', 'Osteoblastoma NOS', 'Chronic lymphoid leukemia', 'T-cell large granular lymphocytic leukemia', 'Bronchial-associated lymphoid tissue lymphoma', 'Melanocytic nevus', 'Dysplastic nevus', 'Neoplasm NOS', 'Undifferentiated round cell sarcoma', 'Tubulolobular carcinoma', 'Pulmonary artery intimal sarcoma', 'Papillary adenofibroma', 'Interstitial cell tumor malignant', 'Chronic myelomonocytic leukemia NOS', 'Infiltrating duct carcinoma NOS', 'Serous cystadenocarcinoma NOS', 'Malignant lymphoma large cell NOS', 'Intraductal papillary adenocarcinoma with invasion', 'Renal cell carcinoma sarcomatoid', 'Malignant lymphoma mixed cell type follicular', 'Adult T-cell lymphoma', 'Lobular and ductal carcinoma', 'Small cell osteosarcoma', 'Adult T-cell lymphoma/leukemia', 'Mixed tumor malignant NOS', 'Papillary serous cystadenocarcinoma', 'Lymphoblastic leukemia NOS', 'T-cell large granular lymphocytosis', 'Precursor T-cell lymphoblastic leukemia', 'unknown', 'Squamous cell carcinoma in situ NOS', 'Burkitt lymphoma NOS (Includes all variants)', 'Haemangiosarcoma', 'Basophil adenocarcinoma', 'Acute lymphoblastic leukemia NOS', 'Melanoma NOS', 'Burkitt cell leukemia', 'Unclassified tumor borderline malignancy', 'Dermatofibroma NOS', 'Combined small cell-squamous cell carcinoma', 'Intraductal papillary adenocarcinoma NOS', 'Rhabdoid meningioma', 'Lymphatic leukemic NOS', 'Carcinoma in adenomatous polyp', 'Malignant lymphoma lymphocytic nodular NOS', 'Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive', 'Renal cell carcinoma NOS', 'Mammary carcinoma in situ', 'Acute leukemia Burkitt type', 'Chronic granulocytic leukemia NOS', 'Peripheral T-cell lymphoma large cell', 'Mixed adenocarcinoma and squamous cell carcinoma', 'Neuroepithelioma NOS', 'Pro-T ALL', 'Nonpigmented nevus', 'Basophil carcinoma', 'Chondroma NOS', 'Tubular carcinoid', 'Intraductal carcinoma noninfiltrating NOS', 'Chronic leukemia NOS', 'Oat cell carcinoma', 'Ganglioglioma NOS', 'Eosinophil carcinoma', 'Mucosal-associated lymphoid tissue lymphoma', 'Combined/mixed carcinoid and adenocarcinoma', 'Pleomorphic adenoma', 'Pulmonary blastoma', 'Sclerosing hemangioma']",,Diagnosis
Gross Tumor Weight,Gross Tumor Weight,GrossTumorWeight,"Numeric value used to describe the gross pathologic tumor weight, measured in grams.",False,,,,Diagnosis
Margin Distance,Margin Distance,MarginDistance,Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.,False,,,,Diagnosis
Tumor Confined to Organ of Origin,Tumor Confined to Organ of Origin,TumorConfinedtoOrganofOrigin,The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Diagnosis
Gleason Grade Group,Gleason Grade Group,GleasonGradeGroup,"The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Group 2', 'Group 5', 'Group 4', 'Group 1', 'Group 3', '']",,Diagnosis
Anaplasia Present,Anaplasia Present,AnaplasiaPresent,Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.,False,,"['Yes - Anaplasia Present', 'Not Reported', 'no', 'unknown', '']",,Diagnosis
IRS Stage,IRS Stage,IRSStage,"The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).",False,,"['3', '2', 'unknown', '1', 'Not Reported', '4', '']",,Diagnosis
AJCC Pathologic T,AJCC Pathologic T,AJCCPathologicT,"Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).",False,,"['T1c', 'Ta', 'T1a1', 'T0', 'T1mi', ""Tis (Paget's)"", 'T2', 'T3d', 'T1a', 'T3c', 'Tis (LCIS)', 'T1a2', 'T4b', 'T2a', 'T1b2', 'T2b', 'Tis (DCIS)', 'T4a', 'T3b', 'T1b', 'T3', 'unknown', 'T2c', 'Not Reported', 'Tis', 'T4e', 'T2d', 'T3a', 'T4', 'T4d', 'T1', 'TX', 'T2a1', 'T1b1', 'T2a2', 'T4c', '']",,Diagnosis
Vascular Invasion Type,Vascular Invasion Type,VascularInvasionType,Text term that represents the type of vascular tumor invasion.,False,,"['Extramural', 'Micro', 'unknown', 'Intramural', 'Macro', 'No Vascular Invasion', 'Not Reported', '']",,Diagnosis
Morphology,Morphology,Morphology,"The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.",True,,,,Diagnosis
Supratentorial Localization,Supratentorial Localization,SupratentorialLocalization,Text term to specify the location of the supratentorial tumor.,False,,"['Spinal Cord', 'Cerebral Cortex', 'unknown', 'White Matter', 'Deep Gray', 'Not Reported', '']",,Diagnosis
IRS Group,IRS Group,IRSGroup,"Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).",False,,"['Group II', 'Group IIc', 'Group III', 'Group Ib', 'Group IIIb', 'unknown', 'Group I', 'Group IV', 'Group IIIa', 'Not Reported', 'Group Ia', 'Group IIa', '']",,Diagnosis
Primary Gleason Grade,Primary Gleason Grade,PrimaryGleasonGrade,"The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Pattern 1', 'Pattern 4', 'Pattern 5', 'Pattern 2', 'Pattern 3', '']",,Diagnosis
AJCC Clinical T,AJCC Clinical T,AJCCClinicalT,Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['T1c', 'Ta', 'T1a1', 'T0', 'T1mi', ""Tis (Paget's)"", 'T2', 'T3d', 'T1a', 'T3c', 'Tis (LCIS)', 'T1a2', 'T4b', 'T2a', 'T1b2', 'T2b', 'Tis (DCIS)', 'T4a', 'T3b', 'T1b', 'T3', 'unknown', 'T2c', 'Not Reported', 'Tis', 'T4e', 'T2d', 'T3a', 'T4', 'T4d', 'T1', 'TX', 'T2a1', 'T1b1', 'T2a2', 'T4c', '']",,Diagnosis
Anaplasia Present Type,Anaplasia Present Type,AnaplasiaPresentType,"The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.",False,,"['Diffuse', 'unknown', 'Equivocal', 'Absent', 'Present', 'Sclerosis', 'Not Reported', 'Focal', '']",,Diagnosis
Laterality,Laterality,Laterality,"For tumors in paired organs, designates the side on which the cancer originates.",False,,"['Right', 'Midline', 'Bilateral', 'unknown', 'Unilateral', 'Not Reported', 'Left', '']",,Diagnosis
Non Nodal Tumor Deposits,Non Nodal Tumor Deposits,NonNodalTumorDeposits,The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Diagnosis
WHO CNS Grade,WHO CNS Grade,WHOCNSGrade,WHO CNS Grade,False,,"['Grade I', 'Grade III', 'Grade Not Assigned', 'unknown', 'Grade IV', 'Grade II', 'Not Reported', '']",,Diagnosis
Mitotic Count,Mitotic Count,MitoticCount,"The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.",False,,,,Diagnosis
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Diagnosis
AJCC Clinical N,AJCC Clinical N,AJCCClinicalN,Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['N2b', 'N1b', 'N0', 'N1c', 'N1', 'N1bI', 'N1bIV', 'NX', 'N2', 'N3', 'N2a', 'N0 (mol+)', 'N3b', 'N3c', 'N0 (mol-)', 'N1a', 'N1bII', 'unknown', 'N4', 'N0 (i+)', 'N2c', 'Not Reported', 'N3a', 'N1bIII', 'N0 (i-)', 'N1mi', '']",,Diagnosis
Margins Involved Site,Margins Involved Site,MarginsInvolvedSite,The text term used to describe the anatomic sites that were involved in the survival margins.,False,,"['Gerota Fascia', 'Renal', 'Renal Sinus', 'Renal Capsule', 'Perinephric Fat', 'Renal Vein', 'Parenchyma', 'Ureter', '']",,Diagnosis
Peritoneal Fluid Cytological Status,Peritoneal Fluid Cytological Status,PeritonealFluidCytologicalStatus,The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.,False,,"['Unsatisfactory', 'Malignant', 'unknown', 'Non-Malignant', 'Atypical', 'Not Reported', '']",,Diagnosis
Metastasis at Diagnosis,Metastasis at Diagnosis,MetastasisatDiagnosis,The text term used to describe the extent of metastatic disease present at diagnosis.,False,,"['No Metastasis', 'unknown', 'Regional Metastasis', 'Metastasis NOS', 'Distant Metastasis', 'Not Reported', '']",,Diagnosis
Classification of Tumor,Classification of Tumor,ClassificationofTumor,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.,False,,"['Not Allowed To Collect', 'Metastasis', 'Recurrence', 'unknown', 'Other', 'Not Reported', 'Primary', '']",,Diagnosis
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Diagnosis
Ovarian Specimen Status,Ovarian Specimen Status,OvarianSpecimenStatus,The text term used to describe the physical condition of the involved ovary.,False,,"['Ovarian Capsule Fragmented', 'Ovarian Capsule Ruptured', 'unknown', 'Ovarian Capsule Intact', 'Not Reported', '']",,Diagnosis
IGCCCG Stage,IGCCCG Stage,IGCCCGStage,"The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.",False,,"['Intermediate Prognosis', 'unknown', 'Good Prognosis', 'Not Reported', 'Poor Prognosis', '']",,Diagnosis
Days to Last Follow up,Days to Last Follow up,DaystoLastFollowup,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'",True,,,,Diagnosis
Prior Treatment,Prior Treatment,PriorTreatment,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.,False,,"['Not Allowed To Collect', 'no', 'unknown', 'Not Reported', 'yes', '']",,Diagnosis
Ovarian Surface Involvement,Ovarian Surface Involvement,OvarianSurfaceInvolvement,The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.,False,,"['Indeterminate', 'unknown', 'Absent', 'Present', 'Not Reported', '']",,Diagnosis
WHO NTE Grade,WHO NTE Grade,WHONTEGrade,WHO NTE Grade,False,,"['G3', 'unknown', 'G2', 'G1', 'Not Reported', 'GX', '']",,Diagnosis
Tumor Grade,Tumor Grade,TumorGrade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.",False,,"['GB', 'Low Grade', 'unknown', 'G3', 'G4', 'High Grade', 'G2', 'G1', 'Not Applicable', 'Not Reported', 'Intermediate Grade', 'GX', '']",,Diagnosis
INRG Stage,INRG Stage,INRGStage,"The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).",False,,"['L2', 'Ms', 'L1', 'unknown', 'Not Reported', 'M', '']",,Diagnosis
AJCC Pathologic M,AJCC Pathologic M,AJCCPathologicM,"Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).",False,,"['M1c', 'M1a', 'M1b', 'M0', 'unknown', 'MX', 'Not Reported', 'M1', 'cM0 (i+)', '']",,Diagnosis
Method of Diagnosis,Method of Diagnosis,MethodofDiagnosis,Text term used to describe the method used to confirm the patients malignant diagnosis.,False,,"['Pap Smear', 'Diagnostic Imaging', 'Surgical Resection', 'Blood Draw', 'Cystoscopy', 'Thoracentesis', 'Pathologic Review', 'Excisional Biopsy', 'Bone Marrow Aspirate', 'Laparotomy', 'Laparoscopy', 'Other', 'Debulking', 'Cytology', 'Core Biopsy', 'unknown', 'Not Reported', 'Biopsy', 'Incisional Biopsy', 'Physical Exam', 'Fine Needle Aspiration', 'Enucleation', 'Autopsy', 'Ultrasound Guided Biopsy', 'Dilation and Curettage Procedure', '']",,Diagnosis
Non Nodal Regional Disease,Non Nodal Regional Disease,NonNodalRegionalDisease,The text term used to describe whether the patient had non-nodal regional disease.,False,,"['Indeterminate', 'unknown', 'Absent', 'Present', 'Not Reported', '']",,Diagnosis
Age at Diagnosis,Age at Diagnosis,AgeatDiagnosis,Age at the time of diagnosis expressed in number of days since birth.,True,,,,Diagnosis
Precancerous Condition Type,Precancerous Condition Type,PrecancerousConditionType,The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).,False,,"['Scar - no residual melanoma', 'Normal', 'Adenocarcinoma in situ - mucinous', 'Adenocarcinoma in situ - non mucinous', 'Melanoma in situ', 'Severe dysplasia', 'Normal WDA', 'Superficial spreading', 'Lentigo maligna type', 'Squamous carcinoma in situ', 'Invasive melanoma - nevoid', 'Invasive melanoma - desmoplastic', 'Hamartoma', 'Invasive melanoma - superficial spreading', 'Neuroendocrine cell hyperplasia', 'Benign tumor NOS', 'Other', 'Persistent melanoma in situ', 'Invasive melanoma - lentigo maligna', 'Mild dysplasia', 'Acral-lentiginous', 'Not Applicable', 'Prostatic Intraepithelial Neoplasia', 'Melanocytic hyperplasia', 'Pancreatic Intraductal Papillary-Mucinous Neoplasm', 'Reserve cell hyperplasia', 'Invasive melanoma - acral lentiginous', 'Moderate dysplasia', 'Melanoma in situ arising in a giant congenital nevus', 'Atypical Adenomatous Lung Hyperplasia', 'Invasive melanoma', 'Squamous metaplasia - mature', 'Atypical adenomatous hyperplasia', 'Atypical melanocytic proliferation', 'Invasive melanoma - nodular type', 'Squamous metaplasia - immature', 'No diagnosis possible', 'Melanoma in situ not otherwise classified', 'Pancreatic Intraepithelial Neoplasia', 'Ductal Carcinoma In Situ', 'Carcinoma NOS', '']",,Diagnosis
Vascular Invasion Present,Vascular Invasion Present,VascularInvasionPresent,The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.,False,,"['Not Allowed To Collect', 'no', 'unknown', 'Not Reported', 'Yes - Vascular Invasion Present', '']",,Diagnosis
Lymph Nodes Positive,Lymph Nodes Positive,LymphNodesPositive,The number of lymph nodes involved with disease as determined by pathologic examination.,False,,,,Diagnosis
Tissue or Organ of Origin,Tissue or Organ of Origin,TissueorOrganofOrigin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Appendix', 'Parametrium', 'Aortic body and other paraganglia', 'Trachea', 'Transverse colon', 'Lateral floor of mouth', 'Paraspinal', 'Cerebellum NOS', 'Paraurethral gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Cloacogenic zone', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Overlapping lesion of bladder', 'Overlapping lesion of retroperitoneum and peritoneum', 'Uterine adnexa', 'Vertebral column', 'Upper lobe lung', 'Overlapping lesion of floor of mouth', 'Spinal meninges', 'Labium minus', 'Hard palate', 'Spleen', 'Breast NOS', 'Middle third of esophagus', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Duodenum', 'Spinal cord', 'Anterior wall of nasopharynx', 'Body of pancreas', 'Fundus uteri', 'Upper third of esophagus', 'Short bones of upper limb and associated joints', 'Overlapping lesion of cervix uteri', 'Lateral wall of bladder', 'Nervous system NOS', 'Upper-outer quadrant of breast', 'Nipple', 'Labium majus', 'Exocervix', 'Vulva NOS', 'Gum NOS', 'Mediastinum NOS', 'Urinary system NOS', 'Medulla of adrenal gland', 'Tongue NOS', 'Overlapping lesion of eye and adnexa', 'Bone marrow', 'Reticuloendothelial system NOS', 'Renal pelvis', 'Brain stem', 'Ureter', 'Overlapping lesion of small intestine', 'unknown primary site', 'Intestinal tract NOS', 'Laryngeal cartilage', 'Scrotum NOS', 'Upper respiratory tract NOS', 'Rectosigmoid junction', 'Overlapping lesion of stomach', 'Sphenoid sinus', 'Lymph nodes of inguinal region or leg', 'Pancreas NOS', 'Kidney NOS', 'Branchial cleft', 'Pharynx NOS', 'Tonsillar pillar', 'Islets of Langerhans', 'Optic nerve', 'Lymph nodes of multiple regions', 'Overlapping lesion of tonsil', 'Posterior wall of hypopharynx', 'Intrahepatic bile duct', 'Lacrimal gland', 'Orbit NOS', 'Bone NOS', 'Submandibular gland', 'Endocervix', 'Corpus uteri', 'Skin of trunk', 'Retina', 'Overlapping lesion of endocrine glands and related structures', 'Ciliary body', 'Overlapping lesion of larynx', 'Anterior mediastinum', 'Lower limb NOS', 'Frontal sinus', 'Superior wall of nasopharynx', 'Prepuce', 'Major salivary gland NOS', 'Stomach NOS', 'Overlapping lesion of rectum anus and anal canal', 'Olfactory nerve', 'Peripheral nerves and autonomic nervous system of thorax', 'Testis NOS', 'Cheek mucosa', 'Abdomen NOS', 'Waldeyer ring', 'Bone of limb NOS', 'Cervical esophagus', 'Intrathoracic lymph nodes', 'Overlapping lesion of digestive system', 'Axillary tail of breast', 'Lower-outer quadrant of breast', 'Overlapping lesion of brain and central nervous system', 'Lymph node NOS', 'Adrenal gland NOS', 'Soft palate NOS', 'Overlapping lesion of pancreas', 'Autonomic nervous system NOS', 'Border of tongue', 'Posterior wall of oropharynx', 'Meninges NOS', 'Colon NOS', 'Lateral wall of oropharynx', 'Supraglottis', 'Overlapping lesion of vulva', 'Fallopian tube', 'Extrahepatic bile duct', 'Posterior wall of nasopharynx', 'External ear', 'skin of upper limb and shoulder', 'Craniopharyngeal duct', 'Specified parts of peritoneum', 'Lingual tonsil', 'Maxillary sinus', 'Lower gum', 'Female genital tract NOS', 'Central portion of breast', 'Overlapping lesion of male genital organs', 'Overlapping lesion of colon', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Mucosa of lower lip', 'Tonsillar fossa', 'Other specified parts of pancreas', 'Anterior wall of bladder', 'Overlapping lesion of esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Connective subcutaneous and other soft tissues of thorax', 'Conjunctiva', 'Nasopharynx NOS', 'Mandible', 'Lung NOS', 'Overlapping lesions of oropharynx', 'External upper lip', 'Vagina NOS', 'Short bones of lower limb and associated joints', 'Placenta', 'Ileum', 'Overlapping lesion of lung', 'Broad ligament', 'Lower third of esophagus', 'Abdominal esophagus', 'External lip NOS', 'Other specified parts of male genital organs', 'Lateral wall of nasopharynx', 'Other specified parts of female genital organs', 'Bones of skull and face and associated joints', 'Palate NOS', 'Retromolar area', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of heart mediastinum and pleura', 'Oropharynx NOS', 'Bladder neck', 'Anal canal', 'Lymph nodes of head face and neck', 'Middle ear', 'Brain NOS', 'Ascending colon', 'Isthmus uteri', 'Ill-defined sites within respiratory system', 'Eye NOS', 'Hematopoietic system NOS', 'Accessory sinus NOS', 'Gastric antrum', 'Trigone of bladder', 'Head face or neck NOS', 'Pylorus', 'Cornea NOS', 'Pelvic lymph nodes', 'Occipital lobe', 'Meckel diverticulum', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Base of tongue NOS', 'Cranial nerve NOS', 'Overlapping lesion of hypopharynx', 'Greater curvature of stomach NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Commissure of lip', 'Overlapping lesion of penis', 'Ovary', 'Cervix uteri', 'Vestibule of mouth', 'Hypopharyngeal aspect of aryepiglottic fold', 'Prostate gland', 'Dome of bladder', 'Parotid gland', 'Pelvis NOS', 'Lower-inner quadrant of breast', 'Connective subcutaneous and other soft tissues of abdomen', 'Pineal gland', 'Fundus of stomach', 'Endocrine gland NOS', 'Cerebrum', 'Splenic flexure of colon', 'Floor of mouth NOS', 'External lower lip', 'Eyelid', 'Carotid body', 'Choroid', 'Overlapping lesion of major salivary glands', 'Mucosa of lip NOS', 'Not Reported', 'Urachus', 'Liver', 'skin of lower limb and hip', 'Overlapping lesion of brain', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Thyroid gland', 'Thoracic esophagus', 'Biliary tract NOS', 'Other ill-defined sites', 'Overlapping lesion of palate', 'Heart', 'Larynx NOS', 'Clitoris', 'Middle lobe lung', 'Peripheral nerves and autonomic nervous system of abdomen', 'Upper gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Parathyroid gland', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lesser curvature of stomach NOS', 'Anterior 2/3 of tongue NOS', 'Thymus', 'Frontal lobe', 'Blood', 'Descending colon', 'Gallbladder', 'Pelvic bones sacrum coccyx and associated joints', 'Lymph nodes of axilla or arm', 'Male genital organs NOS', 'Acoustic nerve', 'Thorax NOS', 'Connective subcutaneous and other soft tissues of pelvis', 'Urethra', 'Body of penis', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Rib sternum clavicle and associated joints', 'Cortex of adrenal gland', 'Jejunum', 'Temporal lobe', 'Overlapping lesion of skin', 'Upper-inner quadrant of breast', 'Bladder NOS', 'Ventral surface of tongue NOS', 'Uterus NOS', 'Anus NOS', 'Overlapping lesion of accessory sinuses', 'Rectum NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Cardia NOS', 'Anterior surface of epiglottis', 'Overlapping lesion of urinary organs', 'Skin of other and unspecified parts of face', 'Skin of scalp and neck', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Lip NOS', 'Posterior mediastinum', 'Sigmoid colon', 'Main bronchus', 'Anterior floor of mouth', 'Overlapping lesion of ill-defined sites', 'Hepatic flexure of colon', 'Overlapping lesion of biliary tract', 'Connective subcutaneous and other soft tissues NOS', 'Tonsil NOS', 'Long bones of upper limb scapula and associated joints', 'Lower lobe lung', 'Myometrium', 'Posterior wall of bladder', 'Hypopharynx NOS', 'Skin of lip NOS', 'Cauda equina', 'Pleura NOS', 'Esophagus NOS', 'Overlapping lesion of breast', 'Cerebral meninges', 'Sublingual gland', 'Penis NOS', 'Overlapping lesion of lip', 'Descended testis', 'Glottis', 'Upper limb NOS', 'Nasal cavity', 'Ethmoid sinus', 'Ampulla of Vater', 'Vallecula', 'Overlapping lesion of tongue', 'skin NOS', 'Epididymis', 'Undescended testis', 'Ventricle NOS', 'Pancreatic duct', 'Body of stomach', 'Endometrium', 'Long bones of lower limb and associated joints', 'Dorsal surface of tongue NOS', 'unknown', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Head of pancreas', 'Gastrointestinal tract NOS', 'Glans penis', 'Postcricoid region', 'Mucosa of upper lip', 'Intra-abdominal lymph nodes', 'Pyriform sinus', 'Round ligament', 'Ureteric orifice', 'Cecum', 'Peritoneum NOS', 'Parietal lobe', 'Subglottis', 'Mouth NOS', 'Small intestine NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of corpus uteri', 'Uvula', 'Spermatic cord', 'Retroperitoneum', 'Tail of pancreas']",,Diagnosis
Synchronous Malignancy,Synchronous Malignancy,SynchronousMalignancy,"A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.",False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Diagnosis
Cog Neuroblastoma Risk Group,Cog Neuroblastoma Risk Group,CogNeuroblastomaRiskGroup,Text term that represents the categorization of patients on the basis of prognostic factors per a system developed by Children's Oncology Group (COG). Risk level is used to assign treatment intensity.,False,,"['Intermediate Risk', 'unknown', 'Low Risk', 'Not Reported', 'High Risk', '']",,Diagnosis
Percent Tumor Invasion,Percent Tumor Invasion,PercentTumorInvasion,The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.,False,,,,Diagnosis
Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Appendix', 'Parametrium', 'Aortic body and other paraganglia', 'Trachea', 'Transverse colon', 'Lateral floor of mouth', 'Paraspinal', 'Cerebellum NOS', 'Paraurethral gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Cloacogenic zone', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Overlapping lesion of bladder', 'Overlapping lesion of retroperitoneum and peritoneum', 'Uterine adnexa', 'Vertebral column', 'Upper lobe lung', 'Overlapping lesion of floor of mouth', 'Spinal meninges', 'Labium minus', 'Hard palate', 'Spleen', 'Breast NOS', 'Middle third of esophagus', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Duodenum', 'Spinal cord', 'Anterior wall of nasopharynx', 'Body of pancreas', 'Fundus uteri', 'Upper third of esophagus', 'Short bones of upper limb and associated joints', 'Overlapping lesion of cervix uteri', 'Lateral wall of bladder', 'Nervous system NOS', 'Upper-outer quadrant of breast', 'Nipple', 'Labium majus', 'Exocervix', 'Vulva NOS', 'Gum NOS', 'Mediastinum NOS', 'Urinary system NOS', 'Medulla of adrenal gland', 'Tongue NOS', 'Overlapping lesion of eye and adnexa', 'Bone marrow', 'Reticuloendothelial system NOS', 'Renal pelvis', 'Brain stem', 'Ureter', 'Overlapping lesion of small intestine', 'unknown primary site', 'Intestinal tract NOS', 'Laryngeal cartilage', 'Scrotum NOS', 'Upper respiratory tract NOS', 'Rectosigmoid junction', 'Overlapping lesion of stomach', 'Sphenoid sinus', 'Lymph nodes of inguinal region or leg', 'Pancreas NOS', 'Kidney NOS', 'Branchial cleft', 'Pharynx NOS', 'Tonsillar pillar', 'Islets of Langerhans', 'Optic nerve', 'Lymph nodes of multiple regions', 'Overlapping lesion of tonsil', 'Posterior wall of hypopharynx', 'Intrahepatic bile duct', 'Lacrimal gland', 'Orbit NOS', 'Bone NOS', 'Submandibular gland', 'Endocervix', 'Corpus uteri', 'Skin of trunk', 'Retina', 'Overlapping lesion of endocrine glands and related structures', 'Ciliary body', 'Overlapping lesion of larynx', 'Anterior mediastinum', 'Lower limb NOS', 'Frontal sinus', 'Superior wall of nasopharynx', 'Prepuce', 'Major salivary gland NOS', 'Stomach NOS', 'Overlapping lesion of rectum anus and anal canal', 'Olfactory nerve', 'Peripheral nerves and autonomic nervous system of thorax', 'Testis NOS', 'Cheek mucosa', 'Abdomen NOS', 'Waldeyer ring', 'Bone of limb NOS', 'Cervical esophagus', 'Intrathoracic lymph nodes', 'Overlapping lesion of digestive system', 'Axillary tail of breast', 'Lower-outer quadrant of breast', 'Overlapping lesion of brain and central nervous system', 'Lymph node NOS', 'Adrenal gland NOS', 'Soft palate NOS', 'Overlapping lesion of pancreas', 'Autonomic nervous system NOS', 'Border of tongue', 'Posterior wall of oropharynx', 'Meninges NOS', 'Colon NOS', 'Lateral wall of oropharynx', 'Supraglottis', 'Overlapping lesion of vulva', 'Fallopian tube', 'Extrahepatic bile duct', 'Posterior wall of nasopharynx', 'External ear', 'skin of upper limb and shoulder', 'Craniopharyngeal duct', 'Specified parts of peritoneum', 'Lingual tonsil', 'Maxillary sinus', 'Lower gum', 'Female genital tract NOS', 'Central portion of breast', 'Overlapping lesion of male genital organs', 'Overlapping lesion of colon', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Mucosa of lower lip', 'Tonsillar fossa', 'Other specified parts of pancreas', 'Anterior wall of bladder', 'Overlapping lesion of esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Connective subcutaneous and other soft tissues of thorax', 'Conjunctiva', 'Nasopharynx NOS', 'Mandible', 'Lung NOS', 'Overlapping lesions of oropharynx', 'External upper lip', 'Vagina NOS', 'Short bones of lower limb and associated joints', 'Placenta', 'Ileum', 'Overlapping lesion of lung', 'Broad ligament', 'Lower third of esophagus', 'Abdominal esophagus', 'External lip NOS', 'Other specified parts of male genital organs', 'Lateral wall of nasopharynx', 'Other specified parts of female genital organs', 'Bones of skull and face and associated joints', 'Palate NOS', 'Retromolar area', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of heart mediastinum and pleura', 'Oropharynx NOS', 'Bladder neck', 'Anal canal', 'Lymph nodes of head face and neck', 'Middle ear', 'Brain NOS', 'Ascending colon', 'Isthmus uteri', 'Ill-defined sites within respiratory system', 'Eye NOS', 'Hematopoietic system NOS', 'Accessory sinus NOS', 'Gastric antrum', 'Trigone of bladder', 'Head face or neck NOS', 'Pylorus', 'Cornea NOS', 'Pelvic lymph nodes', 'Occipital lobe', 'Meckel diverticulum', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Base of tongue NOS', 'Cranial nerve NOS', 'Overlapping lesion of hypopharynx', 'Greater curvature of stomach NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Commissure of lip', 'Overlapping lesion of penis', 'Ovary', 'Cervix uteri', 'Vestibule of mouth', 'Hypopharyngeal aspect of aryepiglottic fold', 'Prostate gland', 'Dome of bladder', 'Parotid gland', 'Pelvis NOS', 'Lower-inner quadrant of breast', 'Connective subcutaneous and other soft tissues of abdomen', 'Pineal gland', 'Fundus of stomach', 'Endocrine gland NOS', 'Cerebrum', 'Splenic flexure of colon', 'Floor of mouth NOS', 'External lower lip', 'Eyelid', 'Carotid body', 'Choroid', 'Overlapping lesion of major salivary glands', 'Mucosa of lip NOS', 'Not Reported', 'Urachus', 'Liver', 'skin of lower limb and hip', 'Overlapping lesion of brain', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Thyroid gland', 'Thoracic esophagus', 'Biliary tract NOS', 'Other ill-defined sites', 'Overlapping lesion of palate', 'Heart', 'Larynx NOS', 'Clitoris', 'Middle lobe lung', 'Peripheral nerves and autonomic nervous system of abdomen', 'Upper gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Parathyroid gland', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lesser curvature of stomach NOS', 'Anterior 2/3 of tongue NOS', 'Thymus', 'Frontal lobe', 'Blood', 'Descending colon', 'Gallbladder', 'Pelvic bones sacrum coccyx and associated joints', 'Lymph nodes of axilla or arm', 'Male genital organs NOS', 'Acoustic nerve', 'Thorax NOS', 'Connective subcutaneous and other soft tissues of pelvis', 'Urethra', 'Body of penis', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Rib sternum clavicle and associated joints', 'Cortex of adrenal gland', 'Jejunum', 'Temporal lobe', 'Overlapping lesion of skin', 'Upper-inner quadrant of breast', 'Bladder NOS', 'Ventral surface of tongue NOS', 'Uterus NOS', 'Anus NOS', 'Overlapping lesion of accessory sinuses', 'Rectum NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Cardia NOS', 'Anterior surface of epiglottis', 'Overlapping lesion of urinary organs', 'Skin of other and unspecified parts of face', 'Skin of scalp and neck', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Lip NOS', 'Posterior mediastinum', 'Sigmoid colon', 'Main bronchus', 'Anterior floor of mouth', 'Overlapping lesion of ill-defined sites', 'Hepatic flexure of colon', 'Overlapping lesion of biliary tract', 'Connective subcutaneous and other soft tissues NOS', 'Tonsil NOS', 'Long bones of upper limb scapula and associated joints', 'Lower lobe lung', 'Myometrium', 'Posterior wall of bladder', 'Hypopharynx NOS', 'Skin of lip NOS', 'Cauda equina', 'Pleura NOS', 'Esophagus NOS', 'Overlapping lesion of breast', 'Cerebral meninges', 'Sublingual gland', 'Penis NOS', 'Overlapping lesion of lip', 'Descended testis', 'Glottis', 'Upper limb NOS', 'Nasal cavity', 'Ethmoid sinus', 'Ampulla of Vater', 'Vallecula', 'Overlapping lesion of tongue', 'skin NOS', 'Epididymis', 'Undescended testis', 'Ventricle NOS', 'Pancreatic duct', 'Body of stomach', 'Endometrium', 'Long bones of lower limb and associated joints', 'Dorsal surface of tongue NOS', 'unknown', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Head of pancreas', 'Gastrointestinal tract NOS', 'Glans penis', 'Postcricoid region', 'Mucosa of upper lip', 'Intra-abdominal lymph nodes', 'Pyriform sinus', 'Round ligament', 'Ureteric orifice', 'Cecum', 'Peritoneum NOS', 'Parietal lobe', 'Subglottis', 'Mouth NOS', 'Small intestine NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of corpus uteri', 'Uvula', 'Spermatic cord', 'Retroperitoneum', 'Tail of pancreas']",,Diagnosis
Secondary Gleason Grade,Secondary Gleason Grade,SecondaryGleasonGrade,"The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Pattern 1', 'Pattern 4', 'Pattern 5', 'Pattern 2', 'Pattern 3', '']",,Diagnosis
Lymph Nodes Tested,Lymph Nodes Tested,LymphNodesTested,The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.,False,,,,Diagnosis
Greatest Tumor Dimension,Greatest Tumor Dimension,GreatestTumorDimension,Numeric value that represents the measurement of the widest portion of the tumor in centimeters.,False,,,,Diagnosis
Year of Diagnosis,Year of Diagnosis,YearofDiagnosis,Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.,False,,,,Diagnosis
Tumor Focality,Tumor Focality,TumorFocality,The text term used to describe whether the patient's disease originated in a single location or multiple locations.,False,,"['Unifocal', 'Not Reported', 'Multifocal', 'unknown', '']",,Diagnosis
AJCC Staging System Edition,AJCC Staging System Edition,AJCCStagingSystemEdition,"The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.",False,,"['1st', '7th', '6th', '5th', '4th', 'unknown', '3rd', '2nd', 'Not Reported', '8th', '']",,Diagnosis
Days to Last Known Disease Status,Days to Last Known Disease Status,DaystoLastKnownDiseaseStatus,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'",True,,,,Diagnosis
First Symptom Prior to Diagnosis,First Symptom Prior to Diagnosis,FirstSymptomPriortoDiagnosis,Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.,False,,"['Visual Changes', 'Sensory Changes', 'Headaches', 'Motor or Movement Changes', 'Altered Mental Status', 'unknown', 'Not Reported', 'Seizures', '']",,Diagnosis
Tumor Largest Dimension Diameter,Tumor Largest Dimension Diameter,TumorLargestDimensionDiameter,"Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.",False,,,,Diagnosis
Gleason Patterns Percent,Gleason Patterns Percent,GleasonPatternsPercent,"Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.",False,,,,Diagnosis
Lymph Node Involved Site,Lymph Node Involved Site,LymphNodeInvolvedSite,The text term used to describe the anatomic site of lymph node involvement.,False,,"['Mesenteric', 'Cervical', 'Submandibular', 'Hilar', 'Paraaortic', 'Popliteal', 'Splenic', 'Iliac', 'NOS', 'Mediastinal', 'Supraclavicular', 'None', 'unknown', 'Parotid', 'Epitrochlear', 'Femoral', 'Not Reported', 'Retroperitoneal', 'Inguinal', 'Occipital', 'Iliac-common', 'Iliac-external', 'Axillary', '']",,Diagnosis
International Prognostic Index,International Prognostic Index,InternationalPrognosticIndex,"The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.",False,,"['High-Intermediate Risk', 'Low-Intermediate Risk', 'Low Risk', 'High Risk', '']",,Diagnosis
Days to Progression Free,Days to Progression Free,DaystoProgressionFree,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis
Days to Progression,Days to Progression,DaystoProgression,Number of days between the date used for index and the date the patient's disease progressed. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis
Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Distant', 'Local', 'Regional', 'unknown', 'Biochemical', 'Not Reported', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis
Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Appendix', 'Parametrium', 'Aortic body and other paraganglia', 'Trachea', 'Transverse colon', 'Lateral floor of mouth', 'Cerebellum NOS', 'Paraurethral gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Cloacogenic zone', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Overlapping lesion of bladder', 'Overlapping lesion of retroperitoneum and peritoneum', 'Uterine adnexa', 'Vertebral column', 'Upper lobe lung', 'Overlapping lesion of floor of mouth', 'Spinal meninges', 'Labium minus', 'Hard palate', 'Spleen', 'Breast NOS', 'Middle third of esophagus', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Duodenum', 'Spinal cord', 'Anterior wall of nasopharynx', 'Body of pancreas', 'Fundus uteri', 'Upper third of esophagus', 'Short bones of upper limb and associated joints', 'Overlapping lesion of cervix uteri', 'Lateral wall of bladder', 'Nervous system NOS', 'Upper-outer quadrant of breast', 'Nipple', 'Labium majus', 'Exocervix', 'Vulva NOS', 'Gum NOS', 'Mediastinum NOS', 'Urinary system NOS', 'Medulla of adrenal gland', 'Tongue NOS', 'Overlapping lesion of eye and adnexa', 'Bone marrow', 'Reticuloendothelial system NOS', 'Renal pelvis', 'Brain stem', 'Ureter', 'Overlapping lesion of small intestine', 'unknown primary site', 'Intestinal tract NOS', 'Laryngeal cartilage', 'Scrotum NOS', 'Upper respiratory tract NOS', 'Rectosigmoid junction', 'Overlapping lesion of stomach', 'Sphenoid sinus', 'Lymph nodes of inguinal region or leg', 'Pancreas NOS', 'Kidney NOS', 'Branchial cleft', 'Pharynx NOS', 'Tonsillar pillar', 'Islets of Langerhans', 'Optic nerve', 'Lymph nodes of multiple regions', 'Overlapping lesion of tonsil', 'Posterior wall of hypopharynx', 'Intrahepatic bile duct', 'Lacrimal gland', 'Orbit NOS', 'Bone NOS', 'Submandibular gland', 'Endocervix', 'Corpus uteri', 'Skin of trunk', 'Retina', 'Overlapping lesion of endocrine glands and related structures', 'Ciliary body', 'Overlapping lesion of larynx', 'Anterior mediastinum', 'Lower limb NOS', 'Frontal sinus', 'Superior wall of nasopharynx', 'Prepuce', 'Major salivary gland NOS', 'Stomach NOS', 'Overlapping lesion of rectum anus and anal canal', 'Olfactory nerve', 'Peripheral nerves and autonomic nervous system of thorax', 'Testis NOS', 'Cheek mucosa', 'Abdomen NOS', 'Waldeyer ring', 'Bone of limb NOS', 'Cervical esophagus', 'Intrathoracic lymph nodes', 'Overlapping lesion of digestive system', 'Axillary tail of breast', 'Lower-outer quadrant of breast', 'Overlapping lesion of brain and central nervous system', 'Lymph node NOS', 'Adrenal gland NOS', 'Soft palate NOS', 'Overlapping lesion of pancreas', 'Autonomic nervous system NOS', 'Border of tongue', 'Posterior wall of oropharynx', 'Meninges NOS', 'Colon NOS', 'Lateral wall of oropharynx', 'Supraglottis', 'Overlapping lesion of vulva', 'Fallopian tube', 'Extrahepatic bile duct', 'Posterior wall of nasopharynx', 'External ear', 'skin of upper limb and shoulder', 'Craniopharyngeal duct', 'Specified parts of peritoneum', 'Lingual tonsil', 'Maxillary sinus', 'Lower gum', 'Female genital tract NOS', 'Central portion of breast', 'Overlapping lesion of male genital organs', 'Overlapping lesion of colon', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Mucosa of lower lip', 'Tonsillar fossa', 'Other specified parts of pancreas', 'Anterior wall of bladder', 'Overlapping lesion of esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Connective subcutaneous and other soft tissues of thorax', 'Conjunctiva', 'Nasopharynx NOS', 'Mandible', 'Lung NOS', 'Overlapping lesions of oropharynx', 'External upper lip', 'Vagina NOS', 'Short bones of lower limb and associated joints', 'Placenta', 'Ileum', 'Overlapping lesion of lung', 'Broad ligament', 'Lower third of esophagus', 'Abdominal esophagus', 'External lip NOS', 'Other specified parts of male genital organs', 'Lateral wall of nasopharynx', 'Other specified parts of female genital organs', 'Bones of skull and face and associated joints', 'Palate NOS', 'Retromolar area', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of heart mediastinum and pleura', 'Oropharynx NOS', 'Bladder neck', 'Anal canal', 'Lymph nodes of head face and neck', 'Middle ear', 'Brain NOS', 'Ascending colon', 'Isthmus uteri', 'Ill-defined sites within respiratory system', 'Eye NOS', 'Hematopoietic system NOS', 'Accessory sinus NOS', 'Gastric antrum', 'Trigone of bladder', 'Head face or neck NOS', 'Pylorus', 'Cornea NOS', 'Pelvic lymph nodes', 'Occipital lobe', 'Meckel diverticulum', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Base of tongue NOS', 'Cranial nerve NOS', 'Overlapping lesion of hypopharynx', 'Greater curvature of stomach NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Commissure of lip', 'Overlapping lesion of penis', 'Ovary', 'Cervix uteri', 'Vestibule of mouth', 'Hypopharyngeal aspect of aryepiglottic fold', 'Prostate gland', 'Dome of bladder', 'Parotid gland', 'Pelvis NOS', 'Lower-inner quadrant of breast', 'Connective subcutaneous and other soft tissues of abdomen', 'Pineal gland', 'Fundus of stomach', 'Endocrine gland NOS', 'Cerebrum', 'Splenic flexure of colon', 'Floor of mouth NOS', 'External lower lip', 'Eyelid', 'Carotid body', 'Choroid', 'Overlapping lesion of major salivary glands', 'Mucosa of lip NOS', 'Not Reported', 'Urachus', 'Liver', 'skin of lower limb and hip', 'Overlapping lesion of brain', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Thyroid gland', 'Thoracic esophagus', 'Biliary tract NOS', 'Other ill-defined sites', 'Overlapping lesion of palate', 'Heart', 'Larynx NOS', 'Clitoris', 'Middle lobe lung', 'Peripheral nerves and autonomic nervous system of abdomen', 'Upper gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Parathyroid gland', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lesser curvature of stomach NOS', 'Anterior 2/3 of tongue NOS', 'Thymus', 'Frontal lobe', 'Blood', 'Descending colon', 'Gallbladder', 'Pelvic bones sacrum coccyx and associated joints', 'Lymph nodes of axilla or arm', 'Male genital organs NOS', 'Acoustic nerve', 'Thorax NOS', 'Urethra', 'Connective subcutaneous and other soft tissues of pelvis', 'Body of penis', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Rib sternum clavicle and associated joints', 'Cortex of adrenal gland', 'Jejunum', 'Temporal lobe', 'Overlapping lesion of skin', 'Upper-inner quadrant of breast', 'Bladder NOS', 'Ventral surface of tongue NOS', 'Uterus NOS', 'Anus NOS', 'Overlapping lesion of accessory sinuses', 'Rectum NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Cardia NOS', 'Anterior surface of epiglottis', 'Overlapping lesion of urinary organs', 'Skin of other and unspecified parts of face', 'Skin of scalp and neck', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Lip NOS', 'Posterior mediastinum', 'Sigmoid colon', 'Main bronchus', 'Anterior floor of mouth', 'Overlapping lesion of ill-defined sites', 'Hepatic flexure of colon', 'Overlapping lesion of biliary tract', 'Connective subcutaneous and other soft tissues NOS', 'Tonsil NOS', 'Long bones of upper limb scapula and associated joints', 'Lower lobe lung', 'Myometrium', 'Posterior wall of bladder', 'Hypopharynx NOS', 'Skin of lip NOS', 'Cauda equina', 'Pleura NOS', 'Esophagus NOS', 'Overlapping lesion of breast', 'Cerebral meninges', 'Sublingual gland', 'Penis NOS', 'Overlapping lesion of lip', 'Descended testis', 'Glottis', 'Upper limb NOS', 'Nasal cavity', 'Ethmoid sinus', 'Ampulla of Vater', 'Vallecula', 'Overlapping lesion of tongue', 'skin NOS', 'Epididymis', 'Undescended testis', 'Ventricle NOS', 'Pancreatic duct', 'Body of stomach', 'Endometrium', 'Long bones of lower limb and associated joints', 'Dorsal surface of tongue NOS', 'unknown', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Head of pancreas', 'Gastrointestinal tract NOS', 'Glans penis', 'Postcricoid region', 'Mucosa of upper lip', 'Intra-abdominal lymph nodes', 'Pyriform sinus', 'Round ligament', 'Ureteric orifice', 'Cecum', 'Peritoneum NOS', 'Parietal lobe', 'Subglottis', 'Mouth NOS', 'Small intestine NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of corpus uteri', 'Uvula', 'Spermatic cord', 'Retroperitoneum', 'Tail of pancreas', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis
Days to Recurrence,Days to Recurrence,DaystoRecurrence,Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis
Chemo Concurrent to Radiation,Chemo Concurrent to Radiation,ChemoConcurrenttoRadiation,The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Therapy
Days to Treatment End,Days to Treatment End,DaystoTreatmentEnd,Number of days between the date used for index and the date the treatment ended. If not applicable please enter 'Not Applicable',False,,,,Therapy
Regimen or Line of Therapy,Regimen or Line of Therapy,RegimenorLineofTherapy,The text term used to describe the regimen or line of therapy.,False,,,,Therapy
Treatment Intent Type,Treatment Intent Type,TreatmentIntentType,Text term to identify the reason for the administration of a treatment regimen. [Manually-curated],False,,"['Cancer Control', 'Neoadjuvant', 'Prevention', 'unknown', 'Adjuvant', 'Palliative', 'Not Reported', 'Cure', '']",,Therapy
Treatment Anatomic Site,Treatment Anatomic Site,TreatmentAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,,"['Appendix', 'Parametrium', 'Aortic body and other paraganglia', 'Trachea', 'Transverse colon', 'Lateral floor of mouth', 'Cerebellum NOS', 'Paraurethral gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Cloacogenic zone', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Overlapping lesion of bladder', 'Overlapping lesion of retroperitoneum and peritoneum', 'Uterine adnexa', 'Vertebral column', 'Upper lobe lung', 'Overlapping lesion of floor of mouth', 'Spinal meninges', 'Labium minus', 'Hard palate', 'Spleen', 'Breast NOS', 'Middle third of esophagus', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Duodenum', 'Spinal cord', 'Anterior wall of nasopharynx', 'Body of pancreas', 'Fundus uteri', 'Upper third of esophagus', 'Short bones of upper limb and associated joints', 'Overlapping lesion of cervix uteri', 'Lateral wall of bladder', 'Nervous system NOS', 'Upper-outer quadrant of breast', 'Nipple', 'Labium majus', 'Exocervix', 'Vulva NOS', 'Gum NOS', 'Mediastinum NOS', 'Urinary system NOS', 'Medulla of adrenal gland', 'Tongue NOS', 'Overlapping lesion of eye and adnexa', 'Bone marrow', 'Reticuloendothelial system NOS', 'Renal pelvis', 'Brain stem', 'Ureter', 'Overlapping lesion of small intestine', 'unknown primary site', 'Intestinal tract NOS', 'Laryngeal cartilage', 'Scrotum NOS', 'Upper respiratory tract NOS', 'Rectosigmoid junction', 'Overlapping lesion of stomach', 'Sphenoid sinus', 'Lymph nodes of inguinal region or leg', 'Pancreas NOS', 'Kidney NOS', 'Branchial cleft', 'Pharynx NOS', 'Tonsillar pillar', 'Islets of Langerhans', 'Optic nerve', 'Lymph nodes of multiple regions', 'Overlapping lesion of tonsil', 'Posterior wall of hypopharynx', 'Intrahepatic bile duct', 'Lacrimal gland', 'Orbit NOS', 'Bone NOS', 'Submandibular gland', 'Endocervix', 'Corpus uteri', 'Skin of trunk', 'Retina', 'Overlapping lesion of endocrine glands and related structures', 'Ciliary body', 'Overlapping lesion of larynx', 'Anterior mediastinum', 'Lower limb NOS', 'Frontal sinus', 'Superior wall of nasopharynx', 'Prepuce', 'Major salivary gland NOS', 'Stomach NOS', 'Overlapping lesion of rectum anus and anal canal', 'Olfactory nerve', 'Peripheral nerves and autonomic nervous system of thorax', 'Testis NOS', 'Cheek mucosa', 'Abdomen NOS', 'Waldeyer ring', 'Bone of limb NOS', 'Cervical esophagus', 'Intrathoracic lymph nodes', 'Overlapping lesion of digestive system', 'Axillary tail of breast', 'Lower-outer quadrant of breast', 'Overlapping lesion of brain and central nervous system', 'Lymph node NOS', 'Adrenal gland NOS', 'Soft palate NOS', 'Overlapping lesion of pancreas', 'Autonomic nervous system NOS', 'Border of tongue', 'Posterior wall of oropharynx', 'Meninges NOS', 'Colon NOS', 'Lateral wall of oropharynx', 'Supraglottis', 'Overlapping lesion of vulva', 'Fallopian tube', 'Extrahepatic bile duct', 'Posterior wall of nasopharynx', 'External ear', 'skin of upper limb and shoulder', 'Craniopharyngeal duct', 'Specified parts of peritoneum', 'Lingual tonsil', 'Maxillary sinus', 'Lower gum', 'Female genital tract NOS', 'Central portion of breast', 'Overlapping lesion of male genital organs', 'Overlapping lesion of colon', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Mucosa of lower lip', 'Tonsillar fossa', 'Other specified parts of pancreas', 'Anterior wall of bladder', 'Overlapping lesion of esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Connective subcutaneous and other soft tissues of thorax', 'Conjunctiva', 'Nasopharynx NOS', 'Mandible', 'Lung NOS', 'Overlapping lesions of oropharynx', 'External upper lip', 'Vagina NOS', 'Short bones of lower limb and associated joints', 'Placenta', 'Ileum', 'Overlapping lesion of lung', 'Broad ligament', 'Lower third of esophagus', 'Abdominal esophagus', 'External lip NOS', 'Other specified parts of male genital organs', 'Lateral wall of nasopharynx', 'Other specified parts of female genital organs', 'Bones of skull and face and associated joints', 'Palate NOS', 'Retromolar area', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of heart mediastinum and pleura', 'Oropharynx NOS', 'Bladder neck', 'Anal canal', 'Lymph nodes of head face and neck', 'Middle ear', 'Brain NOS', 'Ascending colon', 'Isthmus uteri', 'Ill-defined sites within respiratory system', 'Eye NOS', 'Hematopoietic system NOS', 'Accessory sinus NOS', 'Gastric antrum', 'Trigone of bladder', 'Head face or neck NOS', 'Pylorus', 'Cornea NOS', 'Pelvic lymph nodes', 'Occipital lobe', 'Meckel diverticulum', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Base of tongue NOS', 'Cranial nerve NOS', 'Overlapping lesion of hypopharynx', 'Greater curvature of stomach NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Commissure of lip', 'Overlapping lesion of penis', 'Ovary', 'Cervix uteri', 'Vestibule of mouth', 'Hypopharyngeal aspect of aryepiglottic fold', 'Prostate gland', 'Dome of bladder', 'Parotid gland', 'Pelvis NOS', 'Lower-inner quadrant of breast', 'Connective subcutaneous and other soft tissues of abdomen', 'Pineal gland', 'Fundus of stomach', 'Endocrine gland NOS', 'Cerebrum', 'Splenic flexure of colon', 'Floor of mouth NOS', 'External lower lip', 'Eyelid', 'Carotid body', 'Choroid', 'Overlapping lesion of major salivary glands', 'Mucosa of lip NOS', 'Not Reported', 'Urachus', 'Liver', 'skin of lower limb and hip', 'Overlapping lesion of brain', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Thyroid gland', 'Thoracic esophagus', 'Biliary tract NOS', 'Other ill-defined sites', 'Overlapping lesion of palate', 'Heart', 'Larynx NOS', 'Clitoris', 'Middle lobe lung', 'Peripheral nerves and autonomic nervous system of abdomen', 'Upper gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Parathyroid gland', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lesser curvature of stomach NOS', 'Anterior 2/3 of tongue NOS', 'Thymus', 'Frontal lobe', 'Blood', 'Descending colon', 'Gallbladder', 'Pelvic bones sacrum coccyx and associated joints', 'Lymph nodes of axilla or arm', 'Male genital organs NOS', 'Acoustic nerve', 'Thorax NOS', 'Connective subcutaneous and other soft tissues of pelvis', 'Urethra', 'Body of penis', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Rib sternum clavicle and associated joints', 'Cortex of adrenal gland', 'Jejunum', 'Temporal lobe', 'Overlapping lesion of skin', 'Upper-inner quadrant of breast', 'Bladder NOS', 'Ventral surface of tongue NOS', 'Uterus NOS', 'Anus NOS', 'Overlapping lesion of accessory sinuses', 'Rectum NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Cardia NOS', 'Anterior surface of epiglottis', 'Overlapping lesion of urinary organs', 'Skin of other and unspecified parts of face', 'Skin of scalp and neck', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Lip NOS', 'Posterior mediastinum', 'Sigmoid colon', 'Main bronchus', 'Anterior floor of mouth', 'Overlapping lesion of ill-defined sites', 'Hepatic flexure of colon', 'Overlapping lesion of biliary tract', 'Connective subcutaneous and other soft tissues NOS', 'Tonsil NOS', 'Long bones of upper limb scapula and associated joints', 'Lower lobe lung', 'Myometrium', 'Posterior wall of bladder', 'Hypopharynx NOS', 'Skin of lip NOS', 'Cauda equina', 'Pleura NOS', 'Esophagus NOS', 'Overlapping lesion of breast', 'Cerebral meninges', 'Sublingual gland', 'Penis NOS', 'Overlapping lesion of lip', 'Descended testis', 'Glottis', 'Upper limb NOS', 'Nasal cavity', 'Ethmoid sinus', 'Ampulla of Vater', 'Vallecula', 'Overlapping lesion of tongue', 'skin NOS', 'Epididymis', 'Undescended testis', 'Ventricle NOS', 'Pancreatic duct', 'Body of stomach', 'Endometrium', 'Long bones of lower limb and associated joints', 'Dorsal surface of tongue NOS', 'unknown', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Head of pancreas', 'Gastrointestinal tract NOS', 'Glans penis', 'Postcricoid region', 'Mucosa of upper lip', 'Intra-abdominal lymph nodes', 'Pyriform sinus', 'Round ligament', 'Ureteric orifice', 'Cecum', 'Peritoneum NOS', 'Parietal lobe', 'Subglottis', 'Mouth NOS', 'Small intestine NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of corpus uteri', 'Uvula', 'Spermatic cord', 'Retroperitoneum', 'Tail of pancreas', '']",,Therapy
Days to Treatment Start,Days to Treatment Start,DaystoTreatmentStart,Number of days between the date used for index and the date the treatment started. If not applicable please enter 'Not Applicable',False,,,,Therapy
Initial Disease Status,Initial Disease Status,InitialDiseaseStatus,The text term used to describe the status of the patient's malignancy when the treatment began.,False,,"['Residual Disease', 'Recurrent Disease', 'unknown', 'Not Reported', 'Initial Diagnosis', 'Progressive Disease', '']",,Therapy
Number of Cycles,Number of Cycles,NumberofCycles,The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.,False,,,,Therapy
Treatment Effect,Treatment Effect,TreatmentEffect,The text term used to describe the pathologic effect a treatment(s) had on the tumor.,False,,"['Incomplete Necrosis (Viable Tumor Present)', 'No Necrosis', 'Complete Necrosis (No Viable Tumor)', 'unknown', 'Not Reported', '']",,Therapy
Treatment Arm,Treatment Arm,TreatmentArm,Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.,False,,"['EA5142', 'E4512', 'A081105', '']",,Therapy
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Therapy
Treatment Dose,Treatment Dose,TreatmentDose,The numeric value used to describe the dose of an agent the patient received.,False,,,,Therapy
Treatment Effect Indicator,Treatment Effect Indicator,TreatmentEffectIndicator,The text term used to indicate whether the treatment had an effect on the patient.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Therapy
Reason Treatment Ended,Reason Treatment Ended,ReasonTreatmentEnded,The text term used to describe the reason a specific treatment or regimen ended.,False,,"['Disease Progression', 'Adverse Therapy Event', 'Death', 'Withdrawal by Subject', 'Other', 'Course of Therapy Completed', '']",,Therapy
Treatment Outcome,Treatment Outcome,TreatmentOutcome,Text term that describes the patient's final outcome after the treatment was administered.,False,,"['No Response', 'Treatment Ongoing', 'Mixed Response', 'No Measurable Disease', 'Very Good Partial Response', 'Treatment Stopped Due to Toxicity', 'unknown', 'Persistent Disease', 'Stable Disease', 'Not Reported', 'Complete Response', 'Partial Response', 'Progressive Disease', '']",,Therapy
Treatment or Therapy,Treatment or Therapy,TreatmentorTherapy,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Therapy
Treatment Frequency,Treatment Frequency,TreatmentFrequency,The text term used to describe the frequency the patient received an agent or regimen.,False,,"['Four Times Daily', 'Five Times Daily', 'Twice Daily', 'unknown', 'Three Times Daily', 'Twice Weekly', 'Every Hour', 'Once Weekly', 'Not Reported', 'Every Other Day', 'Every 24 Hours', '']",,Therapy
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Therapy
Therapeutic Agents,Therapeutic Agents,TherapeuticAgents,Text identification of the individual agent(s) used as part of a treatment regimen.,False,,,,Therapy
Treatment Dose Units,Treatment Dose Units,TreatmentDoseUnits,The text term used to describe the dose units of an agent the patient received.,False,,"['Gy', 'cGy', '']",,Therapy
Treatment Type,Treatment Type,TreatmentType,Text term that describes the kind of treatment administered.,False,,,,Therapy
Gene Symbol,Gene Symbol,GeneSymbol,"The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",True,,,,MolecularTest
Loci Abnormal Count,Loci Abnormal Count,LociAbnormalCount,Numeric value used to describe the number of loci determined to be abnormal.,False,,,,MolecularTest
Mismatch Repair Mutation,Mismatch Repair Mutation,MismatchRepairMutation,The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,MolecularTest
Second Exon,Second Exon,SecondExon,"The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.",False,,,,MolecularTest
AA Change,AA Change,AAChange,Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest
Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,MolecularTest
Test Result,Test Result,TestResult,The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['High', 'Normal', 'Abnormal NOS', 'Copy Number Reported', 'positive', 'Test Value Reported', 'unknown', 'negative', 'Intermediate', 'Equivocal', 'Overexpressed', 'Low', 'Not Applicable', 'Not Reported', 'Loss of Expression']",,MolecularTest
Laboratory Test,Laboratory Test,LaboratoryTest,"The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.",False,,"['Eosinophil', 'Immunoglobulin M', 'Basophil', 'Platelets', 'Immunoglobulin A', 'Circulating Tumor Cells', 'Human Chorionic Gonadotropin', 'M Protein', 'Lymphoblasts', 'Kappa', 'NOS', 'Creatinine', 'Blood Urea Nitrogen', 'Albumin', 'Total Bilirubin', 'Human Papillomavirus', 'Absolute Neutrophil', 'C-Reactive Protein', 'Myeloblasts', 'Prolymphocytes', 'Promyelocytes', 'Metamyelocytes', 'Segmented Neutrophil', 'Neutrophil Bands', 'Hematocrit', 'Beta 2 Microglobulin', 'Cellularity', 'Immunoglobulin G', 'Leukocytes', 'Lambda', 'Testosterone', 'Alpha Fetoprotein', 'unknown', 'Calcium', 'Not Reported', 'Hemoglobin', 'Total Protein', 'Promonocytes', 'Epstein-Barr Virus', 'Luteinizing Hormone', 'Myelocytes', 'Lactate Dehydrogenase', 'Serum Free Immunoglobulin Light Chain', 'B-cell genotyping', 'Glucose', 'HPV-E6/E7', 'Lymphocytes', '']",,MolecularTest
Copy Number,Copy Number,CopyNumber,"Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest
Loci Count,Loci Count,LociCount,Numeric value used to describe the number of loci tested.,False,,,,MolecularTest
Ploidy,Ploidy,Ploidy,Text term used to describe the number of sets of homologous chromosomes.,False,,"['unknown', 'Hypodiploid', 'Near Diploid', 'Tetraploid', 'Diploid', 'Not Reported', 'Aneuploid', 'Hyperdiploid', '']",,MolecularTest
Histone Family,Histone Family,HistoneFamily,"The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.",False,,"['H1', 'unknown', 'H3', 'H2B', 'H2A', 'H4', 'Not Reported', '']",,MolecularTest
Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Clonal', 'Non-clonal', '']",,MolecularTest
Transcript,Transcript,Transcript,Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest
Locus,Locus,Locus,Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.,False,,,,MolecularTest
Blood Test Normal Range Lower,Blood Test Normal Range Lower,BloodTestNormalRangeLower,Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.,False,,,,MolecularTest
Blood Test Normal Range Upper,Blood Test Normal Range Upper,BloodTestNormalRangeUpper,Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.,False,,,,MolecularTest
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MolecularTest
Molecular Analysis Method,Molecular Analysis Method,MolecularAnalysisMethod,The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['Microsatellite Analysis', 'Flow Cytometry', 'Karyotype', 'IHC', 'Southern Blotting', 'RT-PCR', 'Sequencing NOS', 'FISH', 'Other', 'Not Applicable', 'Targeted Sequencing', 'RNA Sequencing', 'unknown', 'Comparative Genomic Hybridization', 'Not Reported', 'WGS', 'Microarray', 'Cytogenetics NOS', 'Nuclear Staining', 'ISH', 'WXS']",,MolecularTest
Chromosome,Chromosome,Chromosome,"The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,"['chr8', 'chrY', 'chrM', 'chr13', 'chr19', 'chr23', 'chr6', 'chr9', 'chr18', 'chr22', 'chr2', 'chr1', 'chr12', 'chr5', 'chr11', 'chr15', 'chr10', 'unknown', 'chr4', 'chr3', 'chr20', 'Not Reported', 'chr17', 'chr16', 'chr21', 'chr7', 'chr14', 'chrX', '']",,MolecularTest
Cell Count,Cell Count,CellCount,Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest
Pathogenicity,Pathogenicity,Pathogenicity,The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).,False,,"['Uncertain Significance', 'Benign', 'Likely Benign', 'Likely Pathogenic', 'Pathogenic', '']",,MolecularTest
Test Units,Test Units,TestUnits,The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest
Second Gene Symbol,Second Gene Symbol,SecondGeneSymbol,"The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest
Variant Origin,Variant Origin,VariantOrigin,The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Somatic', 'Germline', 'unknown', '']",,MolecularTest
Cytoband,Cytoband,Cytoband,"Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest
Zygosity,Zygosity,Zygosity,The text term used to describe the zygosity of a specific genetic variant.,False,,"['Nullizygous', 'unknown', 'Hemizygous', 'Homozygous', 'Heterozygous', 'Not Reported', '']",,MolecularTest
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MolecularTest
Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,MolecularTest
Intron,Intron,Intron,"Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.",False,,,,MolecularTest
Variant Type,Variant Type,VariantType,The text term used to describe the type of genetic variation.,False,,"['Inversion', 'Mosaicism', 'Gain', 'Substitution', 'Extension', 'Insertion', 'Partial Methylation', 'Translocation', 'Other', 'Conversion', 'Deletion', 'Hypermethylation', 'Deletion-Insertion', 'unknown', 'Rearrangement', 'Not Reported', 'Loss', 'Alleles', 'Splice', 'Chrimerism', 'Repeated Sequences', 'Amplification', 'Duplication', 'Methylation', '']",,MolecularTest
Test Analyte Type,Test Analyte Type,TestAnalyteType,The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Total RNA', 'DNA', 'mRNA', 'unknown', 'Protein Analyte', 'Not Reported', 'miRNA', '']",,MolecularTest
Test Value,Test Value,TestValue,The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here,False,,,,MolecularTest
Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,MolecularTest
Molecular Consequence,Molecular Consequence,MolecularConsequence,The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Upstream Gene Variant', 'Regulatory Region Amplification', 'Stop Gain', 'Transcript Amplification', 'Non-coding Transcript Exon Variant', 'Stop Retained Variant', 'Coding Sequence Variant', 'Inframe Insertion', 'Synonymous Variant', 'Intergenic Variant', 'Splice Region Variant', 'Splice Donor Variant', '5 Prime UTR Variant', 'Regulatory Region Ablation', 'Mature miRNA Variant', 'Missense Variant', 'Protein Altering Variant', 'Incomplete Terminal Codon Variant', 'TFBS Ablation', 'Regulatory Region Variant', 'Inframe Deletion', '3 Prime UTR Variant', 'Splice Acceptor Variant', 'Frameshift Variant', 'Feature Truncation', 'Start Lost', 'Intron Variant', 'NMD Transcript Variant', 'TFBS Amplification', 'TF Binding Site Variant', 'Non-coding Transcript Variant', 'Stop Lost', 'Downstream Gene Variant', 'Feature Elongation', 'Transcript Ablation', '']",,MolecularTest
Antigen,Antigen,Antigen,The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['CD3', 'CD10', 'CD56', 'CEA', 'CD23', 'CD22', 'NSE', 'Mesothelin', 'CA19-9', 'CD79A', 'CD138', 'CD30', 'CD117', 'CA-125', 'HLA-DR', 'CD25', 'Squamous Cell Carcinoma Antigen', 'BCL6', 'unknown', 'CD14', 'CD7', 'Not Reported', 'CD5', 'CD34', 'CCND1', 'CD33', 'CD20', 'CD19', 'CD45', 'CD15', '']",,MolecularTest
Histone Variant,Histone Variant,HistoneVariant,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.",False,,"['H2A.Z.1', 'mH2A.2', 'mH2A', 'H3.X', 'H3.Y', 'H3.2', 'H2A.Z.2.2', 'H3.3', 'H3t (H3.4)', 'H3.5', 'unknown', 'Not Reported', 'H2A.Z.2', 'H3.1', 'H2A.X', 'H2A.Z', 'mH2A.1', 'H2A-Bbd', 'CENP-A', '']",,MolecularTest
Exon,Exon,Exon,"Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest
Specialized Molecular Test,Specialized Molecular Test,SpecializedMolecularTest,Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest
Clinical Biospecimen Type,Clinical Biospecimen Type,ClinicalBiospecimenType,"The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,"['Saliva', 'Blood', 'Buccal Mucosa', 'Embryonic Tissue', 'Soft Tissue', 'Tissue NOS', 'Buffy Coat', 'Peritoneal Fluid', 'Cerebrospinal Fluid', 'Granulocyte', 'Nerve Tissue', 'Skin', 'Muscle Tissue', 'Bone Marrow', 'Serum', 'Plasma', 'Embryonic Fluid', 'Uninvolved Tissue NOS', 'unknown', 'Not Reported', 'Urine', 'Pleural Fluid', 'Feces', 'Connective Tissue', '']",,MolecularTest
Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Urine Biospecimen Type', 'Stool Biospecimen Type', 'Analyte Biospecimen Type', 'Ascites Biospecimen Type', 'Fluids Biospecimen Type', 'Cells Biospecimen Type', 'Bone Marrow Biospecimen Type', 'Sputum Biospecimen Type', 'Blood Biospecimen Type', 'Tissue Biospecimen Type', 'Mouth Rinse Biospecimen Type']",,Biospecimen
Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Surgical Resection', 'Fine Needle Aspirate', 'Excision', 'Endoscopic biopsy', 'Induced sputum', 'Other Acquisition Method', 'Punch Biopsy', 'Fluid collection', 'Lymphadenectomy - Regional Nodes', 'BAL (bronchial alveolar lavage)', 'Core needle biopsy', 'Shave Biopsy', 'Forceps biopsy', 'Biopsy', 'Sentinel Node Biopsy', 'Blood draw', 'Not specified', 'Non induced sputum', 'Cytobrush', 'Autopsy', 'Re-excision']",,Biospecimen
Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['TCL lysis buffer', 'NP40 lysis buffer', 'Formalin', 'Dimethylacetamide', 'Methacarn', 'Unfixed', 'Alcohol', 'Polaxamer', 'Cryo-store', 'Other', ""Carnoy's Fixative"", 'RNAlater', 'Acetone', 'Saline', 'PAXgene tissue', 'None', 'unknown', 'OCT media', 'Carbodiimide', 'Glutaraldehyde', '95% Ethanol', 'Para-benzoquinone', 'Dimidoester']",,Biospecimen
Processing Location,Processing Location,ProcessingLocation,"Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.",False,,,,Biospecimen
Percent Lymphocyte Infiltration,Percent Lymphocyte Infiltration,PercentLymphocyteInfiltration,Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.,False,,,,Biospecimen
Adjacent Biospecimen IDs,Adjacent Biospecimen IDs,AdjacentBiospecimenIDs,"List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...",False,,,,Biospecimen
Percent Inflam Infiltration,Percent Inflam Infiltration,PercentInflamInfiltration,"Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.",False,,,,Biospecimen
Fiducial Marker,Fiducial Marker,FiducialMarker,Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.,False,,"['Grid Slides - Hemocytometer', 'unknown', 'Other', 'Adhesive Markers', 'Fluorescent Beads', 'Nuclear Stain - DAPI', 'Not Reported', '']",,Biospecimen
Histology Assessment By,Histology Assessment By,HistologyAssessmentBy,Text term describing who (in what role) made the histological assessments of the sample,False,,"['Pathologist', 'Other', 'Research Scientist', 'unknown', '']",,Biospecimen
Percent Tumor Nuclei,Percent Tumor Nuclei,PercentTumorNuclei,Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.,False,,,,Biospecimen
Percent Eosinophil Infiltration,Percent Eosinophil Infiltration,PercentEosinophilInfiltration,Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.,False,,,,Biospecimen
Percent Tumor Cells,Percent Tumor Cells,PercentTumorCells,Numeric value that represents the percentage of infiltration by tumor cells in a sample.,False,,,,Biospecimen
Dysplasia Fraction,Dysplasia Fraction,DysplasiaFraction,Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5],False,,,,Biospecimen
Percent Granulocyte Infiltration,Percent Granulocyte Infiltration,PercentGranulocyteInfiltration,Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.,False,,,,Biospecimen
Tumor Infiltrating Lymphocytes,Tumor Infiltrating Lymphocytes,TumorInfiltratingLymphocytes,Measure of Tumor-Infiltrating Lymphocytes [Number],False,,,,Biospecimen
Method of Nucleic Acid Isolation,Method of Nucleic Acid Isolation,MethodofNucleicAcidIsolation,"Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]",False,,,,Biospecimen
HTAN Parent ID,HTAN Parent ID,HTANParentID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,True,,,,Biospecimen
Degree of Dysplasia,Degree of Dysplasia,DegreeofDysplasia,Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.,False,,"['Moderate dysplasia', 'Severe dysplasia', 'unknown', 'Normal or basal cell hyperplasia or metaplasia', 'Mild dysplasia', 'Carcinoma in Situ', '']",,Biospecimen
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,Biospecimen
Percent Necrosis,Percent Necrosis,PercentNecrosis,Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.,False,,,,Biospecimen
Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['Ambient temperature', 'Frozen at -80C', 'Cut slide', '4C in vacuum chamber', 'Desiccant at 4C', 'RNAlater at 25C', 'Frozen at -150C', 'Frozen at -70C', 'Frozen in liquid nitrogen', 'Not Applicable', 'Paraffin block', 'unknown', 'RNAlater at -20C', 'Refrigerated at 4 degrees', 'Refrigerated vacuum chamber', 'RNAlater at 4C', 'Fresh', 'Frozen at -20C', 'Frozen in vapor phase']",,Biospecimen
Processing Days from Index,Processing Days from Index,ProcessingDaysfromIndex,Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable',True,,,,Biospecimen
Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['Scar - no residual melanoma', 'Adenocarcinoma in situ - mucinous', 'Adenocarcinoma in situ - non mucinous', 'Severe dysplasia', 'Melanoma in situ - acral-lentiginous', 'Normal WDA', 'Invasive melanoma - nevoid', 'Melanoma in situ - not otherwise classified', 'Invasive melanoma - desmoplastic', 'Hamartoma', 'Invasive melanoma - superficial spreading', 'Benign tumor NOS', 'Invasive melanoma - other', 'Persistent melanoma in situ', 'Invasive melanoma - lentigo maligna', 'Mild dysplasia', 'Melanocytic hyperplasia', 'Reserve cell hyperplasia', 'Invasive melanoma - acral lentiginous', 'Moderate dysplasia', 'Melanoma in situ - arising in a giant congenital nevus', 'Squamous Carcinoma in situ', 'Squamous metaplasia - mature', 'Atypical adenomatous hyperplasia', 'Melanoma in situ - lentigo maligna type', 'Atypical melanocytic proliferation', 'Invasive melanoma - nodular type', 'Squamous metaplasia - immature', 'No diagnosis possible', 'Melanoma in situ - superficial spreading', 'Carcinoma NOS', '']",,Biospecimen
Percent Stromal Cells,Percent Stromal Cells,PercentStromalCells,"Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.",False,,,,Biospecimen
Slicing Method,Slicing Method,SlicingMethod,Imaging specific: the method by which the tissue was sliced.,False,,"['Sliding microtome', 'Vibratome', 'unknown', 'Other', 'Sectioning', 'Tissue molds', 'Not Reported', 'Cryosectioning', '']",,Biospecimen
Percent Monocyte Infiltration,Percent Monocyte Infiltration,PercentMonocyteInfiltration,Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.,False,,,,Biospecimen
Percent Normal Cells,Percent Normal Cells,PercentNormalCells,Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.,False,,,,Biospecimen
Lysis Buffer,Lysis Buffer,LysisBuffer,scRNA-seq specific: Type of lysis buffer used,False,,,,Biospecimen
Percent Neutrophil Infiltration,Percent Neutrophil Infiltration,PercentNeutrophilInfiltration,Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.,False,,,,Biospecimen
Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['None', 'PBS', 'RPMI', 'RPMI+Serum', 'DMEM+Serum', 'PBS+Serum', 'DMEM', '']",,Biospecimen
Mounting Medium,Mounting Medium,MountingMedium,"The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media",False,,"['Antifade with DAPI', 'Antifade without DAPI', 'PBS', 'Aqueous water based', 'Xylene', 'unknown', 'Not Reported', 'Non-Aqueous Solvent based', 'Toluene', '']",,Biospecimen
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Biospecimen
HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Biospecimen
Site Data Source,Site Data Source,SiteDataSource,"Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.",False,,,,Biospecimen
Number Proliferating Cells,Number Proliferating Cells,NumberProliferatingCells,Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).,False,,,,Biospecimen
Source HTAN Biospecimen ID,Source HTAN Biospecimen ID,SourceHTANBiospecimenID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,False,,,,Biospecimen
Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,Biospecimen
Collection Days from Index,Collection Days from Index,CollectionDaysfromIndex,Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable',True,,,,Biospecimen
Histology Assessment Medium,Histology Assessment Medium,HistologyAssessmentMedium,The method of assessment used to characterize histology,False,,"['Other', 'Microscopy', 'Digital', 'unknown', '']",,Biospecimen
Histologic Morphology Code,Histologic Morphology Code,HistologicMorphologyCode,"The microscopic anatomy of normal and abnormal cells and tissues of the specimen as captured in the morphology codes of the International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3). Example - 8010/0",False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen
Total Volume,Total Volume,TotalVolume,Numeric value for the total amount of sample or specimen,False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen
Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",False,True,"['Appendix', 'Parametrium', 'Aortic body and other paraganglia', 'Trachea', 'Transverse colon', 'Lateral floor of mouth', 'Paraspinal', 'Cerebellum NOS', 'Paraurethral gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Cloacogenic zone', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Overlapping lesion of bladder', 'Overlapping lesion of retroperitoneum and peritoneum', 'Uterine adnexa', 'Vertebral column', 'Upper lobe lung', 'Overlapping lesion of floor of mouth', 'Spinal meninges', 'Labium minus', 'Hard palate', 'Spleen', 'Breast NOS', 'Middle third of esophagus', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Duodenum', 'Spinal cord', 'Anterior wall of nasopharynx', 'Body of pancreas', 'Fundus uteri', 'Upper third of esophagus', 'Short bones of upper limb and associated joints', 'Overlapping lesion of cervix uteri', 'Lateral wall of bladder', 'Nervous system NOS', 'Upper-outer quadrant of breast', 'Nipple', 'Labium majus', 'Exocervix', 'Vulva NOS', 'Gum NOS', 'Mediastinum NOS', 'Urinary system NOS', 'Medulla of adrenal gland', 'Tongue NOS', 'Overlapping lesion of eye and adnexa', 'Bone marrow', 'Reticuloendothelial system NOS', 'Renal pelvis', 'Brain stem', 'Ureter', 'Overlapping lesion of small intestine', 'unknown primary site', 'Intestinal tract NOS', 'Laryngeal cartilage', 'Scrotum NOS', 'Upper respiratory tract NOS', 'Rectosigmoid junction', 'Overlapping lesion of stomach', 'Sphenoid sinus', 'Lymph nodes of inguinal region or leg', 'Pancreas NOS', 'Kidney NOS', 'Branchial cleft', 'Pharynx NOS', 'Tonsillar pillar', 'Islets of Langerhans', 'Optic nerve', 'Lymph nodes of multiple regions', 'Overlapping lesion of tonsil', 'Posterior wall of hypopharynx', 'Intrahepatic bile duct', 'Lacrimal gland', 'Orbit NOS', 'Bone NOS', 'Submandibular gland', 'Endocervix', 'Corpus uteri', 'Skin of trunk', 'Retina', 'Overlapping lesion of endocrine glands and related structures', 'Ciliary body', 'Overlapping lesion of larynx', 'Anterior mediastinum', 'Lower limb NOS', 'Frontal sinus', 'Superior wall of nasopharynx', 'Prepuce', 'Major salivary gland NOS', 'Stomach NOS', 'Overlapping lesion of rectum anus and anal canal', 'Olfactory nerve', 'Peripheral nerves and autonomic nervous system of thorax', 'Testis NOS', 'Cheek mucosa', 'Abdomen NOS', 'Waldeyer ring', 'Bone of limb NOS', 'Cervical esophagus', 'Intrathoracic lymph nodes', 'Overlapping lesion of digestive system', 'Axillary tail of breast', 'Lower-outer quadrant of breast', 'Overlapping lesion of brain and central nervous system', 'Lymph node NOS', 'Adrenal gland NOS', 'Soft palate NOS', 'Overlapping lesion of pancreas', 'Autonomic nervous system NOS', 'Border of tongue', 'Posterior wall of oropharynx', 'Meninges NOS', 'Colon NOS', 'Lateral wall of oropharynx', 'Supraglottis', 'Overlapping lesion of vulva', 'Fallopian tube', 'Extrahepatic bile duct', 'Posterior wall of nasopharynx', 'External ear', 'skin of upper limb and shoulder', 'Craniopharyngeal duct', 'Specified parts of peritoneum', 'Lingual tonsil', 'Maxillary sinus', 'Lower gum', 'Female genital tract NOS', 'Central portion of breast', 'Overlapping lesion of male genital organs', 'Overlapping lesion of colon', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Mucosa of lower lip', 'Tonsillar fossa', 'Other specified parts of pancreas', 'Anterior wall of bladder', 'Overlapping lesion of esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Connective subcutaneous and other soft tissues of thorax', 'Conjunctiva', 'Nasopharynx NOS', 'Mandible', 'Lung NOS', 'Overlapping lesions of oropharynx', 'External upper lip', 'Vagina NOS', 'Short bones of lower limb and associated joints', 'Placenta', 'Ileum', 'Overlapping lesion of lung', 'Broad ligament', 'Lower third of esophagus', 'Abdominal esophagus', 'External lip NOS', 'Other specified parts of male genital organs', 'Lateral wall of nasopharynx', 'Other specified parts of female genital organs', 'Bones of skull and face and associated joints', 'Palate NOS', 'Retromolar area', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of heart mediastinum and pleura', 'Oropharynx NOS', 'Bladder neck', 'Anal canal', 'Lymph nodes of head face and neck', 'Middle ear', 'Brain NOS', 'Ascending colon', 'Isthmus uteri', 'Ill-defined sites within respiratory system', 'Eye NOS', 'Hematopoietic system NOS', 'Accessory sinus NOS', 'Gastric antrum', 'Trigone of bladder', 'Head face or neck NOS', 'Pylorus', 'Cornea NOS', 'Pelvic lymph nodes', 'Occipital lobe', 'Meckel diverticulum', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Base of tongue NOS', 'Cranial nerve NOS', 'Overlapping lesion of hypopharynx', 'Greater curvature of stomach NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Commissure of lip', 'Overlapping lesion of penis', 'Ovary', 'Cervix uteri', 'Vestibule of mouth', 'Hypopharyngeal aspect of aryepiglottic fold', 'Prostate gland', 'Dome of bladder', 'Parotid gland', 'Pelvis NOS', 'Lower-inner quadrant of breast', 'Connective subcutaneous and other soft tissues of abdomen', 'Pineal gland', 'Fundus of stomach', 'Endocrine gland NOS', 'Cerebrum', 'Splenic flexure of colon', 'Floor of mouth NOS', 'External lower lip', 'Eyelid', 'Carotid body', 'Choroid', 'Overlapping lesion of major salivary glands', 'Mucosa of lip NOS', 'Not Reported', 'Urachus', 'Liver', 'skin of lower limb and hip', 'Overlapping lesion of brain', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Thyroid gland', 'Thoracic esophagus', 'Biliary tract NOS', 'Other ill-defined sites', 'Overlapping lesion of palate', 'Heart', 'Larynx NOS', 'Clitoris', 'Middle lobe lung', 'Peripheral nerves and autonomic nervous system of abdomen', 'Upper gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Parathyroid gland', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lesser curvature of stomach NOS', 'Anterior 2/3 of tongue NOS', 'Thymus', 'Frontal lobe', 'Blood', 'Descending colon', 'Gallbladder', 'Pelvic bones sacrum coccyx and associated joints', 'Lymph nodes of axilla or arm', 'Male genital organs NOS', 'Acoustic nerve', 'Thorax NOS', 'Connective subcutaneous and other soft tissues of pelvis', 'Urethra', 'Body of penis', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Rib sternum clavicle and associated joints', 'Cortex of adrenal gland', 'Jejunum', 'Temporal lobe', 'Overlapping lesion of skin', 'Upper-inner quadrant of breast', 'Bladder NOS', 'Ventral surface of tongue NOS', 'Uterus NOS', 'Anus NOS', 'Overlapping lesion of accessory sinuses', 'Rectum NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Cardia NOS', 'Anterior surface of epiglottis', 'Overlapping lesion of urinary organs', 'Skin of other and unspecified parts of face', 'Skin of scalp and neck', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Lip NOS', 'Posterior mediastinum', 'Sigmoid colon', 'Main bronchus', 'Anterior floor of mouth', 'Overlapping lesion of ill-defined sites', 'Hepatic flexure of colon', 'Overlapping lesion of biliary tract', 'Connective subcutaneous and other soft tissues NOS', 'Tonsil NOS', 'Long bones of upper limb scapula and associated joints', 'Lower lobe lung', 'Myometrium', 'Posterior wall of bladder', 'Hypopharynx NOS', 'Skin of lip NOS', 'Cauda equina', 'Pleura NOS', 'Esophagus NOS', 'Overlapping lesion of breast', 'Cerebral meninges', 'Sublingual gland', 'Penis NOS', 'Overlapping lesion of lip', 'Descended testis', 'Glottis', 'Upper limb NOS', 'Nasal cavity', 'Ethmoid sinus', 'Ampulla of Vater', 'Vallecula', 'Overlapping lesion of tongue', 'skin NOS', 'Epididymis', 'Undescended testis', 'Ventricle NOS', 'Pancreatic duct', 'Body of stomach', 'Endometrium', 'Long bones of lower limb and associated joints', 'Dorsal surface of tongue NOS', 'unknown', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Head of pancreas', 'Gastrointestinal tract NOS', 'Glans penis', 'Postcricoid region', 'Mucosa of upper lip', 'Intra-abdominal lymph nodes', 'Pyriform sinus', 'Round ligament', 'Ureteric orifice', 'Cecum', 'Peritoneum NOS', 'Parietal lobe', 'Subglottis', 'Mouth NOS', 'Small intestine NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of corpus uteri', 'Uvula', 'Spermatic cord', 'Retroperitoneum', 'Tail of pancreas', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen
Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,False,True,"['Fresh dissociated and single cell sorted', 'Fresh dissociated', 'Cryopreservation in dry ice - dead tissue', 'Liquid Nitrogen', 'Cryopreserved', 'Fresh dissociated and single cell sorted into plates', 'Formalin fixed-buffered', 'Formalin fixed-unbuffered', 'OCT', 'unknown', 'Cryopreservation in liquid nitrogen - dead tissue', 'Cryopreservation in liquid nitrogen - live cells', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Not Reported', 'Frozen', 'Formalin fixed paraffin embedded - FFPE', 'Fresh', 'Snap Frozen', 'Negative 80 Deg C', 'Methacarn fixed paraffin embedded - MFPE', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen
Portion Weight,Portion Weight,PortionWeight,"Numeric value that represents the sample portion weight, measured in milligrams.",False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen
Specimen Laterality,Specimen Laterality,SpecimenLaterality,"For tumors in paired organs, designates the side on which the specimen was obtained.",False,True,"['Right', 'unknown', 'Bilateral', 'Not Applicable', 'Not Reported', 'Left', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen
Ischemic Time,Ischemic Time,IschemicTime,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Analyte""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen
Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,True,"['Warm Ischemia', '4C wet ice', 'Ambient air', 'Negative -20C', 'unknown', 'Liquid Nitrogen', 'Dry Ice', 'Cold Ischemia', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Analyte""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen
Tumor Tissue Type,Tumor Tissue Type,TumorTissueType,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints),False,True,"['Normal', 'Metastatic', 'Post therapy neoadjuvant', 'Premalignant - in situ', 'Post therapy adjuvant', 'Atypia - hyperplasia', 'Not analyzed', 'Normal adjacent', 'Recurrent', 'Additional Primary', 'Not Otherwise Specified', 'Post therapy', 'Local recurrence', 'Primary', 'Premalignant', 'Normal distant', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen
Section Thickness Value,Section Thickness Value,SectionThicknessValue,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",False,True,,"['Biospecimen is ""Analyte""']",Biospecimen
Sectioning Days from Index,Sectioning Days from Index,SectioningDaysfromIndex,Number of days from the research participant's index date that the biospecimen was sectioned after collection. If not applicable please enter 'Not Applicable',False,True,,"['Biospecimen is ""Analyte""']",Biospecimen
Slide Charge Type,Slide Charge Type,SlideChargeType,A description of the charge on the glass slide.,False,True,"['Uncharged', 'Charged', 'Coverslip', 'Other', 'Not applicable', '']","['Biospecimen is ""Analyte""']",Biospecimen
Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Ambient Pack', 'Specimen at Room Temperature', 'Other Shipping Environment', 'Liquid Nitrogen', 'Not Shipped', 'Ice Pack', 'Dry Ice', 'Cold Pack', '']","['Biospecimen is ""Analyte""', 'Biospecimen is ""Blood""']",Biospecimen
Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,False,True,"['lipid', 'Tissue Section Analyte', 'PBMCs or Plasma or Serum Analyte', 'metabolite', 'RNA Analyte', 'cfDNA Analyte', 'Total RNA Analyte', 'Tissue Block Analyte', 'DNA Analyte', 'cDNA Libraries Analyte', 'PBMCs', 'protein', 'Plasma', 'Serum Analyte', '']","['Biospecimen is ""Analyte""']",Biospecimen
Fixation Duration,Fixation Duration,FixationDuration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",False,True,,"['Biospecimen is ""Analyte""']",Biospecimen
Biospecimen Dimension 3,Biospecimen Dimension 3,BiospecimenDimension3,"Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen
Biospecimen Dimension 2,Biospecimen Dimension 2,BiospecimenDimension2,"Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen
Section Number in Sequence,Section Number in Sequence,SectionNumberinSequence,"Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen
Biospecimen Dimension 1,Biospecimen Dimension 1,BiospecimenDimension1,"First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen
Acquisition Method Other Specify,Acquisition Method Other Specify,AcquisitionMethodOtherSpecify,A custom acquisition method [Text - max length 100 characters],False,True,,"['Acquisition is ""Other Acquisition Method""']",Biospecimen
Total Volume Unit,Total Volume Unit,TotalVolumeUnit,Unit of measurement used for the total amount of sample or specimen,False,,"['cubic millimeter', 'mL', 'square centimeter', '']",,Biospecimen
Dimensions Unit,Dimensions Unit,DimensionsUnit,"Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)",False,,"['mm', 'cm', '']",,Biospecimen
Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Urine Biospecimen Type', 'Stool Biospecimen Type', 'Analyte Biospecimen Type', 'Ascites Biospecimen Type', 'Fluids Biospecimen Type', 'Cells Biospecimen Type', 'Bone Marrow Biospecimen Type', 'Sputum Biospecimen Type', 'Blood Biospecimen Type', 'Tissue Biospecimen Type', 'Mouth Rinse Biospecimen Type']",,SRRSBiospecimen
Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Surgical Resection', 'Fine Needle Aspirate', 'Excision', 'Endoscopic biopsy', 'Induced sputum', 'Other Acquisition Method', 'Punch Biopsy', 'Fluid collection', 'Lymphadenectomy - Regional Nodes', 'BAL (bronchial alveolar lavage)', 'Core needle biopsy', 'Shave Biopsy', 'Forceps biopsy', 'Biopsy', 'Sentinel Node Biopsy', 'Blood draw', 'Not specified', 'Non induced sputum', 'Cytobrush', 'Autopsy', 'Re-excision']",,SRRSBiospecimen
Histologic Morphology Code,Histologic Morphology Code,HistologicMorphologyCode,"The microscopic anatomy of normal and abnormal cells and tissues of the specimen as captured in the morphology codes of the International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3). Example - 8010/0",True,,,,SRRSBiospecimen
Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['TCL lysis buffer', 'NP40 lysis buffer', 'Formalin', 'Dimethylacetamide', 'Methacarn', 'Unfixed', 'Alcohol', 'Polaxamer', 'Cryo-store', 'Other', ""Carnoy's Fixative"", 'RNAlater', 'Acetone', 'Saline', 'PAXgene tissue', 'None', 'unknown', 'OCT media', 'Carbodiimide', 'Glutaraldehyde', '95% Ethanol', 'Para-benzoquinone', 'Dimidoester']",,SRRSBiospecimen
Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,True,,"['Fresh dissociated and single cell sorted', 'Fresh dissociated', 'Cryopreservation in dry ice - dead tissue', 'Liquid Nitrogen', 'Cryopreserved', 'Fresh dissociated and single cell sorted into plates', 'Formalin fixed-buffered', 'Formalin fixed-unbuffered', 'OCT', 'unknown', 'Cryopreservation in liquid nitrogen - dead tissue', 'Cryopreservation in liquid nitrogen - live cells', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Not Reported', 'Frozen', 'Formalin fixed paraffin embedded - FFPE', 'Fresh', 'Snap Frozen', 'Negative 80 Deg C', 'Methacarn fixed paraffin embedded - MFPE']",,SRRSBiospecimen
Adjacent Biospecimen IDs,Adjacent Biospecimen IDs,AdjacentBiospecimenIDs,"List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...",False,,,,SRRSBiospecimen
HTAN Parent ID,HTAN Parent ID,HTANParentID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,True,,,,SRRSBiospecimen
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,SRRSBiospecimen
Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['Ambient temperature', 'Frozen at -80C', 'Cut slide', '4C in vacuum chamber', 'Desiccant at 4C', 'RNAlater at 25C', 'Frozen at -150C', 'Frozen at -70C', 'Frozen in liquid nitrogen', 'Not Applicable', 'Paraffin block', 'unknown', 'RNAlater at -20C', 'Refrigerated at 4 degrees', 'Refrigerated vacuum chamber', 'RNAlater at 4C', 'Fresh', 'Frozen at -20C', 'Frozen in vapor phase']",,SRRSBiospecimen
Processing Days from Index,Processing Days from Index,ProcessingDaysfromIndex,Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable',True,,,,SRRSBiospecimen
Additional Topography,Additional Topography,AdditionalTopography,Topography not included in the ICD-O-3 Topography codes.,False,,"['skin of back', 'skin of lower limb and hip', 'skin of vulva', 'skin of chest', 'skin of nose', 'skin of lip', 'skin of other parts of face', 'skin NOS', 'skin of ear', 'skin of abdomen', 'skin of palm', 'skin of eye lid', 'skin of neck', 'Hilar Airway', 'skin of penis', 'skin of upper limb and shoulder', 'Peri-tumoral Airway', 'Not Reported', 'skin of breast', 'skin of scrotum', 'skin of sole', 'Skin of trunk', 'skin of scalp', '']",,SRRSBiospecimen
Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['Scar - no residual melanoma', 'Adenocarcinoma in situ - mucinous', 'Adenocarcinoma in situ - non mucinous', 'Severe dysplasia', 'Melanoma in situ - acral-lentiginous', 'Normal WDA', 'Invasive melanoma - nevoid', 'Melanoma in situ - not otherwise classified', 'Invasive melanoma - desmoplastic', 'Hamartoma', 'Invasive melanoma - superficial spreading', 'Benign tumor NOS', 'Invasive melanoma - other', 'Persistent melanoma in situ', 'Invasive melanoma - lentigo maligna', 'Mild dysplasia', 'Melanocytic hyperplasia', 'Reserve cell hyperplasia', 'Invasive melanoma - acral lentiginous', 'Moderate dysplasia', 'Melanoma in situ - arising in a giant congenital nevus', 'Squamous Carcinoma in situ', 'Squamous metaplasia - mature', 'Atypical adenomatous hyperplasia', 'Melanoma in situ - lentigo maligna type', 'Atypical melanocytic proliferation', 'Invasive melanoma - nodular type', 'Squamous metaplasia - immature', 'No diagnosis possible', 'Melanoma in situ - superficial spreading', 'Carcinoma NOS', '']",,SRRSBiospecimen
Ischemic Time,Ischemic Time,IschemicTime,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",False,,,,SRRSBiospecimen
Topography Code,Topography Code,TopographyCode,"Topography Code, indicating site within the body, based on ICD-O-3.",False,,"['C63.9', 'C16.6', 'C17.0', 'C72.4', 'C16.0', 'C44.2', 'C00.3', 'C40.1', 'C69.0', 'C67.1', 'C44.3', 'C69.3', 'C75.3', 'C09.8', 'C53.0', 'C18.7', 'C47.0', 'C44.7', 'C21.0', 'C77.4', 'C05.2', 'C47.5', 'C60.2', 'C47.1', 'C24.9', 'C25.8', 'C40.8', 'C10.3', 'C69.1', 'C17.2', 'C04.0', 'C69.6', 'C49.2', 'C11.3', 'C71.4', 'C57.9', 'C14.0', 'C31.1', 'C34.2', 'C72.2', 'C40.9', 'C09.9', 'C11.2', 'C15.8', 'C47.4', 'C41.1', 'C44.5', 'C71.1', 'C41.8', 'C75.0', 'C42.1', 'C34.0', 'C50.4', 'C57.3', 'C38.2', 'C10.9', 'C39.0', 'C70.9', 'C50.1', 'C18.9', 'C49.0', 'C34.3', 'C01.9', 'C73.9', 'C77.5', 'C21.1', 'C00.2', 'C42.3', 'C17.1', 'C72.3', 'C31.8', 'C69.4', 'C15.2', 'C49.4', 'C39.8', 'C09.1', 'C03.1', 'C18.4', 'C38.0', 'C18.1', 'C50.5', 'C42.2', 'C76.4', 'C70.0', 'C02.8', 'C51.2', 'C00.1', 'C14.8', 'C76.5', 'C41.9', 'C10.8', 'C10.2', 'C57.7', 'C31.3', 'C67.8', 'C71.2', 'C11.0', 'C60.1', 'C02.3', 'C16.9', 'C26.8', 'C40.3', 'C77.8', 'C10.1', 'C02.9', 'C51.9', 'C02.2', 'C08.1', 'C44.1', 'C16.1', 'C60.0', 'C75.1', 'C18.2', 'C00.0', 'C72.5', 'C13.8', 'C69.8', 'C51.0', 'C04.1', 'C60.8', 'C68.0', 'C18.8', 'C12.9', 'C04.9', 'C23.9', 'C18.3', 'C13.1', 'C32.8', 'C54.2', 'C06.9', 'C15.3', 'C16.5', 'C15.4', 'C34.1', 'C32.1', 'C00.6', 'C70.1', 'C71.9', 'C31.0', 'C06.2', 'C03.9', 'C32.0', 'C11.8', 'C49.1', 'C72.1', 'C67.2', 'C17.3', 'C09.0', 'C41.0', 'C48.2', 'C77.2', 'C49.3', 'C76.3', 'C16.3', 'C22.0', 'C75.5', 'C48.8', 'C76.0', 'C75.9', 'C54.8', 'C14.2', 'C72.9', 'C44.0', 'C50.6', 'C08.0', 'C55.9', 'C68.1', 'C24.1', 'C62.0', 'C06.1', 'C76.7', 'C48.0', 'C05.1', 'C00.8', 'C15.5', 'C63.0', 'C67.4', 'C24.8', 'C54.9', 'C08.9', 'C38.3', 'C26.9', 'C34.8', 'C25.1', 'C15.9', 'C00.4', 'C26.0', 'C16.4', 'C19.9', 'C18.0', 'C54.0', 'C76.8', 'C63.7', 'C56.9', 'C62.9', 'C11.1', 'C53.8', 'C21.2', 'C63.8', 'Not Reported', 'C10.0', 'C25.7', 'C42.0', 'C71.3', 'C69.9', 'C44.4', 'C57.1', 'C77.9', 'C67.0', 'C05.9', 'C57.8', 'C16.2', 'C34.9', 'C71.8', 'C13.2', 'C51.1', 'C25.3', 'C11.9', 'C41.4', 'C18.6', 'C76.1', 'C41.2', 'C21.8', 'C80.9', 'C75.8', 'C31.9', 'C38.1', 'C37.9', 'C25.0', 'C71.6', 'C25.4', 'C75.2', 'C41.3', 'C49.8', 'C64.9', 'C49.9', 'C47.2', 'C16.8', 'C54.1', 'C22.1', 'C32.3', 'C63.1', 'C72.0', 'C17.8', 'C00.5', 'C02.1', 'C50.2', 'C52.9', 'C40.0', 'C33.9', 'C13.9', 'C57.4', 'C77.1', 'C24.0', 'C57.0', 'C47.9', 'C25.2', 'C71.0', 'C66.9', 'C02.0', 'C50.8', 'C69.5', 'C31.2', 'C71.5', 'C30.1', 'C74.1', 'C38.8', 'C30.0', 'C47.8', 'C60.9', 'C75.4', 'C03.0', 'C17.9', 'C05.8', 'C54.3', 'C77.0', 'C74.9', 'C08.8', 'C25.9', 'C71.7', 'C68.8', 'C67.7', 'C53.1', 'C67.9', 'C67.6', 'C04.8', 'C53.9', 'C13.0', 'C76.2', 'C18.5', 'C02.4', 'unknown', 'C20.9', 'C42.4', 'C61.9', 'C05.0', 'C49.6', 'C07.9', 'C63.2', 'C65.9', 'C47.3', 'C62.1', 'C49.5', 'C57.2', 'C72.8', 'C74.0', 'C06.8', 'C44.6', 'C48.1', 'C69.2', 'C50.3', 'C50.9', 'C15.0', 'C39.9', 'C77.3', 'C06.0', 'C10.4', 'C47.6', 'C68.9', 'C15.1', 'C51.8', 'C50.0', 'C38.4', 'C32.2', 'C32.9', '']",,SRRSBiospecimen
Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,,"['Warm Ischemia', '4C wet ice', 'Ambient air', 'Negative -20C', 'unknown', 'Liquid Nitrogen', 'Dry Ice', 'Cold Ischemia', '']",,SRRSBiospecimen
Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['None', 'PBS', 'RPMI', 'RPMI+Serum', 'DMEM+Serum', 'PBS+Serum', 'DMEM', '']",,SRRSBiospecimen
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SRRSBiospecimen
Source HTAN Biospecimen ID,Source HTAN Biospecimen ID,SourceHTANBiospecimenID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,False,,,,SRRSBiospecimen
HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,SRRSBiospecimen
Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,SRRSBiospecimen
Collection Days from Index,Collection Days from Index,CollectionDaysfromIndex,Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable',True,,,,SRRSBiospecimen
Total Volume,Total Volume,TotalVolume,Numeric value for the total amount of sample or specimen,False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen
Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",False,True,"['Appendix', 'Parametrium', 'Aortic body and other paraganglia', 'Trachea', 'Transverse colon', 'Lateral floor of mouth', 'Paraspinal', 'Cerebellum NOS', 'Paraurethral gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Cloacogenic zone', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Overlapping lesion of bladder', 'Overlapping lesion of retroperitoneum and peritoneum', 'Uterine adnexa', 'Vertebral column', 'Upper lobe lung', 'Overlapping lesion of floor of mouth', 'Spinal meninges', 'Labium minus', 'Hard palate', 'Spleen', 'Breast NOS', 'Middle third of esophagus', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Duodenum', 'Spinal cord', 'Anterior wall of nasopharynx', 'Body of pancreas', 'Fundus uteri', 'Upper third of esophagus', 'Short bones of upper limb and associated joints', 'Overlapping lesion of cervix uteri', 'Lateral wall of bladder', 'Nervous system NOS', 'Upper-outer quadrant of breast', 'Nipple', 'Labium majus', 'Exocervix', 'Vulva NOS', 'Gum NOS', 'Mediastinum NOS', 'Urinary system NOS', 'Medulla of adrenal gland', 'Tongue NOS', 'Overlapping lesion of eye and adnexa', 'Bone marrow', 'Reticuloendothelial system NOS', 'Renal pelvis', 'Brain stem', 'Ureter', 'Overlapping lesion of small intestine', 'unknown primary site', 'Intestinal tract NOS', 'Laryngeal cartilage', 'Scrotum NOS', 'Upper respiratory tract NOS', 'Rectosigmoid junction', 'Overlapping lesion of stomach', 'Sphenoid sinus', 'Lymph nodes of inguinal region or leg', 'Pancreas NOS', 'Kidney NOS', 'Branchial cleft', 'Pharynx NOS', 'Tonsillar pillar', 'Islets of Langerhans', 'Optic nerve', 'Lymph nodes of multiple regions', 'Overlapping lesion of tonsil', 'Posterior wall of hypopharynx', 'Intrahepatic bile duct', 'Lacrimal gland', 'Orbit NOS', 'Bone NOS', 'Submandibular gland', 'Endocervix', 'Corpus uteri', 'Skin of trunk', 'Retina', 'Overlapping lesion of endocrine glands and related structures', 'Ciliary body', 'Overlapping lesion of larynx', 'Anterior mediastinum', 'Lower limb NOS', 'Frontal sinus', 'Superior wall of nasopharynx', 'Prepuce', 'Major salivary gland NOS', 'Stomach NOS', 'Overlapping lesion of rectum anus and anal canal', 'Olfactory nerve', 'Peripheral nerves and autonomic nervous system of thorax', 'Testis NOS', 'Cheek mucosa', 'Abdomen NOS', 'Waldeyer ring', 'Bone of limb NOS', 'Cervical esophagus', 'Intrathoracic lymph nodes', 'Overlapping lesion of digestive system', 'Axillary tail of breast', 'Lower-outer quadrant of breast', 'Overlapping lesion of brain and central nervous system', 'Lymph node NOS', 'Adrenal gland NOS', 'Soft palate NOS', 'Overlapping lesion of pancreas', 'Autonomic nervous system NOS', 'Border of tongue', 'Posterior wall of oropharynx', 'Meninges NOS', 'Colon NOS', 'Lateral wall of oropharynx', 'Supraglottis', 'Overlapping lesion of vulva', 'Fallopian tube', 'Extrahepatic bile duct', 'Posterior wall of nasopharynx', 'External ear', 'skin of upper limb and shoulder', 'Craniopharyngeal duct', 'Specified parts of peritoneum', 'Lingual tonsil', 'Maxillary sinus', 'Lower gum', 'Female genital tract NOS', 'Central portion of breast', 'Overlapping lesion of male genital organs', 'Overlapping lesion of colon', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Mucosa of lower lip', 'Tonsillar fossa', 'Other specified parts of pancreas', 'Anterior wall of bladder', 'Overlapping lesion of esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Connective subcutaneous and other soft tissues of thorax', 'Conjunctiva', 'Nasopharynx NOS', 'Mandible', 'Lung NOS', 'Overlapping lesions of oropharynx', 'External upper lip', 'Vagina NOS', 'Short bones of lower limb and associated joints', 'Placenta', 'Ileum', 'Overlapping lesion of lung', 'Broad ligament', 'Lower third of esophagus', 'Abdominal esophagus', 'External lip NOS', 'Other specified parts of male genital organs', 'Lateral wall of nasopharynx', 'Other specified parts of female genital organs', 'Bones of skull and face and associated joints', 'Palate NOS', 'Retromolar area', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of heart mediastinum and pleura', 'Oropharynx NOS', 'Bladder neck', 'Anal canal', 'Lymph nodes of head face and neck', 'Middle ear', 'Brain NOS', 'Ascending colon', 'Isthmus uteri', 'Ill-defined sites within respiratory system', 'Eye NOS', 'Hematopoietic system NOS', 'Accessory sinus NOS', 'Gastric antrum', 'Trigone of bladder', 'Head face or neck NOS', 'Pylorus', 'Cornea NOS', 'Pelvic lymph nodes', 'Occipital lobe', 'Meckel diverticulum', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Base of tongue NOS', 'Cranial nerve NOS', 'Overlapping lesion of hypopharynx', 'Greater curvature of stomach NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Commissure of lip', 'Overlapping lesion of penis', 'Ovary', 'Cervix uteri', 'Vestibule of mouth', 'Hypopharyngeal aspect of aryepiglottic fold', 'Prostate gland', 'Dome of bladder', 'Parotid gland', 'Pelvis NOS', 'Lower-inner quadrant of breast', 'Connective subcutaneous and other soft tissues of abdomen', 'Pineal gland', 'Fundus of stomach', 'Endocrine gland NOS', 'Cerebrum', 'Splenic flexure of colon', 'Floor of mouth NOS', 'External lower lip', 'Eyelid', 'Carotid body', 'Choroid', 'Overlapping lesion of major salivary glands', 'Mucosa of lip NOS', 'Not Reported', 'Urachus', 'Liver', 'skin of lower limb and hip', 'Overlapping lesion of brain', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Thyroid gland', 'Thoracic esophagus', 'Biliary tract NOS', 'Other ill-defined sites', 'Overlapping lesion of palate', 'Heart', 'Larynx NOS', 'Clitoris', 'Middle lobe lung', 'Peripheral nerves and autonomic nervous system of abdomen', 'Upper gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Parathyroid gland', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lesser curvature of stomach NOS', 'Anterior 2/3 of tongue NOS', 'Thymus', 'Frontal lobe', 'Blood', 'Descending colon', 'Gallbladder', 'Pelvic bones sacrum coccyx and associated joints', 'Lymph nodes of axilla or arm', 'Male genital organs NOS', 'Acoustic nerve', 'Thorax NOS', 'Connective subcutaneous and other soft tissues of pelvis', 'Urethra', 'Body of penis', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Rib sternum clavicle and associated joints', 'Cortex of adrenal gland', 'Jejunum', 'Temporal lobe', 'Overlapping lesion of skin', 'Upper-inner quadrant of breast', 'Bladder NOS', 'Ventral surface of tongue NOS', 'Uterus NOS', 'Anus NOS', 'Overlapping lesion of accessory sinuses', 'Rectum NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Cardia NOS', 'Anterior surface of epiglottis', 'Overlapping lesion of urinary organs', 'Skin of other and unspecified parts of face', 'Skin of scalp and neck', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Lip NOS', 'Posterior mediastinum', 'Sigmoid colon', 'Main bronchus', 'Anterior floor of mouth', 'Overlapping lesion of ill-defined sites', 'Hepatic flexure of colon', 'Overlapping lesion of biliary tract', 'Connective subcutaneous and other soft tissues NOS', 'Tonsil NOS', 'Long bones of upper limb scapula and associated joints', 'Lower lobe lung', 'Myometrium', 'Posterior wall of bladder', 'Hypopharynx NOS', 'Skin of lip NOS', 'Cauda equina', 'Pleura NOS', 'Esophagus NOS', 'Overlapping lesion of breast', 'Cerebral meninges', 'Sublingual gland', 'Penis NOS', 'Overlapping lesion of lip', 'Descended testis', 'Glottis', 'Upper limb NOS', 'Nasal cavity', 'Ethmoid sinus', 'Ampulla of Vater', 'Vallecula', 'Overlapping lesion of tongue', 'skin NOS', 'Epididymis', 'Undescended testis', 'Ventricle NOS', 'Pancreatic duct', 'Body of stomach', 'Endometrium', 'Long bones of lower limb and associated joints', 'Dorsal surface of tongue NOS', 'unknown', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Head of pancreas', 'Gastrointestinal tract NOS', 'Glans penis', 'Postcricoid region', 'Mucosa of upper lip', 'Intra-abdominal lymph nodes', 'Pyriform sinus', 'Round ligament', 'Ureteric orifice', 'Cecum', 'Peritoneum NOS', 'Parietal lobe', 'Subglottis', 'Mouth NOS', 'Small intestine NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of corpus uteri', 'Uvula', 'Spermatic cord', 'Retroperitoneum', 'Tail of pancreas', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen
Portion Weight,Portion Weight,PortionWeight,"Numeric value that represents the sample portion weight, measured in milligrams.",False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen
Specimen Laterality,Specimen Laterality,SpecimenLaterality,"For tumors in paired organs, designates the side on which the specimen was obtained.",False,True,"['Right', 'unknown', 'Bilateral', 'Not Applicable', 'Not Reported', 'Left', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen
Tumor Tissue Type,Tumor Tissue Type,TumorTissueType,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints),False,True,"['Normal', 'Metastatic', 'Post therapy neoadjuvant', 'Premalignant - in situ', 'Post therapy adjuvant', 'Atypia - hyperplasia', 'Not analyzed', 'Normal adjacent', 'Recurrent', 'Additional Primary', 'Not Otherwise Specified', 'Post therapy', 'Local recurrence', 'Primary', 'Premalignant', 'Normal distant', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen
Section Thickness Value,Section Thickness Value,SectionThicknessValue,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",False,True,,"['Biospecimen is ""Analyte""']",SRRSBiospecimen
Sectioning Days from Index,Sectioning Days from Index,SectioningDaysfromIndex,Number of days from the research participant's index date that the biospecimen was sectioned after collection. If not applicable please enter 'Not Applicable',False,True,,"['Biospecimen is ""Analyte""']",SRRSBiospecimen
Slide Charge Type,Slide Charge Type,SlideChargeType,A description of the charge on the glass slide.,False,True,"['Uncharged', 'Charged', 'Coverslip', 'Other', 'Not applicable', '']","['Biospecimen is ""Analyte""']",SRRSBiospecimen
Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Ambient Pack', 'Specimen at Room Temperature', 'Other Shipping Environment', 'Liquid Nitrogen', 'Not Shipped', 'Ice Pack', 'Dry Ice', 'Cold Pack', '']","['Biospecimen is ""Analyte""', 'Biospecimen is ""Blood""']",SRRSBiospecimen
Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,False,True,"['lipid', 'Tissue Section Analyte', 'PBMCs or Plasma or Serum Analyte', 'metabolite', 'RNA Analyte', 'cfDNA Analyte', 'Total RNA Analyte', 'Tissue Block Analyte', 'DNA Analyte', 'cDNA Libraries Analyte', 'PBMCs', 'protein', 'Plasma', 'Serum Analyte', '']","['Biospecimen is ""Analyte""']",SRRSBiospecimen
Fixation Duration,Fixation Duration,FixationDuration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",False,True,,"['Biospecimen is ""Analyte""']",SRRSBiospecimen
Biospecimen Dimension 3,Biospecimen Dimension 3,BiospecimenDimension3,"Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen
Biospecimen Dimension 2,Biospecimen Dimension 2,BiospecimenDimension2,"Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen
Section Number in Sequence,Section Number in Sequence,SectionNumberinSequence,"Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen
Biospecimen Dimension 1,Biospecimen Dimension 1,BiospecimenDimension1,"First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen
Acquisition Method Other Specify,Acquisition Method Other Specify,AcquisitionMethodOtherSpecify,A custom acquisition method [Text - max length 100 characters],False,True,,"['Acquisition is ""Other Acquisition Method""']",SRRSBiospecimen
Total Volume Unit,Total Volume Unit,TotalVolumeUnit,Unit of measurement used for the total amount of sample or specimen,False,,"['cubic millimeter', 'mL', 'square centimeter', '']",,SRRSBiospecimen
Dimensions Unit,Dimensions Unit,DimensionsUnit,"Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)",False,,"['mm', 'cm', '']",,SRRSBiospecimen
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,OtherAssay
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,OtherAssay
Filename,Filename,Filename,Name of a file,True,,,,OtherAssay
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,OtherAssay
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,OtherAssay
Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,OtherAssay
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,ExSeqMinimal
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ExSeqMinimal
Filename,Filename,Filename,Name of a file,True,,,,ExSeqMinimal
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ExSeqMinimal
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ExSeqMinimal
Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,ExSeqMinimal
Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['Enzymatic Digestion', 'Not Applicable', 'Dounce', 'gentleMACS']",,ScRNA-seqLevel1
Total Number of Input Cells,Total Number of Input Cells,TotalNumberofInputCells,Number of cells loaded/placed on plates,True,,,,ScRNA-seqLevel1
Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,ScRNA-seqLevel1
Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,ScRNA-seqLevel1
Input Cells and Nuclei,Input Cells and Nuclei,InputCellsandNuclei,"Number of cells and number of nuclei input; entry format: number, number",True,,,,ScRNA-seqLevel1
Nucleic Acid Capture Days from Index,Nucleic Acid Capture Days from Index,NucleicAcidCaptureDaysfromIndex,Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable',True,,,,ScRNA-seqLevel1
Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScRNA-seqLevel1
Single Cell Dissociation Days from Index,Single Cell Dissociation Days from Index,SingleCellDissociationDaysfromIndex,Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable',True,,,,ScRNA-seqLevel1
Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,,,ScRNA-seqLevel1
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ScRNA-seqLevel1
Cryopreserved Cells in Sample,Cryopreserved Cells in Sample,CryopreservedCellsinSample,Indicate if library preparation was based on revived frozen cells.,True,,"['yes', 'no']",,ScRNA-seqLevel1
Filename,Filename,Filename,Name of a file,True,,,,ScRNA-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,ScRNA-seqLevel1
End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['Full Length Transcript', '5 Prime', '3 Prime']",,ScRNA-seqLevel1
Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['I1', 'R2', 'R1', 'Other', 'R1&R2']",,ScRNA-seqLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,ScRNA-seqLevel1
Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Plates', 'Nuclei Isolation', '10x', 'Droplets', 'Microfluidics Chip', 'FACS']",,ScRNA-seqLevel1
Read1,Read1,Read1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScRNA-seqLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel1
Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV3.1', '10x FLEX', ""10x GEM 5'"", 'inDropsV3', 'Nextera XT', 'Smart-SeqV4', '10xV3', 'CEL-seq2', '10xV2', '10xV1.1', ""10x GEM 3'"", 'sci-ATAC-seq', 'Smart-seq2', 'inDropsV2', '10x Multiome', '10xV1.0', 'TruDrop', 'Drop-seq']",,ScRNA-seqLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel1
Read2,Read2,Read2,Read 2 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScRNA-seqLevel1
Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['Other Spike In', 'No Spike In', 'ERCC', 'PhiX']",,ScRNA-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScRNA-seqLevel1
Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Feature barcoding', 'Poly-dT', 'Random', 'Oligo-dT']",,ScRNA-seqLevel1
Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1
UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1
Cell Barcode Offset,Cell Barcode Offset,CellBarcodeOffset,Offset in sequence for cell barcode read (in bp): number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1
Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1
UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Read2 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1
Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1
cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Read2 is ""cDNA""']",ScRNA-seqLevel1
cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Read2 is ""cDNA""']",ScRNA-seqLevel1
Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,False,True,,"['Library Construction Method is ""CEL-seq2""']",ScRNA-seqLevel1
Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data  is available for each cell in CEL-seq2 assays,False,True,"['yes', 'no', '']","['Library Construction Method is ""CEL-seq2""']",ScRNA-seqLevel1
Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],False,True,,"['Spike In is ""ERCC""']",ScRNA-seqLevel1
Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,,"['Reverse Transcription Primer is ""Feature barcoding""']",ScRNA-seqLevel1
scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cufflinks', 'HCA Optimus', 'DEXSeq', 'HTSeq - FPKM', 'STARsolo', 'Other', 'Differentiation trajectory analysis', 'dropEST', 'SEQC', 'CellRanger', 'Cell annotation']",,ScRNA-seqLevel2
Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScRNA-seqLevel2
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel2
Whitelist Cell Barcode File Link,Whitelist Cell Barcode File Link,WhitelistCellBarcodeFileLink,Link to file listing all possible cell barcodes. URL,True,,,,ScRNA-seqLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel2
Filename,Filename,Filename,Name of a file,True,,,,ScRNA-seqLevel2
Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel2
Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,ScRNA-seqLevel2
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel2
Cell Barcode Tag,Cell Barcode Tag,CellBarcodeTag,SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z),True,,,,ScRNA-seqLevel2
scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel2
Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,ScRNA-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScRNA-seqLevel2
Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,ScRNA-seqLevel2
Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScRNA-seqLevel2
UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,ScRNA-seqLevel2
Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,False,True,,"['Applied Hard Trimming is ""Yes - Applied Hard Trimming""']",ScRNA-seqLevel2
Cell Total,Cell Total,CellTotal,Number of sequenced  cells. Applies to raw counts matrix only.,True,,,,ScRNA-seqLevel3
scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cufflinks', 'HCA Optimus', 'DEXSeq', 'HTSeq - FPKM', 'STARsolo', 'Other', 'Differentiation trajectory analysis', 'dropEST', 'SEQC', 'CellRanger', 'Cell annotation']",,ScRNA-seqLevel3
Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Normalized Counts', 'Batch Corrected Counts']",,ScRNA-seqLevel3
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel3
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel3
Filename,Filename,Filename,Name of a file,True,,,,ScRNA-seqLevel3
Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel3
Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification', 'Gene Expression Quantification', 'Other', 'Exon Expression Quantification']",,ScRNA-seqLevel3
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel3
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel3
scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScRNA-seqLevel3
Cell Median Number Genes,Cell Median Number Genes,CellMedianNumberGenes,Median number of genes detected per cell. Number,True,,,,ScRNA-seqLevel3
Cell Median Number Reads,Cell Median Number Reads,CellMedianNumberReads,Median number of reads per cell. Number,True,,,,ScRNA-seqLevel3
Linked Matrices,Linked Matrices,LinkedMatrices,All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames,False,,,,ScRNA-seqLevel3
scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cufflinks', 'HCA Optimus', 'DEXSeq', 'HTSeq - FPKM', 'STARsolo', 'Other', 'Differentiation trajectory analysis', 'dropEST', 'SEQC', 'CellRanger', 'Cell annotation']",,ScRNA-seqLevel4
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel4
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel4
Filename,Filename,Filename,Name of a file,True,,,,ScRNA-seqLevel4
Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel4
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel4
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel4
scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel4
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScRNA-seqLevel4
Spatial Barcode and UMI,Spatial Barcode and UMI,SpatialBarcodeandUMI,Spot and transcript identifiers,True,,,,Slide-seqLevel1
Spatial Read1,Spatial Read1,SpatialRead1,Read 1 content description,True,,"['Spatial Barcode and UMI', 'cDNA']",,Slide-seqLevel1
Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,Slide-seqLevel1
Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,Slide-seqLevel1
Nucleic Acid Capture Days from Index,Nucleic Acid Capture Days from Index,NucleicAcidCaptureDaysfromIndex,Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable',True,,,,Slide-seqLevel1
Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,Slide-seqLevel1
Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,,,Slide-seqLevel1
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,Slide-seqLevel1
Spatial Barcode Offset,Spatial Barcode Offset,SpatialBarcodeOffset,Offset in sequence for spot barcode read (in bp): number,False,True,,"['Spatial Read1 is ""Spatial Barcode and UMI""']",Slide-seqLevel1
Filename,Filename,Filename,Name of a file,True,,,,Slide-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,Slide-seqLevel1
End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['Full Length Transcript', '5 Prime', '3 Prime']",,Slide-seqLevel1
Spatial Library Construction Method,Spatial Library Construction Method,SpatialLibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV3.1', 'inDropsV3', 'Nextera XT', 'Smart-SeqV4', '10xV3', '10xV2', '10xV1.1', 'Smart-seq2', 'inDropsV2', '10xV1.0', 'TruDrop', 'Drop-seq']",,Slide-seqLevel1
Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['I1', 'R2', 'R1', 'Other', 'R1&R2']",,Slide-seqLevel1
Spatial Read2,Spatial Read2,SpatialRead2,Read 2 content description,True,,"['Spatial Barcode and UMI', 'cDNA']",,Slide-seqLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,Slide-seqLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Slide-seqLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Slide-seqLevel1
Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['Other Spike In', 'No Spike In', 'ERCC', 'PhiX']",,Slide-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,Slide-seqLevel1
Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Feature barcoding', 'Poly-dT', 'Random', 'Oligo-dT']",,Slide-seqLevel1
UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",Slide-seqLevel1
UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",Slide-seqLevel1
Spatial Barcode Length,Spatial Barcode Length,SpatialBarcodeLength,Length of spot barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",Slide-seqLevel1
cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",Slide-seqLevel1
cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",Slide-seqLevel1
Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],False,True,,"['Spike In is ""ERCC""']",Slide-seqLevel1
Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,,"['Reverse Transcription Primer is ""Feature barcoding""']",Slide-seqLevel1
Slide-seq Workflow Parameter Description,Slide-seq Workflow Parameter Description,Slide-seqWorkflowParameterDescription,Parameters used to run the Slide-seq workflow. String,True,,,,Slide-seqLevel2
Spatial Barcode Tag,Spatial Barcode Tag,SpatialBarcodeTag,SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z),True,,,,Slide-seqLevel2
Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,Slide-seqLevel2
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,Slide-seqLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Slide-seqLevel2
Filename,Filename,Filename,Name of a file,True,,,,Slide-seqLevel2
Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,Slide-seqLevel2
Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,Slide-seqLevel2
Slide-seq Workflow Type,Slide-seq Workflow Type,Slide-seqWorkflowType,Generic name for the workflow used to analyze the Slide-seq data set. String,True,,,,Slide-seqLevel2
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,Slide-seqLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Slide-seqLevel2
Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,Slide-seqLevel2
Matched Spatial Barcode Tag,Matched Spatial Barcode Tag,MatchedSpatialBarcodeTag,SAM tag for matched spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z) (Slide-seq specific),True,,,,Slide-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,Slide-seqLevel2
Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,Slide-seqLevel2
Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,Slide-seqLevel2
UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,Slide-seqLevel2
Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,False,True,,"['Applied Hard Trimming is ""Yes - Applied Hard Trimming""']",Slide-seqLevel2
Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,Slide-seqLevel3
Slide-seq Workflow Parameter Description,Slide-seq Workflow Parameter Description,Slide-seqWorkflowParameterDescription,Parameters used to run the Slide-seq workflow. String,True,,,,Slide-seqLevel3
Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Normalized Counts', 'Batch Corrected Counts']",,Slide-seqLevel3
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,Slide-seqLevel3
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Slide-seqLevel3
Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,Slide-seqLevel3
Filename,Filename,Filename,Name of a file,True,,,,Slide-seqLevel3
Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,Slide-seqLevel3
Slide-seq Workflow Type,Slide-seq Workflow Type,Slide-seqWorkflowType,Generic name for the workflow used to analyze the Slide-seq data set. String,True,,,,Slide-seqLevel3
Median Number Genes per Spatial Spot,Median Number Genes per Spatial Spot,MedianNumberGenesperSpatialSpot,The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.,True,,,,Slide-seqLevel3
Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification', 'Gene Expression Quantification', 'Other', 'Exon Expression Quantification']",,Slide-seqLevel3
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Slide-seqLevel3
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,Slide-seqLevel3
Slide-seq Fragment Size,Slide-seq Fragment Size,Slide-seqFragmentSize,Average cDNA length associated with the experiemtn. Integer,False,,,,Slide-seqLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,Slide-seqLevel3
Beads Total,Beads Total,BeadsTotal,Number of sequenced beads. Applies to raw counts matrix only. Integer,False,,,,Slide-seqLevel3
Slide-seq Bead File Type,Slide-seq Bead File Type,Slide-seqBeadFileType,The type of Level 3 file submitted as part of the Slide-seq workflow.,True,,"['Matched Bead Barcodes', 'All Bead Locations', 'Matrix Features', 'Matched Bead Locations', 'Not Applicable', 'All Bead Barcodes', 'Matrix Barcodes']",,Slide-seqLevel3
Median UMI Counts per Spot,Median UMI Counts per Spot,MedianUMICountsperSpot,The median number of UMI counts per tissue covered spot.,True,,,,Slide-seqLevel3
Transcript Integrity Number,Transcript Integrity Number,TranscriptIntegrityNumber,"Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number",False,,,,BulkRNA-seqLevel1
Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1
Fragment Standard Deviation Length,Fragment Standard Deviation Length,FragmentStandardDeviationLength,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkRNA-seqLevel1
Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,BulkRNA-seqLevel1
Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1
Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,BulkRNA-seqLevel1
Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,BulkRNA-seqLevel1
Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,BulkRNA-seqLevel1
Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,BulkRNA-seqLevel1
Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1
Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1
Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,BulkRNA-seqLevel1
Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,BulkRNA-seqLevel1
Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Long Read', 'Single Read', 'Paired End', 'Mid-length']",,BulkRNA-seqLevel1
Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkRNA-seqLevel1
Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1
Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1
Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1
Micro-region Seq Platform,Micro-region Seq Platform,Micro-regionSeqPlatform,The platform used for micro-regional RNA sequencing (if applicable),False,,"['Laser Capture Microdissection', 'Rarecyte Pick-Seq', '']",,BulkRNA-seqLevel1
RIN,RIN,RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,False,,,,BulkRNA-seqLevel1
ROI Tag,ROI Tag,ROITag,The tag or grouping used to identify the ROI in micro-regional RNA sequencing (if applicable). Must match the ROI tag within the count matrix in level 3.,False,,,,BulkRNA-seqLevel1
Filename,Filename,Filename,Name of a file,True,,,,BulkRNA-seqLevel1
Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,BulkRNA-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,BulkRNA-seqLevel1
Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,BulkRNA-seqLevel1
QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,BulkRNA-seqLevel1
Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['Random', 'miRNA Size Fractionation', 'Poly-T Enrichment', 'Affinity Enrichment', 'Other', 'rRNA Depletion', 'Hybrid Selection', 'PCR']",,BulkRNA-seqLevel1
Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkRNA-seqLevel1
Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,BulkRNA-seqLevel1
Library Strand,Library Strand,LibraryStrand,Library stranded-ness.,False,,"['Unstranded', 'Not Applicable', 'First Stranded', 'Second Stranded', '']",,BulkRNA-seqLevel1
Kmer Content,Kmer Content,KmerContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1
Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1
Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['I1', 'R2', 'R1', 'Other', 'R1&R2']",,BulkRNA-seqLevel1
To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['no', 'Yes - Trim Adapter Sequence', '']",,BulkRNA-seqLevel1
Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkRNA-seqLevel1
Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,BulkRNA-seqLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,BulkRNA-seqLevel1
DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,,,BulkRNA-seqLevel1
QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,BulkRNA-seqLevel1
QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,BulkRNA-seqLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel1
Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,BulkRNA-seqLevel1
Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,BulkRNA-seqLevel1
Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,BulkRNA-seqLevel1
Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkRNA-seqLevel1
Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel1
Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,BulkRNA-seqLevel1
Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1
Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['Other Spike In', 'No Spike In', 'ERCC', 'PhiX']",,BulkRNA-seqLevel1
Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkRNA-seqLevel1
Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1
Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1
Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],False,True,,"['Spike In is ""ERCC""']",BulkRNA-seqLevel1
Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkRNA-seqLevel2
Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkRNA-seqLevel2
MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI-low', 'MSI-high', 'MSS', 'MSI', '']",,BulkRNA-seqLevel2
Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkRNA-seqLevel2
Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkRNA-seqLevel2
Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkRNA-seqLevel2
Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,BulkRNA-seqLevel2
Is lowest level,Is lowest level,Islowestlevel,Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing,False,,"['Yes - Is lowest level', 'no', '']",,BulkRNA-seqLevel2
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkRNA-seqLevel2
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkRNA-seqLevel2
Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkRNA-seqLevel2
Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkRNA-seqLevel2
Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkRNA-seqLevel2
Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,BulkRNA-seqLevel2
Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,BulkRNA-seqLevel2
Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,BulkRNA-seqLevel2
Filename,Filename,Filename,Name of a file,True,,,,BulkRNA-seqLevel2
Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkRNA-seqLevel2
Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkRNA-seqLevel2
MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkRNA-seqLevel2
Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkRNA-seqLevel2
Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkRNA-seqLevel2
Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkRNA-seqLevel2
Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BWA-meth', 'Bismark', 'BSMAP', 'STAR 2-Pass Transcriptome', 'STAR 2-Pass Chimeric', 'BWA-mem', 'MethylCoder', 'B-SOLANA', 'Pash', 'BWA', 'SOCS-B', 'BWA with Mark Duplicates and BQSR', 'BS-Seeker2', 'None', 'LAST', 'BatMeth', 'ERNE-BS5', 'BRAT-BW', 'Segemehl', 'STAR 2-Pass Genome', 'GSNAP', 'BWA with BQSR', 'RMAP', 'STAR 2-Pass', 'Bowtie', 'BSmooth', 'Other Alignment Workflow', 'Bisulfighter', 'BWA-aln', 'BS-Seeker']",,BulkRNA-seqLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel2
MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,False,,,,BulkRNA-seqLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkRNA-seqLevel2
Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkRNA-seqLevel2
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,False,True,,"['Is lowest level is ""Yes - Is lowest level""']",BulkRNA-seqLevel2
Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",BulkRNA-seqLevel2
Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Normalized Counts', 'Batch Corrected Counts']",,BulkRNA-seqLevel3
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel3
Filename,Filename,Filename,Name of a file,True,,,,BulkRNA-seqLevel3
Pseudo Alignment Used,Pseudo Alignment Used,PseudoAlignmentUsed,Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.,True,,"['Yes - Pseudo Alignment Used', 'no']",,BulkRNA-seqLevel3
Fusion Gene Identity,Fusion Gene Identity,FusionGeneIdentity,The gene symbols of fused genes.,False,,,,BulkRNA-seqLevel3
Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification', 'Gene Expression Quantification', 'Other', 'Exon Expression Quantification']",,BulkRNA-seqLevel3
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel3
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkRNA-seqLevel3
Expression Units,Expression Units,ExpressionUnits,How quantities are corrected for gene length,True,,"['Counts', 'NA', 'TPM', 'RPKM', 'Other', 'FPKM']",,BulkRNA-seqLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkRNA-seqLevel3
Fusion Gene Detected,Fusion Gene Detected,FusionGeneDetected,Was a fusion gene identified?,False,,"['Yes - Fusion Gene Detected', 'no', 'unknown', '']",,BulkRNA-seqLevel3
Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,False,True,,"['Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""']",BulkRNA-seqLevel3
Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),False,True,,"['Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""']",BulkRNA-seqLevel3
Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),False,True,,"['Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""']",BulkRNA-seqLevel3
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,False,True,,"['Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""']",BulkRNA-seqLevel3
Specify Other Fusion Gene,Specify Other Fusion Gene,SpecifyOtherFusionGene,"Specify fusion gene detected, if not in list",False,True,,"['Fusion Gene Identity is ""Other Fusion Gene""']",BulkRNA-seqLevel3
Fragment Standard Deviation Length,Fragment Standard Deviation Length,FragmentStandardDeviationLength,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkWESLevel1
Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,BulkWESLevel1
Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,BulkWESLevel1
Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,BulkWESLevel1
Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,BulkWESLevel1
Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,BulkWESLevel1
Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,BulkWESLevel1
Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,BulkWESLevel1
Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,BulkWESLevel1
Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Long Read', 'Single Read', 'Paired End', 'Mid-length']",,BulkWESLevel1
Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,BulkWESLevel1
Filename,Filename,Filename,Name of a file,True,,,,BulkWESLevel1
Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,BulkWESLevel1
Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,BulkWESLevel1
Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['Random', 'miRNA Size Fractionation', 'Poly-T Enrichment', 'Affinity Enrichment', 'Other', 'rRNA Depletion', 'Hybrid Selection', 'PCR']",,BulkWESLevel1
Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkWESLevel1
Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['I1', 'R2', 'R1', 'Other', 'R1&R2']",,BulkWESLevel1
To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['no', 'Yes - Trim Adapter Sequence', '']",,BulkWESLevel1
Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkWESLevel1
Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,BulkWESLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,BulkWESLevel1
Target Capture Kit,Target Capture Kit,TargetCaptureKit,"Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.",True,,"['Custom SureSelect GENIE-UHN Panel - 555 Genes', 'Custom AmpliSeq Cancer Hotspot GENIE-MDA Augmented Panel v1 - 46 Genes', 'Custom GENIE-DFCI Oncopanel - 447 Genes', 'Custom MSK IMPACT Panel - 341 Genes', 'Custom SureSelect TARGET-AML_NBL_WT Panel - 2.8 Mb', 'Custom Large Construct Capture TARGET-OS Panel - 8 Genes', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 203 Genes', 'SeqCap EZ HGSC VCRome v2.1', 'Custom SureSelect Human All Exon v1.1 Plus 3 Boosters', 'Foundation Medicine T7 Panel - 429 Genes', 'Custom SureSelect CGCI-HTMCP-CC Panel - 19.7 Mb', 'SureSelect Human All Exon v5 + UTR', 'Custom MSK IMPACT Panel - 468 Genes', 'SureSelect Human All Exon v6', 'Ion AmpliSeq Comprehensive Cancer Panel', 'SeqCap EZ Human Exome v3.0', 'xGen Exome Research Panel v1.0', 'Custom GENIE-DFCI OncoPanel - 275 Genes', '25 rxn xGen Universal Blocking Oligo – TS HT-i7', 'Custom HaloPlex DLBCL Panel - 370 Genes', 'Custom SureSelect CGCI-BLGSP Panel - 4.6 Mb', 'Not Applicable', 'Custom Targets File Provided', 'SureSelect Human All Exon v3', 'Custom Myeloid GENIE-VICC Panel - 37 Genes', 'Custom Personalis ACEcp VAREPOP-APOLLO Panel v2', 'SureSelect Human All Exon v4', 'SureSelect Human All Exon v5', 'TruSight Myeloid Sequencing Panel', 'TruSeq Amplicon Cancer Panel', 'Custom SeqCap EZ TARGET-OS Panel - 7.0 Mb', 'unknown', 'Ion AmpliSeq Cancer Hotspot Panel v2', 'Custom SureSelect CGCI-HTMCP-CC KMT2D And Hotspot Panel - 37.0 Kb', 'Custom MSK IMPACT Panel - 410 Genes', 'Custom GENIE-DFCI Oncopanel - 300 Genes', 'Nextera Rapid Capture Exome v1.2', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v1', 'Custom Twist Broad PanCancer Panel - 396 Genes', 'xGen Universal Blocking Oligo – TS HT-i5 - 25 rxn', 'SeqCap EZ Human Exome v2.0', 'Custom Ion AmpliSeq Hotspot GENIE-MOSC3 Augmented Panel - 74 Genes', 'Custom Twist Broad Exome v1.0 - 35.0 Mb', 'TruSeq RNA Exome', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v2', 'Nextera DNA Exome', 'TruSeq Exome Enrichment - 62 Mb', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 88 Genes', 'Foundation Medicine T5a Panel - 322 Genes', 'Custom Solid Tumor GENIE-VICC Panel - 34 Genes']",,BulkWESLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel1
Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,BulkWESLevel1
Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,BulkWESLevel1
Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1
Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkWESLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel1
Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkWESLevel1
Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkWESLevel2
Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2
Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkWESLevel2
MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI-low', 'MSI-high', 'MSS', 'MSI', '']",,BulkWESLevel2
Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkWESLevel2
Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkWESLevel2
Proportion Coverage 10x,Proportion Coverage 10x,ProportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",False,,,,BulkWESLevel2
Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkWESLevel2
Is lowest level,Is lowest level,Islowestlevel,Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing,False,,"['Yes - Is lowest level', 'no', '']",,BulkWESLevel2
Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkWESLevel2
Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,BulkWESLevel2
Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkWESLevel2
Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2
Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2
Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkWESLevel2
Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkWESLevel2
Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkWESLevel2
Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,BulkWESLevel2
Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,BulkWESLevel2
Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,BulkWESLevel2
Filename,Filename,Filename,Name of a file,True,,,,BulkWESLevel2
Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkWESLevel2
QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,BulkWESLevel2
Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkWESLevel2
MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkWESLevel2
Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,BulkWESLevel2
Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2
Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkWESLevel2
QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,BulkWESLevel2
Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkWESLevel2
QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,BulkWESLevel2
Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkWESLevel2
Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BWA-meth', 'Bismark', 'BSMAP', 'STAR 2-Pass Transcriptome', 'STAR 2-Pass Chimeric', 'BWA-mem', 'MethylCoder', 'B-SOLANA', 'Pash', 'BWA', 'SOCS-B', 'BWA with Mark Duplicates and BQSR', 'BS-Seeker2', 'None', 'LAST', 'BatMeth', 'ERNE-BS5', 'BRAT-BW', 'Segemehl', 'STAR 2-Pass Genome', 'GSNAP', 'BWA with BQSR', 'RMAP', 'STAR 2-Pass', 'Bowtie', 'BSmooth', 'Other Alignment Workflow', 'Bisulfighter', 'BWA-aln', 'BS-Seeker']",,BulkWESLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel2
Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2
MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,False,,,,BulkWESLevel2
Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,BulkWESLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel2
Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2
Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkWESLevel2
Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2
Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkWESLevel2
Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,False,True,,"['Is lowest level is ""Yes - Is lowest level""']",BulkWESLevel2
Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",BulkWESLevel2
Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,BulkWESLevel3
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel3
Somatic Variants Sample Type,Somatic Variants Sample Type,SomaticVariantsSampleType,Is the sample case or control in somatic variant analysis,True,,"['Not Applicable', 'Case Sample', 'Control Sample']",,BulkWESLevel3
Filename,Filename,Filename,Name of a file,True,,,,BulkWESLevel3
Somatic Variants Workflow URL,Somatic Variants Workflow URL,SomaticVariantsWorkflowURL,Generic name for the workflow used to analyze a data set.,True,,,,BulkWESLevel3
Structural Variant Workflow Type,Structural Variant Workflow Type,StructuralVariantWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['None', 'BRASS', 'CNV', 'Other Structural Variant Workflow Type', 'GATK4', 'CNVkit', '']",,BulkWESLevel3
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkWESLevel3
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel3
Germline Variants Workflow Type,Germline Variants Workflow Type,GermlineVariantsWorkflowType,Generic name for the workflow used to analyze a data set,False,,"['Other Germline Variants Workflow Type', 'GATK4', 'None', '']",,BulkWESLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkWESLevel3
Somatic Variants Workflow Type,Somatic Variants Workflow Type,SomaticVariantsWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['CaVEMan', 'MuTect2', 'Pindel', 'None', 'SomaticSniper', 'MuSE', 'Other Somatic Variants Workflow Type', 'VarScan2', 'GATK4', '']",,BulkWESLevel3
Germline Variants Workflow URL,Germline Variants Workflow URL,GermlineVariantsWorkflowURL,"Link to workflow document, e.g. Github, DockStore.org recommended",True,,,,BulkWESLevel3
Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkWESLevel3
Structural Variant Workflow URL,Structural Variant Workflow URL,StructuralVariantWorkflowURL,Link to workflow document. DockStore.org recommended. URL,True,,,,BulkWESLevel3
Custom Structural Variant Workflow Type,Custom Structural Variant Workflow Type,CustomStructuralVariantWorkflowType,Specify the name of a custom workflow name,False,True,,"['Structural is ""Other""']",BulkWESLevel3
Custom Germline Variants Workflow Type,Custom Germline Variants Workflow Type,CustomGermlineVariantsWorkflowType,Specify the name of a custom alignment workflow,False,True,,"['Germline is ""Other""']",BulkWESLevel3
Custom Somatic Variants Workflow Type,Custom Somatic Variants Workflow Type,CustomSomaticVariantsWorkflowType,Specify the name of a custom workflow name,False,True,,"['Somatic is ""Other""']",BulkWESLevel3
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,MicroarrayLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MicroarrayLevel1
Microarray Value Definition,Microarray Value Definition,MicroarrayValueDefinition,What the provided value signifies,True,,,,MicroarrayLevel1
Filename,Filename,Filename,Name of a file,True,,,,MicroarrayLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,MicroarrayLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MicroarrayLevel1
Microarray Platform ID,Microarray Platform ID,MicroarrayPlatformID,The NCBI GEO Microarray Platform ID that links to the table containing the array definition,True,,,,MicroarrayLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,MicroarrayLevel1
Microarray Label,Microarray Label,MicroarrayLabel,Microarray used this kind of label,True,,,,MicroarrayLevel1
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MicroarrayLevel1
Microarray Molecule,Microarray Molecule,MicroarrayMolecule,Microarray is measuring this kind of molecule,True,,"['RNA', 'DNA']",,MicroarrayLevel1
Microarray Protocol Auxiliary File,Microarray Protocol Auxiliary File,MicroarrayProtocolAuxiliaryFile,"Auxiliary file describing the experimental protocols used, as described in the NCBI GEO microarray template, recorded as synapse ID (syn12345).",True,,,,MicroarrayLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,MicroarrayLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MicroarrayLevel2
Filename,Filename,Filename,Name of a file,True,,,,MicroarrayLevel2
Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,MicroarrayLevel2
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MicroarrayLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MicroarrayLevel2
Microarray Platform ID,Microarray Platform ID,MicroarrayPlatformID,The NCBI GEO Microarray Platform ID that links to the table containing the array definition,True,,,,MicroarrayLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,MicroarrayLevel2
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MicroarrayLevel2
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,RPPALevel2
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,RPPALevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,RPPALevel2
Filename,Filename,Filename,Name of a file,True,,,,RPPALevel2
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,RPPALevel2
HTAN RPPA Antibody Table,HTAN RPPA Antibody Table,HTANRPPAAntibodyTable,A table containing antibody level metadata for RPPA,True,,,,RPPALevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",False,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf', '']",,RPPALevel2
Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,RPPALevel2
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,RPPALevel2
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,RPPALevel2
Ab Name Reported on Dataset,Ab Name Reported on Dataset,AbNameReportedonDataset,The antibody name.,False,,,,RPPALevel2
Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Clonal', 'Non-clonal', '']",,RPPALevel2
Catalog Number,Catalog Number,CatalogNumber,Catalog Number,False,,,,RPPALevel2
RPPA Dilution,RPPA Dilution,RPPADilution,The dilution ratio.,False,,,,RPPALevel2
Species,Species,Species,Host animal.,False,,"['Goat', 'Rabbit', 'Mouse', '']",,RPPALevel2
Internal Ab ID,Internal Ab ID,InternalAbID,Internal lab ID for an antibody.,False,,,,RPPALevel2
Antibody Notes,Antibody Notes,AntibodyNotes,Notes on antibodies replacements and antibody recognition observations.,False,,,,RPPALevel2
Phospho Site,Phospho Site,PhosphoSite,The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442),False,,,,RPPALevel2
RPPA Validation Status,RPPA Validation Status,RPPAValidationStatus,Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC),False,,"['Valid', 'Use with Caution', 'Under Evaluation', 'Used for QC', '']",,RPPALevel2
HTAN RPPA Antibody Table ID,HTAN RPPA Antibody Table ID,HTANRPPAAntibodyTableID,HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.,False,,,,RPPALevel2
GENCODE Gene Symbol Target,GENCODE Gene Symbol Target,GENCODEGeneSymbolTarget,The comma separated list of gene symbols targeted by the antibody.,False,,,,RPPALevel2
Vendor,Vendor,Vendor,Vendor,False,,,,RPPALevel2
Phosphoprotein Flag,Phosphoprotein Flag,PhosphoproteinFlag,A flag the denotes if an antibody targets a phosphoprotein.,False,,"['false', 'true', '']",,RPPALevel2
UNIPROT Protein ID Target,UNIPROT Protein ID Target,UNIPROTProteinIDTarget,The comma separated list of UNIPROT IDs targeted by the antibody.,False,,,,RPPALevel2
Clone,Clone,Clone,Clone,False,,,,RPPALevel2
Median Fraction of Reads in Peaks,Median Fraction of Reads in Peaks,MedianFractionofReadsinPeaks,Median fraction of reads in peaks (FRIP),True,,,,ScATAC-seqLevel1
scATACseq Read2,scATACseq Read2,ScATACseqRead2,Read 2 content description,True,,"['DNA Insert', 'Sample Index and DNA Insert', 'Cell Barcode', 'Sample Index', 'Cell Barcode and DNA Insert']",,ScATAC-seqLevel1
Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['Enzymatic Digestion', 'Not Applicable', 'Dounce', 'gentleMACS']",,ScATAC-seqLevel1
scATACseq Read1,scATACseq Read1,ScATACseqRead1,Read 1 content description,True,,"['DNA Insert', 'Sample Index and DNA Insert', 'Cell Barcode', 'Sample Index', 'Cell Barcode and DNA Insert']",,ScATAC-seqLevel1
Total Number of Passing Nuclei,Total Number of Passing Nuclei,TotalNumberofPassingNuclei,Number of nuclei sequenced,True,,,,ScATAC-seqLevel1
Nuclei Barcode Length,Nuclei Barcode Length,NucleiBarcodeLength,Nuclei Barcode Length,True,,,,ScATAC-seqLevel1
Nuclei Barcode Read,Nuclei Barcode Read,NucleiBarcodeRead,Nuclei Barcode Read,True,,,,ScATAC-seqLevel1
Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScATAC-seqLevel1
Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,ScATAC-seqLevel1
Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScATAC-seqLevel1
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScATAC-seqLevel1
Single Nucleus Buffer,Single Nucleus Buffer,SingleNucleusBuffer,Nuclei isolation buffer,True,,"['10x', 'NIB', 'TST', 'Omni']",,ScATAC-seqLevel1
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ScATAC-seqLevel1
Threshold for Minimum Passing Reads,Threshold for Minimum Passing Reads,ThresholdforMinimumPassingReads,Threshold for calling cells,True,,,,ScATAC-seqLevel1
Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel1
Transposition Reaction,Transposition Reaction,TranspositionReaction,"Name of the transposase, transposon sequences",True,,"['Tn5', 'Diagenode-loaded Apex-Bio', 'Diagenode-unloaded Apex-Bio', 'Tn5-059', 'EZ-Tn5', 'In-House', 'Nextera Tn5']",,ScATAC-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,ScATAC-seqLevel1
Nucleus Identifier,Nucleus Identifier,NucleusIdentifier,Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from,True,,['Nuclei Barcode'],,ScATAC-seqLevel1
scATACseq Read3,scATACseq Read3,ScATACseqRead3,Read 3 content description,False,,"['DNA Insert', 'Sample Index and DNA Insert', 'Cell Barcode', 'Sample Index', 'Cell Barcode and DNA Insert', '']",,ScATAC-seqLevel1
Median Passing Read Percentage,Median Passing Read Percentage,MedianPassingReadPercentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,True,,,,ScATAC-seqLevel1
Median Fraction of Reads in Annotated cis DNA Elements,Median Fraction of Reads in Annotated cis DNA Elements,MedianFractionofReadsinAnnotatedcisDNAElements,Median fraction of reads in annotated cis-DNA elements (FRIADE),True,,,,ScATAC-seqLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,ScATAC-seqLevel1
Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Plates', 'Nuclei Isolation', '10x', 'Droplets', 'Microfluidics Chip', 'FACS']",,ScATAC-seqLevel1
scATACseq Library Layout,scATACseq Library Layout,ScATACseqLibraryLayout,Sequencing read type,True,,['scATACseq Paired End'],,ScATAC-seqLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel1
Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV3.1', '10x FLEX', ""10x GEM 5'"", 'inDropsV3', 'Nextera XT', 'Smart-SeqV4', '10xV3', 'CEL-seq2', '10xV2', '10xV1.1', ""10x GEM 3'"", 'sci-ATAC-seq', 'Smart-seq2', 'inDropsV2', '10x Multiome', '10xV1.0', 'TruDrop', 'Drop-seq']",,ScATAC-seqLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScATAC-seqLevel1
Peaks Calling Software,Peaks Calling Software,PeaksCallingSoftware,Generic name of peaks calling tool,False,,,,ScATAC-seqLevel1
Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,False,True,,"['Library Construction Method is ""CEL-seq2""']",ScATAC-seqLevel1
Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data  is available for each cell in CEL-seq2 assays,False,True,"['yes', 'no', '']","['Library Construction Method is ""CEL-seq2""']",ScATAC-seqLevel1
Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScATAC-seqLevel2
Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScATAC-seqLevel2
Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScATAC-seqLevel2
Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScATAC-seqLevel2
Proportion Coverage 10x,Proportion Coverage 10x,ProportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",False,,,,ScATAC-seqLevel2
Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,ScATAC-seqLevel2
Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,ScATAC-seqLevel2
Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScATAC-seqLevel2
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel2
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScATAC-seqLevel2
Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScATAC-seqLevel2
Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScATAC-seqLevel2
Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScATAC-seqLevel2
Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,ScATAC-seqLevel2
Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScATAC-seqLevel2
Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,ScATAC-seqLevel2
Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel2
Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScATAC-seqLevel2
Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScATAC-seqLevel2
Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,ScATAC-seqLevel2
Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScATAC-seqLevel2
Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScATAC-seqLevel2
Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BWA-meth', 'Bismark', 'BSMAP', 'STAR 2-Pass Transcriptome', 'STAR 2-Pass Chimeric', 'BWA-mem', 'MethylCoder', 'B-SOLANA', 'Pash', 'BWA', 'SOCS-B', 'BWA with Mark Duplicates and BQSR', 'BS-Seeker2', 'None', 'LAST', 'BatMeth', 'ERNE-BS5', 'BRAT-BW', 'Segemehl', 'STAR 2-Pass Genome', 'GSNAP', 'BWA with BQSR', 'RMAP', 'STAR 2-Pass', 'Bowtie', 'BSmooth', 'Other Alignment Workflow', 'Bisulfighter', 'BWA-aln', 'BS-Seeker']",,ScATAC-seqLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel2
Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,ScATAC-seqLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel2
MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,ScATAC-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScATAC-seqLevel2
Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScATAC-seqLevel2
Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",ScATAC-seqLevel2
Mitochondrial Read-Pairs,Mitochondrial Read-Pairs,MitochondrialRead-Pairs,Number of read-pairs mapping to mitochondria and non-nuclear contigs,False,,,,ScATAC-seqLevel3
Passed Filters,Passed Filters,PassedFilters,"Number of non-duplicate, usable read-pairs i.e. fragments",False,,,,ScATAC-seqLevel3
MACS2 Start,MACS2 Start,MACS2Start,Genomic starting position in MACS2,False,,,,ScATAC-seqLevel3
scATAC-seq Object ID,scATAC-seq Object ID,ScATAC-seqObjectID,Orig.Ident or scATAC-seq Object ID,False,,,,ScATAC-seqLevel3
MACS2 Width,MACS2 Width,MACS2Width,Width of the peak in bases in MACS2,False,,,,ScATAC-seqLevel3
nFeature RNA,nFeature RNA,NFeatureRNA,Number of genes detected in cell,False,,,,ScATAC-seqLevel3
Blacklist Ratio,Blacklist Ratio,BlacklistRatio,Ratio of reads in blacklist regions,False,,,,ScATAC-seqLevel3
Peak Region Cutsites,Peak Region Cutsites,PeakRegionCutsites,Number of ends of fragments in peak regions,False,,,,ScATAC-seqLevel3
MACS2 Fold Change,MACS2 Fold Change,MACS2FoldChange,Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2,False,,,,ScATAC-seqLevel3
Nucleosome Percentile,Nucleosome Percentile,NucleosomePercentile,Percentile rank of nucleosome score,False,,,,ScATAC-seqLevel3
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel3
TSS Enrichment,TSS Enrichment,TSSEnrichment,Transcription start site (TSS) enrichment score,False,,,,ScATAC-seqLevel3
Promoter Region Fragments,Promoter Region Fragments,PromoterRegionFragments,Number of fragments overlapping promoter regions,False,,,,ScATAC-seqLevel3
Duplicate Read-Pairs,Duplicate Read-Pairs,DuplicateRead-Pairs,Number of duplicate read-pairs,False,,,,ScATAC-seqLevel3
MACS2 Relative Summit Position,MACS2 Relative Summit Position,MACS2RelativeSummitPosition,Position of the peak summit related to the start position in MACS2,False,,,,ScATAC-seqLevel3
MACS2 Name,MACS2 Name,MACS2Name,Name of the peak in MACS2,False,,,,ScATAC-seqLevel3
nCount RNA,nCount RNA,NCountRNA,Total number of fragments in genes,False,,,,ScATAC-seqLevel3
Total Read-Pairs,Total Read-Pairs,TotalRead-Pairs,Total read-pairs,False,,,,ScATAC-seqLevel3
Enhancer Region Fragments,Enhancer Region Fragments,EnhancerRegionFragments,Number of fragments overlapping enhancer regions,False,,,,ScATAC-seqLevel3
Seurat Clusters,Seurat Clusters,SeuratClusters,Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm,False,,,,ScATAC-seqLevel3
Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel3
TSS Percentile,TSS Percentile,TSSPercentile,Percentile rank of TSS score,False,,,,ScATAC-seqLevel3
nCount Peaks,nCount Peaks,NCountPeaks,Total number of fragments in peaks,False,,,,ScATAC-seqLevel3
TSS Fragments,TSS Fragments,TSSFragments,Number of fragments overlapping with TSS regions,False,,,,ScATAC-seqLevel3
Unmapped Read-Pairs,Unmapped Read-Pairs,UnmappedRead-Pairs,Number of read-pairs with at least one end not mapped,False,,,,ScATAC-seqLevel3
LowMapQ,LowMapQ,LowMapQ,Number of read-pairs with <30 mapq on at least one end,False,,,,ScATAC-seqLevel3
DNase Sensitive Region Fragments,DNase Sensitive Region Fragments,DNaseSensitiveRegionFragments,Number of fragments overlapping with DNase sensitive regions,False,,,,ScATAC-seqLevel3
Peak Region Fragments,Peak Region Fragments,PeakRegionFragments,Number of fragments overlapping peaks,False,,,,ScATAC-seqLevel3
MACS2 Score,MACS2 Score,MACS2Score,Peak score (proportional to q-value) in MACS2,False,,,,ScATAC-seqLevel3
MACS2 Neg Log10 pvalue Summit,MACS2 Neg Log10 pvalue Summit,MACS2NegLog10pvalueSummit,Negative log10 p-value for the peak summit in MACS2,False,,,,ScATAC-seqLevel3
Blacklist Region Fragments,Blacklist Region Fragments,BlacklistRegionFragments,Number of fragments overlapping blacklisted regions,False,,,,ScATAC-seqLevel3
MACS2 Seqnames,MACS2 Seqnames,MACS2Seqnames,Chromosome id,False,,,,ScATAC-seqLevel3
MACS2 Strand,MACS2 Strand,MACS2Strand,DNA stand aligned with in MACS2,False,,,,ScATAC-seqLevel3
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel3
MACS2 Neg Log10 qvalue Summit,MACS2 Neg Log10 qvalue Summit,MACS2NegLog10qvalueSummit,Negative log10 q-value for the peak summit in MACS2,False,,,,ScATAC-seqLevel3
MACS2 End,MACS2 End,MACS2End,Genomic ending position in MACS2,False,,,,ScATAC-seqLevel3
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel3
Chimeric Read-Pairs,Chimeric Read-Pairs,ChimericRead-Pairs,Number of chimerically mapped read-pairs,False,,,,ScATAC-seqLevel3
Nucleosome Signal,Nucleosome Signal,NucleosomeSignal,"Nucleosome signal score (strength of the nucleosome signal per cell, computed as the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free))",False,,,,ScATAC-seqLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScATAC-seqLevel3
On Target Fragments,On Target Fragments,OnTargetFragments,"Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)",False,,,,ScATAC-seqLevel3
Pct Reads in Peaks,Pct Reads in Peaks,PctReadsinPeaks,Percentage of reads in peaks,False,,,,ScATAC-seqLevel3
nFeature Peaks,nFeature Peaks,NFeaturePeaks,Number of peaks with at least one read,False,,,,ScATAC-seqLevel3
Peaks Calling Software,Peaks Calling Software,PeaksCallingSoftware,Generic name of peaks calling tool,True,,,,ScmC-seqLevel1
Median Fraction of Reads in Peaks,Median Fraction of Reads in Peaks,MedianFractionofReadsinPeaks,Median fraction of reads in peaks (FRIP),True,,,,ScmC-seqLevel1
Total Number of Passing Nuclei,Total Number of Passing Nuclei,TotalNumberofPassingNuclei,Number of nuclei sequenced,True,,,,ScmC-seqLevel1
Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScmC-seqLevel1
Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,ScmC-seqLevel1
Bisulfite Conversion,Bisulfite Conversion,BisulfiteConversion,Name of the kit used in bisulfite conversion.,True,,"['Agilent SureSelectXT Methyl-Seq', 'Zimo EZ-96 DNA Methylation Deep Kit', 'Zimo EZ-96 DNA Methylation Shallow Kit', 'Zimo EZ DNA Methylation Kit', 'NEBNext Enzymatic Methyl-seq Kit']",,ScmC-seqLevel1
Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScmC-seqLevel1
scmCseq Read2,scmCseq Read2,ScmCseqRead2,Read 2 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScmC-seqLevel1
Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Long Read', 'Single Read', 'Paired End', 'Mid-length']",,ScmC-seqLevel1
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScmC-seqLevel1
Single Nucleus Buffer,Single Nucleus Buffer,SingleNucleusBuffer,Nuclei isolation buffer,True,,"['10x', 'NIB', 'TST', 'Omni']",,ScmC-seqLevel1
Threshold for Minimum Passing Reads,Threshold for Minimum Passing Reads,ThresholdforMinimumPassingReads,Threshold for calling cells,True,,,,ScmC-seqLevel1
Filename,Filename,Filename,Name of a file,True,,,,ScmC-seqLevel1
scmCseq Read3,scmCseq Read3,ScmCseqRead3,Read 3 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScmC-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,ScmC-seqLevel1
Single Nucleus Capture,Single Nucleus Capture,SingleNucleusCapture,Nuclei isolation method,False,,"['Plates', '10x', 'droplet', '']",,ScmC-seqLevel1
Nucleus Identifier,Nucleus Identifier,NucleusIdentifier,Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from,True,,['Nuclei Barcode'],,ScmC-seqLevel1
Median Passing Read Percentage,Median Passing Read Percentage,MedianPassingReadPercentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,True,,,,ScmC-seqLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,ScmC-seqLevel1
Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Plates', 'Nuclei Isolation', '10x', 'Droplets', 'Microfluidics Chip', 'FACS']",,ScmC-seqLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScmC-seqLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScmC-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScmC-seqLevel1
scmCseq Read1,scmCseq Read1,ScmCseqRead1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScmC-seqLevel1
Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1
UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1
Cell Barcode Offset,Cell Barcode Offset,CellBarcodeOffset,Offset in sequence for cell barcode read (in bp): number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1
Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1
UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1
Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1
cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Scmcseq read1 is ""cDNA""']",ScmC-seqLevel1
cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Scmcseq read1 is ""cDNA""']",ScmC-seqLevel1
Nuclei Barcode Length,Nuclei Barcode Length,NucleiBarcodeLength,Nuclei Barcode Length,True,,,,ScmC-seqLevel1
Nuclei Barcode Read,Nuclei Barcode Read,NucleiBarcodeRead,Nuclei Barcode Read,True,,,,ScmC-seqLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,BulkMethylation-seqLevel1
Bulk Methylation Assay Type,Bulk Methylation Assay Type,BulkMethylationAssayType,Assay types normally determine genomic coverage,True,,"['Beadchip Array', 'Targeted Genome', 'Whole genome']",,BulkMethylation-seqLevel1
Total DNA Input,Total DNA Input,TotalDNAInput,"Overall number of reads for a given sample in digits (microgram, nanogram).",False,,,,BulkMethylation-seqLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkMethylation-seqLevel1
Filename,Filename,Filename,Name of a file,True,,,,BulkMethylation-seqLevel1
Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,BulkMethylation-seqLevel1
Bisulfite Conversion,Bisulfite Conversion,BisulfiteConversion,Name of the kit used in bisulfite conversion.,True,,"['Agilent SureSelectXT Methyl-Seq', 'Zimo EZ-96 DNA Methylation Deep Kit', 'Zimo EZ-96 DNA Methylation Shallow Kit', 'Zimo EZ DNA Methylation Kit', 'NEBNext Enzymatic Methyl-seq Kit']",,BulkMethylation-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,BulkMethylation-seqLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkMethylation-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkMethylation-seqLevel1
Replicate Type,Replicate Type,ReplicateType,A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.,True,,"['Not Applicable', 'Technical replicate', 'Biological replicate']",,BulkMethylation-seqLevel1
Beadchip Array,Beadchip Array,BeadchipArray,Assay that uses beads to target a specific locus on the genome.,False,,"['HM27K', 'HM450K', '']",,BulkMethylation-seqLevel1
Targeted Genome,Targeted Genome,TargetedGenome,Assay for analyzing specific mutations in a given sample,False,,"['MeDIP', 'RRBS', '']",,BulkMethylation-seqLevel1
Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScmC-seqLevel2
Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScmC-seqLevel2
Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScmC-seqLevel2
Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScmC-seqLevel2
Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,ScmC-seqLevel2
Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,ScmC-seqLevel2
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScmC-seqLevel2
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScmC-seqLevel2
Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScmC-seqLevel2
Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScmC-seqLevel2
Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScmC-seqLevel2
Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,ScmC-seqLevel2
Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScmC-seqLevel2
Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,ScmC-seqLevel2
Filename,Filename,Filename,Name of a file,True,,,,ScmC-seqLevel2
Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScmC-seqLevel2
Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScmC-seqLevel2
Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,ScmC-seqLevel2
Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScmC-seqLevel2
Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScmC-seqLevel2
Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BWA-meth', 'Bismark', 'BSMAP', 'STAR 2-Pass Transcriptome', 'STAR 2-Pass Chimeric', 'BWA-mem', 'MethylCoder', 'B-SOLANA', 'Pash', 'BWA', 'SOCS-B', 'BWA with Mark Duplicates and BQSR', 'BS-Seeker2', 'None', 'LAST', 'BatMeth', 'ERNE-BS5', 'BRAT-BW', 'Segemehl', 'STAR 2-Pass Genome', 'GSNAP', 'BWA with BQSR', 'RMAP', 'STAR 2-Pass', 'Bowtie', 'BSmooth', 'Other Alignment Workflow', 'Bisulfighter', 'BWA-aln', 'BS-Seeker']",,ScmC-seqLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScmC-seqLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScmC-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScmC-seqLevel2
Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScmC-seqLevel2
Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",ScmC-seqLevel2
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScATAC-seqLevel4
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel4
Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel4
Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScATAC-seqLevel4
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel4
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel4
scATACseq Workflow Parameters Description,scATACseq Workflow Parameters Description,ScATACseqWorkflowParametersDescription,Parameters used to run the scATAC-seq workflow.,True,,,,ScATAC-seqLevel4
scATACseq Workflow Type,scATACseq Workflow Type,ScATACseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,,,ScATAC-seqLevel4
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScATAC-seqLevel4
Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1
Fragment Standard Deviation Length,Fragment Standard Deviation Length,FragmentStandardDeviationLength,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,ScDNA-seqLevel1
Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,ScDNA-seqLevel1
Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,ScDNA-seqLevel1
Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,ScDNA-seqLevel1
Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,ScDNA-seqLevel1
Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,ScDNA-seqLevel1
Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1
Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,ScDNA-seqLevel1
Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,ScDNA-seqLevel1
Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Long Read', 'Single Read', 'Paired End', 'Mid-length']",,ScDNA-seqLevel1
Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScDNA-seqLevel1
Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1
Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1
Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,ScDNA-seqLevel1
Filename,Filename,Filename,Name of a file,True,,,,ScDNA-seqLevel1
Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,ScDNA-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,ScDNA-seqLevel1
Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,ScDNA-seqLevel1
QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,ScDNA-seqLevel1
Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['Random', 'miRNA Size Fractionation', 'Poly-T Enrichment', 'Affinity Enrichment', 'Other', 'rRNA Depletion', 'Hybrid Selection', 'PCR']",,ScDNA-seqLevel1
Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,ScDNA-seqLevel1
Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,ScDNA-seqLevel1
Library Strand,Library Strand,LibraryStrand,Library stranded-ness.,False,,"['Unstranded', 'Not Applicable', 'First Stranded', 'Second Stranded', '']",,ScDNA-seqLevel1
Kmer Content,Kmer Content,KmerContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1
Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1
To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['no', 'Yes - Trim Adapter Sequence', '']",,ScDNA-seqLevel1
Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,ScDNA-seqLevel1
Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,ScDNA-seqLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,ScDNA-seqLevel1
QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,ScDNA-seqLevel1
QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,ScDNA-seqLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScDNA-seqLevel1
Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,ScDNA-seqLevel1
Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,ScDNA-seqLevel1
Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,ScDNA-seqLevel1
Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,ScDNA-seqLevel1
Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScDNA-seqLevel1
Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,ScDNA-seqLevel1
Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1
Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScDNA-seqLevel1
Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1
Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1
Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScDNA-seqLevel2
Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScDNA-seqLevel2
Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScDNA-seqLevel2
Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScDNA-seqLevel2
Proportion Coverage 10x,Proportion Coverage 10x,ProportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",False,,,,ScDNA-seqLevel2
Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,ScDNA-seqLevel2
Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,ScDNA-seqLevel2
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScDNA-seqLevel2
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScDNA-seqLevel2
Proportion Mitochondrial Reads,Proportion Mitochondrial Reads,ProportionMitochondrialReads,Proportion of reads mapping to mitochondria.,False,,,,ScDNA-seqLevel2
Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScDNA-seqLevel2
Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScDNA-seqLevel2
Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScDNA-seqLevel2
Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,ScDNA-seqLevel2
Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScDNA-seqLevel2
Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,ScDNA-seqLevel2
Filename,Filename,Filename,Name of a file,True,,,,ScDNA-seqLevel2
Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScDNA-seqLevel2
Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScDNA-seqLevel2
Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,ScDNA-seqLevel2
Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScDNA-seqLevel2
Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScDNA-seqLevel2
Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BWA-meth', 'Bismark', 'BSMAP', 'STAR 2-Pass Transcriptome', 'STAR 2-Pass Chimeric', 'BWA-mem', 'MethylCoder', 'B-SOLANA', 'Pash', 'BWA', 'SOCS-B', 'BWA with Mark Duplicates and BQSR', 'BS-Seeker2', 'None', 'LAST', 'BatMeth', 'ERNE-BS5', 'BRAT-BW', 'Segemehl', 'STAR 2-Pass Genome', 'GSNAP', 'BWA with BQSR', 'RMAP', 'STAR 2-Pass', 'Bowtie', 'BSmooth', 'Other Alignment Workflow', 'Bisulfighter', 'BWA-aln', 'BS-Seeker']",,ScDNA-seqLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScDNA-seqLevel2
Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,ScDNA-seqLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScDNA-seqLevel2
MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,ScDNA-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScDNA-seqLevel2
Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScDNA-seqLevel2
Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",ScDNA-seqLevel2
Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['Enzymatic Digestion', 'Not Applicable', 'Dounce', 'gentleMACS']",,MultiplexedCITE-seqLevel1
Barcode Folder Synapse ID,Barcode Folder Synapse ID,BarcodeFolderSynapseID,Synapse ID of the folder containing the barcode lists,True,,,,MultiplexedCITE-seqLevel1
Total Number of Input Cells,Total Number of Input Cells,TotalNumberofInputCells,Number of cells loaded/placed on plates,True,,,,MultiplexedCITE-seqLevel1
Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],True,,,,MultiplexedCITE-seqLevel1
Feature Barcode Library Type,Feature Barcode Library Type,FeatureBarcodeLibraryType,The library construction methods for the feature barcode library,True,,"['10x BCR', '10x TCR', '10x ADT – citeseq/hashing']",,MultiplexedCITE-seqLevel1
Barcode Folder File List,Barcode Folder File List,BarcodeFolderFileList,A comma separated list of filenames in the gzipped folder detailing what barcodes are specific to demultiplexing samples versus providing surface protein data,True,,,,MultiplexedCITE-seqLevel1
Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,MultiplexedCITE-seqLevel1
Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,MultiplexedCITE-seqLevel1
Input Cells and Nuclei,Input Cells and Nuclei,InputCellsandNuclei,"Number of cells and number of nuclei input; entry format: number, number",True,,,,MultiplexedCITE-seqLevel1
Nucleic Acid Capture Days from Index,Nucleic Acid Capture Days from Index,NucleicAcidCaptureDaysfromIndex,Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable',True,,,,MultiplexedCITE-seqLevel1
Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel1
Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,MultiplexedCITE-seqLevel1
Single Cell Dissociation Days from Index,Single Cell Dissociation Days from Index,SingleCellDissociationDaysfromIndex,Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable',True,,,,MultiplexedCITE-seqLevel1
Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,,,MultiplexedCITE-seqLevel1
Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data  is available for each cell in CEL-seq2 assays,False,,"['yes', 'no', '']",,MultiplexedCITE-seqLevel1
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,MultiplexedCITE-seqLevel1
Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",True,,,,MultiplexedCITE-seqLevel1
Cryopreserved Cells in Sample,Cryopreserved Cells in Sample,CryopreservedCellsinSample,Indicate if library preparation was based on revived frozen cells.,True,,"['yes', 'no']",,MultiplexedCITE-seqLevel1
Filename,Filename,Filename,Name of a file,True,,,,MultiplexedCITE-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,MultiplexedCITE-seqLevel1
Single Cell Barcode Method Applied,Single Cell Barcode Method Applied,SingleCellBarcodeMethodApplied,The method by which cells are multiplex or labeled with cell surface markers or probes,True,,"['Biolegend Total seq B Human Universal cocktail V1.0', 'Biolegend Total seq C Human Universal cocktail V1.0', 'Biolegend Total seq B Custom', 'Biolegend Total seq C Custom', 'Cell', 'Other', 'Hashtag- multiplex', 'Nuclear Hashtag- multiplex', 'Universal cocktail V1.0', 'Cite-seq custom panel', 'Biolegend Total seq A Custom', 'Biolegend Total seq A Human']",,MultiplexedCITE-seqLevel1
End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['Full Length Transcript', '5 Prime', '3 Prime']",,MultiplexedCITE-seqLevel1
Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['I1', 'R2', 'R1', 'Other', 'R1&R2']",,MultiplexedCITE-seqLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,MultiplexedCITE-seqLevel1
Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Plates', 'Nuclei Isolation', '10x', 'Droplets', 'Microfluidics Chip', 'FACS']",,MultiplexedCITE-seqLevel1
Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,True,,,,MultiplexedCITE-seqLevel1
Read1,Read1,Read1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,MultiplexedCITE-seqLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MultiplexedCITE-seqLevel1
Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV3.1', '10x FLEX', ""10x GEM 5'"", 'inDropsV3', 'Nextera XT', 'Smart-SeqV4', '10xV3', 'CEL-seq2', '10xV2', '10xV1.1', ""10x GEM 3'"", 'sci-ATAC-seq', 'Smart-seq2', 'inDropsV2', '10x Multiome', '10xV1.0', 'TruDrop', 'Drop-seq']",,MultiplexedCITE-seqLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel1
Read2,Read2,Read2,Read 2 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,MultiplexedCITE-seqLevel1
Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['Other Spike In', 'No Spike In', 'ERCC', 'PhiX']",,MultiplexedCITE-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,MultiplexedCITE-seqLevel1
Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Feature barcoding', 'Poly-dT', 'Random', 'Oligo-dT']",,MultiplexedCITE-seqLevel1
Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1
UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1
Cell Barcode Offset,Cell Barcode Offset,CellBarcodeOffset,Offset in sequence for cell barcode read (in bp): number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1
Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1
UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Read2 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1
Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1
cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Read2 is ""cDNA""']",MultiplexedCITE-seqLevel1
cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Read2 is ""cDNA""']",MultiplexedCITE-seqLevel1
Whitelist Cell Barcode File Link,Whitelist Cell Barcode File Link,WhitelistCellBarcodeFileLink,Link to file listing all possible cell barcodes. URL,True,,,,MultiplexedCITE-seqLevel2
Cell Barcode Tag,Cell Barcode Tag,CellBarcodeTag,SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z),True,,,,MultiplexedCITE-seqLevel2
Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,MultiplexedCITE-seqLevel2
Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,MultiplexedCITE-seqLevel2
UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,MultiplexedCITE-seqLevel2
scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cufflinks', 'HCA Optimus', 'DEXSeq', 'HTSeq - FPKM', 'STARsolo', 'Other', 'Differentiation trajectory analysis', 'dropEST', 'SEQC', 'CellRanger', 'Cell annotation']",,MultiplexedCITE-seqLevel2
Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,MultiplexedCITE-seqLevel2
Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel2
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MultiplexedCITE-seqLevel2
Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,MultiplexedCITE-seqLevel2
Filename,Filename,Filename,Name of a file,True,,,,MultiplexedCITE-seqLevel2
Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,MultiplexedCITE-seqLevel2
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,MultiplexedCITE-seqLevel2
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,MultiplexedCITE-seqLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MultiplexedCITE-seqLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel2
scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,MultiplexedCITE-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,MultiplexedCITE-seqLevel2
Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,MultiplexedCITE-seqLevel2
Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,False,True,,"['Applied Hard Trimming is ""Yes - Applied Hard Trimming""']",MultiplexedCITE-seqLevel2
Cell Total,Cell Total,CellTotal,Number of sequenced  cells. Applies to raw counts matrix only.,True,,,,MultiplexedCITE-seqLevel3
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,MultiplexedCITE-seqLevel3
scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cufflinks', 'HCA Optimus', 'DEXSeq', 'HTSeq - FPKM', 'STARsolo', 'Other', 'Differentiation trajectory analysis', 'dropEST', 'SEQC', 'CellRanger', 'Cell annotation']",,MultiplexedCITE-seqLevel3
Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Normalized Counts', 'Batch Corrected Counts']",,MultiplexedCITE-seqLevel3
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,MultiplexedCITE-seqLevel3
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MultiplexedCITE-seqLevel3
Filename,Filename,Filename,Name of a file,True,,,,MultiplexedCITE-seqLevel3
Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,MultiplexedCITE-seqLevel3
Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel3
Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification', 'Gene Expression Quantification', 'Other', 'Exon Expression Quantification']",,MultiplexedCITE-seqLevel3
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel3
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MultiplexedCITE-seqLevel3
scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,MultiplexedCITE-seqLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,MultiplexedCITE-seqLevel3
Cell Median Number Genes,Cell Median Number Genes,CellMedianNumberGenes,Median number of genes detected per cell. Number,True,,,,MultiplexedCITE-seqLevel3
Cell Median Number Reads,Cell Median Number Reads,CellMedianNumberReads,Median number of reads per cell. Number,True,,,,MultiplexedCITE-seqLevel3
Linked Matrices,Linked Matrices,LinkedMatrices,All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames,False,,,,MultiplexedCITE-seqLevel3
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,MultiplexedCITE-seqLevel4
scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cufflinks', 'HCA Optimus', 'DEXSeq', 'HTSeq - FPKM', 'STARsolo', 'Other', 'Differentiation trajectory analysis', 'dropEST', 'SEQC', 'CellRanger', 'Cell annotation']",,MultiplexedCITE-seqLevel4
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,MultiplexedCITE-seqLevel4
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MultiplexedCITE-seqLevel4
Filename,Filename,Filename,Name of a file,True,,,,MultiplexedCITE-seqLevel4
Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,MultiplexedCITE-seqLevel4
Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel4
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MultiplexedCITE-seqLevel4
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel4
scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,MultiplexedCITE-seqLevel4
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,MultiplexedCITE-seqLevel4
Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkMethylation-seqLevel2
Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkMethylation-seqLevel2
Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkMethylation-seqLevel2
Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkMethylation-seqLevel2
Duplicate Removal Software,Duplicate Removal Software,DuplicateRemovalSoftware,Software used for remove duplicate reads,True,,"['picard MarkDuplicates', 'Samtools sort']",,BulkMethylation-seqLevel2
Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkMethylation-seqLevel2
Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,BulkMethylation-seqLevel2
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkMethylation-seqLevel2
Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Long Read', 'Single Read', 'Paired End', 'Mid-length']",,BulkMethylation-seqLevel2
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkMethylation-seqLevel2
Bulk Methylation Genomic Reference,Bulk Methylation Genomic Reference,BulkMethylationGenomicReference,The human genome reference used in the alignment of reads,True,,"['T2T CHM13', 'HG38', 'HG19']",,BulkMethylation-seqLevel2
Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkMethylation-seqLevel2
Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkMethylation-seqLevel2
Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkMethylation-seqLevel2
Trimmer,Trimmer,Trimmer,Software used for trimming,True,,"['Btrim', 'FASTX toolkit', 'ERNE-FILTER', 'Trim Galore!', 'Trimmo-matic', 'Cutadapt', 'ConDeTri', 'Adapter removal', 'SolexaQA', 'PRINSEQ', 'Kraken']",,BulkMethylation-seqLevel2
Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,BulkMethylation-seqLevel2
Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,BulkMethylation-seqLevel2
Filename,Filename,Filename,Name of a file,True,,,,BulkMethylation-seqLevel2
Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkMethylation-seqLevel2
Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkMethylation-seqLevel2
Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkMethylation-seqLevel2
Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkMethylation-seqLevel2
Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkMethylation-seqLevel2
Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BWA-meth', 'Bismark', 'BSMAP', 'STAR 2-Pass Transcriptome', 'STAR 2-Pass Chimeric', 'BWA-mem', 'MethylCoder', 'B-SOLANA', 'Pash', 'BWA', 'SOCS-B', 'BWA with Mark Duplicates and BQSR', 'BS-Seeker2', 'None', 'LAST', 'BatMeth', 'ERNE-BS5', 'BRAT-BW', 'Segemehl', 'STAR 2-Pass Genome', 'GSNAP', 'BWA with BQSR', 'RMAP', 'STAR 2-Pass', 'Bowtie', 'BSmooth', 'Other Alignment Workflow', 'Bisulfighter', 'BWA-aln', 'BS-Seeker']",,BulkMethylation-seqLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkMethylation-seqLevel2
Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,BulkMethylation-seqLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkMethylation-seqLevel2
Proportion of Minimum CpG Coverage 10X,Proportion of Minimum CpG Coverage 10X,ProportionofMinimumCpGCoverage10X,"Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.",False,,,,BulkMethylation-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkMethylation-seqLevel2
Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkMethylation-seqLevel2
Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",BulkMethylation-seqLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkMethylation-seqLevel3
Lambda methylation ratio,Lambda methylation ratio,Lambdamethylationratio,"Methylation ratio of mostly unmethylated lambda control, as a percentage",True,,,,BulkMethylation-seqLevel3
Filename,Filename,Filename,Name of a file,True,,,,BulkMethylation-seqLevel3
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkMethylation-seqLevel3
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkMethylation-seqLevel3
DMC data file format,DMC data file format,DMCdatafileformat,Format of the data files,True,,"['BED', 'bedGraph']",,BulkMethylation-seqLevel3
DMR Calling Workflow URL,DMR Calling Workflow URL,DMRCallingWorkflowURL,Generic name for the workflow used to analyze a data set,True,,,,BulkMethylation-seqLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkMethylation-seqLevel3
DMC Calling Tool,DMC Calling Tool,DMCCallingTool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),True,,"['MOABS', 'DSS-single', 'BSmooth', 'BiSeq', 'MethylSig', 'DSS', 'metilene', 'MACAU', 'MethylKit', 'MethylDackel']",,BulkMethylation-seqLevel3
DMC Calling Workflow URL,DMC Calling Workflow URL,DMCCallingWorkflowURL,Generic name for the workflow used to analyze a data set,True,,,,BulkMethylation-seqLevel3
DMR data file Format,DMR data file Format,DMRdatafileFormat,Format of the data files.,True,,"['BED', 'bedGraph']",,BulkMethylation-seqLevel3
DMR Calling Tool,DMR Calling Tool,DMRCallingTool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),True,,"['MOABS', 'DSS-single', 'BSmooth', 'BiSeq', 'MethylSig', 'DSS', 'metilene', 'MACAU', 'MethylKit']",,BulkMethylation-seqLevel3
pUC19 methylation ratio,pUC19 methylation ratio,PUC19methylationratio,"Methylation ratio of mostly methylated pUC19 control, as a percentage",True,,,,BulkMethylation-seqLevel3
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,ImagingLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel1
Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel1
Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel1
Pre-processing Completed,Pre-processing Completed,Pre-processingCompleted,Pre-processing steps completed to convert level 1 raw data to a single level 2 image,True,,"['None', 'Tile Stitching', 'Other', 'TMA de-arraying', 'Illumination correction', 'Channel/Cycle Registration']",,ImagingLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel1
Pre-processing Required,Pre-processing Required,Pre-processingRequired,Pre-processing steps required to convert level 1 raw data to a single level 2 image,True,,"['None', 'Tile Stitching', 'Other', 'TMA de-arraying', 'Illumination correction', 'Channel/Cycle Registration']",,ImagingLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ImagingLevel1
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel1
Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['MxIF', 'mIHC', 'CODEX', 'SABER', 'IHC', 'H&E', 'MIBI', 'RareCyte Orion', 'IMC', 'GeoMX-DSP', 't-CyCIF', 'Not Applicable', 'ExSeq', 'CyCIF', 'MERFISH']",,ImagingLevel1
Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel1
FOVY,FOVY,FOVY,Field  of view Y dimension. Floating point value,False,,,,ImagingLevel2
FOVX,FOVX,FOVX,Field of view X dimension. Floating point,False,,,,ImagingLevel2
LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel2
WorkingDistance,WorkingDistance,WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",False,,,,ImagingLevel2
Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['yes', 'no']",,ImagingLevel2
PhysicalSizeZUnit,PhysicalSizeZUnit,PhysicalSizeZUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['mm', 'Å', 'nm', 'cm', 'µm']",,ImagingLevel2
SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,ImagingLevel2
Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['false', 'true']",,ImagingLevel2
SizeT,SizeT,SizeT,Number of time points. Integer >= 1,True,,,,ImagingLevel2
MERFISH Positions File,MERFISH Positions File,MERFISHPositionsFile,The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.,False,,,,ImagingLevel2
Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,ImagingLevel2
SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2
NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,ImagingLevel2
PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,ImagingLevel2
FOVXUnit,FOVXUnit,FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ImagingLevel2
Immersion,Immersion,Immersion,Immersion medium,False,,"['Air', 'Other', 'Water', 'Oil', '']",,ImagingLevel2
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,ImagingLevel2
Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['MxIF', 'mIHC', 'CODEX', 'SABER', 'IHC', 'H&E', 'MIBI', 'RareCyte Orion', 'IMC', 'GeoMX-DSP', 't-CyCIF', 'Not Applicable', 'ExSeq', 'CyCIF', 'MERFISH']",,ImagingLevel2
Objective,Objective,Objective,Objective,False,,,,ImagingLevel2
Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['yes', 'no']",,ImagingLevel2
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel2
FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ImagingLevel2
DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['XYTZC', 'XYZTC', 'ZYX', 'XYCTZ', 'XYCZT', 'XYZCT']",,ImagingLevel2
Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel2
SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2
SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2
PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['bit', 'double', 'uint8', 'float', 'int8', 'uint32', 'uint16', 'int32', 'int16']",,ImagingLevel2
Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,ImagingLevel2
MERFISH Codebook File,MERFISH Codebook File,MERFISHCodebookFile,The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.,False,,,,ImagingLevel2
Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['yes', 'no']",,ImagingLevel2
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel2
PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,ImagingLevel2
PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['mm', 'Å', 'nm', 'cm', 'µm']",,ImagingLevel2
FOV number,FOV number,FOVnumber,Index of FOV (as it pertains to its sequence order). Integer >= 1,False,,,,ImagingLevel2
Channel Metadata Filename,Channel Metadata Filename,ChannelMetadataFilename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,True,,,,ImagingLevel2
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,ImagingLevel2
Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,ImagingLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel2
PhysicalSizeZ,PhysicalSizeZ,PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,True,,,,ImagingLevel2
Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel2
WorkingDistanceUnit,WorkingDistanceUnit,WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ImagingLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ImagingLevel2
Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'yes']",,ImagingLevel2
PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,ImagingLevel2
PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ImagingLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel3Segmentation
Imaging Segmentation Data Type,Imaging Segmentation Data Type,ImagingSegmentationDataType,Specifies how the segmentation is stored,True,,"['Polygon', 'Mask', 'Probability Map', 'Outline', 'Point']",,ImagingLevel3Segmentation
Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel3Segmentation
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel3Segmentation
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel3Segmentation
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ImagingLevel3Segmentation
Parameter file,Parameter file,Parameterfile,Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis,False,,,,ImagingLevel3Segmentation
Number of Objects,Number of Objects,NumberofObjects,The number of objects (eg cells) described,True,,,,ImagingLevel3Segmentation
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel3Segmentation
Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,,,ImagingLevel3Segmentation
Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel3Segmentation
Imaging Object Class Description,Imaging Object Class Description,ImagingObjectClassDescription,Free text description of object class [string],False,True,,"['Imaging Object Class is ""Imaging Object Class Other""']",ImagingLevel3Segmentation
FOVY,FOVY,FOVY,Field  of view Y dimension. Floating point value,False,,,,ImagingLevel3Image
FOVX,FOVX,FOVX,Field of view X dimension. Floating point,False,,,,ImagingLevel3Image
LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel3Image
WorkingDistance,WorkingDistance,WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",False,,,,ImagingLevel3Image
Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['yes', 'no']",,ImagingLevel3Image
HTAN Parent Channel Metadata ID,HTAN Parent Channel Metadata ID,HTANParentChannelMetadataID,HTAN ID for a level 3 channels table.,True,,,,ImagingLevel3Image
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel3Image
NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,ImagingLevel3Image
Immersion,Immersion,Immersion,Immersion medium,False,,"['Air', 'Other', 'Water', 'Oil', '']",,ImagingLevel3Image
Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['yes', 'no']",,ImagingLevel3Image
Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['MxIF', 'mIHC', 'CODEX', 'SABER', 'IHC', 'H&E', 'MIBI', 'RareCyte Orion', 'IMC', 'GeoMX-DSP', 't-CyCIF', 'Not Applicable', 'ExSeq', 'CyCIF', 'MERFISH']",,ImagingLevel3Image
Objective,Objective,Objective,Objective,False,,,,ImagingLevel3Image
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel3Image
Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel3Image
Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,ImagingLevel3Image
Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['yes', 'no']",,ImagingLevel3Image
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel3Image
FOV number,FOV number,FOVnumber,Index of FOV (as it pertains to its sequence order). Integer >= 1,False,,,,ImagingLevel3Image
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,ImagingLevel3Image
Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,ImagingLevel3Image
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel3Image
Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel3Image
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel3Image
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ImagingLevel3Image
Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'yes']",,ImagingLevel3Image
FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ImagingLevel3Image
FOVXUnit,FOVXUnit,FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ImagingLevel3Image
WorkingDistanceUnit,WorkingDistanceUnit,WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ImagingLevel3Image
Cycle Number,Cycle Number,CycleNumber,The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles),False,,,,ImagingLevel3Channels
Sub Cycle Number,Sub Cycle Number,SubCycleNumber,Sub cycle number,False,,,,ImagingLevel3Channels
Antibody Name,Antibody Name,AntibodyName,"Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))",True,,,,ImagingLevel3Channels
HTAN Channel Metadata ID,HTAN Channel Metadata ID,HTANChannelMetadataID,HTAN ID for this channel metadata table (same for all rows),True,,,,ImagingLevel3Channels
Emission Wavelength,Emission Wavelength,EmissionWavelength,Center/peak of the emission spectrum (nm),False,,,,ImagingLevel3Channels
Emission Bandwidth,Emission Bandwidth,EmissionBandwidth,Nominal width of emission spectrum (nm),False,,,,ImagingLevel3Channels
Metal Isotope Mass,Metal Isotope Mass,MetalIsotopeMass,Element mass number,False,,,,ImagingLevel3Channels
Oligo Barcode Upper Strand,Oligo Barcode Upper Strand,OligoBarcodeUpperStrand,Oligo Barcode - Upper Strand,False,,,,ImagingLevel3Channels
Concentration,Concentration,Concentration,Concentration (eg 10ug/mL),False,,,,ImagingLevel3Channels
Target Name,Target Name,TargetName,Short descriptive name (abbreviation) for this target (antigen),True,,,,ImagingLevel3Channels
Excitation Bandwidth,Excitation Bandwidth,ExcitationBandwidth,Nominal width of excitation spectrum (nm),False,,,,ImagingLevel3Channels
Excitation Wavelength,Excitation Wavelength,ExcitationWavelength,Center/peak of the excitation spectrum (nm),False,,,,ImagingLevel3Channels
Channel Passed QC,Channel Passed QC,ChannelPassedQC,Identify stains that did not pass QC but are included in the dataset.,True,,"['No - Channel Failed QC', 'yes']",,ImagingLevel3Channels
Lot,Lot,Lot,Lot number from vendor,False,,,,ImagingLevel3Channels
Channel Name,Channel Name,ChannelName,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin'),True,,,,ImagingLevel3Channels
Antibody Role,Antibody Role,AntibodyRole,"""Is this antibody acting as a primary or secondary antibody""",True,,"['Neither-Dye/Stain', 'Secondary', 'Primary']",,ImagingLevel3Channels
Vendor,Vendor,Vendor,Vendor,False,,,,ImagingLevel3Channels
Metal Isotope Element,Metal Isotope Element,MetalIsotopeElement,Element abbreviation. eg “La” or “Nd”,False,,"['Hf', 'At', 'Si', 'Co', 'Rb', 'Er', 'Mg', 'Ru', 'Ar', 'Kr', 'Yb', 'V', 'Cl', 'Sg', 'Ac', 'Pr', 'Cu', 'He', 'Og', 'Mt', 'Rh', 'Xe', 'Mn', 'Y', 'Ne', 'Ni', 'N', 'Sn', 'Po', 'B', 'Tc', 'W', 'Tm', 'Nd', 'Lv', 'Na', 'Gd', 'Pd', 'Ge', 'Sb', 'Ba', 'Hg', 'Rf', 'Fm', 'H', 'Li', 'Cr', 'Eu', 'F', 'Ts', 'Ag', 'Sc', 'Zr', 'Ca', 'Am', 'Es', 'Tl', 'Pu', 'Fl', 'Pt', 'Ta', 'K', 'Cd', 'Dy', 'Sm', 'Lr', 'S', 'Be', 'Pb', 'Ds', 'P', 'Sr', 'Ti', 'Hs', 'Rn', 'Zn', 'Tb', 'I', 'Cf', 'U', 'Mc', 'Cs', 'Ir', 'Te', 'Np', 'Th', 'Fr', 'no', 'Bh', 'Cn', 'Ho', 'Db', 'Br', 'Fe', 'Rg', 'Bi', 'C', 'Md', 'As', 'Ga', 'Al', 'La', 'O', 'Ra', 'Pa', 'Nh', 'Os', 'Bk', 'Pm', 'Ce', 'Re', 'Se', 'Lu', 'Nb', 'In', 'Mo', 'Au', '']",,ImagingLevel3Channels
Oligo Barcode Lower Strand,Oligo Barcode Lower Strand,OligoBarcodeLowerStrand,Oligo Barcode - Lower Strand,False,,,,ImagingLevel3Channels
Fluorophore,Fluorophore,Fluorophore,Fluorescent dye label (eg Alexa Fluor 488),False,,,,ImagingLevel3Channels
Dilution,Dilution,Dilution,Dilution (eg 1:1000),False,,,,ImagingLevel3Channels
Catalog Number,Catalog Number,CatalogNumber,Catalog Number,False,,,,ImagingLevel3Channels
Channel ID,Channel ID,ChannelID,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1'),True,,,,ImagingLevel3Channels
RRID identifier,RRID identifier,RRIDidentifier,Research Resource Identifier (eg “RRID: AB_394606”),True,,,,ImagingLevel3Channels
Clone,Clone,Clone,Clone,False,,,,ImagingLevel3Channels
Channel QC Failure Type,Channel QC Failure Type,ChannelQCFailureType,Reason the channel failed QC,False,True,"['Auto-fluoresence', 'Other/multiple channel QC faliure types', 'Imaging artefact', 'Off-target staining', 'Staining artefacet', '']","['Channel Passed QC is ""No - Channel Failed QC""']",ImagingLevel3Channels
Channel QC Failure Comment,Channel QC Failure Comment,ChannelQCFailureComment,Custom comment on channel QC faliure,False,True,,"['Channel is ""Other/multiple channel QC faliure types""']",ImagingLevel3Channels
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel4
Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel4
Imaging Summary Statistic,Imaging Summary Statistic,ImagingSummaryStatistic,Function used to summarize object/feature intensity,False,,"['Mean', 'Not Specified', 'Median', '']",,ImagingLevel4
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel4
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel4
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ImagingLevel4
Parameter file,Parameter file,Parameterfile,Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis,False,,,,ImagingLevel4
Number of Objects,Number of Objects,NumberofObjects,The number of objects (eg cells) described,True,,,,ImagingLevel4
Number of Features,Number of Features,NumberofFeatures,The number of features (eg channels) described,True,,,,ImagingLevel4
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel4
Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,,,ImagingLevel4
HTAN Parent Channel Metadata ID,HTAN Parent Channel Metadata ID,HTANParentChannelMetadataID,HTAN ID for a level 3 channels table.,True,,,,ImagingLevel4
Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel4
Imaging Object Class Description,Imaging Object Class Description,ImagingObjectClassDescription,Free text description of object class [string],False,True,,"['Imaging Object Class is ""Imaging Object Class Other""']",ImagingLevel4
Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Spatial Read1,Spatial Read1,SpatialRead1,Read 1 content description,True,,"['Spatial Barcode and UMI', 'cDNA']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Permeabilization Time,Permeabilization Time,PermeabilizationTime,Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['C', 'D1', 'C1', 'B', 'A1', 'B1', 'A', 'D', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
RIN,RIN,RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['Full Length Transcript', '5 Prime', '3 Prime']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Spatial Library Construction Method,Spatial Library Construction Method,SpatialLibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV3.1', 'inDropsV3', 'Nextera XT', 'Smart-SeqV4', '10xV3', '10xV2', '10xV1.1', 'Smart-seq2', 'inDropsV2', '10xV1.0', 'TruDrop', 'Drop-seq']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['I1', 'R2', 'R1', 'Other', 'R1&R2']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Spatial Read2,Spatial Read2,SpatialRead2,Read 2 content description,True,,"['Spatial Barcode and UMI', 'cDNA']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Image Re-orientation,Image Re-orientation,ImageRe-orientation,"To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.",False,,"['TRUE', 'FALSE', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Feature barcoding', 'Poly-dT', 'Random', 'Oligo-dT']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Slide Version,Slide Version,SlideVersion,Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.,False,,"['V3', 'V4', 'V2', 'V1', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Spatial Barcode and UMI,Spatial Barcode and UMI,SpatialBarcodeandUMI,Spot and transcript identifiers,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Spatial Barcode Offset,Spatial Barcode Offset,SpatialBarcodeOffset,Offset in sequence for spot barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1
UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1
UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Spatial Barcode Length,Spatial Barcode Length,SpatialBarcodeLength,Length of spot barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1
cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1
cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,,"['Reverse Transcription Primer is ""Feature barcoding""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
Spatial Barcode Tag,Spatial Barcode Tag,SpatialBarcodeTag,SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
Whitelist Spatial Barcode File Link,Whitelist Spatial Barcode File Link,WhitelistSpatialBarcodeFileLink,Link to file listing all possible spatial barcodes. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['C', 'D1', 'C1', 'B', 'A1', 'B1', 'A', 'D', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,False,True,,"['Applied Hard Trimming is ""Yes - Applied Hard Trimming""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel2
Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,,"['unfiltered mex', 'filtered mex', 'detected jpg', 'fiducial image jpg', 'reference jpg', 'json scale factors', 'reference png', 'fiducial image png', 'probe dataset csv', 'tissue_positions', 'features', 'detected image png', 'barcodes', 'high res image', 'low res image', 'qc result html']",,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['C', 'D1', 'C1', 'B', 'A1', 'B1', 'A', 'D', '']",,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,,"['unfiltered mex', 'filtered mex', 'detected jpg', 'fiducial image jpg', 'reference jpg', 'json scale factors', 'reference png', 'fiducial image png', 'probe dataset csv', 'tissue_positions', 'features', 'detected image png', 'barcodes', 'high res image', 'low res image', 'qc result html']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Median Number Genes per Spatial Spot,Median Number Genes per Spatial Spot,MedianNumberGenesperSpatialSpot,The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Spots under tissue,Spots under tissue,Spotsundertissue,The number of barcodes associated with a spot under tissue.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['C', 'D1', 'C1', 'B', 'A1', 'B1', 'A', 'D', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Mean Reads per Spatial Spot,Mean Reads per Spatial Spot,MeanReadsperSpatialSpot,"The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Proportion Reads Mapped to Transcriptome,Proportion Reads Mapped to Transcriptome,ProportionReadsMappedtoTranscriptome,Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Median UMI Counts per Spot,Median UMI Counts per Spot,MedianUMICountsperSpot,The median number of UMI counts per tissue covered spot.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Sequencing Saturation,Sequencing Saturation,SequencingSaturation,"The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
Visium Workflow Type,Visium Workflow Type,VisiumWorkflowType,Generic name for the workflow used to analyze the visium data set.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
Visium Workflow Parameters Description,Visium Workflow Parameters Description,VisiumWorkflowParametersDescription,Parameters used to run the workflow..,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
Synapse ID of GeoMx DSP PKC File,Synapse ID of GeoMx DSP PKC File,SynapseIDofGeoMxDSPPKCFile,The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
GeoMx DSP Library Preparation Kit Version,GeoMx DSP Library Preparation Kit Version,GeoMxDSPLibraryPreparationKitVersion,Version of Library Preparation Kit. String,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
Synapse ID of GeoMx Lab Worksheet File,Synapse ID of GeoMx Lab Worksheet File,SynapseIDofGeoMxLabWorksheetFile,Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
Filename,Filename,Filename,Name of a file,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
GeoMx DSP NGS Library Selection Method,GeoMx DSP NGS Library Selection Method,GeoMxDSPNGSLibrarySelectionMethod,How RNA molecules are isolated.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
GeoMx DSP Library Preparation Kit Vendor,GeoMx DSP Library Preparation Kit Vendor,GeoMxDSPLibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
GeoMx DSP NGS Library Preparation Kit Name,GeoMx DSP NGS Library Preparation Kit Name,GeoMxDSPNGSLibraryPreparationKitName,Name of Library Preparation Kit. String,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
GeoMx DSP NGS Sequencing Platform,GeoMx DSP NGS Sequencing Platform,GeoMxDSPNGSSequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
ROI Y Coordinate,ROI Y Coordinate,ROIYCoordinate,Y location within the image,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
ROI X Coordinate,ROI X Coordinate,ROIXCoordinate,X location within the image,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Nuclei count,Nuclei count,Nucleicount,Number of nuclei detected in the segment (if applicable),True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Scan Offset X,Scan Offset X,ScanOffsetX,Offset X of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Scan name,Scan name,Scanname,GeoMx Scan name (as appears in Segment Summary),True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Raw reads,Raw reads,Rawreads,Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Tags,Tags,Tags,Unique descriptor of a variable group (ie. MAPK+),True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Scan Width,Scan Width,ScanWidth,Width of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Scan Offset Y,Scan Offset Y,ScanOffsetY,Offset Y of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Segment name,Segment name,Segmentname,Name given to segment at time of generation,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Slide name,Slide name,Slidename,"Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).",False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Scan Height,Scan Height,ScanHeight,Height of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Aligned reads,Aligned reads,Alignedreads,Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Deduplicated reads,Deduplicated reads,Deduplicatedreads,Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Biological probe median,Biological probe median,Biologicalprobemedian,Is the median count from all probes except the negative control probes. A measure of signal to background for each segment,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Stitched reads,Stitched reads,Stitchedreads,"Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads",False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
In Situ Negative median,In Situ Negative median,InSituNegativemedian,Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Sequencing Saturation,Sequencing Saturation,SequencingSaturation,"The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).",True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
QC status,QC status,QCstatus,ROI quality control flag as reported by the application,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
ROI Y Coordinate,ROI Y Coordinate,ROIYCoordinate,Y location within the image,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Binding Density,Binding Density,BindingDensity,The binding density as reported by the application,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
ROI X Coordinate,ROI X Coordinate,ROIXCoordinate,X location within the image,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Scan Height,Scan Height,ScanHeight,Height of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Positive norm factor,Positive norm factor,Positivenormfactor,The Positive Control Normalization factor calculated using pos-hyb controls,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Scan name,Scan name,Scanname,GeoMx Scan name (as appears in Segment Summary),True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Tissue Stain,Tissue Stain,TissueStain,e.g. CD45 or PanCK (if masking was performed),False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Tags,Tags,Tags,Unique descriptor of a variable group (ie. MAPK+),True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Scan Width,Scan Width,ScanWidth,Width of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Scan Offset Y,Scan Offset Y,ScanOffsetY,Offset Y of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Nuclei count,Nuclei count,Nucleicount,Number of nuclei detected in the segment (if applicable),True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Segment name,Segment name,Segmentname,Name given to segment at time of generation,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Scan Offset X,Scan Offset X,ScanOffsetX,Offset X of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Normalized Counts', 'Batch Corrected Counts']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
GeoMx DSP Assay Type,GeoMx DSP Assay Type,GeoMxDSPAssayType,The assay type which was used for the GeoMx DSP pipeline.,True,,"['Protein NGS', 'RNA NGS', 'RNA nCounter', 'Protein nCounter']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
Filename,Filename,Filename,Name of a file,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
GeoMx DSP Workflow Type,GeoMx DSP Workflow Type,GeoMxDSPWorkflowType,Generic name for the workflow used to analyze the GeoMx DSP data set.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
GeoMx DSP Workflow Link,GeoMx DSP Workflow Link,GeoMxDSPWorkflowLink,Link to workflow or command. DockStore.org recommended. URL,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
GeoMx DSP Workflow Parameter Description,GeoMx DSP Workflow Parameter Description,GeoMxDSPWorkflowParameterDescription,Parameters used to run the GeoMx DSP workflow.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
GeoMx DSP Genomic Reference,GeoMx DSP Genomic Reference,GeoMxDSPGenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). Only applicable to some applications in GeoMx,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
Synapse ID of GeoMx DSP ROI Segment Annotation File,Synapse ID of GeoMx DSP ROI Segment Annotation File,SynapseIDofGeoMxDSPROISegmentAnnotationFile,Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
GeoMx DSP Unique Probe Count,GeoMx DSP Unique Probe Count,GeoMxDSPUniqueProbeCount,Total number of unique probes reported.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
GeoMx DSP Unique Target Count,GeoMx DSP Unique Target Count,GeoMxDSPUniqueTargetCount,Total number of unique genes reported.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,HI-C-seqLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,HI-C-seqLevel1
Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,HI-C-seqLevel1
Crosslinking Condtion,Crosslinking Condtion,CrosslinkingCondtion,Detailed condition for DNA crosslinking,True,,,,HI-C-seqLevel1
Nuclei Permeabilization Method,Nuclei Permeabilization Method,NucleiPermeabilizationMethod,Detergent and treatment condition for nuclei permeabilization and crosslinking softening,True,,,,HI-C-seqLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,HI-C-seqLevel1
Filename,Filename,Filename,Name of a file,True,,,,HI-C-seqLevel1
Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,HI-C-seqLevel1
Transposition Reaction,Transposition Reaction,TranspositionReaction,"Name of the transposase, transposon sequences",True,,"['Tn5', 'Diagenode-loaded Apex-Bio', 'Diagenode-unloaded Apex-Bio', 'Tn5-059', 'EZ-Tn5', 'In-House', 'Nextera Tn5']",,HI-C-seqLevel1
DNA Digestion Condition,DNA Digestion Condition,DNADigestionCondition,Enzymes and treatment length/temperature for genome digestion,True,,,,HI-C-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,HI-C-seqLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,HI-C-seqLevel1
Ligation Condition,Ligation Condition,LigationCondition,Name of ligase and condition for proximity ligation,True,,,,HI-C-seqLevel1
Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,HI-C-seqLevel1
Biotin Enrichment,Biotin Enrichment,BiotinEnrichment,Whether biotin is used for enriching ligation product,True,,"['yes', 'no']",,HI-C-seqLevel1
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,HI-C-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,HI-C-seqLevel1
DNA Input Amount,DNA Input Amount,DNAInputAmount,"Amount of DNA for library construction, in nanograms.",True,,,,HI-C-seqLevel1
Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,HI-C-seqLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,HI-C-seqLevel2
Filename,Filename,Filename,Name of a file,True,,,,HI-C-seqLevel2
Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,True,,,,HI-C-seqLevel2
Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,HI-C-seqLevel2
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,HI-C-seqLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,HI-C-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,HI-C-seqLevel2
Resolution,Resolution,Resolution,"Binning size used for generating contact matrix, in basepair.",True,,,,HI-C-seqLevel2
Tool,Tool,Tool,Were any software or computational tools generated for this content,True,,"['yes', 'no']",,HI-C-seqLevel2
Loop Calling,Loop Calling,LoopCalling,Tool used for identifying loop interactions,True,,"['Cooltools', 'Other', 'HiCCUPS']",,HI-C-seqLevel3
Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,HI-C-seqLevel3
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,HI-C-seqLevel3
Filename,Filename,Filename,Name of a file,True,,,,HI-C-seqLevel3
Stripe Window,Stripe Window,StripeWindow,Binning size used for calling significant architectural stripes. Can be an integer or comma-separated list of integers indicating bin size and sliding window size if different.,True,,,,HI-C-seqLevel3
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,HI-C-seqLevel3
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,HI-C-seqLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,HI-C-seqLevel3
Loop Window,Loop Window,LoopWindow,Binning size used for calling significant dot interactions (loops),True,,,,HI-C-seqLevel3
Stripe Calling,Stripe Calling,StripeCalling,"Tool used for identifying architectural stripe-forming, interaction hotspots.",True,,"['Other', 'MACS2']",,HI-C-seqLevel3
Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['yes', 'no']",,SRRSImagingLevel2
SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,SRRSImagingLevel2
Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['false', 'true']",,SRRSImagingLevel2
SizeT,SizeT,SizeT,Number of time points. Integer >= 1,True,,,,SRRSImagingLevel2
Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,SRRSImagingLevel2
SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2
NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,SRRSImagingLevel2
PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,SRRSImagingLevel2
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,SRRSImagingLevel2
Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['yes', 'no']",,SRRSImagingLevel2
Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['MxIF', 'mIHC', 'CODEX', 'SABER', 'IHC', 'H&E', 'MIBI', 'RareCyte Orion', 'IMC', 'GeoMX-DSP', 't-CyCIF', 'Not Applicable', 'ExSeq', 'CyCIF', 'MERFISH']",,SRRSImagingLevel2
Objective,Objective,Objective,Objective,False,,,,SRRSImagingLevel2
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,SRRSImagingLevel2
DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['XYTZC', 'XYZTC', 'ZYX', 'XYCTZ', 'XYCZT', 'XYZCT']",,SRRSImagingLevel2
SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2
Filename,Filename,Filename,Name of a file,True,,,,SRRSImagingLevel2
SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2
PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['bit', 'double', 'uint8', 'float', 'int8', 'uint32', 'uint16', 'int32', 'int16']",,SRRSImagingLevel2
Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,SRRSImagingLevel2
Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['yes', 'no']",,SRRSImagingLevel2
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,SRRSImagingLevel2
PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,SRRSImagingLevel2
PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['mm', 'Å', 'nm', 'cm', 'µm']",,SRRSImagingLevel2
Channel Metadata Filename,Channel Metadata Filename,ChannelMetadataFilename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,True,,,,SRRSImagingLevel2
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,SRRSImagingLevel2
Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,SRRSImagingLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SRRSImagingLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,SRRSImagingLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,SRRSImagingLevel2
Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'yes']",,SRRSImagingLevel2
PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,SRRSImagingLevel2
PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,SRRSImagingLevel2
Comment,Comment,Comment,Free text field (generally for QC comment),False,True,,"['Passed QC is ""No - Channels QC""']",SRRSImagingLevel2
Total Number of Cells,Total Number of Cells,TotalNumberofCells,The total number of cells analyzed on the flow cell,True,,,,10XGenomicsXeniumISSExperiment
Xenium IF image HTAN File ID,Xenium IF image HTAN File ID,XeniumIFimageHTANFileID,The HTAN Data File ID of a Imaging Level 2 file,False,,,,10XGenomicsXeniumISSExperiment
Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,10XGenomicsXeniumISSExperiment
Panel Name,Panel Name,PanelName,"The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))",True,,,,10XGenomicsXeniumISSExperiment
Total Number of Targets,Total Number of Targets,TotalNumberofTargets,Refers to the target of an assay. Can be genes/transcripts or probes,True,,,,10XGenomicsXeniumISSExperiment
Experiment IF Channels,Experiment IF Channels,ExperimentIFChannels,"A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)",True,,,,10XGenomicsXeniumISSExperiment
ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,True,,,,10XGenomicsXeniumISSExperiment
Xenium HE image HTAN File ID,Xenium HE image HTAN File ID,XeniumHEimageHTANFileID,The HTAN Data File ID of a Imaging Level 2 file,False,,,,10XGenomicsXeniumISSExperiment
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,10XGenomicsXeniumISSExperiment
Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,10XGenomicsXeniumISSExperiment
Filename,Filename,Filename,Name of a file,True,,,,10XGenomicsXeniumISSExperiment
Decoded Transcripts,Decoded Transcripts,DecodedTranscripts,"In Xenium, this is the number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area to get a transcript density (units are reported in 100um^2).",True,,,,10XGenomicsXeniumISSExperiment
Transcripts per Cell,Transcripts per Cell,TranscriptsperCell,Mean or Median transcript count per cell analyzed on the flow cell or slide,True,,,,10XGenomicsXeniumISSExperiment
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,10XGenomicsXeniumISSExperiment
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,10XGenomicsXeniumISSExperiment
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10XGenomicsXeniumISSExperiment
Xenium Bundle Contents,Xenium Bundle Contents,XeniumBundleContents,A comma separated list of filenames within the Xenium bundle zip file,True,,,,10XGenomicsXeniumISSExperiment
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10XGenomicsXeniumISSExperiment
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,10XGenomicsXeniumISSExperiment
Percent of Transcripts within Cells,Percent of Transcripts within Cells,PercentofTranscriptswithinCells,The percentage of transcripts assigned to assayed cells,True,,,,10XGenomicsXeniumISSExperiment
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,RPPALevel3
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,RPPALevel3
Filename,Filename,Filename,Name of a file,True,,,,RPPALevel3
Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,RPPALevel3
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel3
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,RPPALevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,RPPALevel3
Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,RPPALevel3
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,RPPALevel3
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,RPPALevel3
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,RPPALevel4
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,RPPALevel4
Filename,Filename,Filename,Name of a file,True,,,,RPPALevel4
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel4
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,RPPALevel4
Batch Correction Method,Batch Correction Method,BatchCorrectionMethod,Method that was used to batch correct Level 3 data,False,,,,RPPALevel4
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,RPPALevel4
Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,RPPALevel4
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,RPPALevel4
Total Number of Cells,Total Number of Cells,TotalNumberofCells,The total number of cells analyzed on the flow cell,True,,,,NanostringCosMxSMIExperiment
Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,NanostringCosMxSMIExperiment
Number of FOVs,Number of FOVs,NumberofFOVs,The total number of FOVs recorded for the sample on a single flow cell,True,,,,NanostringCosMxSMIExperiment
Panel Name,Panel Name,PanelName,"The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))",True,,,,NanostringCosMxSMIExperiment
Total Number of Targets,Total Number of Targets,TotalNumberofTargets,Refers to the target of an assay. Can be genes/transcripts or probes,True,,,,NanostringCosMxSMIExperiment
Experiment IF Channels,Experiment IF Channels,ExperimentIFChannels,"A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)",True,,,,NanostringCosMxSMIExperiment
Unique Genes,Unique Genes,UniqueGenes,The total unique genes detected above background,False,,,,NanostringCosMxSMIExperiment
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,NanostringCosMxSMIExperiment
Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,NanostringCosMxSMIExperiment
CosMx Bundle Contents,CosMx Bundle Contents,CosMxBundleContents,A comma separated list of filenames within the CosMx bundle zip file,True,,,,NanostringCosMxSMIExperiment
CosMx Assay Type,CosMx Assay Type,CosMxAssayType,The specification for barcodes on each image. Either RNA probe or protein antibody according to the assay,True,,"['RNA', 'protein']",,NanostringCosMxSMIExperiment
Filename,Filename,Filename,Name of a file,True,,,,NanostringCosMxSMIExperiment
Transcripts per Cell,Transcripts per Cell,TranscriptsperCell,Mean or Median transcript count per cell analyzed on the flow cell or slide,True,,,,NanostringCosMxSMIExperiment
Total Negative Probe Counts,Total Negative Probe Counts,TotalNegativeProbeCounts,Mean Total Negative probe counts/cell,True,,,,NanostringCosMxSMIExperiment
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,NanostringCosMxSMIExperiment
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,NanostringCosMxSMIExperiment
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,NanostringCosMxSMIExperiment
Mean Total Transcripts per Area,Mean Total Transcripts per Area,MeanTotalTranscriptsperArea,The mean total transcripts per um3,True,,,,NanostringCosMxSMIExperiment
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,NanostringCosMxSMIExperiment
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,NanostringCosMxSMIExperiment
Percent of Transcripts within Cells,Percent of Transcripts within Cells,PercentofTranscriptswithinCells,The percentage of transcripts assigned to assayed cells,True,,,,NanostringCosMxSMIExperiment
LC Flow Rate,LC Flow Rate,LCFlowRate,LC flow rate in nL/min.,True,,,,MassSpectrometryLevel1
MS-based Targeted,MS-based Targeted,MS-basedTargeted,Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. Example: The MALDI Imaging analyte is lipids.,True,,"['Targeted', 'Untargeted']",,MassSpectrometryLevel1
LC Column Vendor and Model,LC Column Vendor and Model,LCColumnVendorandModel,"The manufacturer of the LC Column unless self-packed, pulled tip capilary is used and the model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter 'Pulled tip capilary'",True,,,,MassSpectrometryLevel1
LC Length Value,LC Length Value,LCLengthValue,LC column length in cm.,True,,,,MassSpectrometryLevel1
Mass Range Low Value,Mass Range Low Value,MassRangeLowValue,The low value of the scanned mass range for MS1 in m/z.,True,,,,MassSpectrometryLevel1
Mass Range High Value,Mass Range High Value,MassRangeHighValue,The high value of the scanned mass range for MS1 in m/z.,True,,,,MassSpectrometryLevel1
MS Scan Mode,MS Scan Mode,MSScanMode,"Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)",True,,"['Other', 'MS', 'MS3', 'MS/MS']",,MassSpectrometryLevel1
MS Instrument Metadata File,MS Instrument Metadata File,MSInstrumentMetadataFile,Additional file containing instrument metadata details. Use either synapse_path or entity_Id,False,,,,MassSpectrometryLevel1
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,MassSpectrometryLevel1
MS Batch ID,MS Batch ID,MSBatchID,Batch ID indicating a set of samples that were run together.,True,,,,MassSpectrometryLevel1
MS-based Assay Type,MS-based Assay Type,MS-basedAssayType,Analytes are the target molecules being measured with the assay.,True,,"['TMT', 'LC-MS/MS', 'MS', 'LC-MS']",,MassSpectrometryLevel1
Filename,Filename,Filename,Name of a file,True,,,,MassSpectrometryLevel1
Data Collection Mode,Data Collection Mode,DataCollectionMode,Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.,True,,"['Other', 'DIA', 'DDA']",,MassSpectrometryLevel1
Polarity,Polarity,Polarity,The polarity of the mass analysis (positive or negative ion modes),True,,"['negative', 'positive']",,MassSpectrometryLevel1
LC ID Value,LC ID Value,LCIDValue,LC column inner diameter in microns.,True,,,,MassSpectrometryLevel1
Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,True,,"['lipid', 'Tissue Section Analyte', 'PBMCs or Plasma or Serum Analyte', 'metabolite', 'RNA Analyte', 'cfDNA Analyte', 'Total RNA Analyte', 'Tissue Block Analyte', 'DNA Analyte', 'cDNA Libraries Analyte', 'PBMCs', 'protein', 'Plasma', 'Serum Analyte']",,MassSpectrometryLevel1
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel1
LC Temp Value,LC Temp Value,LCTempValue,LC temperature in C.,True,,,,MassSpectrometryLevel1
MS Instrument Vendor and Model,MS Instrument Vendor and Model,MSInstrumentVendorandModel,An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.,True,,,,MassSpectrometryLevel1
LC Gradient,LC Gradient,LCGradient,The program dictates the mobile phase solvent composition over the course of the chromatographic run.,True,,,,MassSpectrometryLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,MassSpectrometryLevel1
LC Resin,LC Resin,LCResin,"Details of the resin used for lc, including vendor, particle size, pore size",True,,,,MassSpectrometryLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MassSpectrometryLevel1
MS Labeling,MS Labeling,MSLabeling,"Indicates whether samples were labeled prior to MS analysis (e.g., TMT)",True,,,,MassSpectrometryLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel1
MS Source,MS Source,MSSource,"The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)",True,,"['nESI', 'MALDI', 'MALDI-2', 'SIMS', 'DESI', 'Other']",,MassSpectrometryLevel1
LC Mobile Phase B,LC Mobile Phase B,LCMobilePhaseB,Composition of mobile phase B,True,,,,MassSpectrometryLevel1
LC Instrument Vendor and Model,LC Instrument Vendor and Model,LCInstrumentVendorandModel,The manufacturer of the instrument used for LC.,True,,,,MassSpectrometryLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,MassSpectrometryLevel1
LC Mobile Phase A,LC Mobile Phase A,LCMobilePhaseA,Composition of mobile phase A,True,,,,MassSpectrometryLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,MassSpectrometryLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MassSpectrometryLevel2
Filename,Filename,Filename,Name of a file,True,,,,MassSpectrometryLevel2
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MassSpectrometryLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel2
MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel2
Mass Spectrometry Auxiliary File,Mass Spectrometry Auxiliary File,MassSpectrometryAuxiliaryFile,"Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).",False,,,,MassSpectrometryLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",False,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf', '']",,MassSpectrometryLevel2
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel2
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,MassSpectrometryLevel3
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MassSpectrometryLevel3
Filename,Filename,Filename,Name of a file,True,,,,MassSpectrometryLevel3
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MassSpectrometryLevel3
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel3
MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel3
Mass Spectrometry Auxiliary File,Mass Spectrometry Auxiliary File,MassSpectrometryAuxiliaryFile,"Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).",False,,,,MassSpectrometryLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",False,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf', '']",,MassSpectrometryLevel3
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel3
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,MassSpectrometryLevel4
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MassSpectrometryLevel4
Filename,Filename,Filename,Name of a file,True,,,,MassSpectrometryLevel4
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MassSpectrometryLevel4
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel4
MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel4
Mass Spectrometry Auxiliary File,Mass Spectrometry Auxiliary File,MassSpectrometryAuxiliaryFile,"Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).",False,,,,MassSpectrometryLevel4
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",False,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf', '']",,MassSpectrometryLevel4
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel4
PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,ElectronMicroscopyLevel1
EM signal or contrast mech,EM signal or contrast mech,EMsignalorcontrastmech,How the electron microscopy signal is generated from the sample,True,,"['SE', 'phase', 'BSE', 'bright-field', 'dark-field']",,ElectronMicroscopyLevel1
EM contrast type,EM contrast type,EMcontrasttype,Does the image use standard SEM contrast or TEM contrast,False,,"['SEM', 'TEM', '']",,ElectronMicroscopyLevel1
SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,ElectronMicroscopyLevel1
SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,ElectronMicroscopyLevel1
EM method,EM method,EMmethod,Electron microscopy method used,True,,"['cryo ET', 'ssTEM', 'ET', 'TEM', 'SBF-SEM', 'SEM', 'FIB-SEM', 'AT']",,ElectronMicroscopyLevel1
EM stage tilt,EM stage tilt,EMstagetilt,Physical stage tilt in degrees with respect to the electron beam,False,,,,ElectronMicroscopyLevel1
Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ElectronMicroscopyLevel1
EM spot size,EM spot size,EMspotsize,Beam spot size in micrometers (µm),False,,,,ElectronMicroscopyLevel1
Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel1
SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,ElectronMicroscopyLevel1
EM instrument,EM instrument,EMinstrument,Make and model of the EM instrument used,True,,,,ElectronMicroscopyLevel1
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ElectronMicroscopyLevel1
PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,ElectronMicroscopyLevel1
HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,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,,,,ElectronMicroscopyLevel1
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ElectronMicroscopyLevel1
PhysicalSizeZ,PhysicalSizeZ,PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,True,,,,ElectronMicroscopyLevel1
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel1
EM signal processing,EM signal processing,EMsignalprocessing,SNR improvement strategies used,False,,"['frame averaging', 'line integration', 'frame integration', 'None', '']",,ElectronMicroscopyLevel1
EM dwell or exposure time,EM dwell or exposure time,EMdwellorexposuretime,Duration in microseconds (µs) of electron beam data collection per pixel or frame,False,,,,ElectronMicroscopyLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ElectronMicroscopyLevel1
EM voltage,EM voltage,EMvoltage,Accelerating voltage in kiloelectronvolts (keV),False,,,,ElectronMicroscopyLevel1
SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,ElectronMicroscopyLevel1
EM beam current,EM beam current,EMbeamcurrent,Beam current in nanoamps (nA),False,,,,ElectronMicroscopyLevel1
PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ElectronMicroscopyLevel1
PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ElectronMicroscopyLevel1
PhysicalSizeZUnit,PhysicalSizeZUnit,PhysicalSizeZUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ElectronMicroscopyLevel1
Tile overlap Y,Tile overlap Y,TileoverlapY,Percentage of image overlap to allow tile stitching in x direction,True,,,,ElectronMicroscopyLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ElectronMicroscopyLevel2
Tile overlap X,Tile overlap X,TileoverlapX,Percentage of image overlap to allow tile stitching in x direction,True,,,,ElectronMicroscopyLevel2
Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel2
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ElectronMicroscopyLevel2
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ElectronMicroscopyLevel2
EM contrast type,EM contrast type,EMcontrasttype,Does the image use standard SEM contrast or TEM contrast,False,,"['SEM', 'TEM', '']",,ElectronMicroscopyLevel2
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ElectronMicroscopyLevel3
Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel3
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ElectronMicroscopyLevel3
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ElectronMicroscopyLevel3
Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,,,ElectronMicroscopyLevel3
Imaging Object Class Description,Imaging Object Class Description,ImagingObjectClassDescription,Free text description of object class [string],False,True,,"['Imaging Object Class is ""Imaging Object Class Other""']",ElectronMicroscopyLevel3
Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ElectronMicroscopyLevel4
Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel4
Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ElectronMicroscopyLevel4
HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ElectronMicroscopyLevel4
HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel4
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ElectronMicroscopyLevel4