HTAN.dependencies.csv

Unnamed: 0,Attribute,Label,Description,Required,Cond_Req,Valid Values,Conditional Requirements,Component
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
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Patient
Country of Residence,Country of Residence,CountryofResidence,Country of Residence at enrollment,False,,"['Italy', 'Lebanon', 'Canada', 'Macau', 'Israel', 'Malta', 'Curacao', 'Mauritius', 'Gabon', 'Samoa', 'Sao Tome and Principe', 'Wallis and Futuna', 'Finland', 'Iraq', 'Indonesia', 'Lesotho', 'Mali', 'Qatar', 'Solomon Islands', 'Niger', 'Hong Kong', 'Algeria', 'Pakistan', 'Holy See', 'Bermuda', 'Barbados', 'Croatia', 'Iceland', 'Saint Kitts and Nevis', 'Saint Vincent and the Grenadines', 'Virgin Islands U.S.', 'Equatorial Guinea', 'Guinea', 'Costa Rica', 'Romania', 'Switzerland', 'Albania', 'Guatemala', 'Senegal', 'Serbia', 'Cyprus', 'Uzbekistan', 'Kenya', 'Djibouti', 'Brazil', 'Papua New Guinea', 'Tajikistan', 'India', 'Congo', 'Aruba', 'Nepal', 'Togo', 'Guadeloupe', ""Cote d'Ivoire"", 'Czech Republic (Czechia)', 'Kuwait', 'Zambia', 'Madagascar', 'Fiji', 'Sri Lanka', 'New Zealand', 'Tanzania', 'Antigua and Barbuda', 'Monaco', 'Jamaica', 'Australia', 'Argentina', 'Luxembourg', 'Guinea-Bissau', 'United Arab Emirates', 'South Sudan', 'Benin', 'Burundi', 'Denmark', 'Jordan', 'Saint Helena Ascension and Tristan da Cunha', 'United Kingdom', 'Zimbabwe', 'Bolivia', 'Guernsey', 'Nigeria', 'Mexico', 'Guam', 'Honduras', 'Grenada', 'Palau', 'Yemen', 'Panama', 'Isle of Man', 'Gibraltar', 'Uruguay', 'Dominica', 'Laos', 'Anguilla', 'Kyrgyzstan', 'Venezuela', 'Cuba', 'Bhutan', 'El Salvador', 'Cambodia', 'Liechtenstein', 'Myanmar', 'Nauru', 'Portugal', 'Japan', 'Kiribati', 'Democratic Republic of the Congo', 'Sweden', 'Nicaragua', 'Guyana', 'Malaysia', 'Marshall Islands', 'Belize', 'Saint Lucia', 'Virgin Islands British', 'Mayotte', 'Seychelles', 'South Korea', 'Armenia', 'Philippines', 'Svalbard & Jan Mayen Islands', 'Kazakhstan', 'Slovenia', 'Greece', 'Northern Mariana Islands', 'Mongolia', 'Morocco', 'Saint Pierre and Miquelon', 'Slovakia', 'State of Palestine', 'Saudi Arabia', 'Tunisia', 'Spain', 'Oman', 'Comoros', 'French Guiana', 'Ireland', 'Western Sahara', 'Lithuania', 'Ukraine', 'Eritrea', 'Eswatini', 'Trinidad and Tobago', 'North Macedonia', 'Burkina Faso', 'Hungary', 'South Africa', 'Niue', 'Chad', 'Poland', 'Dominican Republic', 'Timor-Leste', 'Faroe Islands', 'Tokelau', 'Cook Islands', 'Turkmenistan', 'Tuvalu', 'Taiwan', 'China', 'Falkland Islands (Malvinas)', 'Cayman Islands', 'Montenegro', 'Libya', 'Colombia', 'Jersey', 'Paraguay', 'Vietnam', 'Bosnia and Herzegovina', 'Malawi', 'Gambia', 'Turkey', 'United States', 'French Polynesia', 'Sudan', 'Liberia', 'Belarus', 'Austria', 'Reunion', 'Central African Republic', 'Azerbaijan', 'Brunei', 'Norway', 'Cameroon', 'San Marino', 'Ghana', 'Moldova', 'Ethiopia', 'Bangladesh', 'North Korea', 'Singapore', 'Sierra Leone', 'Bahamas', 'Maldives', 'Bulgaria', 'Greenland', 'Netherlands', 'Rwanda', 'Suriname', 'Federated States of Micronesia', 'Somalia', 'Botswana', 'Georgia', 'Montserrat', 'Germany', 'Kosovo', 'Mozambique', 'Andorra', 'Puerto Rico', 'Haiti', 'Martinique', 'Afghanistan', 'Egypt', 'Namibia', 'Tonga', 'Uganda', 'Iran', 'Latvia', 'Peru', 'Bahrain', 'Cape Verde', 'Ecuador', 'Chile', 'Russia', 'Thailand', 'Angola', 'Syria', 'France', 'Belgium', 'Estonia', 'New Caledonia', 'Vanuatu', 'Mauritania', '']",,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
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', 'no', 'unknown', 'yes', '']",,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
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,,"['Unspecified', 'Not Reported', 'unknown', 'Female', 'Male']",,Demographics
Year Of Birth,Year Of Birth,YearOfBirth,Numeric value to represent the calendar year in which an individual was born.,False,,,,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,,"['true', 'false', '']",,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
Vital Status,Vital Status,VitalStatus,The survival state of the person registered on the protocol.,True,,"['Not Reported', 'Alive', 'unknown', 'Dead']",,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 Reported', 'hispanic or latino', 'not allowed to collect', 'unknown', 'not hispanic or latino']",,Demographics
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,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 Reported', 'Other', 'black or african american', 'asian', 'not allowed to collect', 'american indian or alaska native', 'unknown', 'white', 'native hawaiian or other pacific islander']",,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
Cause of Death,Cause of Death,CauseofDeath,The cause of death,False,True,"['Not Reported', 'Cancer Related', 'End-stage Renal Disease', 'Cardiovascular Disorder NOS', 'Not Applicable', 'Surgical Complications', 'Toxicity', 'Infection', 'Renal Disorder NOS', 'Not Cancer Related', 'unknown', 'Spinal Muscular Atrophy', '']","['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,"['Not Reported', 'Death Certificate', 'Obituary', 'Medical Record', 'unknown', 'Social Security Death Index', 'Autopsy', '']","['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
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
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
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,,"['Not Reported', 'None', 'unknown', '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
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,"['Unspecified', 'Not Reported', 'unknown', 'Female', 'Male', '']","['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,"['Half Brother', 'Paternal Grandmother', 'Aunt', 'Natural Son', 'Identical Twin Sister', 'Maternal Half Sibling', 'Natural Grandchild', 'Natural Mother', 'Paternal Uncle', 'Spouse', 'Foster Daughter', 'Maternal Great Uncle', 'Adoptive Sister', 'Maternal Great Aunt', 'Natural Grandmother', 'Adoptive Mother', 'Adopted Daughter', 'Maternal Grandparent', 'Paternal First Cousin Once Removed', 'Natural Child', 'Wife', 'Daughter-in-law', 'Adoptive Brother', 'Stepfather', 'Natural Father', 'Cousin', 'Paternal Great Aunt', 'Grandmother', 'Niece Second Degree Relative', 'Natural Brother', 'Natural Sibling', 'Natural Grandfather', 'Sister', 'Stepsister', 'Refused', 'Fraternal Twin Sister', 'Grandfather', 'Natural Sister', 'Foster Brother', 'Identical Twin Sibling', 'Maternal Half Sister', 'Mother-in-law', 'Paternal Half Brother', 'Step Sibling', 'Identical Twin Brother', 'Maternal Grandmother', 'Sister-in-law', 'Grandchild', 'Female Cousin', 'Uncle', 'Paternal Aunt', 'Natural Daughter', 'Son-in-law', 'First Cousin', 'Stepbrother', 'Twin Sibling', 'Adopted Son', 'Full Sister', 'Paternal Grandparent', 'Step Child', 'Father', 'Maternal Uncle', 'Foster Sister', 'Foster Son', 'Granddaughter', 'Full Brother', 'Male Cousin', 'Natural Parent', 'Foster Father', 'Other', 'Foster Mother', 'Paternal Half Sister', 'Natural Grandparent', 'Paternal Great Grandparent', 'Son', 'First Cousin Once Removed', 'Fraternal Twin Sibling', 'Nephew', 'Maternal Grandfather', 'Unrelated', 'Sibling', 'Fraternal Twin Brother', 'Brother-in-law', 'Niece', 'Maternal First Cousin', 'Paternal Grandfather', 'Not Reported', 'Grand Niece', 'Grandson', 'Mother', 'Stepson', 'Stepdaughter', 'Adoptive Father', 'Maternal First Cousin Once Removed', 'Parent', 'Maternal Half Brother', 'unknown', 'Child', 'Grandparent', 'Daughter', 'Paternal Half Sibling', 'Brother', 'Half Sibling', 'Stepmother', 'Half Sister', 'Grand Nephew', 'Husband', 'Paternal Great Uncle', 'Maternal Aunt', 'Great Grandchild', 'Ward', 'Maternal Great Grandparent', 'Paternal First Cousin', 'Domestic Partner', 'Father-in-law', 'Legal Guardian', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",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 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,"['Not Reported', 'Blood Cancer', 'Osteosarcoma', 'Head and Neck Cancer', 'Rectal Cancer', 'Mesothelioma', 'Wilms Tumor', 'Ewing Sarcoma', 'Leukemia', 'Lymphoma', 'Melanoma', 'Bone Cancer', 'unknown', 'Bile Duct Cancer', 'Adrenal Gland Cancer', 'Laryngeal Cancer', 'Lung Cancer', 'Tonsillar Cancer', 'Glioblastoma', 'Breast Cancer', 'Esophageal Cancer', 'Basal Cell Cancer', 'Colorectal Cancer', 'CNS Cancer', 'Chondrosarcoma', 'Cervical Cancer', 'Gastric Cancer', 'Prostate Cancer', 'Uterine Cancer', 'Skin Cancer', 'Throat Cancer', 'Kidney Cancer', 'Thyroid Cancer', 'Bladder Cancer', 'Cancer', 'Kaposi Sarcoma', 'Multiple Myeloma', 'Tongue Cancer', 'Gallbladder Cancer', 'Hematologic Cancer', 'Liver Cancer', 'Lymph Node Cancer', 'Pancreas Cancer', 'Testicular Cancer', 'Spleen Cancer', 'Sarcoma', 'Neuroblastoma', 'Ovarian Cancer', 'Rhabdomyosarcoma', 'Gynecologic Cancer', 'Brain Cancer', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory
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,,"['no', 'unknown', 'yes', '']",,Exposure
Asbestos Exposure,Asbestos Exposure,AsbestosExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,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,,"['no', 'unknown', 'yes', '']",,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,,"['no', 'unknown', 'yes', '']",,Exposure
Radon Exposure,Radon Exposure,RadonExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to radon.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,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
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
Alcohol Exposure,Alcohol Exposure,AlcoholExposure,Indicate if individual has alcohol exposure,True,,"['Not Reported', 'Yes - Alcohol Exposure', 'No - Alcohol Exposure']",,Exposure
Smoking Exposure,Smoking Exposure,SmokingExposure,Indicate if individual has smoking exposure,True,,"['Not Reported', 'No - Smoking Exposure', 'Yes - Smoking Exposure']",,Exposure
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,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,"['Not Reported', 'Lifelong Non-Drinker', 'Drinker', 'Heavy Drinker', 'Occasional Drinker', 'Non-Drinker', 'unknown', '']","['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', 'no', 'unknown', 'yes', '']","['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 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 Type,Alcohol Type,AlcoholType,Type of alcohol use,False,True,"['Not Reported', 'Other', 'Liquor', 'Wine', 'unknown', 'Beer', '']","['Alcohol Exposure is ""Yes - Alcohol 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,"['6-30 Minutes', 'Within 5 Minutes', '31-60 Minutes', 'unknown', 'After 60 Minutes', '']","['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,"['Not Reported', 'Pipe', 'Other', 'Electronic Cigarette', 'Cigarettes', 'Cigar', 'Smokeless Tobacco', 'unknown', 'Marijuana', '']","['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
Smokeless Tobacco Quit Age,Smokeless Tobacco Quit Age,SmokelessTobaccoQuitAge,Smokeless tobacco quit age,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,"['Not Reported', 'Lifelong Non-Smoker', 'Smoking history not documented', 'Duration Not Specified', 'Current Smoker', 'unknown', 'Current Reformed Smoker for < or = 15 yrs', 'Current Reformed Smoker', 'Current Reformed Smoker for > 15 yrs', '']","['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
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,"['Volcanic smoke', 'Wood burning smoke factory', 'Workrelated smoke generators', 'Workrelated smoke NOS', 'Workrelated smoke paint baking', 'Workrelated smoke plumbing', 'Grilling smoke', 'Workrelated smoke fire fighting', 'unknown', 'Wood burning smoke NOS', 'Accidental building fire smoke', 'Accidental forest fire smoke', 'Accidental fire smoke NOS', 'Indoor coal burning stove or fireplace smoke', 'Workrelated smoke soldering/welding', 'Hashish smoke', 'Indoor stove or fireplace smoke NOS', 'Fire smoke NOS', 'Electrical fire smoke', 'Environmental tobacco smoke', 'Workrelated smoke military', 'Accidental vehicle fire smoke', 'Oil burning smoke Kerosene', 'Oil burning smoke NOS', 'Burning tree smoke', 'Smoke exposure NOS', 'Furnace or boiler smoke', 'Workrelated smoke foundry', 'Smokehouse smoke', 'Marijuana smoke', 'Workrelated smoke plastics factory', 'Cooking related smoke NOS', 'Gas burning smoke propane', 'Tobacco smoke cigarettes', 'Factory smokestack smoke', 'Workrelated smoke artificial smoke machines', 'Field burning smoke', 'Electronic cigarette smoke NOS', 'Coal smoke NOS', 'Aircraft smoke', 'Recreational fire smoke', 'Waste burning smoke', 'Machine smoke', 'Tobacco smoke cigar', 'No Smoke Exposure', 'Indoor wood burning stove or fireplace smoke', 'Accidental grass fire smoke', 'Tobacco smoke pipe', 'Grease fire smoke', '']","['Smoking Exposure is ""Yes - Smoking 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', 'no', 'unknown', 'yes', '']","['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
Cigarettes per Day,Cigarettes per Day,CigarettesperDay,The average number of cigarettes smoked per day.,False,True,,"['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
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
Smoking Frequency,Smoking Frequency,SmokingFrequency,The text term used to generally decribe how often the patient smokes.,False,True,"['Every day', 'unknown', 'Some days', '']","['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
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
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', 'unknown', 'no']",,FollowUp
Imaging Type,Imaging Type,ImagingType,The text term used to describe the type of imaging or scan performed on the patient.,False,,"['MRI', '99mTc Bone Scintigraphy', 'PET', 'CT Scan', '']",,FollowUp
BMI,BMI,BMI,A calculated numerical quantity that represents an individual's weight to height ratio.,False,,,,FollowUp
Disease Response,Disease Response,DiseaseResponse,Code assigned to describe the patient's response or outcome to the disease.,False,,"['Not Reported', 'BED-Biochemical Evidence of Disease', 'RP-Response', 'WT-With Tumor', 'CPD-Clinical Progression', 'DU-Disease Unchanged', 'sCR-Stringent Complete Response', 'unknown', 'PSR-Pseudoresponse', 'Non-CR/Non-PD-Non-CR/Non-PD', 'IPD-Immunoprogression', 'IMR-Immunoresponse', 'RPD-Radiographic Progressive Disease', 'SPD-Surgical Progression', 'VGPR-Very Good Partial Response', 'PA-Palliative Therapy', 'MR-Minimal/Marginal response', 'CRU-Complete Response Unconfirmed', 'PDM-Persistent Distant Metastasis', 'RD-Responsive Disease', 'PR-Partial Response', 'MX-Mixed Response', 'SD-Stable Disease', 'PPD-Pseudoprogression', 'PB-Palliative Benefit', 'NPB-No Palliative Benefit', 'CR-Complete Response', 'PLD-Persistent Locoregional Disease', 'AJ-Adjuvant Therapy', 'NR-No Response', 'TF-Tumor Free', 'PD-Progressive Disease', 'TE-Too Early', '']",,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
Hysterectomy Type,Hysterectomy Type,HysterectomyType,The text term used to describe the type of hysterectomy the patient had.,False,,"['Not Reported', 'Radical Hysterectomy', 'Not performed', 'unknown', 'Hysterectomy NOS', 'Simple Hysterectomy', '']",,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,,"['Ureteric Anastomotic Leak', 'Salivary Duct Inflammation', 'Voice Alteration', 'Cecal Hemorrhage', 'Stoma Site Infection', 'Hyperglycemia', 'IVth Nerve Disorder', 'Osteonecrosis of Jaw', 'Middle Ear Inflammation', 'Vital Capacity Abnormal', 'Postoperative Thoracic Procedure Complication', 'Vaginal Inflammation', 'Alopecia', 'Photophobia', 'Myalgia', 'Feminization Acquired', 'Chronic Kidney Disease', 'Accessory Nerve Disorder', 'Rash Acneiform', 'Pancreatic Duct Stenosis', 'Stridor', 'Bladder Spasm', 'Endocrine Disorders Other', 'Lymphocele', 'Pancreatic Hemorrhage', 'Nipple Deformity', 'Pulmonary Hypertension', 'Pleural Infection', 'Laryngeal Obstruction', 'Glossopharyngeal Nerve Disorder', 'Buttock Pain', 'Growth Hormone Abnormal', 'Colonic Hemorrhage', 'Delirium', 'Small Intestinal Mucositis', 'Hypocalcemia', 'Vaginal Hemorrhage', 'Encephalitis Infection', 'Abducens Nerve Disorder', 'Alanine Aminotransferase Increased', 'External Ear Inflammation', 'Hemolysis', 'Bloating', 'Hemoglobinuria', 'Sudden Death NOS', 'Electrocardiogram QT Corrected Interval Prolonged', 'Myelodysplastic Syndrome', 'Rectal Necrosis', 'Intraoperative Hepatobiliary Injury', 'Bladder Anastomotic Leak', 'Anaphylaxis', 'Hypothermia', 'Cardiac Troponin T Increased', 'Dental Caries', 'Mediastinal Hemorrhage', 'Vaginal Dryness', 'Gastrointestinal Anastomotic Leak', 'Supraventricular Tachycardia', 'Investigations Other', 'Anal Necrosis', 'Scalp Pain', 'Otitis Media', 'Bullous Dermatitis', 'Retinal Detachment', 'Spermatic Cord Hemorrhage', 'Vaginal Anastomotic Leak', 'Prostate Infection', 'Mucosal Infection', 'Localized Edema', 'Flashing Lights', 'Nausea', 'Intraoperative Head and Neck Injury', 'Platelet Count Decreased', 'Ileus', 'Pruritus', 'Tracheitis', 'Hepatic Pain', 'Skin Infection', 'Virilization', 'Laryngeal Edema', 'Corneal Ulcer', 'Laryngopharyngeal Dysesthesia', 'Myositis', 'Azoospermia', 'Hemorrhoids', 'Conjunctivitis Infective', 'Ileal Stenosis', 'Rash Maculo-Papular', 'Peripheral Sensory Neuropathy', 'Lactation Disorder', 'Pregnancy', 'Lung Infection', 'Pelvic Floor Muscle Weakness', 'Biliary Fistula', 'Intraoperative Gastrointestinal Injury', 'Colonic Obstruction', 'Eye Disorders Other', 'Serum Sickness', 'Pelvic Infection', 'Confusion', 'Urinary Tract Infection', 'Haptoglobin Decreased', 'Insomnia', 'Skin Hyperpigmentation', 'Palmar-Plantar Erythrodysesthesia Syndrome', 'Gastric Stenosis', 'Sepsis', 'Back Pain', 'Prostatic Obstruction', 'Intraoperative Cardiac Injury', 'GGT Increased', 'Pleuritic Pain', 'Social Circumstances Other', 'Intraoperative Skin Injury', 'Intraoperative Arterial Injury', 'Osteoporosis', 'Anorgasmia', 'Ovarian Hemorrhage', 'Hypoparathyroidism', 'Paronychia', 'Heart Failure', 'Flushing', 'dyspnea', 'Pain of Skin', 'Malaise', 'Soft Tissue Necrosis Lower Limb', 'Ischemia Cerebrovascular', 'Conjunctivitis', 'Injury to Carotid Artery', 'Infective Myositis', 'Keratitis', 'Capillary Leak Syndrome', 'Gallbladder Fistula', 'Muscle Weakness Right-Sided', 'Head Soft Tissue Necrosis', 'Infections and Infestations Other', 'Body Odor', 'Lipase Increased', 'Mobitz (Type) II Atrioventricular Block', 'Skin Ulceration', 'Mediastinal Infection', 'Hypercalcemia', 'Vulval Infection', 'Visceral Arterial Ischemia', 'Watering Eyes', 'Esophageal Obstruction', 'Intestinal Stoma Site Bleeding', 'Hemolytic Uremic Syndrome', 'Arthralgia', 'Psychiatric Disorders Other', 'Vitreous Hemorrhage', 'Death Neonatal', 'Constrictive Pericarditis', 'Meningitis', 'Hepatic Necrosis', 'Retinal Vascular Disorder', 'Pneumothorax', 'Pancreatic Fistula', 'Photosensitivity', 'Edema Cerebral', 'Aortic Injury', 'Intraoperative Neurological Injury', 'Right Ventricular Dysfunction', 'Neck Pain', 'Hepatic Hemorrhage', 'Euphoria', 'Kyphosis', 'Glaucoma', 'Phlebitis', 'Joint Effusion', 'Laryngospasm', 'Hyperthyroidism', 'Ileal Obstruction', 'Uterine Anastomotic Leak', 'Hyperuricemia', 'Gastric Ulcer', 'Skin Hypopigmentation', 'Left Ventricular Systolic Dysfunction', 'Pharyngolaryngeal Pain', 'Vasovagal Reaction', 'Erythroderma', 'Intraoperative Musculoskeletal Injury', 'Aphonia', 'Tremor', 'Olfactory Nerve Disorder', 'Presyncope', 'Depression', 'Hyperhidrosis', 'Bronchospasm', 'Pulmonary Valve Disease', 'Neck Soft Tissue Necrosis', 'Irregular Menstruation', 'Intraoperative Endocrine Injury', 'Anal Mucositis', 'Libido Increased', 'Neutrophil Count Decreased', 'Constipation', 'Splenic Infection', 'Tricuspid Valve Disease', 'Laryngeal Hemorrhage', 'Hemorrhoidal Hemorrhage', 'Prolapse of Urostomy', 'Peripheral Motor Neuropathy', 'Gastritis', 'CPK Increased', 'Personality Change', 'Oral Pain', 'Depressed Level of Consciousness', 'Hip Fracture', 'Recurrent Laryngeal Nerve Palsy', 'Growth Suppression', 'Cecal Infection', 'External Ear Pain', 'Phlebitis Infective', 'Prostatic Pain', 'Aortic Valve Disease', 'CD4 Lymphocytes Decreased', 'Aspiration', 'Fatigue', 'Uterine Perforation', 'Reproductive System and Breast Disorders Other', 'Myelitis', 'Soft Tissue Infection', 'Forced Expiratory Volume Decreased', 'Penile Infection', 'Acute Coronary Syndrome', 'Portal Hypertension', 'Glucose Intolerance', 'Intracranial Hemorrhage', 'Mania', 'Lipohypertrophy', 'Atrioventricular Block First Degree', 'Treatment Related Secondary Malignancy', 'Familial and Genetic Disorders Other', 'Nervous System Disorders Other', 'Periorbital Infection', 'Cholesterol High', 'Arthritis', 'Arterial Injury', 'Flu Like Symptoms', 'Uterine Fistula', 'Erythema Multiforme', 'Musculoskeletal Deformity', 'Fibrinogen Decreased', 'Pyramidal Tract Syndrome', 'Cytokine Release Syndrome', 'Bone Marrow Hypocellular', 'Paroxysmal Atrial Tachycardia', 'Toxic Epidermal Necrolysis', 'Musculoskeletal and Connective Tissue Disorders Other', 'Corneal Infection', 'Hydrocephalus', 'Rectal Mucositis', 'Cough', 'Gastrointestinal Disorders Other', 'Hematosalpinx', 'Nystagmus', 'Bronchopulmonary Hemorrhage', 'Appendicitis Perforated', 'Enterocolitis', 'Esophageal Varices Hemorrhage', 'Intra-Abdominal Hemorrhage', 'Trismus', 'Optic Nerve Disorder', 'Urinary Tract Pain', 'Weight Loss', 'Perforation Bile Duct', 'Cushingoid', 'Fibrosis Deep Connective Tissue', 'Infusion Site Extravasation', 'Lethargy', 'Dry Mouth', 'Rectal Fistula', 'Duodenal Hemorrhage', 'Penile Pain', 'Portal Vein Thrombosis', 'Amnesia', 'Colonic Stenosis', 'Large Intestinal Anastomotic Leak', 'Mucositis Oral', 'Adult Respiratory Distress Syndrome', 'Alkalosis', 'Premature Menopause', 'Eye Infection', 'Urostomy Leak', 'Muscle Weakness Upper Limb', 'Pancreatic Anastomotic Leak', 'Asystole', 'Stevens-Johnson Syndrome', 'Bladder Infection', 'Epistaxis', 'Lordosis', 'Lymph Gland Infection', 'Leukocytosis', 'Pancreatitis', 'Hyponatremia', 'Hypertriglyceridemia', 'Small Intestinal Obstruction', 'Ventricular Fibrillation', 'Esophageal Stenosis', 'Skin Atrophy', 'Fever', 'Breast Pain', 'Enterocolitis Infectious', 'Memory Impairment', 'Blurred Vision', 'Ventricular Arrhythmia', 'Flank Pain', 'Perineal Pain', 'Fracture', 'Lymphocyte Count Decreased', 'Acoustic Nerve Disorder NOS', 'Hepatitis Viral', 'Spermatic Cord Anastomotic Leak', 'Pericarditis', 'Flatulence', 'Hypophosphatemia', 'Rhinitis Infective', 'Bone Pain', 'Retinopathy', 'Duodenal Fistula', 'Appendicitis', 'Laryngeal Mucositis', 'Gallbladder Infection', 'Biliary Anastomotic Leak', 'Intraoperative Venous Injury', 'Malignant and Unspecified (Incl Cysts and Polyps) Other', 'Allergic Rhinitis', 'Gastroparesis', 'Dehydration', 'Syncope', 'Suicide Attempt', 'Gait Disturbance', 'Esophageal Fistula', 'Hypomagnesemia', 'Periodontal Disease', 'Duodenal Ulcer', 'Nasal Congestion', 'Gum Infection', 'Pancreatic Necrosis', 'Jejunal Fistula', 'Vasculitis', 'Encephalopathy', 'Hoarseness', 'Atrial Fibrillation', 'Menorrhagia', 'Ventricular Tachycardia', 'Female Genital Tract Fistula', 'Hypermagnesemia', 'Wrist Fracture', 'Rectal Pain', 'Dyspepsia', 'Hyperparathyroidism', 'Postoperative Hemorrhage', 'Wound Dehiscence', 'Biliary Tract Infection', 'Dyspareunia', 'Hepatic Infection', 'Sinus Pain', 'Sick Sinus Syndrome', 'Tracheostomy Site Bleeding', 'Anal Pain', 'Ileal Ulcer', 'Hypokalemia', 'Pancreas Infection', 'Muscle Weakness Lower Limb', 'Breast Atrophy', 'Dry Skin', 'Palpitations', 'Paresthesia', 'Salivary Gland Fistula', 'Bruising', 'Puerperium and Perinatal Conditions Other', 'Proctitis', 'Brachial Plexopathy', 'Pharyngeal Anastomotic Leak', 'Laryngeal Inflammation', 'Leukemia Secondary to Oncology Chemotherapy', 'Neoplasms Benign', 'Hypertrichosis', 'Superior Vena Cava Syndrome', 'Urinary Retention', 'Cervicitis Infection', 'Vas Deferens Anastomotic Leak', 'Myocardial Infarction', 'Ileal Perforation', 'Urinary Urgency', 'Ovarian Rupture', 'Periorbital Edema', 'Gastrointestinal Fistula', 'Ear and Labyrinth Disorders Other', 'Hepatobiliary Disorders Other', 'Pleural Hemorrhage', 'Hypothyroidism', 'Radiation Recall Reaction (Dermatologic)', 'Acidosis', 'Arachnoiditis', 'Lymphedema', 'Agitation', 'Gastric Necrosis', 'Concentration Impairment', 'Febrile Neutropenia', 'Delusions', 'Sinus Disorder', 'Generalized Muscle Weakness', 'Trigeminal Nerve Disorder', 'Urinary Frequency', 'Productive Cough', 'Hiccups', 'Sinus Bradycardia', 'Obesity', 'Poisoning and Procedural Complications Other', 'Movements Involuntary', 'Intestinal Stoma Leak', 'Tooth Discoloration', 'Encephalomyelitis Infection', 'Vaginal Stricture', 'Thrombotic Thrombocytopenic Purpura', 'Pharyngeal Stenosis', 'Urine Discoloration', 'Vaginal Pain', 'Delayed Orgasm', 'Pharyngeal Mucositis', 'Conduction Disorder', 'Ankle Fracture', 'Fetal Growth Retardation', 'Hemoglobin Increased', 'Colonic Fistula', 'Mitral Valve Disease', 'Hepatic Failure', 'Jejunal Hemorrhage', 'Pericardial Tamponade', 'Spleen Disorder', 'Vaginal Infection', 'Spermatic Cord Obstruction', 'Hypotension', 'Urostomy Stenosis', 'Urine Output Decreased', 'Gallbladder Pain', 'Premature Delivery', 'Weight Gain', 'Lymph Node Pain', 'Soft Tissue Necrosis Upper Limb', 'Spasticity', 'Tinnitus', 'Vagus Nerve Disorder', 'Vaginal Perforation', 'Chest Pain Cardiac', 'Vaginismus', 'Respiratory', 'Hypoalbuminemia', 'Laryngeal Stenosis', 'Scrotal Infection', 'Purpura', 'Superficial Soft Tissue Fibrosis', 'Scrotal Pain', 'Small Intestine Infection', 'Lower Gastrointestinal Hemorrhage', 'Respiratory Failure', 'Gastric Hemorrhage', 'Edema Face', 'Otitis Externa', 'Anxiety', 'Papilledema', 'Sinusitis', 'Duodenal Infection', 'Tumor Lysis Syndrome', 'Anal Stenosis', 'Exostosis', 'Seizure', 'Retroperitoneal Hemorrhage', 'Gastric Anastomotic Leak', 'Injection Site Reaction', 'Bronchopleural Fistula', 'Uterine Pain', 'Cardiac Troponin I Increased', 'Gallbladder Necrosis', 'Genital Edema', 'Duodenal Stenosis', 'Pain', 'Thoracic and Mediastinal Disorders Other', 'Fallopian Tube Perforation', 'Rash Pustular', 'Intraoperative Urinary Injury', 'Serum Amylase Increased', 'Sneezing', 'Pain in Extremity', 'Endophthalmitis', 'Central Nervous System Necrosis', 'Esophageal Pain', 'Cardiac Disorders Other', 'Ovarian Infection', 'Rectal Ulcer', 'Testicular Pain', 'Testicular Disorder', 'Ear Pain', 'Lip Pain', 'Ovulation Pain', 'Unequal Limb Length', 'Allergic Reaction', 'Blood Corticotrophin Decreased', 'Joint Infection', 'Hypersomnia', 'Nail Discoloration', 'Gallbladder Perforation', 'Night Blindness', 'Anorexia', 'Peritoneal Infection', 'Dry Eye', 'Edema Limbs', 'Hypertension', 'Colonic Perforation', 'Ascites', 'Intraoperative Splenic Injury', 'Jejunal Ulcer', 'Abdominal Soft Tissue Necrosis', 'Small Intestinal Anastomotic Leak', 'Nail Loss', 'Jejunal Stenosis', 'Papulopustular Rash', 'Urethral Anastomotic Leak', 'Enterovesical Fistula', 'Uterine Obstruction', 'Mobitz Type I', 'Akathisia', 'Blood Antidiuretic Hormone Abnormal', 'Hot Flashes', 'Menopause', 'Pharyngeal Necrosis', 'Facial Nerve Disorder', 'Renal Calculi', 'Gastric Fistula', 'Salivary Gland Infection', 'Urinary Fistula', 'Gastric Perforation', 'Rectal Perforation', 'Tumor Pain', 'Peritoneal Necrosis', 'Pleural Effusion', 'Retinoic Acid Syndrome', 'Psychosis', 'Vaginal Fistula', 'Facial Muscle Weakness', 'Wolff-Parkinson-White Syndrome', 'Muscle Weakness Trunk', 'Superficial Thrombophlebitis', 'Anal Fistula', 'Pelvic Soft Tissue Necrosis', 'Uterine Infection', 'Intestinal Stoma Obstruction', 'Chylothorax', 'Ejaculation Disorder', 'Fallopian Tube Anastomotic Leak', 'Testicular Hemorrhage', 'Growth Accelerated', 'Dysphasia', 'Tooth Infection', 'Vaginal Discharge', 'Prolapse of Intestinal Stoma', 'Retinal Tear', 'Telangiectasia', 'Leukoencephalopathy', 'Injury to Superior Vena Cava', 'Irritability', 'Uterine Hemorrhage', 'Atrial Flutter', 'Venous Injury', 'Tooth Development Disorder', 'Hirsutism', 'Headache', 'Pulmonary Edema', 'Device Related Infection', 'Oral Dysesthesia', 'Urethral Infection', 'Intraoperative Ocular Injury', 'Abdominal Distension', 'Anorectal Infection', 'Renal Hemorrhage', 'Intraoperative Ear Injury', 'Pericardial Effusion', 'Sore Throat', 'Lip Infection', 'Stomach Pain', 'White Blood Cell Decreased', 'Cataract', 'Catheter Related Infection', 'Erectile Dysfunction', 'Renal Colic', 'Dysarthria', 'Fallopian Tube Stenosis', 'Injury to Jugular Vein', 'Abdominal Infection', 'Pelvic Pain', 'Eyelid Function Disorder', 'Laryngitis', 'Small Intestinal Perforation', 'Blood and Lymphatic System Disorders Other', 'Laryngeal Fistula', 'Anal Hemorrhage', 'Intraoperative Respiratory Injury', 'Dysesthesia', 'Dysmenorrhea', 'Jejunal Perforation', 'Peripheral Nerve Infection', 'Tracheal Fistula', 'Vomiting', 'Pulmonary Fibrosis', 'Precocious Puberty', 'Stroke', 'Bone Infection', 'Acute Kidney Injury', 'Eye Pain', 'Facial Pain', 'Gallbladder Obstruction', 'Malabsorption', 'Hearing Impaired', 'Bronchial Infection', 'Anal Ulcer', 'Gingival Pain', 'Gastrointestinal Stoma Necrosis', 'Injury to Inferior Vena Cava', 'Esophageal Ulcer', 'Bronchial Stricture', 'Oral Hemorrhage', 'Oculomotor Nerve Disorder', 'Rectal Anastomotic Leak', 'Ejection Fraction Decreased', 'Dizziness', 'Tracheal Hemorrhage', 'Esophageal Infection', 'Fall', 'Breast Infection', 'Jejunal Obstruction', 'Wound Complication', 'Chills', 'Ileal Fistula', 'Tracheal Obstruction', 'Phantom Pain', 'Vestibular Disorder', 'Intraoperative Renal Injury', 'Creatinine Increased', 'Immune System Disorders Other', 'Pharyngeal Hemorrhage', 'Sinus Tachycardia', 'Stomal Ulcer', 'Unintended Pregnancy', 'Vascular Access Complication', 'dysphagia', 'Meningismus', 'Reversible Posterior Leukoencephalopathy Syndrome', 'Typhlitis', 'Kidney Infection', 'Peripheral Ischemia', 'Pneumonitis', 'Duodenal Perforation', 'Urinary Tract Obstruction', 'Upper Respiratory Infection', 'Fat Atrophy', 'Floaters', 'Hematoma', 'Joint Range of Motion Decreased', 'Hematuria', 'Small Intestinal Stenosis', 'Avascular Necrosis', 'Autoimmune Disorder', 'Fallopian Tube Obstruction', 'Disseminated Intravascular Coagulation', 'Atelectasis', 'Edema Trunk', 'Muscle Weakness Left-Sided', 'Oral Cavity Fistula', 'Pancreatic Enzymes Decreased', 'Cranial Nerve Infection', 'Apnea', 'Blood Gonadotrophin Abnormal', 'Neuralgia', 'Iron Overload', 'Pharyngitis', 'Cholecystitis', 'Alkaline Phosphatase Increased', 'Upper Gastrointestinal Hemorrhage', 'Nail Ridging', 'Kidney Anastomotic Leak', 'Rectal Stenosis', 'Arteritis Infective', 'Surgical and Medical Procedures Other', 'Postnasal Drip', 'Ileal Hemorrhage', 'Hypohidrosis', 'Skin Induration', 'Cardiac Arrest', 'Chest Wall Pain', 'Prostatic Hemorrhage', 'Scoliosis', 'Hallucinations', 'Joint Range of Motion Decreased Cervical Spine', 'Wound Infection', 'Gynecomastia', 'Colitis', 'Restlessness', 'Infusion Related Reaction', 'Tracheal Mucositis', 'Adrenal Insufficiency', 'Toothache', 'Ataxia', 'Somnolence', 'Hyperkalemia', 'Esophagitis', 'Thromboembolic Event', 'Esophageal Hemorrhage', 'Radiculitis', 'Oligospermia', 'Renal and Urinary Disorders Other', 'Vertigo', 'Burn', 'Urostomy Obstruction', 'Vascular Disorders Other', 'Scleral Disorder', 'Dysgeusia', 'Cerebrospinal Fluid Leakage', 'General Disorders and Administration Site Conditions Other', 'Rectal Hemorrhage', 'Blood Bilirubin Increased', 'Urticaria', 'Carbon Monoxide Diffusing Capacity Decreased', 'Joint Range of Motion Decreased Lumbar Spine', 'Transient Ischemic Attacks', 'Aspartate Aminotransferase Increased', 'Stenosis of Gastrointestinal Stoma', 'Fetal Death', 'Hypernatremia', 'Esophageal Anastomotic Leak', 'Multi-Organ Failure', 'Sleep Apnea', 'Activated Partial Thromboplastin Time Prolonged', 'Lymph Leakage', 'wheezing', 'Abdominal Pain', 'Anemia', 'Atrioventricular Block Complete', 'Urostomy Site Bleeding', 'Colonic Ulcer', 'Lymphocyte Count Increased', 'Nail Infection', 'Neck Edema', 'Delayed Puberty', 'INR Increased', 'Libido Decreased', 'Bile Duct Stenosis', 'Myocarditis', 'Pharyngeal Fistula', 'Tracheal Stenosis', 'Vaginal Obstruction', 'Urinary Incontinence', 'Hypoglossal Nerve Disorder', 'Extraocular Muscle Paresis', 'Metabolism and Nutrition Disorders Other', 'Esophageal Perforation', 'Pulmonary Fistula', 'Rectal Obstruction', 'Duodenal Obstruction', 'Bronchial Fistula', 'Intraoperative Hemorrhage', 'Bladder Perforation', 'Intraoperative Reproductive Tract Injury', 'Seroma', 'Intraoperative Breast Injury', 'Small Intestine Ulcer', 'Gastroesophageal Reflux Disease', 'Gastrointestinal Pain', 'Esophageal Necrosis', 'Suicidal Ideation', 'Congenital', 'Skin and Subcutaneous Tissue Disorders Other', 'Alcohol Intolerance', 'Proteinuria', 'Restrictive Cardiomyopathy', 'Fecal Incontinence', 'Cognitive Disturbance', 'Hypoglycemia', 'Bronchial Obstruction', 'Uveitis', 'Dermatitis Radiation', 'Non-Cardiac Chest Pain', 'Extrapyramidal Disorder', 'Hypoxia', 'Cystitis Noninfective', 'Endocarditis Infective', 'Cheilitis', 'Diarrhea', 'Injury', 'Spinal Fracture', 'Obstruction Gastric', 'Death NOS', 'Blood Prolactin Abnormal', '']",,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', 'no', 'unknown', 'yes', '']",,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
Imaging Result,Imaging Result,ImagingResult,The text term used to describe the result of the imaging or scan performed on the patient.,False,,"['Not Reported', 'Indeterminate', 'unknown', 'positive', 'negative', 'Not Performed', '']",,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,,"['Not Reported', 'HBV Core Antibody', 'HBV Surface Antibody', 'Hepatitis C Antibody', 'unknown', 'HCV Genotype', 'HBV DNA', 'Hepatitis C Virus RNA', 'HBV Genotype', 'Hepatitis B Surface Antigen', '']",,FollowUp
Weight,Weight,Weight,The weight of the patient measured in kilograms.,False,,,,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,,"['Not Reported', 'Transfusion Recipient', 'Intravenous Drug User', 'None', 'Heterosexual Contact', 'unknown', 'Hemophiliac', 'Homosexual Contact', '']",,FollowUp
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
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,,"['Not Reported', 'Pathology', 'Histology', 'unknown', 'Radiology', '']",,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
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 2', 'Grade 4', 'Grade 1', 'Grade 5', 'Grade 3', '']",,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
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
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
Comorbidity,Comorbidity,Comorbidity,"The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.",False,,"['Peripheral Neuropathy', 'Peutz-Jeghers Disease', 'Hepatitis B Infection', 'Bone Fracture(s)', 'Hyperglycemia', 'Hypothyroidism', 'Other Nonmalignant Systemic Disease', 'Psoriasis', 'Tyrosinemia', 'Cholelithiasis', 'Adrenocortical Insufficiency', 'Congestive Heart Failure (CHF)', 'Obesity', 'Pulmonary Fibrosis', 'Stroke', 'Neuroendocrine Tumor', 'Transient Ischemic Attack', ""Hashimoto's Thyroiditis"", 'ITP', 'Hepatitis A Infection', 'Hemorrhagic Cystitis', 'MAI', 'Rheumatoid Arthritis', 'Li-Fraumeni Syndrome', 'HUS/TTP', 'Hepatitis', 'Osteoarthritis', 'Celiac Disease', 'Pregnancy in Patient or Partner', 'Renal Insufficiency', 'Renal Failure (Requiring Dialysis)', 'Other Cancer Within 5 Years', 'Arthritis', 'Hepatitis C Infection', 'Ulcerative Colitis', 'Acute Renal Failure', 'Asthma', 'Alpha-1 Antitrypsin', 'DVT/PE', 'Heart Disease', 'Renal Dialysis', ""Crohn's Disease"", 'Cataracts', 'Fibrosis', 'Ischemic Heart Disease', ""Behcet's Disease"", 'Liver Cirrhosis (Liver Disease)', 'Turcot Syndrome', 'Dyslipidemia', 'Avascular Necrosis', 'Epilepsy', 'Peptic Ulcer (Ulcer)', 'Diet Controlled Diabetes', 'Cerebrovascular Disease', 'Tuberculosis', 'Herpes', 'Anxiety', 'Hereditary Non-polyposis Colon Cancer', 'Smoking', 'Iron Overload', 'Cancer', 'Rubinstein-Taybi Syndrome', 'Seizure', 'Colon Polyps', 'Type II', 'Intraductal Papillary Mucinous Neoplasm', 'Arrhythmia', 'Wagr Syndrome', 'Pancreatitis', 'Interstitial Pneumontis or ARDS', 'Eczema', 'Calcium Channel Blockers', 'Myasthenia Gravis', 'Epstein-Barr Virus', 'Chronic Renal Failure', 'Kidney Disease', 'H. pylori Infection', 'Denys-Drash Syndrome', 'Gout', 'High Grade Liver Dysplastic Nodule', 'Glycogen Storage Disease', 'Sarcoidosis', 'Organ transplant (site)', 'Inflammatory Bowel Disease', 'Bronchitis', 'Blood Clots', 'Other', 'Deep Vein Thrombosis / Thromboembolism', 'Hypertension', 'Lupus', 'Allergies', 'Fanconi Anemia', 'Peripheral Vascular Disease', 'GERD', 'Hyperlipidemia', 'Other Pulmonary Complications', 'Nonalcoholic Steatohepatitis', 'Common Variable Immunodeficiency', 'Pulmonary Hemorrhage', 'Anemia', ""Barrett's Esophagus"", 'Not Reported', 'Hypospadias', 'Basal Cell Carcinoma', 'Familial Adenomatous Polyposis', 'Hemihypertrophy', 'Biliary Disorder', 'Sleep apnea', 'Cirrhosis', 'Lynch Syndrome', 'Atrial Fibrillation', 'Hypercalcemia', 'Liver Toxicity (Non-Infectious)', 'unknown', 'Gorlin Syndrome', 'Pain (Various)', 'HIV / AIDS', 'Coronary Artery Disease', 'Human Papillomavirus Infection', 'Connective Tissue Disorder', 'Beckwith-Wiedemann', 'Chronic Hepatitis', 'Osteoporosis or Osteopenia', 'Gastroesophageal Reflux Disease', 'Insulin Controlled Diabetes', 'Rheumatologic Disease', 'Gonadal Dysfunction', 'Adenomatous Polyposis Coli', 'Diverticulitis', 'Hypercholesterolemia', 'Glaucoma', 'Headache', 'Cryptogenic Organizing Pneumonia', 'Diabetes', 'Joint Replacement', 'Adenocarcinoma', 'Low Grade Liver Dysplastic Nodule', 'Diabetic Neuropathy', 'Myocardial Infarction', 'Primary Sclerosing Cholangitis', 'Depression', 'Steatosis', 'unknown Etiology', 'COPD', '']",,FollowUp
Pregnancy Outcome,Pregnancy Outcome,PregnancyOutcome,The text term used to describe the type of pregnancy the patient had,False,,"['Not Reported', 'Ectopic Pregnancy', 'Miscarriage', 'Stillbirth', 'unknown', 'Live Birth', 'Induced Abortion', '']",,FollowUp
Karnofsky Performance Status,Karnofsky Performance Status,KarnofskyPerformanceStatus,Text term used to describe the classification used of the functional capabilities of a person.,False,,"['Not Reported', '""70""', '""20""', '""60""', '""30""', '""90""', '""10""', '""50""', 'unknown', '""100""', '""40""', '""80""', '""0""', '']",,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,,"['Not Reported', 'Bladder', 'Vagina', 'None', 'unknown', 'Microscopic Parametrium', 'Macroscopic Parametrium', '']",,FollowUp
Height,Height,Height,The height of the patient in centimeters.,False,,,,FollowUp
Barretts Esophagus Goblet Cells Present,Barretts Esophagus Goblet Cells Present,BarrettsEsophagusGobletCellsPresent,Presence or absennce of Barretts esophagus goblet cells.,False,,"['no', 'yes', '']",,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
Diabetes Treatment Type,Diabetes Treatment Type,DiabetesTreatmentType,Text term used to describe the types of treatment used to manage diabetes.,False,,"['Not Reported', 'Injected Insulin', 'Other', 'Alpha-Glucosidase Inhibitor', 'Oral Hypoglycemic', 'Thiazolidinedione', 'Biguanide', 'Insulin', 'Sulfonylurea', 'unknown', 'Diet', '']",,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
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
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
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
Immunosuppressive Treatment Type,Immunosuppressive Treatment Type,ImmunosuppressiveTreatmentType,The text term used to describe the type of immunosuppresive treatment the patient received.,False,,"['Not Reported', 'Anti-TNFTherapy', 'Other', 'Cyclophosphamide', 'None', 'unknown', 'Azathioprine', 'Methotrexate', '']",,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,,"['Hepatitis B Infection', 'Undescended Testis', 'Allergy Animal NOS', 'Cholelithiasis', 'Allergy Food NOS', 'HIV', 'Obesity', 'Allergy Eggs', 'Hepatic Encephalopathy', 'Hay Fever', ""Hashimoto's Thyroiditis"", 'Diabetes NOS', 'Li-Fraumeni Syndrome', 'Thyroid Nodular Hyperplasia', 'Serous tubal intraepithelial carcinoma (STIC)', 'Alpha-1 Antitrypsin Deficiency', 'Parasitic Disease of Biliary Tract', 'Hepatitis C Infection', 'Recurrent Pyogenic Cholangitis', ""Gilbert's Syndrome"", 'Tattoo', 'Nonalcoholic Fatty Liver Disease', 'Allergy Ant', 'Autoimmune Atrophic Chronic Gastritis', 'Fibrosis', ""Behcet's Disease"", 'Tobacco Smoking', 'Turcot Syndrome', 'Gastric Polyp(s)', 'Tobacco Smokeless', 'Iron Overload', 'Cancer', 'Rubinstein-Taybi Syndrome', 'Intestinal Metaplasia', 'Seizure', 'Colon Polyps', 'Hematologic Disorder NOS', 'Wagr Syndrome', 'Pancreatitis', 'Eczema', 'Myasthenia Gravis', 'Epstein-Barr Virus', 'Common variable immune deficiency (CVID)', 'Low Grade Dysplasia', 'Denys-Drash Syndrome', 'Helicobacter Pylori-Associated Gastritis', 'Sarcoidosis', 'Tobacco NOS', 'Hepatitis NOS', 'Sensory Changes', 'Fanconi Anemia', 'Endometriosis', 'Nonalcoholic Steatohepatitis', 'Alcohol Consumption', 'Allergy Nuts', 'Diet', ""Barrett's Esophagus"", 'Not Reported', 'Hypospadias', 'Allergy Fruit', 'Allergy Seafood', 'Diabetes Type I', 'Familial Adenomatous Polyposis', 'Hemihypertrophy', 'Cirrhosis', 'Allergy Dog', 'High Grade Dysplasia', 'Lynch Syndrome', 'Allergy Bee', 'unknown', 'Gorlin Syndrome', 'Diabetes Type II', 'Human Papillomavirus Infection', 'Allergy Wasp', 'Endosalpingiosis', 'Beckwith-Wiedemann', 'Oral Contraceptives', 'Vision Changes', 'Chronic Hepatitis', 'Alcoholic Liver Disease', 'Lymphocytic Thyroiditis', 'Diverticulitis', 'Allergy Dairy or Lactose', 'Headache', 'Hemochromatosis', 'Allergy Mold or Dust', 'Allergy Meat', 'Allergy Processed Foods', 'Reflux Disease', 'Primary Sclerosing Cholangitis', 'Steatosis', 'Allergy Cat', 'Rheumatoid Arthritis', '']",,FollowUp
Pancreatitis Onset Year,Pancreatitis Onset Year,PancreatitisOnsetYear,Date of onset of pancreatitis.,False,,,,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
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
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', 'Coccidioidomycosis', 'Isosporiasis', 'Salmonella Septicemia', 'Mycobacterium avium Complex', 'Herpes Simplex Virus', 'Mycobacterium', 'Nocardiosis', 'NOS', 'Toxoplasmosis', 'Cytomegalovirus', 'Cryptococcosis', 'pneumonia', 'Progressive Multifocal Leukoencephalopathy', 'Candidiasis', 'Wasting Syndrome', 'Histoplasmosis', 'Mycobacterium tuberculosis', 'Pneumocystis Pneumonia', '']",,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,,"['Not Reported', 'Not Applicable', 'Proton Pump Inhibitors', 'H2 Blockers', 'unknown', 'No Treatment', 'Surgically Treated', 'Antacids', 'Medically Treated', '']",,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,,"['Not Reported', 'Current User', 'Never Used', 'Former User', 'unknown', '']",,FollowUp
ECOG Performance Status,ECOG Performance Status,ECOGPerformanceStatus,The ECOG functional performance status of the patient/participant.,False,,"['Not Reported', '""5""', '""3""', '""0.0""', '""2""', '""1""', '""2.0""', '""1.0""', '""4.0""', '""4""', '""3.0""', 'unknown', '""5.0""', '""0""', '']",,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', 'no', 'unknown', 'yes', '']",,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', 'Axumin', 'PSMA', 'Choline', 'Sodium Fluoride', '']",,FollowUp
Menopause Status,Menopause Status,MenopauseStatus,Text term used to describe the patient's menopause status.,False,,"['Not Reported', 'Postmenopausal', 'Perimenopausal', 'unknown', 'Premenopausal', '']",,FollowUp
HPV Positive Type,HPV Positive Type,HPVPositiveType,Text classification to represent the strain or type of human papillomavirus identified in an individual.,False,,"['Not Reported', '""70""', '""33""', '""63""', 'unknown', '""16""', '""56""', '""26""', '""18""', '""31""', '""45""', 'Other', '""68""', '""58""', '""51""', '""59""', '""39""', '""35""', '""82""', '""73""', '""52""', '""66""', '""53""', '']",,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', 'no', 'unknown', 'yes', '']",,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
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,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,,"['Positive Biomarkers', 'Convincing Image Source', 'Biopsy with Histologic Confirmation', '']",,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
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,"['Spinal meninges', 'Palate NOS', 'Body of pancreas', 'Biliary tract NOS', 'Small intestine NOS', 'Bone marrow', 'Lower limb NOS', 'Trigone of bladder', 'Liver', 'Intestinal tract NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Waldeyer ring', 'Lung NOS', 'External lip NOS', 'Connective subcutaneous and other soft tissues of abdomen', 'Cervix uteri', 'Overlapping lesion of endocrine glands and related structures', 'Thoracic esophagus', 'Round ligament', 'Greater curvature of stomach NOS', 'Ileum', 'Connective subcutaneous and other soft tissues of thorax', 'Cortex of adrenal gland', 'Splenic flexure of colon', 'Endometrium', 'Intrathoracic lymph nodes', 'Lateral wall of oropharynx', 'Pharynx NOS', 'Blood', 'Overlapping lesion of breast', 'Overlapping lesion of biliary tract', 'Paraurethral gland', 'Glans penis', 'Anus NOS', 'Posterior wall of nasopharynx', 'Parietal lobe', 'unknown primary site', 'Anterior wall of nasopharynx', 'Ampulla of Vater', 'Lateral wall of nasopharynx', 'Subglottis', 'Head face or neck NOS', 'Anterior wall of bladder', 'Head of pancreas', 'Lip NOS', 'Myometrium', 'Cerebrum', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Peripheral nerves and autonomic nervous system of thorax', 'Overlapping lesion of small intestine', 'Other specified parts of female genital organs', 'Overlapping lesion of rectum anus and anal canal', 'Pineal gland', 'Lymph node NOS', 'Acoustic nerve', 'Middle ear', 'External ear', 'Overlapping lesion of penis', 'Long bones of upper limb scapula and associated joints', 'Anterior surface of epiglottis', 'Overlapping lesion of skin', 'Overlapping lesion of eye and adnexa', 'Pelvic bones sacrum coccyx and associated joints', 'Body of penis', 'Lower-inner quadrant of breast', 'Central portion of breast', 'Vertebral column', 'Thymus', 'Overlapping lesion of larynx', 'Female genital tract NOS', 'Penis NOS', 'Pancreatic duct', 'Anterior mediastinum', 'Overlapping lesion of esophagus', 'Pyriform sinus', 'Gastrointestinal tract NOS', 'Retina', 'Axillary tail of breast', 'Extrahepatic bile duct', 'Lower third of esophagus', 'Tongue NOS', 'Orbit NOS', 'Overlapping lesion of vulva', 'Frontal sinus', 'Connective subcutaneous and other soft tissues NOS', 'Lower gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cornea NOS', 'Bladder NOS', 'Overlapping lesion of brain and central nervous system', 'Long bones of lower limb and associated joints', 'Sphenoid sinus', 'Main bronchus', 'Bladder neck', 'Lateral wall of bladder', 'Major salivary gland NOS', 'Overlapping lesion of cervix uteri', 'Overlapping lesion of tongue', 'Upper gum', 'Intra-abdominal lymph nodes', 'Oropharynx NOS', 'Tail of pancreas', 'Autonomic nervous system NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Body of stomach', 'Trachea', 'Overlapping lesion of brain', 'Vestibule of mouth', 'Prostate gland', 'Breast NOS', 'Epididymis', 'Overlapping lesion of stomach', 'Pelvic lymph nodes', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Urachus', 'Aortic body and other paraganglia', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Mucosa of lower lip', 'Tonsil NOS', 'Fundus uteri', 'Choroid', 'Other specified parts of pancreas', 'Overlapping lesion of palate', 'Cerebral meninges', 'External upper lip', 'Uvula', 'Gum NOS', 'Bone NOS', 'Lymph nodes of multiple regions', 'Cranial nerve NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Brain NOS', 'Abdominal esophagus', 'Pancreas NOS', 'Descending colon', 'Anterior 2/3 of tongue NOS', 'Branchial cleft', 'Peritoneum NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Rectum NOS', 'Cloacogenic zone', 'Submandibular gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Cheek mucosa', 'Retromolar area', 'Anterior floor of mouth', 'Lesser curvature of stomach NOS', 'Temporal lobe', 'Mandible', 'Vagina NOS', 'Thorax NOS', 'Lymph nodes of head face and neck', 'Abdomen NOS', 'Urethra', 'Optic nerve', 'Labium majus', 'Overlapping lesion of pancreas', 'skin of upper limb and shoulder', 'Tonsillar pillar', 'Overlapping lesion of digestive system', 'Parathyroid gland', 'Craniopharyngeal duct', 'Overlapping lesion of corpus uteri', 'Lingual tonsil', 'Ovary', 'Undescended testis', 'Endocervix', 'Lymph nodes of axilla or arm', 'Hypopharyngeal aspect of aryepiglottic fold', 'Dome of bladder', 'Thyroid gland', 'Ascending colon', 'Overlapping lesion of floor of mouth', 'Spermatic cord', 'Pelvis NOS', 'Cervical esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Broad ligament', 'Parametrium', 'Nasopharynx NOS', 'Nipple', 'Occipital lobe', 'Bone of limb NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Eyelid', 'Gallbladder', 'Dorsal surface of tongue NOS', 'Skin of scalp and neck', 'Carotid body', 'Upper lobe lung', 'Cerebellum NOS', 'Hypopharynx NOS', 'Overlapping lesion of colon', 'Male genital organs NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Accessory sinus NOS', 'Hard palate', 'Overlapping lesion of retroperitoneum and peritoneum', 'Mucosa of upper lip', 'Colon NOS', 'Upper limb NOS', 'Ventral surface of tongue NOS', 'Middle third of esophagus', 'Laryngeal cartilage', 'Adrenal gland NOS', 'Olfactory nerve', 'Gastric antrum', 'Mucosa of lip NOS', 'Overlapping lesion of tonsil', 'Overlapping lesions of oropharynx', 'Ureter', 'Maxillary sinus', 'Posterior wall of oropharynx', 'skin of lower limb and hip', 'Overlapping lesion of heart mediastinum and pleura', 'Connective subcutaneous and other soft tissues of head face and neck', 'Not Reported', 'Other ill-defined sites', 'External lower lip', 'unknown', 'Cauda equina', 'Base of tongue NOS', 'Rib sternum clavicle and associated joints', 'Descended testis', 'Lateral floor of mouth', 'Conjunctiva', 'Peripheral nerves and autonomic nervous system of pelvis', 'Clitoris', 'Hepatic flexure of colon', 'Parotid gland', 'Other specified parts of male genital organs', 'Overlapping lesion of ill-defined sites', 'Lower-outer quadrant of breast', 'Nervous system NOS', 'Overlapping lesion of accessory sinuses', 'Endocrine gland NOS', 'Superior wall of nasopharynx', 'Exocervix', 'Labium minus', 'Tonsillar fossa', 'Spinal cord', 'Frontal lobe', 'Overlapping lesion of hypopharynx', 'Stomach NOS', 'Posterior mediastinum', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Glottis', 'Pleura NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Esophagus NOS', 'Jejunum', 'Bones of skull and face and associated joints', 'Placenta', 'Ethmoid sinus', 'Fundus of stomach', 'Pylorus', 'Larynx NOS', 'Medulla of adrenal gland', 'Transverse colon', 'Uterus NOS', 'Soft palate NOS', 'Cardia NOS', 'Corpus uteri', 'skin NOS', 'Short bones of lower limb and associated joints', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sublingual gland', 'Scrotum NOS', 'Appendix', 'Hematopoietic system NOS', 'Rectosigmoid junction', 'Islets of Langerhans', 'Lacrimal gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Posterior wall of bladder', 'Posterior wall of hypopharynx', 'Commissure of lip', 'Short bones of upper limb and associated joints', 'Floor of mouth NOS', 'Mediastinum NOS', 'Overlapping lesion of bladder', 'Ventricle NOS', 'Lower lobe lung', 'Skin of lip NOS', 'Kidney NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of major salivary glands', 'Vulva NOS', 'Upper third of esophagus', 'Sigmoid colon', 'Duodenum', 'Ureteric orifice', 'Lymph nodes of inguinal region or leg', 'Overlapping lesion of urinary organs', 'Upper respiratory tract NOS', 'Intrahepatic bile duct', 'Retroperitoneum', 'Vallecula', 'Middle lobe lung', 'Urinary system NOS', 'Postcricoid region', 'Supraglottis', 'Eye NOS', 'Anal canal', 'Meninges NOS', 'Upper-inner quadrant of breast', 'Spleen', 'Overlapping lesion of lung', 'Uterine adnexa', 'Specified parts of peritoneum', 'Prepuce', 'Upper-outer quadrant of breast', 'Nasal cavity', 'Cecum', 'Isthmus uteri', 'Testis NOS', 'Fallopian tube', 'Overlapping lesion of lip', 'Skin of other and unspecified parts of face', 'Mouth NOS', 'Renal pelvis', 'Overlapping lesion of male genital organs', 'Meckel diverticulum', 'Reticuloendothelial system NOS', 'Skin of trunk', 'Brain stem', 'Ill-defined sites within respiratory system', 'Border of tongue', 'Heart', 'Ciliary body', '']","['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
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,"['Not Reported', 'Distant', 'Biochemical', 'Regional', 'Local', 'unknown', '']","['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
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,,"['Not Reported', 'MX', 'M1a', 'M0', 'M1b', 'cM0 (i+)', 'unknown', 'M1c', 'M1', '']",,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', 'no', 'unknown', 'yes', '']",,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,,"['Intraductal papillary adenocarcinoma with invasion', 'Multiple myeloma', 'Teratoma malignant NOS', 'Intraductal carcinoma noninfiltrating NOS', 'Renal medullary carcinoma', 'Diffuse melanocytosis', 'Tubulovillous adenoma NOS', 'Mucosal-associated lymphoid tissue lymphoma', 'Hepatoid adenocarcinoma', 'Osteoblastoma malignant', 'Cervical intraepithelial neoplasia low grade', 'Non-Hodgkin lymphoma NOS', 'Therapy related myeloid neoplasm', 'Classical Hodgkin lymphoma nodular sclerosis grade 1', 'Glioblastoma', 'Rhabdomyoma NOS', 'Precursor T-cell lymphoblastic lymphoma', 'Mixed medullary-follicular carcinoma', 'Chronic monocytic leukemia', 'Squamous cell carcinoma clear cell type', 'Hepatocellular adenoma', 'Non-small cell carcinoma', 'Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis', 'Malignant melanoma in congenital melanocytic nevus', 'Neuroepithelioma NOS', 'Bronchiolar carcinoma', 'Adenocarcinoma in situ in adenomatous polyp', 'Melanoma in situ', 'Splenic B-cell lymphoma/leukemia unclassifiable', 'Chondrosarcoma grade 2/3', 'Eosinophil adenoma', 'Transitional cell carcinoma in situ', 'Tubulocystic renal cell carcinoma', 'Intraepidermal squamous cell carcinoma Bowen type', 'c-ALL', 'Burkitt lymphoma NOS (Includes all variants)', 'Pleomorphic carcinoma', 'Adenocarcinoma in situ non-mucinous', 'Adenocarcinoma metastatic NOS', 'Papillary urothelial carcinoma', 'Carcinoma in situ in adenomatous polyp', 'Basophil carcinoma', 'Large cell carcinoma NOS', 'Papillary cystadenoma NOS', 'Chronic myelogenous leukemia BCR-ABL positive', 'Papillary carcinoma NOS', 'Eosinophil carcinoma', 'Malignant lymphoma lymphoblastic NOS', 'Meningioma malignant', 'Malignant lymphoma small B lymphocytic NOS', 'Undifferentiated pleomorphic sarcoma', 'Adenocarcinoma diffuse type', 'Glioma malignant', 'Paget disease extramammary', 'Papillotubular adenocarcinoma', 'Bronchiolo-alveolar carcinoma Clara cell and goblet cell type', 'Kaposi sarcoma', 'Melanotic medulloblastoma', 'Hodgkin granuloma', 'Hodgkin lymphoma nodular sclerosis NOS', 'Bronchio-alveolar carcinoma mucinous', 'Precancerous melanosis NOS', 'High-grade serous carcinoma', 'Hepatoid carcinoma', 'Splenic diffuse red pulp small B-cell lymphoma', 'Neoplasm metastatic', 'Secondary carcinoma', 'Lymphoma NOS', 'Precursor B-cell lymphoblastic leukemia', 'T-cell large granular lymphocytic leukemia', 'Astrocytoma anaplastic', 'Renal cell adenocarcinoma', 'Papillary transitional cell carcinoma', 'Pancreatoblastoma', 'Pleomorphic lobular carcinoma in situ', 'Bronchiolo-alveolar carcinoma indeterminate type', 'Paraganglioma malignant', 'Sclerosing hepatic carcinoma', 'Infiltrating duct carcinoma NOS', 'Acute leukemia Burkitt type', 'Gastrinoma NOS', 'Teratoma NOS', 'Renal carcinoma collecting duct type', 'Capillary hemangioma', 'Unclassified tumor borderline malignancy', 'Undifferentiated round cell sarcoma', 'Burkitt tumor', 'Tubular adenocarcinoma', 'Medullary osteosarcoma', 'Intraductal tubulopapillary neoplasm', 'Liposarcoma NOS', 'Mixed tumor NOS', 'Papillary microcarcinoma', 'Adenocarcinoma in polypoid adenoma', 'Carcinoma intestinal type', 'Esophageal squamous intraepithelial neoplasia (dysplasia) low grade', 'Meningioma NOS', 'Papillary meningioma', 'Mixed adenocarcinoma and epidermoid carcinoma', 'Adenocarcinoma NOS', 'Combined small cell-adenocarcinoma', 'Gastrin cell tumor', 'Haemangioblastoma', 'Gastrin cell tumor malignant', 'Acute lymphoblastic leukemia-lymphoma NOS', 'Liver cell adenoma', 'Myeloid leukemia NOS', 'Undifferentiated spindle cell sarcoma', 'Tumor secondary', 'Basal cell adenocarcinoma', 'Papillary serous cystadenocarcinoma', 'Mammary carcinoma in situ', 'Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL)', 'Pigmented nevus NOS', 'Ganglioglioma NOS', 'Malignant lymphoma immunoblastic NOS', 'Tumor embolus', 'Malignant melanoma regressing', 'Dermatofibroma NOS', 'Pleomorphic lobular carcinoma', 'Nephroblastoma NOS', 'Meningioma anaplastic', 'Hodgkin paragranuloma NOS', 'Hodgkin disease NOS', 'Capillary lymphangioma', 'Malignancy', 'Interstitial cell tumor malignant', 'Papillary serous adenocarcinoma', 'Sarcoma NOS', 'Meningeal melanoma', 'Chronic myeloproliferative disease NOS', 'Basophil adenocarcinoma', 'Malignant lymphoma large B-cell NOS', 'Tubular carcinoid', 'Unclassified tumor malignant uncertain whether primary or metastatic', 'Chronic myelomonocytic leukemia NOS', 'Acute myeloid leukemia MLL', 'Intraductal carcinoma clinging', 'Malignant lymphoma Hodgkin', 'Osteosarcoma NOS', 'Adenocarcinoid tumor', 'Nevus NOS', 'Hodgkin lymphoma NOS', 'Tubular adenoma NOS', 'Eosinophilic granuloma', 'Esophageal glandular dysplasia (intraepithelial neoplasia) low grade', 'B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL)', 'Intradermal nevus', 'Malignant lymphoma lymphocytic diffuse NOS', 'Intraductal and lobular carcinoma', 'Pituitary carcinoma NOS', 'Medullary carcinoma NOS', 'Melanotic progonoma', 'Epidermoid carcinoma NOS', 'Basal cell tumor', 'Mixed small cell carcinoma', 'Acute lymphoid leukemia', 'Bile duct adenocarcinoma', 'Serous cystadenocarcinoma NOS', 'Small cell sarcoma', 'Juvenile myelomonocytic leukemia', 'Adenocarcinoma in villous adenoma', 'Eosinophil adenocarcinoma', 'Pancreatic endocrine tumor benign', 'Squamous cell carcinoma adenoid', 'Tubulolobular carcinoma', 'Bronchial adenoma carcinoid', 'Melanotic neurofibroma', 'Bile duct carcinoma', 'Intraductal papillary carcinoma', 'Malignant lymphoma mixed cell type nodular', 'Pulmonary artery intimal sarcoma', 'Melanocytic nevus', 'Chronic lymphoid leukemia', 'Precursor B-cell lymphoblastic lymphoma', 'Precursor T-cell lymphoblastic leukemia', 'Preleukemia', 'Acute basophilic leukaemia', 'Adenocarcinoma in situ NOS', 'Malignant lymphoma large B-cell diffuse NOS', 'Burkitt cell leukemia', 'Composite Hodgkin and non-Hodgkin lymphoma', 'Mixed squamous cell and glandular papilloma', 'Papillomatosis NOS', 'Combined large cell neuroendocrine carcinoma', 'Mucous adenocarcinoma', 'Bronchiolar adenocarcinoma', 'Epidermoid carcinoma in situ NOS', 'Malignant melanoma in giant pigmented nevus', 'Chronic myelomonocytic leukemia Type II', 'Typical carcinoid', 'Bronchiolo-alveolar adenocarcinoma NOS', 'Monocytic leukemia NOS', 'Rhabdoid meningioma', 'Adenocarcinoma of anal glands', 'Papillary squamous cell carcinoma in situ', 'Myeloma NOS', 'Adenocarcinoma of anal ducts', 'Pulmonary blastoma', 'Tumor cells benign', 'Carcinoma in a polyp NOS', 'Interstitial cell tumor NOS', 'Epithelial tumor benign', 'Tubular androblastoma with lipid storage', 'Burkitt-like lymphoma', 'Malignant lymphoma lymphocytic nodular NOS', 'Adenocarcinoma in situ mucinous', 'Preleukemic syndrome', 'Ductal carcinoma in situ NOS', 'Intraepidermal carcinoma NOS', 'Malignant lymphoma mixed cell type follicular', 'Papillary adenocarcinoma NOS', 'B-ALL', 'Carcinoma undifferentiated NOS', 'Cementoma NOS', 'Pancreatobiliary-type carcinoma', 'Papillary tumor of the pineal region', 'Chronic myelomonocytic leukemia in transformation', 'Endometrioid adenocarcinoma NOS', 'Papillary serous cystadenoma NOS', 'Interstitial cell tumor benign', 'Neoplasm benign', 'Lobular and ductal carcinoma', 'Mixed adenocarcinoma and squamous cell carcinoma', 'Melanocytoma NOS', 'Acute lymphatic leukemia', 'Acute lymphoblastic leukemia mature B-cell type', 'Chronic granulocytic leukemia NOS', 'Malignant lymphoma nodular NOS', 'Squamous cell carcinoma in situ NOS', 'Acute lymphoblastic leukemia precursor cell type', 'Infiltrating duct and cribriform carcinoma', 'Meningeal melanocytoma', 'Familial adenomatous polyposis', 'Malignant lymphoma non-Hodgkin NOS', 'Papillotubular adenoma', 'Mixed pancreatic endocrine and exocrine tumor malignant', 'Small congenital nevus', 'Esophageal glandular dysplasia (intraepithelial neoplasia) high grade', 'Mixed medullary-papillary carcinoma', 'Esophageal intraepithelial neoplasia high grade', 'Melanoma NOS', 'Bile duct adenoma', 'Neoplasm NOS', 'Gastrointestinal stromal tumor malignant', 'Tumor NOS', 'Chondroma NOS', 'Precursor cell lymphoblastic leukemia NOS', 'Basal cell carcinoma NOS', 'Squamous cell carcinoma NOS', 'Transitional carcinoma', 'Undifferentiated sarcoma', 'Undifferentiated epithelioid sarcoma', 'Neoplasm malignant uncertain whether primary or metastatic', 'Papillary and follicular carcinoma', 'Pro-T ALL', 'Rhabdoid sarcoma', 'Renal cell carcinoma unclassified', 'Adult T-cell lymphoma', 'Papillary epidermoid carcinoma', 'Hodgkin lymphoma mixed cellularity NOS', 'Unclassified tumor benign', 'Classical Hodgkin lymphoma lymphocyte-rich', 'Undifferentiated leukaemia', 'Classical Hodgkin lymphoma nodular sclerosis cellular phase', 'Liposarcoma well differentiated', 'Paget disease of breast', 'Chronic lymphocytic leukemia', 'Renal cell carcinoma NOS', 'Adenocarcinoma intestinal type', 'Duct carcinoma NOS', 'Malignant lymphoma diffuse NOS', 'Diffuse large B-cell lymphoma NOS', 'Inflammatory carcinoma', 'Chronic myeloid leukemia NOS', 'Carcinoma metastatic NOS', 'Transitional cell carcinoma', 'Tumor metastatic', 'Melanotic MPNST', 'Papillary adenoma NOS', 'Pancreatic endocrine tumor NOS', 'Tubular carcinoma', 'T-cell lymphoma NOS', 'Astrocytoma NOS', 'Bronchiolo-alveolar carcinoma goblet cell type', 'Malignant melanoma in precancerous melanosis', 'Glioma NOS', 'Chronic lymphatic leukemia', 'Lymphocytic leukemia NOS', 'Duct adenocarcinoma NOS', 'Bronchial-associated lymphoid tissue lymphoma', 'Central neurocytoma', 'Hodgkin sarcoma', 'Papillary squamous cell carcinoma', 'Pulmonary adenomatosis', 'Malignant melanoma in Hutchinson melanotic freckle', 'Classical Hodgkin lymphoma nodular sclerosis grade 2', 'Dysplastic nevus', 'Cancer', 'Lobular carcinoma NOS', 'Mixed tumor malignant NOS', 'Sclerosing hemangioma', 'Chronic myeloproliferative disorder', 'Non-lymphocytic leukemia NOS', 'Adenocarcinoma pancreatobiliary type', 'Intraductal tubular-papillary neoplasm high grade', 'Neoplasm secondary', 'Hepatocarcinoma', 'Classical Hodgkin lymphoma lymphocyte depletion reticular', 'Classical Hodgkin lymphoma nodular sclerosis NOS', 'Bronchio-alveolar carcinoma mixed mucinous and non-mucinous', 'Renal cell carcinoma sarcomatoid', 'Renal cell carcinoma chromophobe type', 'Lobular carcinoma noninfiltrating', 'Melanoameloblastoma', 'Cerebellar sarcoma NOS', 'Diffuse astrocytoma IDH-wildtype', 'Tubulo-papillary adenoma', 'Rhabdomyosarcoma with ganglionic differentiation', 'Non-invasive low grade serous carcinoma', 'Serous surface papillary carcinoma', 'Adenocarcinoma endocervical type', 'B-cell lymphocytic leukemia/small lymphocytic lymphoma', 'Peripheral T-cell lymphoma large cell', 'Pancreatic microadenoma', 'Acute myelomonocytic leukemia', 'Ependymoma NOS', 'T-cell large granular lymphocytosis', 'Pancreatic endocrine tumor malignant', 'Liposarcoma differentiated', 'Undifferentiated high-grade pleomorphic sarcoma', 'Chronic neutrophilic leukemia', 'Malignant lymphoma NOS', 'Combined hepatocellular carcinoma and cholangiocarcinoma', 'Malignant melanoma in junctional nevus', 'Hepatocellular carcinoma NOS', 'Malignant lymphoma lymphocytic NOS', 'Pleomorphic lipoma', 'Papilloma of bladder', 'Bronchiolo-alveolar carcinoma NOS', 'Acute lymphoblastic leukemia NOS', 'Pituitary adenoma NOS', 'Adult T-cell lymphoma/leukemia', 'Not Reported', 'Tumor cells uncertain whether benign or malignant', 'Splenic lymphoma with villous lymphocytes', 'unknown', 'Renal cell carcinoma spindle cell', 'Pleomorphic adenoma', 'Paget disease and infiltrating duct carcinoma of breast', 'Duct carcinoma desmoplastic type', 'Oat cell carcinoma', 'Nonpigmented nevus', 'Endometrioid adenofibroma NOS', 'Paget disease and intraductal carcinoma of breast', 'Unclassified tumor uncertain whether benign or malignant', 'Tumorlet benign', 'Bronchial adenoma NOS', 'B lymphoblastic leukemia/lymphoma with hyperdiploidy', 'Carcinoma in situ in a polyp NOS', 'Chronic myelocytic leukemia NOS', 'Adenocarcinoma in a polyp NOS', 'Adult rhabdomyoma', 'Paget disease mammary', 'Melanotic neuroectodermal tumor', 'Neuroblastoma NOS', 'Intravascular B-cell lymphoma', 'Malignant lymphoma large cell NOS', 'Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive', 'Inflammatory adenocarcinoma', 'Prostatic intraepithelial neoplasia grade III', 'Gastrinoma malignant', 'Bronchiolo-alveolar carcinoma non-mucinous', 'Pleomorphic liposarcoma', 'Rhabdosarcoma', 'Intraductal carcinoma NOS', 'Primary amyloidosis', 'Small cell neuroendocrine carcinoma', 'Intraductal micropapillary carcinoma', 'Intraductal papillary adenocarcinoma NOS', 'Combined/mixed carcinoid and adenocarcinoma', 'Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive', 'Neoplasm malignant', 'Papillary glioneuronal tumor', 'Adenocarcinoma combined with other types of carcinoma', 'Adenocarcinoma in adenomatous polyp', 'Liver cell carcinoma', 'Endometrioid carcinoma NOS', 'Neoplasm uncertain whether benign or malignant', 'Papillary carcinoma in situ', 'Carcinoma in situ NOS', 'Papillary adenocarcinoma follicular variant', 'Spindle cell melanoma NOS', 'Undifferentiated uterine sarcoma', 'Classical Hodgkin lymphoma mixed cellularity NOS', 'Intraductal carcinoma solid type', 'Pro-B ALL', 'Rhabdomyosarcoma NOS', 'Dermal nevus', 'Combined small cell carcinoma', 'Ductal carcinoma NOS', 'Pagetoid reticulosis', 'Chronic granulocytic leukemia BCR/ABL', 'Medulloblastoma NOS', 'Secretory carcinoma of breast', 'Bronchial adenoma cylindroid', 'Infiltrating duct and colloid carcinoma', 'Diffuse astrocytoma IDH-mutant', 'Bile duct cystadenoma', 'Cervical intraepithelial neoplasia grade III', 'Splenic marginal zone B-cell lymphoma', 'Medullary adenocarcinoma', 'Small cell osteosarcoma', 'Papilloma NOS', 'B lymphoblastic leukemia/lymphoma NOS', 'Pigmented basal cell carcinoma', 'Lobular adenocarcinoma', 'Melanoma malignant of soft parts', 'Infiltrating basal cell carcinoma NOS', 'Combined small cell-large carcinoma', 'Paraganglioma NOS', 'Adenocarcinoma in situ in a polyp NOS', 'Carcinoma in adenomatous polyp', 'Acute leukemia NOS', 'Chronic leukemia NOS', 'Adenocarcinoma in situ in tubular adenoma', 'Cerebellar liponeurocytoma', 'Melanotic psammomatous MPNST', 'Bile duct cystadenocarcinoma', 'Tumor malignant NOS', 'Myelocytic leukemia NOS', 'Unclassified tumor malignant', 'Lymphatic leukemic NOS', 'Malignant lymphoma mixed cell type diffuse', 'Pancreatic endocrine tumor nonfunctioning', 'Eosinophilic leukemia', 'Acute myeloid leukemia minimal differentiation', 'Neurofibroma NOS', 'Endometrial sarcoma NOS', 'Basophil adenoma', 'Malignant melanoma NOS', 'Melanocytoma eyeball', 'Small cell carcinoma NOS', 'Mixed pineal tumor', 'Classical Hodgkin lymphoma lymphocyte depletion NOS', 'Combined small cell-squamous cell carcinoma', 'Duct adenoma NOS', 'Intraductal carcinoma and lobular carcinoma in situ', 'Intracystic papilloma', 'Adenocarcinoma in tubular adenoma', 'Micropapillary carcinoma NOS', 'Paraganglioma benign', 'Splenic marginal zone lymphoma NOS', 'Carcinoma NOS', 'Tubulopapillary adenocarcinoma', 'Ewing sarcoma', 'Neurofibrosarcoma', 'Carcinoma diffuse type', 'Diffuse astrocytoma low grade', 'Pancreatobiliary neoplasm non-invasive', 'Rodent ulcer', 'Rhabdoid tumor NOS', 'Basal cell adenoma', 'Tumor benign', 'Neuroendocrine carcinoma NOS', 'Carcinoma in pleomorphic adenoma', 'Peripheral T-cell lymphoma NOS', 'Tubular androblastoma NOS', 'Carcinosarcoma NOS', 'Astrocytoma low grade', 'Osteoblastoma NOS', 'Hepatocholangiocarcinoma', 'Acinar cell carcinoma', 'Epithelial tumor malignant', 'Endometrioid adenoma NOS', 'Acute lymphocytic leukemia', 'Myoepithelioma', 'Pigmented adenoma', 'Lymphoblastoma', 'Papillomatosis glandular', 'Lymphoblastic leukemia NOS', 'Duct cell carcinoma', 'Acute myeloid leukemia NOS', 'Bronchiolo-alveolar carcinoma Clara cell', 'Chronic myelomonocytic leukemia Type 1', 'Intraductal tubular-papillary neoplasm low grade', 'Esophageal squamous intraepithelial neoplasia (dysplasia) high grade', 'Acute promyelocytic leukemia NOS', 'Intraductal adenocarcinoma noninfiltrating NOS', 'Carcinoma anaplastic NOS', 'Lobular carcinoma in situ NOS', 'T lymphoblastic leukemia/lymphoma', 'Tumor cells malignant', 'Papillary adenofibroma', 'Neurofibromatosis NOS', 'Neurosarcoma', 'Papillary renal cell carcinoma', 'Central neuroblastoma', 'Basal cell epithelioma', 'Haemangiosarcoma', 'Tumor cells NOS', 'Melanotic schwannoma', 'B cell lymphoma NOS', 'Skin appendage carcinoma', 'Spindle cell carcinoma NOS']",,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,,"['Not Reported', 'Unifocal', 'Multifocal', 'unknown', '']",,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', 'Favorable', 'Unfavorable', 'unknown', '']",,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', 'no', 'unknown', 'yes', '']",,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
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,,"['Not Reported', 'N1bII', 'N0', 'N3c', 'N0 (mol+)', 'N2', 'unknown', 'N1bIV', 'N0 (i+)', 'N2a', 'N0 (i-)', 'N3', 'N2b', 'N1b', 'NX', 'N4', 'N1c', 'N2c', 'N3b', 'N1bI', 'N1', 'N3a', 'N1mi', 'N1bIII', 'N1a', 'N0 (mol-)', '']",,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
Non Nodal Regional Disease,Non Nodal Regional Disease,NonNodalRegionalDisease,The text term used to describe whether the patient had non-nodal regional disease.,False,,"['Not Reported', 'Indeterminate', 'unknown', 'Present', 'Absent', '']",,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,,"['Not Reported', 'Stage IB', 'Stage 0', 'Stage IB2', 'Stage 0is', 'Stage III', 'Stage IIA', 'Stage II', 'Stage IS', 'unknown', 'Stage IIA1', 'Stage Tis', 'Stage IIIA', 'Stage IA1', 'Stage IVA', 'Stage IIC', 'Stage IVB', 'Stage IIIC', 'Stage IV', 'Stage IB1', 'Stage IIIB', 'Stage I', 'Stage IA2', 'Stage X', 'Stage IC', 'Stage IIIC2', 'Stage IIC1', 'Stage IIB', 'Stage 0a', 'Stage IVC', 'Stage IA', 'Stage IIIC1', 'Stage IIA2', '']",,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
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 Reported', 'Recurrence', 'Other', 'Primary', 'Not Allowed To Collect', 'unknown', 'Metastasis', '']",,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,,"['Low-Intermediate Risk', 'High Risk', 'Low Risk', 'High-Intermediate Risk', '']",,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 5', 'Group 3', 'Group 4', 'Group 2', 'Group 1', '']",,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', 'no', 'unknown', 'yes', '']",,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 5', 'Pattern 2', 'Pattern 1', 'Pattern 3', 'Pattern 4', '']",,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
Tumor Grade,Tumor Grade,TumorGrade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.",False,,"['Not Reported', 'Low Grade', 'Not Applicable', 'G2', 'High Grade', 'G3', 'G4', 'G1', 'GX', 'unknown', 'Intermediate Grade', 'GB', '']",,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,,"['Not Reported', '2', '1', '3', 'unknown', '4', '']",,Diagnosis
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
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,,"['Not Reported', 'Biochemical evidence of disease without structural correlate', 'Not Applicable', 'unknown tumor status', 'Loco-regional recurrence/progression', 'Not Allowed To Collect', 'Tumor free', 'With tumor', 'Distant met recurrence/progression']",,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,,"['Not Reported', 'Lymph Node NOS', 'Pleura', 'Abdomen', 'Distant Nodes', 'unknown', 'Soft Tissue', 'Scalp', 'Distant Organ', 'Kidney', 'Adrenal Gland', 'Peritoneal Cavity', 'Peritoneum', 'Pelvis', 'Central Nervous System', 'Ovary', 'Skin', 'Liver', 'Spinal Cord', 'Bone Marrow', 'Ascites', 'Bone', 'Brain', 'Groin', 'Cerebrospinal Fluid', 'Lung', 'Inguinal', 'Colon', 'Lymph Node', 'Mediastinum', 'Axillary', 'Omentum', 'Small Intestine', '']",,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,,"['Not Reported', 'T1b1', 'Tis (LCIS)', 'T4a', 'T4b', 'unknown', 'T2a', 'T4e', 'T3b', 'T1a', 'T2a2', 'T1mi', 'T4d', 'Tis', 'T4c', 'T3c', 'T4', 'Ta', 'T0', 'T1a1', 'T2a1', 'T1b', 'T1a2', 'T1', 'T2d', 'T3d', 'T2c', 'T1b2', 'T1c', 'T3', 'T2b', 'TX', ""Tis (Paget's)"", 'T2', 'T3a', 'Tis (DCIS)', '']",,Diagnosis
Gross Tumor Weight,Gross Tumor Weight,GrossTumorWeight,"Numeric value used to describe the gross pathologic tumor weight, measured in grams.",False,,,,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,,"['Not Reported', 'Indeterminate', 'unknown', 'Present', 'Absent', '']",,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
Laterality,Laterality,Laterality,"For tumors in paired organs, designates the side on which the cancer originates.",False,,"['Not Reported', 'Unilateral', 'Bilateral', 'unknown', 'Right', 'Midline', 'Left', '']",,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
Greatest Tumor Dimension,Greatest Tumor Dimension,GreatestTumorDimension,Numeric value that represents the measurement of the widest portion of the tumor in centimeters.,False,,,,Diagnosis
Tumor Depth,Tumor Depth,TumorDepth,"Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).",False,,,,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,,"['Not Reported', 'High Risk', 'Intermediate Risk', 'unknown', 'Low Risk', '']",,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 Reported', 'no', 'Not Allowed To Collect', 'Yes - Vascular Invasion Present', 'unknown', '']",,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,,"['Not Reported', 'High Risk', 'Intermediate Risk', 'unknown', 'Low Risk', '']",,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,,"['Not Reported', 'Poor Prognosis', 'Intermediate Prognosis', 'unknown', 'Good Prognosis', '']",,Diagnosis
Lymph Node Involved Site,Lymph Node Involved Site,LymphNodeInvolvedSite,The text term used to describe the anatomic site of lymph node involvement.,False,,"['Not Reported', 'Iliac', 'unknown', 'Paraaortic', 'Iliac-external', 'Supraclavicular', 'Occipital', 'Hilar', 'Parotid', 'NOS', 'Retroperitoneal', 'Femoral', 'Submandibular', 'Inguinal', 'Popliteal', 'Splenic', 'Cervical', 'Epitrochlear', 'Axillary', 'None', 'Mediastinal', 'Iliac-common', 'Mesenteric', '']",,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', 'unknown', 'Present', 'Absent', '']",,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,,"['Not Reported', 'White Matter', 'Deep Gray', 'unknown', 'Spinal Cord', 'Cerebral Cortex', '']",,Diagnosis
Method of Diagnosis,Method of Diagnosis,MethodofDiagnosis,Text term used to describe the method used to confirm the patients malignant diagnosis.,False,,"['Not Reported', 'Surgical Resection', 'Excisional Biopsy', 'unknown', 'Autopsy', 'Incisional Biopsy', 'Thoracentesis', 'Fine Needle Aspiration', 'Cytology', 'Ultrasound Guided Biopsy', 'Laparotomy', 'Bone Marrow Aspirate', 'Other', 'Diagnostic Imaging', 'Pap Smear', 'Laparoscopy', 'Debulking', 'Blood Draw', 'Biopsy', 'Physical Exam', 'Core Biopsy', 'Cystoscopy', 'Pathologic Review', 'Enucleation', 'Dilation and Curettage Procedure', '']",,Diagnosis
Best Overall Response,Best Overall Response,BestOverallResponse,The best improvement achieved throughout the entire course of protocol treatment.,False,,"['RP-Response', 'DU-Disease Unchanged', 'CPD-Clinical Progression', 'sCR-Stringent Complete Response', 'PSR-Pseudoresponse', 'Non-CR/Non-PD-Non-CR/Non-PD', 'IPD-Immunoprogression', 'IMR-Immunoresponse', 'RPD-Radiographic Progressive Disease', 'MR-Minimal/Marginal Response', 'SPD-Surgical Progression', 'VGPR-Very Good Partial Response', 'PA-Palliative Therapy', 'CRU-Complete Response Unconfirmed', 'RD-Responsive Disease', 'PR-Partial Response', 'MX-Mixed Response', 'SD-Stable Disease', 'PPD-Pseudoprogression', 'PB-Palliative Benefit', 'NPB-No Palliative Benefit', 'CR-Complete Response', 'AJ-Adjuvant Therapy', 'NR-No Response', 'PD-Progressive Disease', 'TE-Too Early', '']",,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,,"['Not Reported', 'N1bII', 'N0', 'N3c', 'N0 (mol+)', 'N2', 'unknown', 'N1bIV', 'N0 (i+)', 'N2a', 'N0 (i-)', 'N3', 'N2b', 'N1b', 'NX', 'N4', 'N1c', 'N2c', 'N3b', 'N1bI', 'N1', 'N3a', 'N1mi', 'N1bIII', 'N1a', 'N0 (mol-)', '']",,Diagnosis
Ovarian Specimen Status,Ovarian Specimen Status,OvarianSpecimenStatus,The text term used to describe the physical condition of the involved ovary.,False,,"['Not Reported', 'Ovarian Capsule Fragmented', 'Ovarian Capsule Intact', 'Ovarian Capsule Ruptured', 'unknown', '']",,Diagnosis
ISS Stage,ISS Stage,ISSStage,The multiple myeloma disease stage at diagnosis.,False,,"['Not Reported', 'I', 'II', 'unknown', 'III', '']",,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,,"['Not Reported', 'Non-Malignant', 'Malignant', 'Unsatisfactory', 'unknown', 'Atypical', '']",,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 Reported', 'no', 'yes', 'Not Allowed To Collect', 'unknown', '']",,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,,"['Spinal meninges', 'Palate NOS', 'Body of pancreas', 'Biliary tract NOS', 'Small intestine NOS', 'Bone marrow', 'Lower limb NOS', 'Trigone of bladder', 'Liver', 'Intestinal tract NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Waldeyer ring', 'Lung NOS', 'External lip NOS', 'Connective subcutaneous and other soft tissues of abdomen', 'Cervix uteri', 'Overlapping lesion of endocrine glands and related structures', 'Thoracic esophagus', 'Round ligament', 'Greater curvature of stomach NOS', 'Ileum', 'Connective subcutaneous and other soft tissues of thorax', 'Cortex of adrenal gland', 'Splenic flexure of colon', 'Endometrium', 'Intrathoracic lymph nodes', 'Lateral wall of oropharynx', 'Pharynx NOS', 'Blood', 'Overlapping lesion of breast', 'Overlapping lesion of biliary tract', 'Paraurethral gland', 'Glans penis', 'Anus NOS', 'Posterior wall of nasopharynx', 'Parietal lobe', 'unknown primary site', 'Anterior wall of nasopharynx', 'Ampulla of Vater', 'Lateral wall of nasopharynx', 'Subglottis', 'Head face or neck NOS', 'Anterior wall of bladder', 'Head of pancreas', 'Lip NOS', 'Myometrium', 'Cerebrum', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Peripheral nerves and autonomic nervous system of thorax', 'Overlapping lesion of small intestine', 'Other specified parts of female genital organs', 'Overlapping lesion of rectum anus and anal canal', 'Pineal gland', 'Lymph node NOS', 'Acoustic nerve', 'Middle ear', 'External ear', 'Overlapping lesion of penis', 'Long bones of upper limb scapula and associated joints', 'Anterior surface of epiglottis', 'Overlapping lesion of skin', 'Overlapping lesion of eye and adnexa', 'Pelvic bones sacrum coccyx and associated joints', 'Body of penis', 'Lower-inner quadrant of breast', 'Central portion of breast', 'Vertebral column', 'Thymus', 'Overlapping lesion of larynx', 'Female genital tract NOS', 'Penis NOS', 'Pancreatic duct', 'Anterior mediastinum', 'Overlapping lesion of esophagus', 'Pyriform sinus', 'Gastrointestinal tract NOS', 'Axillary tail of breast', 'Retina', 'Extrahepatic bile duct', 'Lower third of esophagus', 'Tongue NOS', 'Orbit NOS', 'Overlapping lesion of vulva', 'Frontal sinus', 'Connective subcutaneous and other soft tissues NOS', 'Lower gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cornea NOS', 'Bladder NOS', 'Overlapping lesion of brain and central nervous system', 'Long bones of lower limb and associated joints', 'Sphenoid sinus', 'Main bronchus', 'Bladder neck', 'Lateral wall of bladder', 'Major salivary gland NOS', 'Overlapping lesion of cervix uteri', 'Overlapping lesion of tongue', 'Upper gum', 'Intra-abdominal lymph nodes', 'Oropharynx NOS', 'Tail of pancreas', 'Autonomic nervous system NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Body of stomach', 'Trachea', 'Overlapping lesion of brain', 'Vestibule of mouth', 'Prostate gland', 'Breast NOS', 'Epididymis', 'Overlapping lesion of stomach', 'Pelvic lymph nodes', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Urachus', 'Aortic body and other paraganglia', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Mucosa of lower lip', 'Tonsil NOS', 'Fundus uteri', 'Choroid', 'Other specified parts of pancreas', 'Overlapping lesion of palate', 'Cerebral meninges', 'External upper lip', 'Uvula', 'Gum NOS', 'Bone NOS', 'Lymph nodes of multiple regions', 'Cranial nerve NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Brain NOS', 'Abdominal esophagus', 'Pancreas NOS', 'Descending colon', 'Anterior 2/3 of tongue NOS', 'Branchial cleft', 'Peritoneum NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Rectum NOS', 'Cloacogenic zone', 'Submandibular gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Cheek mucosa', 'Retromolar area', 'Anterior floor of mouth', 'Lesser curvature of stomach NOS', 'Temporal lobe', 'Mandible', 'Vagina NOS', 'Thorax NOS', 'Lymph nodes of head face and neck', 'Abdomen NOS', 'Urethra', 'Optic nerve', 'Labium majus', 'Overlapping lesion of pancreas', 'skin of upper limb and shoulder', 'Tonsillar pillar', 'Overlapping lesion of digestive system', 'Parathyroid gland', 'Craniopharyngeal duct', 'Overlapping lesion of corpus uteri', 'Lingual tonsil', 'Ovary', 'Undescended testis', 'Endocervix', 'Lymph nodes of axilla or arm', 'Hypopharyngeal aspect of aryepiglottic fold', 'Dome of bladder', 'Thyroid gland', 'Ascending colon', 'Overlapping lesion of floor of mouth', 'Spermatic cord', 'Pelvis NOS', 'Cervical esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Broad ligament', 'Nasopharynx NOS', 'Parametrium', 'Nipple', 'Occipital lobe', 'Bone of limb NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Eyelid', 'Gallbladder', 'Dorsal surface of tongue NOS', 'Skin of scalp and neck', 'Carotid body', 'Upper lobe lung', 'Cerebellum NOS', 'Hypopharynx NOS', 'Overlapping lesion of colon', 'Male genital organs NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Accessory sinus NOS', 'Hard palate', 'Overlapping lesion of retroperitoneum and peritoneum', 'Mucosa of upper lip', 'Colon NOS', 'Upper limb NOS', 'Ventral surface of tongue NOS', 'Middle third of esophagus', 'Laryngeal cartilage', 'Adrenal gland NOS', 'Olfactory nerve', 'Gastric antrum', 'Mucosa of lip NOS', 'Overlapping lesion of tonsil', 'Overlapping lesions of oropharynx', 'Ureter', 'Maxillary sinus', 'Posterior wall of oropharynx', 'skin of lower limb and hip', 'Paraspinal', 'Overlapping lesion of heart mediastinum and pleura', 'Connective subcutaneous and other soft tissues of head face and neck', 'Not Reported', 'Other ill-defined sites', 'External lower lip', 'unknown', 'Cauda equina', 'Base of tongue NOS', 'Rib sternum clavicle and associated joints', 'Descended testis', 'Lateral floor of mouth', 'Conjunctiva', 'Peripheral nerves and autonomic nervous system of pelvis', 'Clitoris', 'Hepatic flexure of colon', 'Parotid gland', 'Other specified parts of male genital organs', 'Overlapping lesion of ill-defined sites', 'Lower-outer quadrant of breast', 'Nervous system NOS', 'Overlapping lesion of accessory sinuses', 'Endocrine gland NOS', 'Superior wall of nasopharynx', 'Exocervix', 'Labium minus', 'Tonsillar fossa', 'Spinal cord', 'Frontal lobe', 'Overlapping lesion of hypopharynx', 'Stomach NOS', 'Posterior mediastinum', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Glottis', 'Pleura NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Esophagus NOS', 'Jejunum', 'Bones of skull and face and associated joints', 'Placenta', 'Ethmoid sinus', 'Fundus of stomach', 'Pylorus', 'Larynx NOS', 'Medulla of adrenal gland', 'Transverse colon', 'Uterus NOS', 'Soft palate NOS', 'Cardia NOS', 'Corpus uteri', 'skin NOS', 'Short bones of lower limb and associated joints', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sublingual gland', 'Scrotum NOS', 'Appendix', 'Hematopoietic system NOS', 'Rectosigmoid junction', 'Islets of Langerhans', 'Lacrimal gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Posterior wall of bladder', 'Posterior wall of hypopharynx', 'Commissure of lip', 'Short bones of upper limb and associated joints', 'Floor of mouth NOS', 'Mediastinum NOS', 'Overlapping lesion of bladder', 'Ventricle NOS', 'Lower lobe lung', 'Skin of lip NOS', 'Kidney NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of major salivary glands', 'Vulva NOS', 'Upper third of esophagus', 'Sigmoid colon', 'Duodenum', 'Ureteric orifice', 'Lymph nodes of inguinal region or leg', 'Overlapping lesion of urinary organs', 'Upper respiratory tract NOS', 'Intrahepatic bile duct', 'Retroperitoneum', 'Vallecula', 'Middle lobe lung', 'Urinary system NOS', 'Postcricoid region', 'Supraglottis', 'Eye NOS', 'Anal canal', 'Meninges NOS', 'Upper-inner quadrant of breast', 'Spleen', 'Overlapping lesion of lung', 'Uterine adnexa', 'Specified parts of peritoneum', 'Prepuce', 'Upper-outer quadrant of breast', 'Nasal cavity', 'Cecum', 'Isthmus uteri', 'Testis NOS', 'Fallopian tube', 'Overlapping lesion of lip', 'Skin of other and unspecified parts of face', 'Mouth NOS', 'Renal pelvis', 'Overlapping lesion of male genital organs', 'Meckel diverticulum', 'Reticuloendothelial system NOS', 'Skin of trunk', 'Brain stem', 'Ill-defined sites within respiratory system', 'Border of tongue', 'Heart', 'Ciliary body']",,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', 'no', 'unknown', 'yes', '']",,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
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', 'unknown', 'no']",,Diagnosis
Lymph Nodes Positive,Lymph Nodes Positive,LymphNodesPositive,The number of lymph nodes involved with disease as determined by pathologic examination.,False,,,,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,,"['Not Reported', 'L1', 'M', 'unknown', 'L2', 'Ms', '']",,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,,"['Not Reported', 'MX', 'M1a', 'M0', 'M1b', 'cM0 (i+)', 'unknown', 'M1c', 'M1', '']",,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,,"['Not Reported', 'T1b1', 'Tis (LCIS)', 'T4a', 'T4b', 'unknown', 'T2a', 'T4e', 'T3b', 'T1a', 'T2a2', 'T1mi', 'T4d', 'Tis', 'T4c', 'T3c', 'T4', 'Ta', 'T0', 'T1a1', 'T2a1', 'T1b', 'T1a2', 'T1', 'T2d', 'T3d', 'T2c', 'T1b2', 'T1c', 'T3', 'T2b', 'TX', ""Tis (Paget's)"", 'T2', 'T3a', 'Tis (DCIS)', '']",,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
Residual Disease,Residual Disease,ResidualDisease,Text terms to describe the status of a tissue margin following surgical resection.,False,,"['Not Reported', 'R0', 'R1', 'unknown', 'RX', 'R2', '']",,Diagnosis
Margin Distance,Margin Distance,MarginDistance,Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.,False,,,,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,,"['Not Reported', 'Low', 'Intermediate', 'unknown', 'High', '']",,Diagnosis
WHO CNS Grade,WHO CNS Grade,WHOCNSGrade,WHO CNS Grade,False,,"['Not Reported', 'Grade III', 'Grade IV', 'Grade II', 'Grade I', 'Grade Not Assigned', 'unknown', '']",,Diagnosis
WHO NTE Grade,WHO NTE Grade,WHONTEGrade,WHO NTE Grade,False,,"['Not Reported', 'G2', 'G3', 'G1', 'GX', 'unknown', '']",,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,,"['Ureter', 'Renal Capsule', 'Perinephric Fat', 'Gerota Fascia', 'Parenchyma', 'Renal', 'Renal Sinus', 'Renal Vein', '']",,Diagnosis
Age at Diagnosis,Age at Diagnosis,AgeatDiagnosis,Age at the time of diagnosis expressed in number of days since birth.,True,,,,Diagnosis
Metastasis at Diagnosis,Metastasis at Diagnosis,MetastasisatDiagnosis,The text term used to describe the extent of metastatic disease present at diagnosis.,False,,"['Not Reported', 'Regional Metastasis', 'No Metastasis', 'Distant Metastasis', 'Metastasis NOS', 'unknown', '']",,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', 'no', 'unknown', 'yes', '']",,Diagnosis
Prior Malignancy,Prior Malignancy,PriorMalignancy,The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.,False,,"['Not Reported', 'no', 'yes', 'Not Allowed To Collect', 'unknown', '']",,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,,"['Spinal meninges', 'Palate NOS', 'Body of pancreas', 'Biliary tract NOS', 'Small intestine NOS', 'Bone marrow', 'Lower limb NOS', 'Trigone of bladder', 'Liver', 'Intestinal tract NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Waldeyer ring', 'Lung NOS', 'External lip NOS', 'Connective subcutaneous and other soft tissues of abdomen', 'Cervix uteri', 'Overlapping lesion of endocrine glands and related structures', 'Thoracic esophagus', 'Round ligament', 'Greater curvature of stomach NOS', 'Ileum', 'Connective subcutaneous and other soft tissues of thorax', 'Cortex of adrenal gland', 'Splenic flexure of colon', 'Endometrium', 'Intrathoracic lymph nodes', 'Lateral wall of oropharynx', 'Pharynx NOS', 'Blood', 'Overlapping lesion of breast', 'Overlapping lesion of biliary tract', 'Paraurethral gland', 'Glans penis', 'Anus NOS', 'Posterior wall of nasopharynx', 'Parietal lobe', 'unknown primary site', 'Anterior wall of nasopharynx', 'Ampulla of Vater', 'Lateral wall of nasopharynx', 'Subglottis', 'Head face or neck NOS', 'Anterior wall of bladder', 'Head of pancreas', 'Lip NOS', 'Myometrium', 'Cerebrum', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Peripheral nerves and autonomic nervous system of thorax', 'Overlapping lesion of small intestine', 'Other specified parts of female genital organs', 'Overlapping lesion of rectum anus and anal canal', 'Pineal gland', 'Lymph node NOS', 'Acoustic nerve', 'Middle ear', 'External ear', 'Overlapping lesion of penis', 'Long bones of upper limb scapula and associated joints', 'Anterior surface of epiglottis', 'Overlapping lesion of skin', 'Overlapping lesion of eye and adnexa', 'Pelvic bones sacrum coccyx and associated joints', 'Body of penis', 'Lower-inner quadrant of breast', 'Central portion of breast', 'Vertebral column', 'Thymus', 'Overlapping lesion of larynx', 'Female genital tract NOS', 'Penis NOS', 'Pancreatic duct', 'Anterior mediastinum', 'Overlapping lesion of esophagus', 'Pyriform sinus', 'Gastrointestinal tract NOS', 'Axillary tail of breast', 'Retina', 'Extrahepatic bile duct', 'Lower third of esophagus', 'Tongue NOS', 'Orbit NOS', 'Overlapping lesion of vulva', 'Frontal sinus', 'Connective subcutaneous and other soft tissues NOS', 'Lower gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cornea NOS', 'Bladder NOS', 'Overlapping lesion of brain and central nervous system', 'Long bones of lower limb and associated joints', 'Sphenoid sinus', 'Main bronchus', 'Bladder neck', 'Lateral wall of bladder', 'Major salivary gland NOS', 'Overlapping lesion of cervix uteri', 'Overlapping lesion of tongue', 'Upper gum', 'Intra-abdominal lymph nodes', 'Oropharynx NOS', 'Tail of pancreas', 'Autonomic nervous system NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Body of stomach', 'Trachea', 'Overlapping lesion of brain', 'Vestibule of mouth', 'Prostate gland', 'Breast NOS', 'Epididymis', 'Overlapping lesion of stomach', 'Pelvic lymph nodes', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Urachus', 'Aortic body and other paraganglia', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Mucosa of lower lip', 'Tonsil NOS', 'Fundus uteri', 'Choroid', 'Other specified parts of pancreas', 'Overlapping lesion of palate', 'Cerebral meninges', 'External upper lip', 'Uvula', 'Gum NOS', 'Bone NOS', 'Lymph nodes of multiple regions', 'Cranial nerve NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Brain NOS', 'Abdominal esophagus', 'Pancreas NOS', 'Descending colon', 'Anterior 2/3 of tongue NOS', 'Branchial cleft', 'Peritoneum NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Rectum NOS', 'Cloacogenic zone', 'Submandibular gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Cheek mucosa', 'Retromolar area', 'Anterior floor of mouth', 'Lesser curvature of stomach NOS', 'Temporal lobe', 'Mandible', 'Vagina NOS', 'Thorax NOS', 'Lymph nodes of head face and neck', 'Abdomen NOS', 'Urethra', 'Optic nerve', 'Labium majus', 'Overlapping lesion of pancreas', 'skin of upper limb and shoulder', 'Tonsillar pillar', 'Overlapping lesion of digestive system', 'Parathyroid gland', 'Craniopharyngeal duct', 'Overlapping lesion of corpus uteri', 'Lingual tonsil', 'Ovary', 'Undescended testis', 'Endocervix', 'Lymph nodes of axilla or arm', 'Hypopharyngeal aspect of aryepiglottic fold', 'Dome of bladder', 'Thyroid gland', 'Ascending colon', 'Overlapping lesion of floor of mouth', 'Spermatic cord', 'Pelvis NOS', 'Cervical esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Broad ligament', 'Nasopharynx NOS', 'Parametrium', 'Nipple', 'Occipital lobe', 'Bone of limb NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Eyelid', 'Gallbladder', 'Dorsal surface of tongue NOS', 'Skin of scalp and neck', 'Carotid body', 'Upper lobe lung', 'Cerebellum NOS', 'Hypopharynx NOS', 'Overlapping lesion of colon', 'Male genital organs NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Accessory sinus NOS', 'Hard palate', 'Overlapping lesion of retroperitoneum and peritoneum', 'Mucosa of upper lip', 'Colon NOS', 'Upper limb NOS', 'Ventral surface of tongue NOS', 'Middle third of esophagus', 'Laryngeal cartilage', 'Adrenal gland NOS', 'Olfactory nerve', 'Gastric antrum', 'Mucosa of lip NOS', 'Overlapping lesion of tonsil', 'Overlapping lesions of oropharynx', 'Ureter', 'Maxillary sinus', 'Posterior wall of oropharynx', 'skin of lower limb and hip', 'Paraspinal', 'Overlapping lesion of heart mediastinum and pleura', 'Connective subcutaneous and other soft tissues of head face and neck', 'Not Reported', 'Other ill-defined sites', 'External lower lip', 'unknown', 'Cauda equina', 'Base of tongue NOS', 'Rib sternum clavicle and associated joints', 'Descended testis', 'Lateral floor of mouth', 'Conjunctiva', 'Peripheral nerves and autonomic nervous system of pelvis', 'Clitoris', 'Hepatic flexure of colon', 'Parotid gland', 'Other specified parts of male genital organs', 'Overlapping lesion of ill-defined sites', 'Lower-outer quadrant of breast', 'Nervous system NOS', 'Overlapping lesion of accessory sinuses', 'Endocrine gland NOS', 'Superior wall of nasopharynx', 'Exocervix', 'Labium minus', 'Tonsillar fossa', 'Spinal cord', 'Frontal lobe', 'Overlapping lesion of hypopharynx', 'Stomach NOS', 'Posterior mediastinum', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Glottis', 'Pleura NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Esophagus NOS', 'Jejunum', 'Bones of skull and face and associated joints', 'Placenta', 'Ethmoid sinus', 'Fundus of stomach', 'Pylorus', 'Larynx NOS', 'Medulla of adrenal gland', 'Transverse colon', 'Uterus NOS', 'Soft palate NOS', 'Cardia NOS', 'Corpus uteri', 'skin NOS', 'Short bones of lower limb and associated joints', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sublingual gland', 'Scrotum NOS', 'Appendix', 'Hematopoietic system NOS', 'Rectosigmoid junction', 'Islets of Langerhans', 'Lacrimal gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Posterior wall of bladder', 'Posterior wall of hypopharynx', 'Commissure of lip', 'Short bones of upper limb and associated joints', 'Floor of mouth NOS', 'Mediastinum NOS', 'Overlapping lesion of bladder', 'Ventricle NOS', 'Lower lobe lung', 'Skin of lip NOS', 'Kidney NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of major salivary glands', 'Vulva NOS', 'Upper third of esophagus', 'Sigmoid colon', 'Duodenum', 'Ureteric orifice', 'Lymph nodes of inguinal region or leg', 'Overlapping lesion of urinary organs', 'Upper respiratory tract NOS', 'Intrahepatic bile duct', 'Retroperitoneum', 'Vallecula', 'Middle lobe lung', 'Urinary system NOS', 'Postcricoid region', 'Supraglottis', 'Eye NOS', 'Anal canal', 'Meninges NOS', 'Upper-inner quadrant of breast', 'Spleen', 'Overlapping lesion of lung', 'Uterine adnexa', 'Specified parts of peritoneum', 'Prepuce', 'Upper-outer quadrant of breast', 'Nasal cavity', 'Cecum', 'Isthmus uteri', 'Testis NOS', 'Fallopian tube', 'Overlapping lesion of lip', 'Skin of other and unspecified parts of face', 'Mouth NOS', 'Renal pelvis', 'Overlapping lesion of male genital organs', 'Meckel diverticulum', 'Reticuloendothelial system NOS', 'Skin of trunk', 'Brain stem', 'Ill-defined sites within respiratory system', 'Border of tongue', 'Heart', 'Ciliary body']",,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,,"['Not Reported', 'Stage 4', 'Stage 3', 'Stage 1', 'Stage 2A', 'unknown', 'Stage 2B', 'Stage 4S', '']",,Diagnosis
Medulloblastoma Molecular Classification,Medulloblastoma Molecular Classification,MedulloblastomaMolecularClassification,The text term used to describe the classification of medulloblastoma tumors based on molecular features.,False,,"['Not Reported', 'WNT-Activated', 'Not Determined', 'Non-WNT/non-SHH Activated', 'SHH-Activated', 'unknown', '']",,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
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,,"['Invasive melanoma', 'Not Applicable', 'No diagnosis possible', 'Invasive melanoma - superficial spreading', 'Severe dysplasia', 'Invasive melanoma - lentigo maligna', 'Atypical melanocytic proliferation', 'Squamous metaplasia - immature', 'Adenocarcinoma in situ - mucinous', 'Mild dysplasia', 'Atypical adenomatous hyperplasia', 'Scar - no residual melanoma', 'Squamous metaplasia - mature', 'Melanocytic hyperplasia', 'Invasive melanoma - acral lentiginous', 'Invasive melanoma - desmoplastic', 'Other', 'Acral-lentiginous', 'Reserve cell hyperplasia', 'Superficial spreading', 'Benign tumor NOS', 'Invasive melanoma - nevoid', 'Pancreatic Intraductal Papillary-Mucinous Neoplasm', 'Atypical Adenomatous Lung Hyperplasia', 'Normal', 'Normal WDA', 'Melanoma in situ not otherwise classified', 'Melanoma in situ', 'Prostatic Intraepithelial Neoplasia', 'Hamartoma', 'Neuroendocrine cell hyperplasia', 'Persistent melanoma in situ', 'Adenocarcinoma in situ - non mucinous', 'Lentigo maligna type', 'Melanoma in situ arising in a giant congenital nevus', 'Squamous carcinoma in situ', 'Carcinoma NOS', 'Pancreatic Intraepithelial Neoplasia', 'Ductal Carcinoma In Situ', 'Invasive melanoma - nodular type', 'Moderate dysplasia', '']",,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,,"['Not Reported', 'Headaches', 'Motor or Movement Changes', 'Visual Changes', 'Sensory Changes', 'unknown', 'Altered Mental Status', 'Seizures', '']",,Diagnosis
Vascular Invasion Type,Vascular Invasion Type,VascularInvasionType,Text term that represents the type of vascular tumor invasion.,False,,"['Not Reported', 'No Vascular Invasion', 'Micro', 'Macro', 'Intramural', 'unknown', 'Extramural', '']",,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
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,,"['Not Reported', 'Diffuse', 'Focal', 'Sclerosis', 'unknown', 'Present', 'Absent', 'Equivocal', '']",,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,,"['Not Reported', 'Stage IB', 'Stage 0', 'Stage IB2', 'Stage 0is', 'Stage III', 'Stage IIA', 'Stage II', 'Stage IS', 'unknown', 'Stage IIA1', 'Stage Tis', 'Stage IIIA', 'Stage IA1', 'Stage IVA', 'Stage IIC', 'Stage IVB', 'Stage IIIC', 'Stage IV', 'Stage IB1', 'Stage IIIB', 'Stage I', 'Stage IA2', 'Stage X', 'Stage IC', 'Stage IIIC2', 'Stage IIC1', 'Stage IIB', 'Stage 0a', 'Stage IVC', 'Stage IA', 'Stage IIIC1', 'Stage IIA2', '']",,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,,"['Not Reported', '7th', '4th', '6th', '8th', '1st', '3rd', '2nd', 'unknown', '5th', '']",,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
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,,"['Not Reported', 'Undifferentiated', 'Differentiating', 'unknown', 'Poorly Differentiated', '']",,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', 'no', 'unknown', 'yes', '']",,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,,"['Not Reported', 'Group III', 'Group IIIa', 'Group IIIb', 'Group II', 'Group Ia', 'Group IIa', 'Group IIc', 'Group Ib', 'unknown', 'Group I', 'Group IV', '']",,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 5', 'Pattern 2', 'Pattern 1', 'Pattern 3', 'Pattern 4', '']",,Diagnosis
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,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,,"['Not Reported', 'Yes - Anaplasia Present', 'unknown', 'no', '']",,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
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,"['Spinal meninges', 'Palate NOS', 'Body of pancreas', 'Biliary tract NOS', 'Small intestine NOS', 'Bone marrow', 'Lower limb NOS', 'Trigone of bladder', 'Liver', 'Intestinal tract NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Waldeyer ring', 'Lung NOS', 'External lip NOS', 'Connective subcutaneous and other soft tissues of abdomen', 'Cervix uteri', 'Overlapping lesion of endocrine glands and related structures', 'Thoracic esophagus', 'Round ligament', 'Greater curvature of stomach NOS', 'Ileum', 'Connective subcutaneous and other soft tissues of thorax', 'Cortex of adrenal gland', 'Splenic flexure of colon', 'Endometrium', 'Intrathoracic lymph nodes', 'Lateral wall of oropharynx', 'Pharynx NOS', 'Blood', 'Overlapping lesion of breast', 'Overlapping lesion of biliary tract', 'Paraurethral gland', 'Glans penis', 'Anus NOS', 'Posterior wall of nasopharynx', 'Parietal lobe', 'unknown primary site', 'Anterior wall of nasopharynx', 'Ampulla of Vater', 'Lateral wall of nasopharynx', 'Subglottis', 'Head face or neck NOS', 'Anterior wall of bladder', 'Head of pancreas', 'Lip NOS', 'Myometrium', 'Cerebrum', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Peripheral nerves and autonomic nervous system of thorax', 'Overlapping lesion of small intestine', 'Other specified parts of female genital organs', 'Overlapping lesion of rectum anus and anal canal', 'Pineal gland', 'Lymph node NOS', 'Acoustic nerve', 'Middle ear', 'External ear', 'Overlapping lesion of penis', 'Long bones of upper limb scapula and associated joints', 'Anterior surface of epiglottis', 'Overlapping lesion of skin', 'Overlapping lesion of eye and adnexa', 'Pelvic bones sacrum coccyx and associated joints', 'Body of penis', 'Lower-inner quadrant of breast', 'Central portion of breast', 'Vertebral column', 'Thymus', 'Overlapping lesion of larynx', 'Female genital tract NOS', 'Penis NOS', 'Pancreatic duct', 'Anterior mediastinum', 'Overlapping lesion of esophagus', 'Pyriform sinus', 'Gastrointestinal tract NOS', 'Retina', 'Axillary tail of breast', 'Extrahepatic bile duct', 'Lower third of esophagus', 'Tongue NOS', 'Orbit NOS', 'Overlapping lesion of vulva', 'Frontal sinus', 'Connective subcutaneous and other soft tissues NOS', 'Lower gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cornea NOS', 'Bladder NOS', 'Overlapping lesion of brain and central nervous system', 'Long bones of lower limb and associated joints', 'Sphenoid sinus', 'Main bronchus', 'Bladder neck', 'Lateral wall of bladder', 'Major salivary gland NOS', 'Overlapping lesion of cervix uteri', 'Overlapping lesion of tongue', 'Upper gum', 'Intra-abdominal lymph nodes', 'Oropharynx NOS', 'Tail of pancreas', 'Autonomic nervous system NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Body of stomach', 'Trachea', 'Overlapping lesion of brain', 'Vestibule of mouth', 'Prostate gland', 'Breast NOS', 'Epididymis', 'Overlapping lesion of stomach', 'Pelvic lymph nodes', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Urachus', 'Aortic body and other paraganglia', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Mucosa of lower lip', 'Tonsil NOS', 'Fundus uteri', 'Choroid', 'Other specified parts of pancreas', 'Overlapping lesion of palate', 'Cerebral meninges', 'External upper lip', 'Uvula', 'Gum NOS', 'Bone NOS', 'Lymph nodes of multiple regions', 'Cranial nerve NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Brain NOS', 'Abdominal esophagus', 'Pancreas NOS', 'Descending colon', 'Anterior 2/3 of tongue NOS', 'Branchial cleft', 'Peritoneum NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Rectum NOS', 'Cloacogenic zone', 'Submandibular gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Cheek mucosa', 'Retromolar area', 'Anterior floor of mouth', 'Lesser curvature of stomach NOS', 'Temporal lobe', 'Mandible', 'Vagina NOS', 'Thorax NOS', 'Lymph nodes of head face and neck', 'Abdomen NOS', 'Urethra', 'Optic nerve', 'Labium majus', 'Overlapping lesion of pancreas', 'skin of upper limb and shoulder', 'Tonsillar pillar', 'Overlapping lesion of digestive system', 'Parathyroid gland', 'Craniopharyngeal duct', 'Overlapping lesion of corpus uteri', 'Lingual tonsil', 'Ovary', 'Undescended testis', 'Endocervix', 'Lymph nodes of axilla or arm', 'Hypopharyngeal aspect of aryepiglottic fold', 'Dome of bladder', 'Thyroid gland', 'Ascending colon', 'Overlapping lesion of floor of mouth', 'Spermatic cord', 'Pelvis NOS', 'Cervical esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Broad ligament', 'Parametrium', 'Nasopharynx NOS', 'Nipple', 'Occipital lobe', 'Bone of limb NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Eyelid', 'Gallbladder', 'Dorsal surface of tongue NOS', 'Skin of scalp and neck', 'Carotid body', 'Upper lobe lung', 'Cerebellum NOS', 'Hypopharynx NOS', 'Overlapping lesion of colon', 'Male genital organs NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Accessory sinus NOS', 'Hard palate', 'Overlapping lesion of retroperitoneum and peritoneum', 'Mucosa of upper lip', 'Colon NOS', 'Upper limb NOS', 'Ventral surface of tongue NOS', 'Middle third of esophagus', 'Laryngeal cartilage', 'Adrenal gland NOS', 'Olfactory nerve', 'Gastric antrum', 'Mucosa of lip NOS', 'Overlapping lesion of tonsil', 'Overlapping lesions of oropharynx', 'Ureter', 'Maxillary sinus', 'Posterior wall of oropharynx', 'skin of lower limb and hip', 'Overlapping lesion of heart mediastinum and pleura', 'Connective subcutaneous and other soft tissues of head face and neck', 'Not Reported', 'Other ill-defined sites', 'External lower lip', 'unknown', 'Cauda equina', 'Base of tongue NOS', 'Rib sternum clavicle and associated joints', 'Descended testis', 'Lateral floor of mouth', 'Conjunctiva', 'Peripheral nerves and autonomic nervous system of pelvis', 'Clitoris', 'Hepatic flexure of colon', 'Parotid gland', 'Other specified parts of male genital organs', 'Overlapping lesion of ill-defined sites', 'Lower-outer quadrant of breast', 'Nervous system NOS', 'Overlapping lesion of accessory sinuses', 'Endocrine gland NOS', 'Superior wall of nasopharynx', 'Exocervix', 'Labium minus', 'Tonsillar fossa', 'Spinal cord', 'Frontal lobe', 'Overlapping lesion of hypopharynx', 'Stomach NOS', 'Posterior mediastinum', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Glottis', 'Pleura NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Esophagus NOS', 'Jejunum', 'Bones of skull and face and associated joints', 'Placenta', 'Ethmoid sinus', 'Fundus of stomach', 'Pylorus', 'Larynx NOS', 'Medulla of adrenal gland', 'Transverse colon', 'Uterus NOS', 'Soft palate NOS', 'Cardia NOS', 'Corpus uteri', 'skin NOS', 'Short bones of lower limb and associated joints', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sublingual gland', 'Scrotum NOS', 'Appendix', 'Hematopoietic system NOS', 'Rectosigmoid junction', 'Islets of Langerhans', 'Lacrimal gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Posterior wall of bladder', 'Posterior wall of hypopharynx', 'Commissure of lip', 'Short bones of upper limb and associated joints', 'Floor of mouth NOS', 'Mediastinum NOS', 'Overlapping lesion of bladder', 'Ventricle NOS', 'Lower lobe lung', 'Skin of lip NOS', 'Kidney NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of major salivary glands', 'Vulva NOS', 'Upper third of esophagus', 'Sigmoid colon', 'Duodenum', 'Ureteric orifice', 'Lymph nodes of inguinal region or leg', 'Overlapping lesion of urinary organs', 'Upper respiratory tract NOS', 'Intrahepatic bile duct', 'Retroperitoneum', 'Vallecula', 'Middle lobe lung', 'Urinary system NOS', 'Postcricoid region', 'Supraglottis', 'Eye NOS', 'Anal canal', 'Meninges NOS', 'Upper-inner quadrant of breast', 'Spleen', 'Overlapping lesion of lung', 'Uterine adnexa', 'Specified parts of peritoneum', 'Prepuce', 'Upper-outer quadrant of breast', 'Nasal cavity', 'Cecum', 'Isthmus uteri', 'Testis NOS', 'Fallopian tube', 'Overlapping lesion of lip', 'Skin of other and unspecified parts of face', 'Mouth NOS', 'Renal pelvis', 'Overlapping lesion of male genital organs', 'Meckel diverticulum', 'Reticuloendothelial system NOS', 'Skin of trunk', 'Brain stem', 'Ill-defined sites within respiratory system', 'Border of tongue', 'Heart', 'Ciliary body', '']","['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
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,"['Not Reported', 'Distant', 'Biochemical', 'Regional', 'Local', 'unknown', '']","['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
Therapeutic Agents,Therapeutic Agents,TherapeuticAgents,Text identification of the individual agent(s) used as part of a treatment regimen.,False,,,,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
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,,"['Spinal meninges', 'Palate NOS', 'Body of pancreas', 'Biliary tract NOS', 'Small intestine NOS', 'Bone marrow', 'Lower limb NOS', 'Trigone of bladder', 'Liver', 'Intestinal tract NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Waldeyer ring', 'Lung NOS', 'External lip NOS', 'Connective subcutaneous and other soft tissues of abdomen', 'Cervix uteri', 'Overlapping lesion of endocrine glands and related structures', 'Thoracic esophagus', 'Round ligament', 'Greater curvature of stomach NOS', 'Ileum', 'Connective subcutaneous and other soft tissues of thorax', 'Cortex of adrenal gland', 'Splenic flexure of colon', 'Endometrium', 'Intrathoracic lymph nodes', 'Lateral wall of oropharynx', 'Pharynx NOS', 'Blood', 'Overlapping lesion of breast', 'Overlapping lesion of biliary tract', 'Paraurethral gland', 'Glans penis', 'Anus NOS', 'Posterior wall of nasopharynx', 'Parietal lobe', 'unknown primary site', 'Anterior wall of nasopharynx', 'Ampulla of Vater', 'Lateral wall of nasopharynx', 'Subglottis', 'Head face or neck NOS', 'Anterior wall of bladder', 'Head of pancreas', 'Lip NOS', 'Myometrium', 'Cerebrum', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Peripheral nerves and autonomic nervous system of thorax', 'Overlapping lesion of small intestine', 'Other specified parts of female genital organs', 'Overlapping lesion of rectum anus and anal canal', 'Pineal gland', 'Lymph node NOS', 'Acoustic nerve', 'Middle ear', 'External ear', 'Overlapping lesion of penis', 'Long bones of upper limb scapula and associated joints', 'Anterior surface of epiglottis', 'Overlapping lesion of skin', 'Overlapping lesion of eye and adnexa', 'Pelvic bones sacrum coccyx and associated joints', 'Body of penis', 'Lower-inner quadrant of breast', 'Central portion of breast', 'Vertebral column', 'Thymus', 'Overlapping lesion of larynx', 'Female genital tract NOS', 'Penis NOS', 'Pancreatic duct', 'Anterior mediastinum', 'Overlapping lesion of esophagus', 'Pyriform sinus', 'Gastrointestinal tract NOS', 'Axillary tail of breast', 'Retina', 'Extrahepatic bile duct', 'Lower third of esophagus', 'Tongue NOS', 'Orbit NOS', 'Overlapping lesion of vulva', 'Frontal sinus', 'Connective subcutaneous and other soft tissues NOS', 'Lower gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cornea NOS', 'Bladder NOS', 'Overlapping lesion of brain and central nervous system', 'Long bones of lower limb and associated joints', 'Sphenoid sinus', 'Main bronchus', 'Bladder neck', 'Lateral wall of bladder', 'Major salivary gland NOS', 'Overlapping lesion of cervix uteri', 'Overlapping lesion of tongue', 'Upper gum', 'Intra-abdominal lymph nodes', 'Oropharynx NOS', 'Tail of pancreas', 'Autonomic nervous system NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Body of stomach', 'Trachea', 'Overlapping lesion of brain', 'Vestibule of mouth', 'Prostate gland', 'Breast NOS', 'Epididymis', 'Overlapping lesion of stomach', 'Pelvic lymph nodes', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Urachus', 'Aortic body and other paraganglia', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Mucosa of lower lip', 'Tonsil NOS', 'Fundus uteri', 'Choroid', 'Other specified parts of pancreas', 'Overlapping lesion of palate', 'Cerebral meninges', 'External upper lip', 'Uvula', 'Gum NOS', 'Bone NOS', 'Lymph nodes of multiple regions', 'Cranial nerve NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Brain NOS', 'Abdominal esophagus', 'Pancreas NOS', 'Descending colon', 'Anterior 2/3 of tongue NOS', 'Branchial cleft', 'Peritoneum NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Rectum NOS', 'Cloacogenic zone', 'Submandibular gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Cheek mucosa', 'Retromolar area', 'Anterior floor of mouth', 'Lesser curvature of stomach NOS', 'Temporal lobe', 'Mandible', 'Vagina NOS', 'Thorax NOS', 'Lymph nodes of head face and neck', 'Abdomen NOS', 'Urethra', 'Optic nerve', 'Labium majus', 'Overlapping lesion of pancreas', 'skin of upper limb and shoulder', 'Tonsillar pillar', 'Overlapping lesion of digestive system', 'Parathyroid gland', 'Craniopharyngeal duct', 'Overlapping lesion of corpus uteri', 'Lingual tonsil', 'Ovary', 'Undescended testis', 'Endocervix', 'Lymph nodes of axilla or arm', 'Hypopharyngeal aspect of aryepiglottic fold', 'Dome of bladder', 'Thyroid gland', 'Ascending colon', 'Overlapping lesion of floor of mouth', 'Spermatic cord', 'Pelvis NOS', 'Cervical esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Broad ligament', 'Nasopharynx NOS', 'Parametrium', 'Nipple', 'Occipital lobe', 'Bone of limb NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Eyelid', 'Gallbladder', 'Dorsal surface of tongue NOS', 'Skin of scalp and neck', 'Carotid body', 'Upper lobe lung', 'Cerebellum NOS', 'Hypopharynx NOS', 'Overlapping lesion of colon', 'Male genital organs NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Accessory sinus NOS', 'Hard palate', 'Overlapping lesion of retroperitoneum and peritoneum', 'Mucosa of upper lip', 'Colon NOS', 'Upper limb NOS', 'Ventral surface of tongue NOS', 'Middle third of esophagus', 'Laryngeal cartilage', 'Adrenal gland NOS', 'Olfactory nerve', 'Gastric antrum', 'Mucosa of lip NOS', 'Overlapping lesion of tonsil', 'Overlapping lesions of oropharynx', 'Ureter', 'Maxillary sinus', 'Posterior wall of oropharynx', 'skin of lower limb and hip', 'Overlapping lesion of heart mediastinum and pleura', 'Connective subcutaneous and other soft tissues of head face and neck', 'Not Reported', 'Other ill-defined sites', 'External lower lip', 'unknown', 'Cauda equina', 'Base of tongue NOS', 'Rib sternum clavicle and associated joints', 'Descended testis', 'Lateral floor of mouth', 'Conjunctiva', 'Peripheral nerves and autonomic nervous system of pelvis', 'Clitoris', 'Hepatic flexure of colon', 'Parotid gland', 'Other specified parts of male genital organs', 'Overlapping lesion of ill-defined sites', 'Lower-outer quadrant of breast', 'Nervous system NOS', 'Overlapping lesion of accessory sinuses', 'Endocrine gland NOS', 'Superior wall of nasopharynx', 'Exocervix', 'Labium minus', 'Tonsillar fossa', 'Spinal cord', 'Frontal lobe', 'Overlapping lesion of hypopharynx', 'Stomach NOS', 'Posterior mediastinum', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Glottis', 'Pleura NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Esophagus NOS', 'Jejunum', 'Bones of skull and face and associated joints', 'Placenta', 'Ethmoid sinus', 'Fundus of stomach', 'Pylorus', 'Larynx NOS', 'Medulla of adrenal gland', 'Transverse colon', 'Uterus NOS', 'Soft palate NOS', 'Cardia NOS', 'Corpus uteri', 'skin NOS', 'Short bones of lower limb and associated joints', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sublingual gland', 'Scrotum NOS', 'Appendix', 'Hematopoietic system NOS', 'Rectosigmoid junction', 'Islets of Langerhans', 'Lacrimal gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Posterior wall of bladder', 'Posterior wall of hypopharynx', 'Commissure of lip', 'Short bones of upper limb and associated joints', 'Floor of mouth NOS', 'Mediastinum NOS', 'Overlapping lesion of bladder', 'Ventricle NOS', 'Lower lobe lung', 'Skin of lip NOS', 'Kidney NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of major salivary glands', 'Vulva NOS', 'Upper third of esophagus', 'Sigmoid colon', 'Duodenum', 'Ureteric orifice', 'Lymph nodes of inguinal region or leg', 'Overlapping lesion of urinary organs', 'Upper respiratory tract NOS', 'Intrahepatic bile duct', 'Retroperitoneum', 'Vallecula', 'Middle lobe lung', 'Urinary system NOS', 'Postcricoid region', 'Supraglottis', 'Eye NOS', 'Anal canal', 'Meninges NOS', 'Upper-inner quadrant of breast', 'Spleen', 'Overlapping lesion of lung', 'Uterine adnexa', 'Specified parts of peritoneum', 'Prepuce', 'Upper-outer quadrant of breast', 'Nasal cavity', 'Cecum', 'Isthmus uteri', 'Testis NOS', 'Fallopian tube', 'Overlapping lesion of lip', 'Skin of other and unspecified parts of face', 'Mouth NOS', 'Renal pelvis', 'Overlapping lesion of male genital organs', 'Meckel diverticulum', 'Reticuloendothelial system NOS', 'Skin of trunk', 'Brain stem', 'Ill-defined sites within respiratory system', 'Border of tongue', 'Heart', 'Ciliary body', '']",,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
Treatment Outcome,Treatment Outcome,TreatmentOutcome,Text term that describes the patient's final outcome after the treatment was administered.,False,,"['Not Reported', 'Partial Response', 'Very Good Partial Response', 'Progressive Disease', 'Mixed Response', 'Complete Response', 'Stable Disease', 'No Response', 'Persistent Disease', 'unknown', 'Treatment Stopped Due to Toxicity', 'No Measurable Disease', 'Treatment Ongoing', '']",,Therapy
Reason Treatment Ended,Reason Treatment Ended,ReasonTreatmentEnded,The text term used to describe the reason a specific treatment or regimen ended.,False,,"['Other', 'Adverse Therapy Event', 'Death', 'Disease Progression', 'Course of Therapy Completed', 'Withdrawal by Subject', '']",,Therapy
Treatment Type,Treatment Type,TreatmentType,Text term that describes the kind of treatment administered.,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,,"['Not Reported', 'Neoadjuvant', 'Prevention', 'Adjuvant', 'Palliative', 'Cancer Control', 'Cure', 'unknown', '']",,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,,"['Not Reported', 'Recurrent Disease', 'Progressive Disease', 'unknown', 'Initial Diagnosis', 'Residual Disease', '']",,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
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', 'no', 'unknown', 'yes', '']",,Therapy
Treatment Effect,Treatment Effect,TreatmentEffect,The text term used to describe the pathologic effect a treatment(s) had on the tumor.,False,,"['Not Reported', 'No Necrosis', 'Complete Necrosis (No Viable Tumor)', 'unknown', 'Incomplete Necrosis (Viable Tumor Present)', '']",,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', 'no', 'unknown', 'yes', '']",,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 Indicator,Treatment Effect Indicator,TreatmentEffectIndicator,The text term used to indicate whether the treatment had an effect on the patient.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,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
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
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 Frequency,Treatment Frequency,TreatmentFrequency,The text term used to describe the frequency the patient received an agent or regimen.,False,,"['Not Reported', 'Every Other Day', 'Once Weekly', 'Twice Weekly', 'Four Times Daily', 'Three Times Daily', 'unknown', 'Every Hour', 'Twice Daily', 'Five Times Daily', 'Every 24 Hours', '']",,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
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,,"['Not Reported', 'chrM', 'chr16', 'chr10', 'chr20', 'chr1', 'unknown', 'chrY', 'chr17', 'chr3', 'chr11', 'chr6', 'chr7', 'chr21', 'chr22', 'chr5', 'chr18', 'chr2', 'chr8', 'chr13', 'chr9', 'chr15', 'chr19', 'chrX', 'chr14', 'chr4', 'chr12', 'chr23', '']",,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
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
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
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', 'no', 'unknown', 'yes', '']",,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
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,,"['Not Reported', 'Copy Number Reported', 'Low', 'Not Applicable', 'Intermediate', 'Overexpressed', 'Test Value Reported', 'Normal', 'unknown', 'positive', 'negative', 'Equivocal', 'High', 'Loss of Expression', 'Abnormal NOS']",,MolecularTest
Ploidy,Ploidy,Ploidy,Text term used to describe the number of sets of homologous chromosomes.,False,,"['Not Reported', 'Hypodiploid', 'Diploid', 'Hyperdiploid', 'Tetraploid', 'Near Diploid', 'unknown', 'Aneuploid', '']",,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,,"['Inframe Insertion', 'Inframe Deletion', 'Missense Variant', 'Upstream Gene Variant', 'Regulatory Region Ablation', 'TFBS Ablation', 'Start Lost', 'Splice Acceptor Variant', 'Synonymous Variant', 'Transcript Amplification', 'Stop Lost', 'TF Binding Site Variant', 'Regulatory Region Amplification', 'NMD Transcript Variant', 'Feature Truncation', 'Incomplete Terminal Codon Variant', 'TFBS Amplification', 'Transcript Ablation', '3 Prime UTR Variant', 'Feature Elongation', 'Regulatory Region Variant', 'Splice Region Variant', 'Intergenic Variant', 'Protein Altering Variant', 'Stop Retained Variant', 'Frameshift Variant', '5 Prime UTR Variant', 'Coding Sequence Variant', 'Non-coding Transcript Variant', 'Mature miRNA Variant', 'Splice Donor Variant', 'Non-coding Transcript Exon Variant', 'Intron Variant', 'Stop Gain', 'Downstream Gene Variant', '']",,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
Variant Type,Variant Type,VariantType,The text term used to describe the type of genetic variation.,False,,"['Not Reported', 'Translocation', 'Alleles', 'unknown', 'Hypermethylation', 'Repeated Sequences', 'Deletion', 'Mosaicism', 'Loss', 'Other', 'Inversion', 'Splice', 'Chrimerism', 'Gain', 'Amplification', 'Deletion-Insertion', 'Extension', 'Duplication', 'Conversion', 'Substitution', 'Insertion', 'Rearrangement', 'Methylation', 'Partial Methylation', '']",,MolecularTest
Loci Count,Loci Count,LociCount,Numeric value used to describe the number of loci tested.,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
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', 'unknown', 'Germline', '']",,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
Loci Abnormal Count,Loci Abnormal Count,LociAbnormalCount,Numeric value used to describe the number of loci determined to be abnormal.,False,,,,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,,"['Not Reported', 'Comparative Genomic Hybridization', 'Microarray', 'Microsatellite Analysis', 'Not Applicable', 'Southern Blotting', 'unknown', 'Flow Cytometry', 'Nuclear Staining', 'Other', 'WXS', 'WGS', 'ISH', 'FISH', 'Cytogenetics NOS', 'Karyotype', 'RNA Sequencing', 'Sequencing NOS', 'Targeted Sequencing', 'IHC', 'RT-PCR']",,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
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
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,,"['Not Reported', 'Segmented Neutrophil', 'Myeloblasts', 'Epstein-Barr Virus', 'Glucose', 'Lymphoblasts', 'unknown', 'Basophil', 'Myelocytes', 'Platelets', 'Kappa', 'Alpha Fetoprotein', 'Lactate Dehydrogenase', 'Luteinizing Hormone', 'Eosinophil', 'Lymphocytes', 'Hematocrit', 'Prolymphocytes', 'Human Chorionic Gonadotropin', 'Immunoglobulin A', 'Albumin', 'Beta 2 Microglobulin', 'Total Bilirubin', 'M Protein', 'Blood Urea Nitrogen', 'Calcium', 'NOS', 'B-cell genotyping', 'Serum Free Immunoglobulin Light Chain', 'Promonocytes', 'Leukocytes', 'Promyelocytes', 'Total Protein', 'Metamyelocytes', 'Hemoglobin', 'Creatinine', 'Human Papillomavirus', 'Immunoglobulin G', 'Immunoglobulin M', 'Neutrophil Bands', 'Lambda', 'C-Reactive Protein', 'Circulating Tumor Cells', 'Testosterone', 'HPV-E6/E7', 'Absolute Neutrophil', 'Cellularity', '']",,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
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,,"['Likely Benign', 'Benign', 'Likely Pathogenic', 'Uncertain Significance', 'Pathogenic', '']",,MolecularTest
Zygosity,Zygosity,Zygosity,The text term used to describe the zygosity of a specific genetic variant.,False,,"['Not Reported', 'Heterozygous', 'Hemizygous', 'Nullizygous', 'unknown', 'Homozygous', '']",,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
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,,"['Not Reported', 'Total RNA', 'DNA', 'miRNA', 'unknown', 'Protein Analyte', 'mRNA', '']",,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
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
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
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,,"['Not Reported', 'CD138', 'CD25', 'CCND1', 'unknown', 'CD19', 'CD5', 'CA-125', 'CD30', 'BCL6', 'CD20', 'Squamous Cell Carcinoma Antigen', 'CD7', 'CD79A', 'CD14', 'CD56', 'NSE', 'CD33', 'CD3', 'CD23', 'CA19-9', 'CD34', 'Mesothelin', 'CD10', 'CD117', 'HLA-DR', 'CD45', 'CD15', 'CD22', 'CEA', '']",,MolecularTest
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
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,,"['Not Reported', 'H2A.Z.2.2', 'unknown', 'H2A.Z.1', 'H3.5', 'H3t (H3.4)', 'H3.X', 'H2A.Z.2', 'mH2A.1', 'H2A.Z', 'H3.1', 'H2A.X', 'H3.2', 'mH2A', 'mH2A.2', 'CENP-A', 'H3.3', 'H3.Y', 'H2A-Bbd', '']",,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,,"['Not Reported', 'Embryonic Fluid', 'Blood', 'unknown', 'Soft Tissue', 'Connective Tissue', 'Muscle Tissue', 'Skin', 'Peritoneal Fluid', 'Tissue NOS', 'Plasma', 'Bone Marrow', 'Saliva', 'Nerve Tissue', 'Cerebrospinal Fluid', 'Embryonic Tissue', 'Uninvolved Tissue NOS', 'Granulocyte', 'Serum', 'Pleural Fluid', 'Feces', 'Urine', 'Buffy Coat', 'Buccal Mucosa', '']",,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
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
Locus,Locus,Locus,Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.,False,,,,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
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
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,,"['Not Reported', 'H3', 'H2A', 'H2B', 'H1', 'unknown', 'H4', '']",,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
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MolecularTest
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
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 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
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
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
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,,"['Not Reported', 'Aqueous water based', 'PBS', 'Antifade without DAPI', 'Antifade with DAPI', 'Non-Aqueous Solvent based', 'unknown', 'Xylene', 'Toluene', '']",,Biospecimen
Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Mouth Rinse Biospecimen Type', 'Urine Biospecimen Type', 'Analyte Biospecimen Type', 'Bone Marrow Biospecimen Type', 'Sputum Biospecimen Type', 'Ascites Biospecimen Type', 'Cells Biospecimen Type', 'Blood Biospecimen Type', 'Tissue Biospecimen Type', 'Fluids Biospecimen Type', 'Stool Biospecimen Type']",,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
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
Histology Assessment Medium,Histology Assessment Medium,HistologyAssessmentMedium,The method of assessment used to characterize histology,False,,"['Digital', 'Microscopy', 'Other', 'unknown', '']",,Biospecimen
Lysis Buffer,Lysis Buffer,LysisBuffer,scRNA-seq specific: Type of lysis buffer used,False,,,,Biospecimen
Percent Necrosis,Percent Necrosis,PercentNecrosis,Numeric value to represent the percentage of cell death in a malignant tumor 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
Slicing Method,Slicing Method,SlicingMethod,Imaging specific: the method by which the tissue was sliced.,False,,"['Not Reported', 'Other', 'Sliding microtome', 'Cryosectioning', 'Tissue molds', 'Sectioning', 'unknown', 'Vibratome', '']",,Biospecimen
Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['Not Applicable', 'Refrigerated vacuum chamber', 'unknown', 'Ambient temperature', 'Cut slide', 'Frozen at -20C', 'Frozen at -70C', 'RNAlater at -20C', 'Desiccant at 4C', 'Frozen at -150C', '4C in vacuum chamber', 'Paraffin block', 'RNAlater at 25C', 'Fresh', 'Frozen in liquid nitrogen', 'Frozen at -80C', 'Frozen in vapor phase', 'RNAlater at 4C', 'Refrigerated at 4 degrees']",,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
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
Fiducial Marker,Fiducial Marker,FiducialMarker,Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.,False,,"['Not Reported', 'Other', 'Grid Slides - Hemocytometer', 'Fluorescent Beads', 'unknown', 'Nuclear Stain - DAPI', 'Adhesive Markers', '']",,Biospecimen
Percent Tumor Cells,Percent Tumor Cells,PercentTumorCells,Numeric value that represents the percentage of infiltration by tumor cells in a sample.,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
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
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
HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,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
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
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
Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['PBS+Serum', 'PBS', 'RPMI', 'DMEM+Serum', 'None', 'RPMI+Serum', 'DMEM', '']",,Biospecimen
Tumor Infiltrating Lymphocytes,Tumor Infiltrating Lymphocytes,TumorInfiltratingLymphocytes,Measure of Tumor-Infiltrating Lymphocytes [Number],False,,,,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
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
Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['No diagnosis possible', 'Invasive melanoma - superficial spreading', 'Severe dysplasia', 'Invasive melanoma - lentigo maligna', 'Atypical melanocytic proliferation', 'Squamous metaplasia - immature', 'Adenocarcinoma in situ - mucinous', 'Mild dysplasia', 'Atypical adenomatous hyperplasia', 'Scar - no residual melanoma', 'Invasive melanoma - other', 'Squamous metaplasia - mature', 'Melanocytic hyperplasia', 'Invasive melanoma - acral lentiginous', 'Invasive melanoma - desmoplastic', 'Melanoma in situ - acral-lentiginous', 'Reserve cell hyperplasia', 'Benign tumor NOS', 'Invasive melanoma - nevoid', 'Normal WDA', 'Squamous Carcinoma in situ', 'Melanoma in situ - arising in a giant congenital nevus', 'Persistent melanoma in situ', 'Hamartoma', 'Adenocarcinoma in situ - non mucinous', 'Melanoma in situ - not otherwise classified', 'Carcinoma NOS', 'Melanoma in situ - lentigo maligna type', 'Melanoma in situ - superficial spreading', 'Invasive melanoma - nodular type', 'Moderate dysplasia', '']",,Biospecimen
Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Endoscopic biopsy', 'Re-excision', 'Surgical Resection', 'Cytobrush', 'Shave Biopsy', 'Fine Needle Aspirate', 'Autopsy', 'Forceps biopsy', 'Induced sputum', 'BAL (bronchial alveolar lavage)', 'Non induced sputum', 'Core needle biopsy', 'Sentinel Node Biopsy', 'Blood draw', 'Lymphadenectomy - Regional Nodes', 'Not specified', 'Biopsy', 'Other Acquisition Method', 'Punch Biopsy', 'Fluid collection', 'Excision']",,Biospecimen
Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['Methacarn', 'unknown', 'Carbodiimide', 'NP40 lysis buffer', 'Other', 'Cryo-store', '95% Ethanol', 'Dimidoester', 'Alcohol', 'Formalin', 'Saline', 'PAXgene tissue', 'Dimethylacetamide', 'Unfixed', 'Acetone', 'OCT media', 'Para-benzoquinone', ""Carnoy's Fixative"", 'Glutaraldehyde', 'Polaxamer', 'None', 'RNAlater', 'TCL lysis buffer']",,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
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
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,,"['Severe dysplasia', 'Mild dysplasia', 'unknown', 'Moderate dysplasia', 'Carcinoma in Situ', 'Normal or basal cell hyperplasia or metaplasia', '']",,Biospecimen
Percent Monocyte Infiltration,Percent Monocyte Infiltration,PercentMonocyteInfiltration,Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.,False,,,,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
Histology Assessment By,Histology Assessment By,HistologyAssessmentBy,Text term describing who (in what role) made the histological assessments of the sample,False,,"['Pathologist', 'Other', 'unknown', 'Research Scientist', '']",,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,"['Spinal meninges', 'Palate NOS', 'Body of pancreas', 'Biliary tract NOS', 'Small intestine NOS', 'Bone marrow', 'Lower limb NOS', 'Trigone of bladder', 'Liver', 'Intestinal tract NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Waldeyer ring', 'Lung NOS', 'External lip NOS', 'Connective subcutaneous and other soft tissues of abdomen', 'Cervix uteri', 'Overlapping lesion of endocrine glands and related structures', 'Thoracic esophagus', 'Round ligament', 'Greater curvature of stomach NOS', 'Ileum', 'Connective subcutaneous and other soft tissues of thorax', 'Cortex of adrenal gland', 'Splenic flexure of colon', 'Endometrium', 'Intrathoracic lymph nodes', 'Lateral wall of oropharynx', 'Pharynx NOS', 'Blood', 'Overlapping lesion of breast', 'Overlapping lesion of biliary tract', 'Paraurethral gland', 'Glans penis', 'Anus NOS', 'Posterior wall of nasopharynx', 'Parietal lobe', 'unknown primary site', 'Anterior wall of nasopharynx', 'Ampulla of Vater', 'Lateral wall of nasopharynx', 'Subglottis', 'Head face or neck NOS', 'Anterior wall of bladder', 'Head of pancreas', 'Lip NOS', 'Myometrium', 'Cerebrum', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Peripheral nerves and autonomic nervous system of thorax', 'Overlapping lesion of small intestine', 'Other specified parts of female genital organs', 'Overlapping lesion of rectum anus and anal canal', 'Pineal gland', 'Lymph node NOS', 'Acoustic nerve', 'Middle ear', 'External ear', 'Overlapping lesion of penis', 'Long bones of upper limb scapula and associated joints', 'Anterior surface of epiglottis', 'Overlapping lesion of skin', 'Overlapping lesion of eye and adnexa', 'Pelvic bones sacrum coccyx and associated joints', 'Body of penis', 'Lower-inner quadrant of breast', 'Central portion of breast', 'Vertebral column', 'Thymus', 'Overlapping lesion of larynx', 'Female genital tract NOS', 'Penis NOS', 'Pancreatic duct', 'Anterior mediastinum', 'Overlapping lesion of esophagus', 'Pyriform sinus', 'Gastrointestinal tract NOS', 'Axillary tail of breast', 'Retina', 'Extrahepatic bile duct', 'Lower third of esophagus', 'Tongue NOS', 'Orbit NOS', 'Overlapping lesion of vulva', 'Frontal sinus', 'Connective subcutaneous and other soft tissues NOS', 'Lower gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cornea NOS', 'Bladder NOS', 'Overlapping lesion of brain and central nervous system', 'Long bones of lower limb and associated joints', 'Sphenoid sinus', 'Main bronchus', 'Bladder neck', 'Lateral wall of bladder', 'Major salivary gland NOS', 'Overlapping lesion of cervix uteri', 'Overlapping lesion of tongue', 'Upper gum', 'Intra-abdominal lymph nodes', 'Oropharynx NOS', 'Tail of pancreas', 'Autonomic nervous system NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Body of stomach', 'Trachea', 'Overlapping lesion of brain', 'Vestibule of mouth', 'Prostate gland', 'Breast NOS', 'Epididymis', 'Overlapping lesion of stomach', 'Pelvic lymph nodes', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Urachus', 'Aortic body and other paraganglia', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Mucosa of lower lip', 'Tonsil NOS', 'Fundus uteri', 'Choroid', 'Other specified parts of pancreas', 'Overlapping lesion of palate', 'Cerebral meninges', 'External upper lip', 'Uvula', 'Gum NOS', 'Bone NOS', 'Lymph nodes of multiple regions', 'Cranial nerve NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Brain NOS', 'Abdominal esophagus', 'Pancreas NOS', 'Descending colon', 'Anterior 2/3 of tongue NOS', 'Branchial cleft', 'Peritoneum NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Rectum NOS', 'Cloacogenic zone', 'Submandibular gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Cheek mucosa', 'Retromolar area', 'Anterior floor of mouth', 'Lesser curvature of stomach NOS', 'Temporal lobe', 'Mandible', 'Vagina NOS', 'Thorax NOS', 'Lymph nodes of head face and neck', 'Abdomen NOS', 'Urethra', 'Optic nerve', 'Labium majus', 'Overlapping lesion of pancreas', 'skin of upper limb and shoulder', 'Tonsillar pillar', 'Overlapping lesion of digestive system', 'Parathyroid gland', 'Craniopharyngeal duct', 'Overlapping lesion of corpus uteri', 'Lingual tonsil', 'Ovary', 'Undescended testis', 'Endocervix', 'Lymph nodes of axilla or arm', 'Hypopharyngeal aspect of aryepiglottic fold', 'Dome of bladder', 'Thyroid gland', 'Ascending colon', 'Overlapping lesion of floor of mouth', 'Spermatic cord', 'Pelvis NOS', 'Cervical esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Broad ligament', 'Nasopharynx NOS', 'Parametrium', 'Nipple', 'Occipital lobe', 'Bone of limb NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Eyelid', 'Gallbladder', 'Dorsal surface of tongue NOS', 'Skin of scalp and neck', 'Carotid body', 'Upper lobe lung', 'Cerebellum NOS', 'Hypopharynx NOS', 'Overlapping lesion of colon', 'Male genital organs NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Accessory sinus NOS', 'Hard palate', 'Overlapping lesion of retroperitoneum and peritoneum', 'Mucosa of upper lip', 'Colon NOS', 'Upper limb NOS', 'Ventral surface of tongue NOS', 'Middle third of esophagus', 'Laryngeal cartilage', 'Adrenal gland NOS', 'Olfactory nerve', 'Gastric antrum', 'Mucosa of lip NOS', 'Overlapping lesion of tonsil', 'Overlapping lesions of oropharynx', 'Ureter', 'Maxillary sinus', 'Posterior wall of oropharynx', 'skin of lower limb and hip', 'Paraspinal', 'Overlapping lesion of heart mediastinum and pleura', 'Connective subcutaneous and other soft tissues of head face and neck', 'Not Reported', 'Other ill-defined sites', 'External lower lip', 'unknown', 'Cauda equina', 'Base of tongue NOS', 'Rib sternum clavicle and associated joints', 'Descended testis', 'Lateral floor of mouth', 'Conjunctiva', 'Peripheral nerves and autonomic nervous system of pelvis', 'Clitoris', 'Hepatic flexure of colon', 'Parotid gland', 'Other specified parts of male genital organs', 'Overlapping lesion of ill-defined sites', 'Lower-outer quadrant of breast', 'Nervous system NOS', 'Overlapping lesion of accessory sinuses', 'Endocrine gland NOS', 'Superior wall of nasopharynx', 'Exocervix', 'Labium minus', 'Tonsillar fossa', 'Spinal cord', 'Frontal lobe', 'Overlapping lesion of hypopharynx', 'Stomach NOS', 'Posterior mediastinum', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Glottis', 'Pleura NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Esophagus NOS', 'Jejunum', 'Bones of skull and face and associated joints', 'Placenta', 'Ethmoid sinus', 'Fundus of stomach', 'Pylorus', 'Larynx NOS', 'Medulla of adrenal gland', 'Transverse colon', 'Uterus NOS', 'Soft palate NOS', 'Cardia NOS', 'Corpus uteri', 'skin NOS', 'Short bones of lower limb and associated joints', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sublingual gland', 'Scrotum NOS', 'Appendix', 'Hematopoietic system NOS', 'Rectosigmoid junction', 'Islets of Langerhans', 'Lacrimal gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Posterior wall of bladder', 'Posterior wall of hypopharynx', 'Commissure of lip', 'Short bones of upper limb and associated joints', 'Floor of mouth NOS', 'Mediastinum NOS', 'Overlapping lesion of bladder', 'Ventricle NOS', 'Lower lobe lung', 'Skin of lip NOS', 'Kidney NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of major salivary glands', 'Vulva NOS', 'Upper third of esophagus', 'Sigmoid colon', 'Duodenum', 'Ureteric orifice', 'Lymph nodes of inguinal region or leg', 'Overlapping lesion of urinary organs', 'Upper respiratory tract NOS', 'Intrahepatic bile duct', 'Retroperitoneum', 'Vallecula', 'Middle lobe lung', 'Urinary system NOS', 'Postcricoid region', 'Supraglottis', 'Eye NOS', 'Anal canal', 'Meninges NOS', 'Upper-inner quadrant of breast', 'Spleen', 'Overlapping lesion of lung', 'Uterine adnexa', 'Specified parts of peritoneum', 'Prepuce', 'Upper-outer quadrant of breast', 'Nasal cavity', 'Cecum', 'Isthmus uteri', 'Testis NOS', 'Fallopian tube', 'Overlapping lesion of lip', 'Skin of other and unspecified parts of face', 'Mouth NOS', 'Renal pelvis', 'Overlapping lesion of male genital organs', 'Meckel diverticulum', 'Reticuloendothelial system NOS', 'Skin of trunk', 'Brain stem', 'Ill-defined sites within respiratory system', 'Border of tongue', 'Heart', 'Ciliary body', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen
Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,True,"['Liquid Nitrogen', 'Warm Ischemia', 'Negative -20C', 'Cold Ischemia', 'Dry Ice', 'unknown', 'Ambient air', '4C wet ice', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Analyte""', '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
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
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,"['Metastatic', 'Normal adjacent', 'Recurrent', 'Post therapy', 'Normal distant', 'Primary', 'Post therapy adjuvant', 'Not analyzed', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Premalignant - in situ', 'Normal', 'Premalignant', 'Post therapy neoadjuvant', 'Additional Primary', 'Local recurrence', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",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
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
Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,False,True,"['Not Reported', 'OCT', 'Negative 80 Deg C', 'Cryopreservation in liquid nitrogen - live cells', 'unknown', 'Formalin fixed-buffered', 'Liquid Nitrogen', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Cryopreservation in liquid nitrogen - dead tissue', 'Fresh dissociated and single cell sorted into plates', 'Formalin fixed paraffin embedded - FFPE', 'Cryopreserved', 'Fresh dissociated', 'Fresh', 'Cryopreservation in dry ice - dead tissue', 'Fresh dissociated and single cell sorted', 'Formalin fixed-unbuffered', 'Snap Frozen', 'Methacarn fixed paraffin embedded - MFPE', 'Frozen', '']","['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,"['Not Reported', 'Not Applicable', 'unknown', 'Bilateral', 'Right', 'Left', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",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
Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Liquid Nitrogen', 'Cold Pack', 'Ambient Pack', 'Ice Pack', 'Not Shipped', 'Dry Ice', 'Other Shipping Environment', 'Specimen at Room Temperature', '']","['Biospecimen is ""Analyte""', 'Biospecimen is ""Blood""']",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,"['Coverslip', 'Other', 'Not applicable', 'Uncharged', 'Charged', '']","['Biospecimen is ""Analyte""']",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,"['cDNA Libraries Analyte', 'Total RNA Analyte', 'Tissue Block Analyte', 'cfDNA Analyte', 'Plasma', 'DNA Analyte', 'PBMCs or Plasma or Serum Analyte', 'Serum Analyte', 'protein', 'PBMCs', 'lipid', 'metabolite', 'RNA Analyte', 'Tissue Section Analyte', '']","['Biospecimen is ""Analyte""']",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
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 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
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
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
Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Mouth Rinse Biospecimen Type', 'Urine Biospecimen Type', 'Analyte Biospecimen Type', 'Bone Marrow Biospecimen Type', 'Sputum Biospecimen Type', 'Ascites Biospecimen Type', 'Cells Biospecimen Type', 'Blood Biospecimen Type', 'Tissue Biospecimen Type', 'Fluids Biospecimen Type', 'Stool Biospecimen Type']",,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
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
Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['Not Applicable', 'Refrigerated vacuum chamber', 'unknown', 'Ambient temperature', 'Cut slide', 'Frozen at -20C', 'Frozen at -70C', 'RNAlater at -20C', 'Desiccant at 4C', 'Frozen at -150C', '4C in vacuum chamber', 'Paraffin block', 'RNAlater at 25C', 'Fresh', 'Frozen in liquid nitrogen', 'Frozen at -80C', 'Frozen in vapor phase', 'RNAlater at 4C', 'Refrigerated at 4 degrees']",,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
Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,True,,"['Not Reported', 'OCT', 'Negative 80 Deg C', 'Cryopreservation in liquid nitrogen - live cells', 'unknown', 'Formalin fixed-buffered', 'Liquid Nitrogen', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Cryopreservation in liquid nitrogen - dead tissue', 'Fresh dissociated and single cell sorted into plates', 'Formalin fixed paraffin embedded - FFPE', 'Cryopreserved', 'Fresh dissociated', 'Fresh', 'Cryopreservation in dry ice - dead tissue', 'Fresh dissociated and single cell sorted', 'Formalin fixed-unbuffered', 'Snap Frozen', 'Methacarn fixed paraffin embedded - MFPE', 'Frozen']",,SRRSBiospecimen
Topography Code,Topography Code,TopographyCode,"Topography Code, indicating site within the body, based on ICD-O-3.",False,,"['C25.0', 'C31.9', 'C11.3', 'C53.0', 'C51.2', 'C68.8', 'C38.2', 'C57.9', 'C71.5', 'C02.3', 'C57.3', 'C74.1', 'C11.8', 'C03.9', 'C62.1', 'C38.8', 'C31.3', 'C05.2', 'C08.0', 'C21.2', 'C69.8', 'C49.1', 'C57.2', 'C24.9', 'C72.8', 'C51.0', 'C51.1', 'C42.3', 'C62.9', 'C56.9', 'C71.1', 'C75.3', 'C02.8', 'C70.0', 'C34.3', 'C49.2', 'C17.2', 'C69.0', 'C73.9', 'C39.0', 'C69.1', 'C00.5', 'C49.5', 'C50.1', 'C60.9', 'C75.8', 'C16.4', 'C06.9', 'C11.9', 'C09.8', 'C00.1', 'C60.2', 'C41.2', 'C69.6', 'C12.9', 'C68.9', 'C22.0', 'C02.1', 'C74.0', 'C68.0', 'C47.0', 'C38.3', 'C54.0', 'C24.8', 'C20.9', 'C32.3', 'C71.6', 'C08.1', 'C63.1', 'C41.3', 'C53.1', 'C32.8', 'C48.1', 'C54.8', 'C02.9', 'C40.3', 'C76.3', 'C25.8', 'C76.8', 'C50.8', 'C44.5', 'C30.1', 'C70.9', 'C71.7', 'C38.1', 'C18.1', 'C50.6', 'C13.9', 'C25.7', 'C00.0', 'C11.0', 'C00.2', 'C54.3', 'C13.0', 'C77.0', 'C26.9', 'C40.8', 'C47.9', 'C00.4', 'C77.4', 'C00.8', 'C75.2', 'C41.9', 'C74.9', 'C69.9', 'C52.9', 'C39.9', 'C72.5', 'C18.0', 'C47.6', 'C76.4', 'C10.0', 'C16.6', 'C10.9', 'C76.1', 'C47.1', 'C67.1', 'C48.0', 'C49.8', 'C05.8', 'C34.0', 'C15.4', 'C14.2', 'C16.9', 'C00.6', 'C04.9', 'C51.8', 'C72.1', 'C11.1', 'C49.4', 'C72.4', 'C50.4', 'C63.2', 'C14.8', 'C18.8', 'C50.5', 'C34.1', 'C67.8', 'C19.9', 'C49.6', 'C04.8', 'C18.3', 'C60.8', 'C16.5', 'C75.9', 'C17.8', 'C32.2', 'C67.2', 'C21.1', 'C18.4', 'C08.9', 'C77.2', 'C62.0', 'C16.0', 'C65.9', 'C04.0', 'C25.9', 'C18.6', 'C47.5', 'C15.8', 'C75.4', 'C40.1', 'C13.2', 'C03.1', 'C71.4', 'C31.8', 'C49.3', 'C25.1', 'C06.1', 'C41.0', 'C75.1', 'C67.4', 'C05.9', 'C18.5', 'C01.9', 'C63.8', 'C72.9', 'C47.4', 'C25.3', 'C38.0', 'C60.0', 'C14.0', 'C77.5', 'C44.2', 'C18.7', 'C26.8', 'C39.8', 'C10.4', 'C76.7', 'C50.2', 'C44.1', 'C71.0', 'C63.9', 'C17.0', 'C05.1', 'C44.3', 'C71.2', 'C53.8', 'C26.0', 'C72.3', 'C71.9', 'C17.1', 'C24.0', 'C77.1', 'C44.4', 'C25.2', 'C42.0', 'C04.1', 'C15.5', 'C69.5', 'C40.0', 'C18.9', 'C38.4', 'C17.9', 'C49.0', 'C49.9', 'C76.0', 'C31.1', 'C40.9', 'C17.3', 'C47.3', 'C44.7', 'C09.1', 'C68.1', 'Not Reported', 'C13.8', 'C57.8', 'C50.0', 'C03.0', 'C44.0', 'unknown', 'C21.0', 'C69.2', 'C50.3', 'C32.1', 'C77.9', 'C34.8', 'C09.9', 'C64.9', 'C71.8', 'C57.0', 'C24.1', 'C16.2', 'C11.2', 'C77.8', 'C63.7', 'C77.3', 'C21.8', 'C02.0', 'C08.8', 'C67.7', 'C70.1', 'C41.4', 'C41.8', 'C53.9', 'C06.8', 'C15.3', 'C15.1', 'C32.0', 'C37.9', 'C60.1', 'C25.4', 'C34.2', 'C10.2', 'C47.2', 'C57.7', 'C33.9', 'C05.0', 'C69.4', 'C72.0', 'C06.2', 'C15.2', 'C75.0', 'C67.0', 'C22.1', 'C16.3', 'C42.2', 'C09.0', 'C13.1', 'C54.1', 'C47.8', 'C67.9', 'C72.2', 'C42.4', 'C10.1', 'C41.1', 'C32.9', 'C54.2', 'C76.2', 'C15.9', 'C23.9', 'C80.9', 'C76.5', 'C69.3', 'C10.8', 'C63.0', 'C51.9', 'C57.4', 'C02.2', 'C15.0', 'C34.9', 'C48.8', 'C44.6', 'C71.3', 'C54.9', 'C31.0', 'C48.2', 'C50.9', 'C07.9', 'C06.0', 'C67.6', 'C57.1', 'C00.3', 'C42.1', 'C02.4', 'C16.1', 'C75.5', 'C31.2', 'C61.9', 'C10.3', 'C18.2', 'C30.0', 'C55.9', 'C16.8', 'C66.9', '']",,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
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
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
Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['PBS+Serum', 'PBS', 'RPMI', 'DMEM+Serum', 'None', 'RPMI+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
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
Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['No diagnosis possible', 'Invasive melanoma - superficial spreading', 'Severe dysplasia', 'Invasive melanoma - lentigo maligna', 'Atypical melanocytic proliferation', 'Squamous metaplasia - immature', 'Adenocarcinoma in situ - mucinous', 'Mild dysplasia', 'Atypical adenomatous hyperplasia', 'Scar - no residual melanoma', 'Invasive melanoma - other', 'Squamous metaplasia - mature', 'Melanocytic hyperplasia', 'Invasive melanoma - acral lentiginous', 'Invasive melanoma - desmoplastic', 'Melanoma in situ - acral-lentiginous', 'Reserve cell hyperplasia', 'Benign tumor NOS', 'Invasive melanoma - nevoid', 'Normal WDA', 'Squamous Carcinoma in situ', 'Melanoma in situ - arising in a giant congenital nevus', 'Persistent melanoma in situ', 'Hamartoma', 'Adenocarcinoma in situ - non mucinous', 'Melanoma in situ - not otherwise classified', 'Carcinoma NOS', 'Melanoma in situ - lentigo maligna type', 'Melanoma in situ - superficial spreading', 'Invasive melanoma - nodular type', 'Moderate dysplasia', '']",,SRRSBiospecimen
Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Endoscopic biopsy', 'Re-excision', 'Surgical Resection', 'Cytobrush', 'Shave Biopsy', 'Fine Needle Aspirate', 'Autopsy', 'Forceps biopsy', 'Induced sputum', 'BAL (bronchial alveolar lavage)', 'Non induced sputum', 'Core needle biopsy', 'Sentinel Node Biopsy', 'Blood draw', 'Lymphadenectomy - Regional Nodes', 'Not specified', 'Biopsy', 'Other Acquisition Method', 'Punch Biopsy', 'Fluid collection', 'Excision']",,SRRSBiospecimen
Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['Methacarn', 'unknown', 'Carbodiimide', 'NP40 lysis buffer', 'Other', 'Cryo-store', '95% Ethanol', 'Dimidoester', 'Alcohol', 'Formalin', 'Saline', 'PAXgene tissue', 'Dimethylacetamide', 'Unfixed', 'Acetone', 'OCT media', 'Para-benzoquinone', ""Carnoy's Fixative"", 'Glutaraldehyde', 'Polaxamer', 'None', 'RNAlater', 'TCL lysis buffer']",,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
Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,,"['Liquid Nitrogen', 'Warm Ischemia', 'Negative -20C', 'Cold Ischemia', 'Dry Ice', 'unknown', 'Ambient air', '4C wet ice', '']",,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
Additional Topography,Additional Topography,AdditionalTopography,Topography not included in the ICD-O-3 Topography codes.,False,,"['Not Reported', 'skin of penis', 'skin of nose', 'skin of neck', 'skin of breast', 'skin of upper limb and shoulder', 'skin of vulva', 'skin NOS', 'skin of back', 'skin of abdomen', 'Peri-tumoral Airway', 'Skin of trunk', 'skin of palm', 'skin of eye lid', 'skin of sole', 'skin of chest', 'skin of lower limb and hip', 'skin of lip', 'Hilar Airway', 'skin of scalp', 'skin of other parts of face', 'skin of scrotum', 'skin of ear', '']",,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,"['Spinal meninges', 'Palate NOS', 'Body of pancreas', 'Biliary tract NOS', 'Small intestine NOS', 'Bone marrow', 'Lower limb NOS', 'Trigone of bladder', 'Liver', 'Intestinal tract NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Waldeyer ring', 'Lung NOS', 'External lip NOS', 'Connective subcutaneous and other soft tissues of abdomen', 'Cervix uteri', 'Overlapping lesion of endocrine glands and related structures', 'Thoracic esophagus', 'Round ligament', 'Greater curvature of stomach NOS', 'Ileum', 'Connective subcutaneous and other soft tissues of thorax', 'Cortex of adrenal gland', 'Splenic flexure of colon', 'Endometrium', 'Intrathoracic lymph nodes', 'Lateral wall of oropharynx', 'Pharynx NOS', 'Blood', 'Overlapping lesion of breast', 'Overlapping lesion of biliary tract', 'Paraurethral gland', 'Glans penis', 'Anus NOS', 'Posterior wall of nasopharynx', 'Parietal lobe', 'unknown primary site', 'Anterior wall of nasopharynx', 'Ampulla of Vater', 'Lateral wall of nasopharynx', 'Subglottis', 'Head face or neck NOS', 'Anterior wall of bladder', 'Head of pancreas', 'Lip NOS', 'Myometrium', 'Cerebrum', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Peripheral nerves and autonomic nervous system of thorax', 'Overlapping lesion of small intestine', 'Other specified parts of female genital organs', 'Overlapping lesion of rectum anus and anal canal', 'Pineal gland', 'Lymph node NOS', 'Acoustic nerve', 'Middle ear', 'External ear', 'Overlapping lesion of penis', 'Long bones of upper limb scapula and associated joints', 'Anterior surface of epiglottis', 'Overlapping lesion of skin', 'Overlapping lesion of eye and adnexa', 'Pelvic bones sacrum coccyx and associated joints', 'Body of penis', 'Lower-inner quadrant of breast', 'Central portion of breast', 'Vertebral column', 'Thymus', 'Overlapping lesion of larynx', 'Female genital tract NOS', 'Penis NOS', 'Pancreatic duct', 'Anterior mediastinum', 'Overlapping lesion of esophagus', 'Pyriform sinus', 'Gastrointestinal tract NOS', 'Axillary tail of breast', 'Retina', 'Extrahepatic bile duct', 'Lower third of esophagus', 'Tongue NOS', 'Orbit NOS', 'Overlapping lesion of vulva', 'Frontal sinus', 'Connective subcutaneous and other soft tissues NOS', 'Lower gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cornea NOS', 'Bladder NOS', 'Overlapping lesion of brain and central nervous system', 'Long bones of lower limb and associated joints', 'Sphenoid sinus', 'Main bronchus', 'Bladder neck', 'Lateral wall of bladder', 'Major salivary gland NOS', 'Overlapping lesion of cervix uteri', 'Overlapping lesion of tongue', 'Upper gum', 'Intra-abdominal lymph nodes', 'Oropharynx NOS', 'Tail of pancreas', 'Autonomic nervous system NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Body of stomach', 'Trachea', 'Overlapping lesion of brain', 'Vestibule of mouth', 'Prostate gland', 'Breast NOS', 'Epididymis', 'Overlapping lesion of stomach', 'Pelvic lymph nodes', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Urachus', 'Aortic body and other paraganglia', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Mucosa of lower lip', 'Tonsil NOS', 'Fundus uteri', 'Choroid', 'Other specified parts of pancreas', 'Overlapping lesion of palate', 'Cerebral meninges', 'External upper lip', 'Uvula', 'Gum NOS', 'Bone NOS', 'Lymph nodes of multiple regions', 'Cranial nerve NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Brain NOS', 'Abdominal esophagus', 'Pancreas NOS', 'Descending colon', 'Anterior 2/3 of tongue NOS', 'Branchial cleft', 'Peritoneum NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Rectum NOS', 'Cloacogenic zone', 'Submandibular gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Cheek mucosa', 'Retromolar area', 'Anterior floor of mouth', 'Lesser curvature of stomach NOS', 'Temporal lobe', 'Mandible', 'Vagina NOS', 'Thorax NOS', 'Lymph nodes of head face and neck', 'Abdomen NOS', 'Urethra', 'Optic nerve', 'Labium majus', 'Overlapping lesion of pancreas', 'skin of upper limb and shoulder', 'Tonsillar pillar', 'Overlapping lesion of digestive system', 'Parathyroid gland', 'Craniopharyngeal duct', 'Overlapping lesion of corpus uteri', 'Lingual tonsil', 'Ovary', 'Undescended testis', 'Endocervix', 'Lymph nodes of axilla or arm', 'Hypopharyngeal aspect of aryepiglottic fold', 'Dome of bladder', 'Thyroid gland', 'Ascending colon', 'Overlapping lesion of floor of mouth', 'Spermatic cord', 'Pelvis NOS', 'Cervical esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Broad ligament', 'Nasopharynx NOS', 'Parametrium', 'Nipple', 'Occipital lobe', 'Bone of limb NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Eyelid', 'Gallbladder', 'Dorsal surface of tongue NOS', 'Skin of scalp and neck', 'Carotid body', 'Upper lobe lung', 'Cerebellum NOS', 'Hypopharynx NOS', 'Overlapping lesion of colon', 'Male genital organs NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Accessory sinus NOS', 'Hard palate', 'Overlapping lesion of retroperitoneum and peritoneum', 'Mucosa of upper lip', 'Colon NOS', 'Upper limb NOS', 'Ventral surface of tongue NOS', 'Middle third of esophagus', 'Laryngeal cartilage', 'Adrenal gland NOS', 'Olfactory nerve', 'Gastric antrum', 'Mucosa of lip NOS', 'Overlapping lesion of tonsil', 'Overlapping lesions of oropharynx', 'Ureter', 'Maxillary sinus', 'Posterior wall of oropharynx', 'skin of lower limb and hip', 'Paraspinal', 'Overlapping lesion of heart mediastinum and pleura', 'Connective subcutaneous and other soft tissues of head face and neck', 'Not Reported', 'Other ill-defined sites', 'External lower lip', 'unknown', 'Cauda equina', 'Base of tongue NOS', 'Rib sternum clavicle and associated joints', 'Descended testis', 'Lateral floor of mouth', 'Conjunctiva', 'Peripheral nerves and autonomic nervous system of pelvis', 'Clitoris', 'Hepatic flexure of colon', 'Parotid gland', 'Other specified parts of male genital organs', 'Overlapping lesion of ill-defined sites', 'Lower-outer quadrant of breast', 'Nervous system NOS', 'Overlapping lesion of accessory sinuses', 'Endocrine gland NOS', 'Superior wall of nasopharynx', 'Exocervix', 'Labium minus', 'Tonsillar fossa', 'Spinal cord', 'Frontal lobe', 'Overlapping lesion of hypopharynx', 'Stomach NOS', 'Posterior mediastinum', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Glottis', 'Pleura NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Esophagus NOS', 'Jejunum', 'Bones of skull and face and associated joints', 'Placenta', 'Ethmoid sinus', 'Fundus of stomach', 'Pylorus', 'Larynx NOS', 'Medulla of adrenal gland', 'Transverse colon', 'Uterus NOS', 'Soft palate NOS', 'Cardia NOS', 'Corpus uteri', 'skin NOS', 'Short bones of lower limb and associated joints', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sublingual gland', 'Scrotum NOS', 'Appendix', 'Hematopoietic system NOS', 'Rectosigmoid junction', 'Islets of Langerhans', 'Lacrimal gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Posterior wall of bladder', 'Posterior wall of hypopharynx', 'Commissure of lip', 'Short bones of upper limb and associated joints', 'Floor of mouth NOS', 'Mediastinum NOS', 'Overlapping lesion of bladder', 'Ventricle NOS', 'Lower lobe lung', 'Skin of lip NOS', 'Kidney NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of major salivary glands', 'Vulva NOS', 'Upper third of esophagus', 'Sigmoid colon', 'Duodenum', 'Ureteric orifice', 'Lymph nodes of inguinal region or leg', 'Overlapping lesion of urinary organs', 'Upper respiratory tract NOS', 'Intrahepatic bile duct', 'Retroperitoneum', 'Vallecula', 'Middle lobe lung', 'Urinary system NOS', 'Postcricoid region', 'Supraglottis', 'Eye NOS', 'Anal canal', 'Meninges NOS', 'Upper-inner quadrant of breast', 'Spleen', 'Overlapping lesion of lung', 'Uterine adnexa', 'Specified parts of peritoneum', 'Prepuce', 'Upper-outer quadrant of breast', 'Nasal cavity', 'Cecum', 'Isthmus uteri', 'Testis NOS', 'Fallopian tube', 'Overlapping lesion of lip', 'Skin of other and unspecified parts of face', 'Mouth NOS', 'Renal pelvis', 'Overlapping lesion of male genital organs', 'Meckel diverticulum', 'Reticuloendothelial system NOS', 'Skin of trunk', 'Brain stem', 'Ill-defined sites within respiratory system', 'Border of tongue', 'Heart', 'Ciliary body', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",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
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,"['Metastatic', 'Normal adjacent', 'Recurrent', 'Post therapy', 'Normal distant', 'Primary', 'Post therapy adjuvant', 'Not analyzed', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Premalignant - in situ', 'Normal', 'Premalignant', 'Post therapy neoadjuvant', 'Additional Primary', 'Local recurrence', '']","['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,"['Not Reported', 'Not Applicable', 'unknown', 'Bilateral', 'Right', 'Left', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",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
Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Liquid Nitrogen', 'Cold Pack', 'Ambient Pack', 'Ice Pack', 'Not Shipped', 'Dry Ice', 'Other Shipping Environment', 'Specimen at Room Temperature', '']","['Biospecimen is ""Analyte""', 'Biospecimen is ""Blood""']",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,"['Coverslip', 'Other', 'Not applicable', 'Uncharged', 'Charged', '']","['Biospecimen is ""Analyte""']",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,"['cDNA Libraries Analyte', 'Total RNA Analyte', 'Tissue Block Analyte', 'cfDNA Analyte', 'Plasma', 'DNA Analyte', 'PBMCs or Plasma or Serum Analyte', 'Serum Analyte', 'protein', 'PBMCs', 'lipid', 'metabolite', 'RNA Analyte', 'Tissue Section Analyte', '']","['Biospecimen is ""Analyte""']",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
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 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
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
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
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
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,OtherAssay
Filename,Filename,Filename,Name of a file,True,,,,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
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
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
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ExSeqMinimal
Filename,Filename,Filename,Name of a file,True,,,,ExSeqMinimal
Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",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,,,,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
Total Number of Input Cells,Total Number of Input Cells,TotalNumberofInputCells,Number of cells loaded/placed on plates,True,,,,ScRNA-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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,,"['3 Prime', '5 Prime', 'Full Length Transcript']",,ScRNA-seqLevel1
Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,ScRNA-seqLevel1
Cryopreserved Cells in Sample,Cryopreserved Cells in Sample,CryopreservedCellsinSample,Indicate if library preparation was based on revived frozen cells.,True,,"['no', 'yes']",,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
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
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
Input Cells and Nuclei,Input Cells and Nuclei,InputCellsandNuclei,"Number of cells and number of nuclei input; entry format: number, number",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,,"['Microfluidics Chip', '10x', 'Nuclei Isolation', 'Droplets', 'Plates', 'FACS']",,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,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,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
Read2,Read2,Read2,Read 2 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,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,,"['Poly-dT', 'Feature barcoding', 'Oligo-dT', 'Random']",,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 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
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
Filename,Filename,Filename,Name of a file,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,,"['Nextera XT', 'Drop-seq', 'CEL-seq2', '10xV2', '10xV1.1', 'inDropsV2', 'sci-ATAC-seq', '10x Multiome', '10xV3', 'Smart-seq2', '10xV1.0', 'TruDrop', 'inDropsV3', ""10x GEM 3'"", '10xV3.1', 'Smart-SeqV4', ""10x GEM 5'"", '10x FLEX']",,ScRNA-seqLevel1
Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['gentleMACS', 'Enzymatic Digestion', 'Not Applicable', 'Dounce']",,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,,"['No Spike In', 'ERCC', 'PhiX', 'Other Spike In']",,ScRNA-seqLevel1
Read1,Read1,Read1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScRNA-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,ScRNA-seqLevel1
Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1
Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1
Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1
UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Read1 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,,"['Read1 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,,"['Read1 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1
cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Read1 is ""cDNA""']",ScRNA-seqLevel1
cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Read1 is ""cDNA""']",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
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,"['no', 'yes', '']","['Library Construction Method is ""CEL-seq2""']",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
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
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
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),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
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
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
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
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
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
scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['HCA Optimus', 'dropEST', 'Other', 'Differentiation trajectory analysis', 'Cell annotation', 'DEXSeq', 'STARsolo', 'Cufflinks', 'CellRanger', 'HTSeq - FPKM', 'SEQC']",,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
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScRNA-seqLevel2
Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,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
Checksum,Checksum,Checksum,MD5 checksum of the BAM file,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
Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Other', 'Gene Expression Quantification', 'Exon Expression Quantification', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification']",,ScRNA-seqLevel3
Cell Total,Cell Total,CellTotal,Number of sequenced  cells. Applies to raw counts matrix only.,True,,,,ScRNA-seqLevel3
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel3
Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Batch Corrected Counts', 'Normalized Counts']",,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
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
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 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
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
scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['HCA Optimus', 'dropEST', 'Other', 'Differentiation trajectory analysis', 'Cell annotation', 'DEXSeq', 'STARsolo', 'Cufflinks', 'CellRanger', 'HTSeq - FPKM', 'SEQC']",,ScRNA-seqLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScRNA-seqLevel3
Cell Median Number Reads,Cell Median Number Reads,CellMedianNumberReads,Median number of reads per cell. Number,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
Cell Median Number Genes,Cell Median Number Genes,CellMedianNumberGenes,Median number of genes detected per cell. Number,True,,,,ScRNA-seqLevel3
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),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
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
scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['HCA Optimus', 'dropEST', 'Other', 'Differentiation trajectory analysis', 'Cell annotation', 'DEXSeq', 'STARsolo', 'Cufflinks', 'CellRanger', 'HTSeq - FPKM', 'SEQC']",,ScRNA-seqLevel4
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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 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
Spatial Barcode Offset,Spatial Barcode Offset,SpatialBarcodeOffset,Offset in sequence for spot barcode read (in bp): number,True,,,,Slide-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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,,"['3 Prime', '5 Prime', 'Full Length Transcript']",,Slide-seqLevel1
Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,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 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,,"['Nextera XT', 'Drop-seq', '10xV2', '10xV1.1', 'inDropsV2', '10xV3', 'Smart-seq2', '10xV1.0', 'TruDrop', 'inDropsV3', '10xV3.1', 'Smart-SeqV4']",,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
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
Spatial Barcode and UMI,Spatial Barcode and UMI,SpatialBarcodeandUMI,Spot and transcript identifiers,True,,,,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,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,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
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,,"['Poly-dT', 'Feature barcoding', 'Oligo-dT', 'Random']",,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 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
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
Spatial Read1,Spatial Read1,SpatialRead1,Read 1 content description,True,,"['cDNA', 'Spatial Barcode and UMI']",,Slide-seqLevel1
Spatial Read2,Spatial Read2,SpatialRead2,Read 2 content description,True,,"['cDNA', 'Spatial Barcode and UMI']",,Slide-seqLevel1
Filename,Filename,Filename,Name of a file,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,,"['No Spike In', 'ERCC', 'PhiX', 'Other Spike In']",,Slide-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,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
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
cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",Slide-seqLevel1
cDNA Length,cDNA Length,CDNALength,Length of 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
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),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
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
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
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
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
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
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
Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,Slide-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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
Slide-seq Workflow Parameter Description,Slide-seq Workflow Parameter Description,Slide-seqWorkflowParameterDescription,Parameters used to run the Slide-seq workflow. String,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
Checksum,Checksum,Checksum,MD5 checksum of the BAM file,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
Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Other', 'Gene Expression Quantification', 'Exon Expression Quantification', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification']",,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
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,Slide-seqLevel3
Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Batch Corrected Counts', 'Normalized Counts']",,Slide-seqLevel3
Beads Total,Beads Total,BeadsTotal,Number of sequenced beads. Applies to raw counts matrix only. Integer,False,,,,Slide-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,,,,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
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
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
Slide-seq Fragment Size,Slide-seq Fragment Size,Slide-seqFragmentSize,Average cDNA length associated with the experiemtn. Integer,False,,,,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
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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 Parameter Description,Slide-seq Workflow Parameter Description,Slide-seqWorkflowParameterDescription,Parameters used to run the Slide-seq workflow. String,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
Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,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,,"['All Bead Locations', 'Not Applicable', 'Matched Bead Locations', 'Matched Bead Barcodes', 'All Bead Barcodes', 'Matrix Barcodes', 'Matrix Features']",,Slide-seqLevel3
Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Single Read', 'Long Read', 'Mid-length', 'Paired End']",,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
Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,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
Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkRNA-seqLevel1
Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['rRNA Depletion', 'Random', 'Other', 'PCR', 'Affinity Enrichment', 'miRNA Size Fractionation', 'Hybrid Selection', 'Poly-T Enrichment']",,BulkRNA-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkRNA-seqLevel1
Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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
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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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
Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,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
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1
Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,BulkRNA-seqLevel1
QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1
Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,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
Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,BulkRNA-seqLevel1
Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,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
Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,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
Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1
Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,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
Filename,Filename,Filename,Name of a file,True,,,,BulkRNA-seqLevel1
Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. 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
To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['Yes - Trim Adapter Sequence', 'no', '']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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
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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1
DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1
Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. 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
Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,BulkRNA-seqLevel1
Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,BulkRNA-seqLevel1
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
Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['No Spike In', 'ERCC', 'PhiX', 'Other Spike In']",,BulkRNA-seqLevel1
Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,BulkRNA-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,BulkRNA-seqLevel1
Library Strand,Library Strand,LibraryStrand,Library stranded-ness.,False,,"['Unstranded', 'Second Stranded', 'Not Applicable', 'First Stranded', '']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1
QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,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
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
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 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
Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkRNA-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkRNA-seqLevel2
Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,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
MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkRNA-seqLevel2
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,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
Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkRNA-seqLevel2
Contamination Error,Contamination Error,ContaminationError,Estimation error of 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
Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,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
Filename,Filename,Filename,Name of a file,True,,,,BulkRNA-seqLevel2
Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STAR 2-Pass Transcriptome', 'BSmooth', 'Bismark', 'BWA-aln', 'SOCS-B', 'Bowtie', 'BRAT-BW', 'BatMeth', 'BWA', 'BWA-meth', 'GSNAP', 'STAR 2-Pass Chimeric', 'Bisulfighter', 'BWA with BQSR', 'LAST', 'STAR 2-Pass', 'STAR 2-Pass Genome', 'BWA with Mark Duplicates and BQSR', 'ERNE-BS5', 'BS-Seeker2', 'MethylCoder', 'Other Alignment Workflow', 'Segemehl', 'BSMAP', 'Pash', 'None', 'B-SOLANA', 'RMAP', 'BWA-mem', 'BS-Seeker']",,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
MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI', 'MSI-low', 'MSS', 'MSI-high', '']",,BulkRNA-seqLevel2
Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,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
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
Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,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
Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,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
Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkRNA-seqLevel2
MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,False,,,,BulkRNA-seqLevel2
Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,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
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
Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Other', 'Gene Expression Quantification', 'Exon Expression Quantification', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification']",,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 Detected,Fusion Gene Detected,FusionGeneDetected,Was a fusion gene identified?,False,,"['Yes - Fusion Gene Detected', 'unknown', 'no', '']",,BulkRNA-seqLevel3
Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Batch Corrected Counts', 'Normalized Counts']",,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
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
Expression Units,Expression Units,ExpressionUnits,How quantities are corrected for gene length,True,,"['Other', 'RPKM', 'FPKM', 'TPM', 'NA', '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
Fusion Gene Identity,Fusion Gene Identity,FusionGeneIdentity,The gene symbols of fused genes.,False,,,,BulkRNA-seqLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkRNA-seqLevel3
Filename,Filename,Filename,Name of a file,True,,,,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
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
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
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
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
Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Single Read', 'Long Read', 'Mid-length', 'Paired End']",,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
Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,BulkWESLevel1
Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkWESLevel1
Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkWESLevel1
Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['rRNA Depletion', 'Random', 'Other', 'PCR', 'Affinity Enrichment', 'miRNA Size Fractionation', 'Hybrid Selection', 'Poly-T Enrichment']",,BulkWESLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkWESLevel1
Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,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
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
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
Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. 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
Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,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,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,BulkWESLevel1
Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,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
Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,BulkWESLevel1
Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,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
Filename,Filename,Filename,Name of a file,True,,,,BulkWESLevel1
Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. 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
To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['Yes - Trim Adapter Sequence', 'no', '']",,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,,"['SureSelect Human All Exon v3', 'Custom SeqCap EZ TARGET-OS Panel - 7.0 Mb', 'TruSeq Exome Enrichment - 62 Mb', 'Custom Ion AmpliSeq Hotspot GENIE-MOSC3 Augmented Panel - 74 Genes', 'Not Applicable', 'Custom Myeloid GENIE-VICC Panel - 37 Genes', '25 rxn xGen Universal Blocking Oligo – TS HT-i7', 'Custom SureSelect CGCI-HTMCP-CC KMT2D And Hotspot Panel - 37.0 Kb', 'Custom Twist Broad Exome v1.0 - 35.0 Mb', 'unknown', 'Nextera Rapid Capture Exome v1.2', 'SureSelect Human All Exon v5 + UTR', 'Custom Twist Broad PanCancer Panel - 396 Genes', 'SeqCap EZ Human Exome v3.0', 'xGen Exome Research Panel v1.0', 'Custom SureSelect GENIE-UHN Panel - 555 Genes', 'Custom Targets File Provided', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 203 Genes', 'Custom MSK IMPACT Panel - 410 Genes', 'Custom SureSelect CGCI-HTMCP-CC Panel - 19.7 Mb', 'Custom MSK IMPACT Panel - 341 Genes', 'Nextera DNA Exome', 'SeqCap EZ HGSC VCRome v2.1', 'SureSelect Human All Exon v5', 'TruSight Myeloid Sequencing Panel', 'TruSeq RNA Exome', 'Custom Personalis ACEcp VAREPOP-APOLLO Panel v2', 'Custom SureSelect Human All Exon v1.1 Plus 3 Boosters', 'Foundation Medicine T5a Panel - 322 Genes', 'Custom AmpliSeq Cancer Hotspot GENIE-MDA Augmented Panel v1 - 46 Genes', 'Custom GENIE-DFCI Oncopanel - 300 Genes', 'Custom Large Construct Capture TARGET-OS Panel - 8 Genes', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v1', 'Custom Solid Tumor GENIE-VICC Panel - 34 Genes', 'xGen Universal Blocking Oligo – TS HT-i5 - 25 rxn', 'Ion AmpliSeq Comprehensive Cancer Panel', 'SureSelect Human All Exon v6', 'Foundation Medicine T7 Panel - 429 Genes', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v2', 'Custom GENIE-DFCI Oncopanel - 447 Genes', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 88 Genes', 'SeqCap EZ Human Exome v2.0', 'TruSeq Amplicon Cancer Panel', 'Custom SureSelect TARGET-AML_NBL_WT Panel - 2.8 Mb', 'Custom GENIE-DFCI OncoPanel - 275 Genes', 'SureSelect Human All Exon v4', 'Custom MSK IMPACT Panel - 468 Genes', 'Custom HaloPlex DLBCL Panel - 370 Genes', 'Custom SureSelect CGCI-BLGSP Panel - 4.6 Mb', 'Ion AmpliSeq Cancer Hotspot Panel v2']",,BulkWESLevel1
Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,BulkWESLevel1
Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1
Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1
Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,BulkWESLevel1
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
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
Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkWESLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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
Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2
Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,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
MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkWESLevel2
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2
QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,BulkWESLevel2
Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. 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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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
Contamination Error,Contamination Error,ContaminationError,Estimation error of 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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2
Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkWESLevel2
Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,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
Filename,Filename,Filename,Name of a file,True,,,,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2
Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STAR 2-Pass Transcriptome', 'BSmooth', 'Bismark', 'BWA-aln', 'SOCS-B', 'Bowtie', 'BRAT-BW', 'BatMeth', 'BWA', 'BWA-meth', 'GSNAP', 'STAR 2-Pass Chimeric', 'Bisulfighter', 'BWA with BQSR', 'LAST', 'STAR 2-Pass', 'STAR 2-Pass Genome', 'BWA with Mark Duplicates and BQSR', 'ERNE-BS5', 'BS-Seeker2', 'MethylCoder', 'Other Alignment Workflow', 'Segemehl', 'BSMAP', 'Pash', 'None', 'B-SOLANA', 'RMAP', 'BWA-mem', 'BS-Seeker']",,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
MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI', 'MSI-low', 'MSS', 'MSI-high', '']",,BulkWESLevel2
Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,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
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
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
Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. 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
Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkWESLevel2
Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. 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
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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2
Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkWESLevel2
MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2
Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkWESLevel2
Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",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
Somatic Variants Workflow Type,Somatic Variants Workflow Type,SomaticVariantsWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['MuTect2', 'Pindel', 'SomaticSniper', 'CaVEMan', 'VarScan2', 'Other Somatic Variants Workflow Type', 'None', 'MuSE', 'GATK4', '']",,BulkWESLevel3
Structural Variant Workflow Type,Structural Variant Workflow Type,StructuralVariantWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['BRASS', 'CNVkit', 'Other Structural Variant Workflow Type', 'None', 'CNV', 'GATK4', '']",,BulkWESLevel3
Somatic Variants Workflow URL,Somatic Variants Workflow URL,SomaticVariantsWorkflowURL,Generic name for the workflow used to analyze a data set.,True,,,,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
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
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
Somatic Variants Sample Type,Somatic Variants Sample Type,SomaticVariantsSampleType,Is the sample case or control in somatic variant analysis,True,,"['Case Sample', 'Not Applicable', 'Control Sample']",,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
Germline Variants Workflow URL,Germline Variants Workflow URL,GermlineVariantsWorkflowURL,"Link to workflow document, e.g. Github, DockStore.org recommended",True,,,,BulkWESLevel3
Structural Variant Workflow URL,Structural Variant Workflow URL,StructuralVariantWorkflowURL,Link to workflow document. DockStore.org recommended. URL,True,,,,BulkWESLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkWESLevel3
Filename,Filename,Filename,Name of a file,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', 'None', 'GATK4', '']",,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
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
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,,,,MicroarrayLevel1
Microarray Molecule,Microarray Molecule,MicroarrayMolecule,Microarray is measuring this kind of molecule,True,,"['RNA', 'DNA']",,MicroarrayLevel1
Microarray Value Definition,Microarray Value Definition,MicroarrayValueDefinition,What the provided value signifies,True,,,,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
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
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,MicroarrayLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MicroarrayLevel1
Filename,Filename,Filename,Name of a file,True,,,,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 Platform ID,Microarray Platform ID,MicroarrayPlatformID,The NCBI GEO Microarray Platform ID that links to the table containing the array definition,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
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
Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,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
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MicroarrayLevel2
Filename,Filename,Filename,Name of a file,True,,,,MicroarrayLevel2
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),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
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
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
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
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,RPPALevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",False,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am', '']",,RPPALevel2
Filename,Filename,Filename,Name of a file,False,,,,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
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
Phosphoprotein Flag,Phosphoprotein Flag,PhosphoproteinFlag,A flag the denotes if an antibody targets a phosphoprotein.,False,,"['true', 'false', '']",,RPPALevel2
Vendor,Vendor,Vendor,Vendor,False,,,,RPPALevel2
Antibody Notes,Antibody Notes,AntibodyNotes,Notes on antibodies replacements and antibody recognition observations.,False,,,,RPPALevel2
Ab Name Reported on Dataset,Ab Name Reported on Dataset,AbNameReportedonDataset,The antibody name.,False,,,,RPPALevel2
GENCODE Gene Symbol Target,GENCODE Gene Symbol Target,GENCODEGeneSymbolTarget,The comma separated list of gene symbols targeted by the antibody.,False,,,,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
Species,Species,Species,Host animal.,False,,"['Rabbit', 'Mouse', 'Goat', '']",,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
Clone,Clone,Clone,Clone,False,,,,RPPALevel2
UNIPROT Protein ID Target,UNIPROT Protein ID Target,UNIPROTProteinIDTarget,The comma separated list of UNIPROT IDs targeted by the antibody.,False,,,,RPPALevel2
Internal Ab ID,Internal Ab ID,InternalAbID,Internal lab ID for an antibody.,False,,,,RPPALevel2
RPPA Dilution,RPPA Dilution,RPPADilution,The dilution ratio.,False,,,,RPPALevel2
Phospho Site,Phospho Site,PhosphoSite,The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442),False,,,,RPPALevel2
Catalog Number,Catalog Number,CatalogNumber,Catalog Number,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,,"['Used for QC', 'Under Evaluation', 'Valid', 'Use with Caution', '']",,RPPALevel2
Nucleus Identifier,Nucleus Identifier,NucleusIdentifier,Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from,True,,['Nuclei Barcode'],,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
scATACseq Read2,scATACseq Read2,ScATACseqRead2,Read 2 content description,True,,"['Sample Index', 'Cell Barcode and DNA Insert', 'Sample Index and DNA Insert', 'Cell Barcode', 'DNA Insert']",,ScATAC-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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
scATACseq Library Layout,scATACseq Library Layout,ScATACseqLibraryLayout,Sequencing read type,True,,['scATACseq Paired End'],,ScATAC-seqLevel1
scATACseq Read3,scATACseq Read3,ScATACseqRead3,Read 3 content description,False,,"['Sample Index', 'Cell Barcode and DNA Insert', 'Sample Index and DNA Insert', 'Cell Barcode', 'DNA Insert', '']",,ScATAC-seqLevel1
Total Number of Passing Nuclei,Total Number of Passing Nuclei,TotalNumberofPassingNuclei,Number of nuclei sequenced,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,,"['Microfluidics Chip', '10x', 'Nuclei Isolation', 'Droplets', 'Plates', 'FACS']",,ScATAC-seqLevel1
scATACseq Read1,scATACseq Read1,ScATACseqRead1,Read 1 content description,True,,"['Sample Index', 'Cell Barcode and DNA Insert', 'Sample Index and DNA Insert', 'Cell Barcode', 'DNA Insert']",,ScATAC-seqLevel1
Nuclei Barcode Length,Nuclei Barcode Length,NucleiBarcodeLength,Nuclei Barcode Length,True,,,,ScATAC-seqLevel1
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScATAC-seqLevel1
Threshold for Minimum Passing Reads,Threshold for Minimum Passing Reads,ThresholdforMinimumPassingReads,Threshold for calling cells,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
Single Nucleus Buffer,Single Nucleus Buffer,SingleNucleusBuffer,Nuclei isolation buffer,True,,"['10x', 'Omni', 'TST', 'NIB']",,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,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', '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
Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,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
Filename,Filename,Filename,Name of a file,True,,,,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
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,,"['Nextera XT', 'Drop-seq', 'CEL-seq2', '10xV2', '10xV1.1', 'inDropsV2', 'sci-ATAC-seq', '10x Multiome', '10xV3', 'Smart-seq2', '10xV1.0', 'TruDrop', 'inDropsV3', ""10x GEM 3'"", '10xV3.1', 'Smart-SeqV4', ""10x GEM 5'"", '10x FLEX']",,ScATAC-seqLevel1
Transposition Reaction,Transposition Reaction,TranspositionReaction,"Name of the transposase, transposon sequences",True,,"['Nextera Tn5', 'Tn5-059', 'In-House', 'Diagenode-unloaded Apex-Bio', 'Tn5', 'EZ-Tn5', 'Diagenode-loaded Apex-Bio']",,ScATAC-seqLevel1
Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['gentleMACS', 'Enzymatic Digestion', 'Not Applicable', 'Dounce']",,ScATAC-seqLevel1
Nuclei Barcode Read,Nuclei Barcode Read,NucleiBarcodeRead,Nuclei Barcode Read,True,,,,ScATAC-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,ScATAC-seqLevel1
Median Fraction of Reads in Peaks,Median Fraction of Reads in Peaks,MedianFractionofReadsinPeaks,Median fraction of reads in peaks (FRIP),True,,,,ScATAC-seqLevel1
Peaks Calling Software,Peaks Calling Software,PeaksCallingSoftware,Generic name of peaks calling tool,False,,,,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,"['no', 'yes', '']","['Library Construction Method is ""CEL-seq2""']",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
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
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
Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScATAC-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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
Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,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
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
Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScATAC-seqLevel2
Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScATAC-seqLevel2
MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,ScATAC-seqLevel2
Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScATAC-seqLevel2
Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,ScATAC-seqLevel2
Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,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
Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel2
Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STAR 2-Pass Transcriptome', 'BSmooth', 'Bismark', 'BWA-aln', 'SOCS-B', 'Bowtie', 'BRAT-BW', 'BatMeth', 'BWA', 'BWA-meth', 'GSNAP', 'STAR 2-Pass Chimeric', 'Bisulfighter', 'BWA with BQSR', 'LAST', 'STAR 2-Pass', 'STAR 2-Pass Genome', 'BWA with Mark Duplicates and BQSR', 'ERNE-BS5', 'BS-Seeker2', 'MethylCoder', 'Other Alignment Workflow', 'Segemehl', 'BSMAP', 'Pash', 'None', 'B-SOLANA', 'RMAP', 'BWA-mem', 'BS-Seeker']",,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
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
Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,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
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
Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,ScATAC-seqLevel2
Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,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 Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScATAC-seqLevel2
Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,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
MACS2 Seqnames,MACS2 Seqnames,MACS2Seqnames,Chromosome id,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
MACS2 Score,MACS2 Score,MACS2Score,Peak score (proportional to q-value) in MACS2,False,,,,ScATAC-seqLevel3
nFeature Peaks,nFeature Peaks,NFeaturePeaks,Number of peaks with at least one read,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
MACS2 Start,MACS2 Start,MACS2Start,Genomic starting position in MACS2,False,,,,ScATAC-seqLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScATAC-seqLevel3
Peak Region Cutsites,Peak Region Cutsites,PeakRegionCutsites,Number of ends of fragments in peak regions,False,,,,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
Blacklist Ratio,Blacklist Ratio,BlacklistRatio,Ratio of reads in blacklist regions,False,,,,ScATAC-seqLevel3
MACS2 Name,MACS2 Name,MACS2Name,Name of the peak in MACS2,False,,,,ScATAC-seqLevel3
Chimeric Read-Pairs,Chimeric Read-Pairs,ChimericRead-Pairs,Number of chimerically mapped read-pairs,False,,,,ScATAC-seqLevel3
scATAC-seq Object ID,scATAC-seq Object ID,ScATAC-seqObjectID,Orig.Ident or scATAC-seq Object ID,False,,,,ScATAC-seqLevel3
DNase Sensitive Region Fragments,DNase Sensitive Region Fragments,DNaseSensitiveRegionFragments,Number of fragments overlapping with DNase sensitive regions,False,,,,ScATAC-seqLevel3
MACS2 End,MACS2 End,MACS2End,Genomic ending position in MACS2,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
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
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
nFeature RNA,nFeature RNA,NFeatureRNA,Number of genes detected in cell,False,,,,ScATAC-seqLevel3
Promoter Region Fragments,Promoter Region Fragments,PromoterRegionFragments,Number of fragments overlapping promoter 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
nCount RNA,nCount RNA,NCountRNA,Total number of fragments in genes,False,,,,ScATAC-seqLevel3
Duplicate Read-Pairs,Duplicate Read-Pairs,DuplicateRead-Pairs,Number of duplicate read-pairs,False,,,,ScATAC-seqLevel3
MACS2 Strand,MACS2 Strand,MACS2Strand,DNA stand aligned with in MACS2,False,,,,ScATAC-seqLevel3
Total Read-Pairs,Total Read-Pairs,TotalRead-Pairs,Total read-pairs,False,,,,ScATAC-seqLevel3
TSS Fragments,TSS Fragments,TSSFragments,Number of fragments overlapping with TSS regions,False,,,,ScATAC-seqLevel3
Pct Reads in Peaks,Pct Reads in Peaks,PctReadsinPeaks,Percentage of reads in peaks,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
Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel3
TSS Percentile,TSS Percentile,TSSPercentile,Percentile rank of TSS score,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
MACS2 Relative Summit Position,MACS2 Relative Summit Position,MACS2RelativeSummitPosition,Position of the peak summit related to the start position in MACS2,False,,,,ScATAC-seqLevel3
Blacklist Region Fragments,Blacklist Region Fragments,BlacklistRegionFragments,Number of fragments overlapping blacklisted regions,False,,,,ScATAC-seqLevel3
Peak Region Fragments,Peak Region Fragments,PeakRegionFragments,Number of fragments overlapping peaks,False,,,,ScATAC-seqLevel3
Passed Filters,Passed Filters,PassedFilters,"Number of non-duplicate, usable read-pairs i.e. fragments",False,,,,ScATAC-seqLevel3
Nucleosome Percentile,Nucleosome Percentile,NucleosomePercentile,Percentile rank of nucleosome score,False,,,,ScATAC-seqLevel3
Enhancer Region Fragments,Enhancer Region Fragments,EnhancerRegionFragments,Number of fragments overlapping enhancer regions,False,,,,ScATAC-seqLevel3
nCount Peaks,nCount Peaks,NCountPeaks,Total number of fragments in peaks,False,,,,ScATAC-seqLevel3
LowMapQ,LowMapQ,LowMapQ,Number of read-pairs with <30 mapq on at least one end,False,,,,ScATAC-seqLevel3
MACS2 Width,MACS2 Width,MACS2Width,Width of the peak in bases in MACS2,False,,,,ScATAC-seqLevel3
Mitochondrial Read-Pairs,Mitochondrial Read-Pairs,MitochondrialRead-Pairs,Number of read-pairs mapping to mitochondria and non-nuclear contigs,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
TSS Enrichment,TSS Enrichment,TSSEnrichment,Transcription start site (TSS) enrichment score,False,,,,ScATAC-seqLevel3
Nucleus Identifier,Nucleus Identifier,NucleusIdentifier,Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from,True,,['Nuclei Barcode'],,ScmC-seqLevel1
Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Single Read', 'Long Read', 'Mid-length', 'Paired End']",,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,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScmC-seqLevel1
Single Nucleus Capture,Single Nucleus Capture,SingleNucleusCapture,Nuclei isolation method,False,,"['10x', 'droplet', 'Plates', '']",,ScmC-seqLevel1
Total Number of Passing Nuclei,Total Number of Passing Nuclei,TotalNumberofPassingNuclei,Number of nuclei sequenced,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
scmCseq Read2,scmCseq Read2,ScmCseqRead2,Read 2 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,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,,"['Microfluidics Chip', '10x', 'Nuclei Isolation', 'Droplets', 'Plates', 'FACS']",,ScmC-seqLevel1
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScmC-seqLevel1
scmCseq Read3,scmCseq Read3,ScmCseqRead3,Read 3 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScmC-seqLevel1
Threshold for Minimum Passing Reads,Threshold for Minimum Passing Reads,ThresholdforMinimumPassingReads,Threshold for calling cells,True,,,,ScmC-seqLevel1
Single Nucleus Buffer,Single Nucleus Buffer,SingleNucleusBuffer,Nuclei isolation buffer,True,,"['10x', 'Omni', 'TST', 'NIB']",,ScmC-seqLevel1
Peaks Calling Software,Peaks Calling Software,PeaksCallingSoftware,Generic name of peaks calling tool,True,,,,ScmC-seqLevel1
scmCseq Read1,scmCseq Read1,ScmCseqRead1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,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,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,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
Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,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
Filename,Filename,Filename,Name of a file,True,,,,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
Bisulfite Conversion,Bisulfite Conversion,BisulfiteConversion,Name of the kit used in bisulfite conversion.,True,,"['Zimo EZ-96 DNA Methylation Deep Kit', 'Agilent SureSelectXT Methyl-Seq', 'Zimo EZ DNA Methylation Kit', 'NEBNext Enzymatic Methyl-seq Kit', 'Zimo EZ-96 DNA Methylation Shallow Kit']",,ScmC-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,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
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
Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,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
Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,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
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 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
cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Scmcseq read1 is ""cDNA""']",ScmC-seqLevel1
cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Scmcseq read1 is ""cDNA""']",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
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,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,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
Total DNA Input,Total DNA Input,TotalDNAInput,"Overall number of reads for a given sample in digits (microgram, nanogram).",False,,,,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,,"['Technical replicate', 'Not Applicable', 'Biological replicate']",,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
Bisulfite Conversion,Bisulfite Conversion,BisulfiteConversion,Name of the kit used in bisulfite conversion.,True,,"['Zimo EZ-96 DNA Methylation Deep Kit', 'Agilent SureSelectXT Methyl-Seq', 'Zimo EZ DNA Methylation Kit', 'NEBNext Enzymatic Methyl-seq Kit', 'Zimo EZ-96 DNA Methylation Shallow Kit']",,BulkMethylation-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,BulkMethylation-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkMethylation-seqLevel1
Bulk Methylation Assay Type,Bulk Methylation Assay Type,BulkMethylationAssayType,Assay types normally determine genomic coverage,True,,"['Beadchip Array', 'Whole genome', 'Targeted Genome']",,BulkMethylation-seqLevel1
Filename,Filename,Filename,Name of a file,True,,,,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
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
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
Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScmC-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScmC-seqLevel2
Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,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
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
Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScmC-seqLevel2
Contamination Error,Contamination Error,ContaminationError,Estimation error of 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
Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,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
Filename,Filename,Filename,Name of a file,True,,,,ScmC-seqLevel2
Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STAR 2-Pass Transcriptome', 'BSmooth', 'Bismark', 'BWA-aln', 'SOCS-B', 'Bowtie', 'BRAT-BW', 'BatMeth', 'BWA', 'BWA-meth', 'GSNAP', 'STAR 2-Pass Chimeric', 'Bisulfighter', 'BWA with BQSR', 'LAST', 'STAR 2-Pass', 'STAR 2-Pass Genome', 'BWA with Mark Duplicates and BQSR', 'ERNE-BS5', 'BS-Seeker2', 'MethylCoder', 'Other Alignment Workflow', 'Segemehl', 'BSMAP', 'Pash', 'None', 'B-SOLANA', 'RMAP', 'BWA-mem', 'BS-Seeker']",,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
Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,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
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
Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,ScmC-seqLevel2
Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,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 Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScmC-seqLevel2
Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,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
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 Type,scATACseq Workflow Type,ScATACseqWorkflowType,Generic name for the workflow used to analyze a data set.,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
scATACseq Workflow Parameters Description,scATACseq Workflow Parameters Description,ScATACseqWorkflowParametersDescription,Parameters used to run the scATAC-seq workflow.,True,,,,ScATAC-seqLevel4
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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
Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Single Read', 'Long Read', 'Mid-length', 'Paired End']",,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
Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,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
Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,ScDNA-seqLevel1
Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['rRNA Depletion', 'Random', 'Other', 'PCR', 'Affinity Enrichment', 'miRNA Size Fractionation', 'Hybrid Selection', 'Poly-T Enrichment']",,ScDNA-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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
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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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
Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,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
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1
Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,ScDNA-seqLevel1
QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1
Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,ScDNA-seqLevel1
QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,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
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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1
Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,ScDNA-seqLevel1
Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,ScDNA-seqLevel1
Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,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
Filename,Filename,Filename,Name of a file,True,,,,ScDNA-seqLevel1
Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. 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
To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['Yes - Trim Adapter Sequence', 'no', '']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1
Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. 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
Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,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
QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,ScDNA-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,ScDNA-seqLevel1
Library Strand,Library Strand,LibraryStrand,Library stranded-ness.,False,,"['Unstranded', 'Second Stranded', 'Not Applicable', 'First Stranded', '']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,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,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1
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
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
Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScDNA-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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
Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,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
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
Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScDNA-seqLevel2
Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScDNA-seqLevel2
MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,ScDNA-seqLevel2
Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScDNA-seqLevel2
Proportion Mitochondrial Reads,Proportion Mitochondrial Reads,ProportionMitochondrialReads,Proportion of reads mapping to mitochondria.,False,,,,ScDNA-seqLevel2
Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,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
Filename,Filename,Filename,Name of a file,True,,,,ScDNA-seqLevel2
Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STAR 2-Pass Transcriptome', 'BSmooth', 'Bismark', 'BWA-aln', 'SOCS-B', 'Bowtie', 'BRAT-BW', 'BatMeth', 'BWA', 'BWA-meth', 'GSNAP', 'STAR 2-Pass Chimeric', 'Bisulfighter', 'BWA with BQSR', 'LAST', 'STAR 2-Pass', 'STAR 2-Pass Genome', 'BWA with Mark Duplicates and BQSR', 'ERNE-BS5', 'BS-Seeker2', 'MethylCoder', 'Other Alignment Workflow', 'Segemehl', 'BSMAP', 'Pash', 'None', 'B-SOLANA', 'RMAP', 'BWA-mem', 'BS-Seeker']",,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
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
Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,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
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
Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,ScDNA-seqLevel2
Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,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 Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScDNA-seqLevel2
Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,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
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,,"['Hashtag- multiplex', 'Cite-seq custom panel', 'Other', 'Biolegend Total seq B Human Universal cocktail V1.0', 'Nuclear Hashtag- multiplex', 'Biolegend Total seq A Custom', 'Biolegend Total seq C Custom', 'Biolegend Total seq B Custom', 'Biolegend Total seq A Human', 'Biolegend Total seq C Human Universal cocktail V1.0', 'Cell', 'Universal cocktail V1.0']",,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
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
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
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
Total Number of Input Cells,Total Number of Input Cells,TotalNumberofInputCells,Number of cells loaded/placed on plates,True,,,,MultiplexedCITE-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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,,"['3 Prime', '5 Prime', 'Full Length Transcript']",,MultiplexedCITE-seqLevel1
Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,MultiplexedCITE-seqLevel1
Cryopreserved Cells in Sample,Cryopreserved Cells in Sample,CryopreservedCellsinSample,Indicate if library preparation was based on revived frozen cells.,True,,"['no', 'yes']",,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,,"['no', 'yes', '']",,MultiplexedCITE-seqLevel1
Barcode Folder Synapse ID,Barcode Folder Synapse ID,BarcodeFolderSynapseID,Synapse ID of the folder containing the barcode lists,True,,,,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 Barcode Library Type,Feature Barcode Library Type,FeatureBarcodeLibraryType,The library construction methods for the feature barcode library,True,,"['10x ADT – citeseq/hashing', '10x TCR', '10x BCR']",,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
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
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
Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,True,,,,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
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,,"['Microfluidics Chip', '10x', 'Nuclei Isolation', 'Droplets', 'Plates', 'FACS']",,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
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,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,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
Read2,Read2,Read2,Read 2 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,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,,"['Poly-dT', 'Feature barcoding', 'Oligo-dT', 'Random']",,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 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
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
Filename,Filename,Filename,Name of a file,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,,"['Nextera XT', 'Drop-seq', 'CEL-seq2', '10xV2', '10xV1.1', 'inDropsV2', 'sci-ATAC-seq', '10x Multiome', '10xV3', 'Smart-seq2', '10xV1.0', 'TruDrop', 'inDropsV3', ""10x GEM 3'"", '10xV3.1', 'Smart-SeqV4', ""10x GEM 5'"", '10x FLEX']",,MultiplexedCITE-seqLevel1
Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['gentleMACS', 'Enzymatic Digestion', 'Not Applicable', 'Dounce']",,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,,"['No Spike In', 'ERCC', 'PhiX', 'Other Spike In']",,MultiplexedCITE-seqLevel1
Read1,Read1,Read1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,MultiplexedCITE-seqLevel1
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,MultiplexedCITE-seqLevel1
Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1
Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1
Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1
UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Read1 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,,"['Read1 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,,"['Read1 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1
cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Read1 is ""cDNA""']",MultiplexedCITE-seqLevel1
cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Read1 is ""cDNA""']",MultiplexedCITE-seqLevel1
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
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
Whitelist Cell Barcode File Link,Whitelist Cell Barcode File Link,WhitelistCellBarcodeFileLink,Link to file listing all possible cell barcodes. URL,True,,,,MultiplexedCITE-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MultiplexedCITE-seqLevel2
Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,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
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
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
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
Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,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 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
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
scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['HCA Optimus', 'dropEST', 'Other', 'Differentiation trajectory analysis', 'Cell annotation', 'DEXSeq', 'STARsolo', 'Cufflinks', 'CellRanger', 'HTSeq - FPKM', 'SEQC']",,MultiplexedCITE-seqLevel2
Filename,Filename,Filename,Name of a file,True,,,,MultiplexedCITE-seqLevel2
Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,MultiplexedCITE-seqLevel2
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),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
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
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
Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Other', 'Gene Expression Quantification', 'Exon Expression Quantification', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification']",,MultiplexedCITE-seqLevel3
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
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,MultiplexedCITE-seqLevel3
Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Batch Corrected Counts', 'Normalized Counts']",,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
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
Linked Matrices,Linked Matrices,LinkedMatrices,All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames,False,,,,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
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
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
scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['HCA Optimus', 'dropEST', 'Other', 'Differentiation trajectory analysis', 'Cell annotation', 'DEXSeq', 'STARsolo', 'Cufflinks', 'CellRanger', 'HTSeq - FPKM', 'SEQC']",,MultiplexedCITE-seqLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MultiplexedCITE-seqLevel3
Cell Median Number Reads,Cell Median Number Reads,CellMedianNumberReads,Median number of reads per cell. Number,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
Cell Median Number Genes,Cell Median Number Genes,CellMedianNumberGenes,Median number of genes detected per cell. Number,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-seqLevel4
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),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
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
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
scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['HCA Optimus', 'dropEST', 'Other', 'Differentiation trajectory analysis', 'Cell annotation', 'DEXSeq', 'STARsolo', 'Cufflinks', 'CellRanger', 'HTSeq - FPKM', 'SEQC']",,MultiplexedCITE-seqLevel4
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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
Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Single Read', 'Long Read', 'Mid-length', 'Paired End']",,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
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
Duplicate Removal Software,Duplicate Removal Software,DuplicateRemovalSoftware,Software used for remove duplicate reads,True,,"['Samtools sort', 'picard MarkDuplicates']",,BulkMethylation-seqLevel2
Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkMethylation-seqLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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
Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,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
Bulk Methylation Genomic Reference,Bulk Methylation Genomic Reference,BulkMethylationGenomicReference,The human genome reference used in the alignment of reads,True,,"['HG19', 'T2T CHM13', 'HG38']",,BulkMethylation-seqLevel2
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,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
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
Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkMethylation-seqLevel2
Contamination Error,Contamination Error,ContaminationError,Estimation error of 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
Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,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
Filename,Filename,Filename,Name of a file,True,,,,BulkMethylation-seqLevel2
Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STAR 2-Pass Transcriptome', 'BSmooth', 'Bismark', 'BWA-aln', 'SOCS-B', 'Bowtie', 'BRAT-BW', 'BatMeth', 'BWA', 'BWA-meth', 'GSNAP', 'STAR 2-Pass Chimeric', 'Bisulfighter', 'BWA with BQSR', 'LAST', 'STAR 2-Pass', 'STAR 2-Pass Genome', 'BWA with Mark Duplicates and BQSR', 'ERNE-BS5', 'BS-Seeker2', 'MethylCoder', 'Other Alignment Workflow', 'Segemehl', 'BSMAP', 'Pash', 'None', 'B-SOLANA', 'RMAP', 'BWA-mem', 'BS-Seeker']",,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
Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,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
Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,BulkMethylation-seqLevel2
Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,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 Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkMethylation-seqLevel2
Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkMethylation-seqLevel2
Trimmer,Trimmer,Trimmer,Software used for trimming,True,,"['Trim Galore!', 'FASTX toolkit', 'ConDeTri', 'ERNE-FILTER', 'Adapter removal', 'Kraken', 'Cutadapt', 'PRINSEQ', 'SolexaQA', 'Trimmo-matic', 'Btrim']",,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
Lambda methylation ratio,Lambda methylation ratio,Lambdamethylationratio,"Methylation ratio of mostly unmethylated lambda control, as a percentage",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
DMR Calling Tool,DMR Calling Tool,DMRCallingTool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),True,,"['metilene', 'DSS', 'MethylSig', 'DSS-single', 'BiSeq', 'MACAU', 'BSmooth', 'MethylKit', 'MOABS']",,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
DMR data file Format,DMR data file Format,DMRdatafileFormat,Format of the data files.,True,,"['BED', 'bedGraph']",,BulkMethylation-seqLevel3
DMC Calling Tool,DMC Calling Tool,DMCCallingTool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),True,,"['metilene', 'DSS', 'MethylSig', 'DSS-single', 'BiSeq', 'MACAU', 'MethylDackel', 'BSmooth', 'MethylKit', 'MOABS']",,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
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
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkMethylation-seqLevel3
pUC19 methylation ratio,pUC19 methylation ratio,PUC19methylationratio,"Methylation ratio of mostly methylated pUC19 control, as a percentage",True,,,,BulkMethylation-seqLevel3
Filename,Filename,Filename,Name of a file,True,,,,BulkMethylation-seqLevel3
DMC data file format,DMC data file format,DMCdatafileformat,Format of the data files,True,,"['BED', 'bedGraph']",,BulkMethylation-seqLevel3
Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,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
Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel1
Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 'MxIF', 'IMC', 'Not Applicable', 'ExSeq', 'H&E', 'SABER', 'mIHC', 't-CyCIF', 'CODEX', 'MIBI', 'GeoMX-DSP', 'MERFISH', 'RareCyte Orion', 'IHC']",,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
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
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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,,"['Other', 'Channel/Cycle Registration', 'TMA de-arraying', 'None', 'Illumination correction', 'Tile Stitching']",,ImagingLevel1
Filename,Filename,Filename,Name of a file,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,,"['Other', 'Channel/Cycle Registration', 'TMA de-arraying', 'None', 'Illumination correction', 'Tile Stitching']",,ImagingLevel1
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
WorkingDistance,WorkingDistance,WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",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
Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['no', 'yes']",,ImagingLevel2
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ImagingLevel2
Objective,Objective,Objective,Objective,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
FOVXUnit,FOVXUnit,FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ImagingLevel2
Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['no', 'yes']",,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
Immersion,Immersion,Immersion,Immersion medium,False,,"['Oil', 'Water', 'Other', 'Air', '']",,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),True,,"['nm', 'mm', 'cm', 'Å', 'µm']",,ImagingLevel2
SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,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,,"['nm', 'mm', 'cm', 'Å', 'µm']",,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
PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['uint32', 'int32', 'bit', 'uint16', 'double', 'uint8', 'float', 'int8', 'int16']",,ImagingLevel2
PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. 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),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ImagingLevel2
SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2
Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'yes']",,ImagingLevel2
Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,ImagingLevel2
FOVX,FOVX,FOVX,Field of view X dimension. Floating point,False,,,,ImagingLevel2
PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,ImagingLevel2
SizeT,SizeT,SizeT,Number of time points. Integer >= 1,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
SizeC,SizeC,SizeC,Number of channels. Integer >= 1,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,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ImagingLevel2
SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2
Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 'MxIF', 'IMC', 'Not Applicable', 'ExSeq', 'H&E', 'SABER', 'mIHC', 't-CyCIF', 'CODEX', 'MIBI', 'GeoMX-DSP', 'MERFISH', 'RareCyte Orion', 'IHC']",,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
FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ImagingLevel2
FOVY,FOVY,FOVY,Field  of view Y dimension. Floating point value,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
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
Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel2
Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,ImagingLevel2
PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,ImagingLevel2
Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel2
DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['ZYX', 'XYCTZ', 'XYZTC', 'XYCZT', 'XYZCT', 'XYTZC']",,ImagingLevel2
Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['no', 'yes']",,ImagingLevel2
FOV number,FOV number,FOVnumber,Index of FOV (as it pertains to its sequence order). Integer >= 1,False,,,,ImagingLevel2
PhysicalSizeZ,PhysicalSizeZ,PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,True,,,,ImagingLevel2
Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['true', 'false']",,ImagingLevel2
LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel2
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,ImagingLevel2
Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,ImagingLevel2
Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel3Segmentation
Imaging Segmentation Data Type,Imaging Segmentation Data Type,ImagingSegmentationDataType,Specifies how the segmentation is stored,True,,"['Probability Map', 'Mask', 'Point', 'Polygon', 'Outline']",,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
Number of Objects,Number of Objects,NumberofObjects,The number of objects (eg cells) described,True,,,,ImagingLevel3Segmentation
Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,,,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
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
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel3Segmentation
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ImagingLevel3Segmentation
Filename,Filename,Filename,Name of a file,True,,,,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
WorkingDistance,WorkingDistance,WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",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
Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['no', 'yes']",,ImagingLevel3Image
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel3Image
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ImagingLevel3Image
Objective,Objective,Objective,Objective,False,,,,ImagingLevel3Image
Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['no', 'yes']",,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
Immersion,Immersion,Immersion,Immersion medium,False,,"['Oil', 'Water', 'Other', 'Air', '']",,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
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
Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'yes']",,ImagingLevel3Image
FOVX,FOVX,FOVX,Field of view X dimension. Floating point,False,,,,ImagingLevel3Image
Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 'MxIF', 'IMC', 'Not Applicable', 'ExSeq', 'H&E', 'SABER', 'mIHC', 't-CyCIF', 'CODEX', 'MIBI', 'GeoMX-DSP', 'MERFISH', 'RareCyte Orion', 'IHC']",,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
FOVY,FOVY,FOVY,Field  of view Y dimension. Floating point value,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
Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel3Image
Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,ImagingLevel3Image
Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel3Image
Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['no', 'yes']",,ImagingLevel3Image
HTAN Parent Channel Metadata ID,HTAN Parent Channel Metadata ID,HTANParentChannelMetadataID,HTAN ID for a level 3 channels table.,True,,,,ImagingLevel3Image
FOV number,FOV number,FOVnumber,Index of FOV (as it pertains to its sequence order). Integer >= 1,False,,,,ImagingLevel3Image
LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel3Image
Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,ImagingLevel3Image
WorkingDistanceUnit,WorkingDistanceUnit,WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'cm', 'Å', '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,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ImagingLevel3Image
FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ImagingLevel3Image
Vendor,Vendor,Vendor,Vendor,False,,,,ImagingLevel3Channels
Emission Wavelength,Emission Wavelength,EmissionWavelength,Center/peak of the emission 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
Excitation Wavelength,Excitation Wavelength,ExcitationWavelength,Center/peak of the excitation spectrum (nm),False,,,,ImagingLevel3Channels
Antibody Name,Antibody Name,AntibodyName,"Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))",True,,,,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
Clone,Clone,Clone,Clone,False,,,,ImagingLevel3Channels
Excitation Bandwidth,Excitation Bandwidth,ExcitationBandwidth,Nominal width of excitation spectrum (nm),False,,,,ImagingLevel3Channels
Catalog Number,Catalog Number,CatalogNumber,Catalog Number,False,,,,ImagingLevel3Channels
HTAN Channel Metadata ID,HTAN Channel Metadata ID,HTANChannelMetadataID,HTAN ID for this channel metadata table (same for all rows),True,,,,ImagingLevel3Channels
Emission Bandwidth,Emission Bandwidth,EmissionBandwidth,Nominal width of emission spectrum (nm),False,,,,ImagingLevel3Channels
Oligo Barcode Upper Strand,Oligo Barcode Upper Strand,OligoBarcodeUpperStrand,Oligo Barcode - Upper Strand,False,,,,ImagingLevel3Channels
Dilution,Dilution,Dilution,Dilution (eg 1:1000),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,,"['Primary', 'Neither-Dye/Stain', 'Secondary']",,ImagingLevel3Channels
Channel ID,Channel ID,ChannelID,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1'),True,,,,ImagingLevel3Channels
Concentration,Concentration,Concentration,Concentration (eg 10ug/mL),False,,,,ImagingLevel3Channels
Metal Isotope Mass,Metal Isotope Mass,MetalIsotopeMass,Element mass number,False,,,,ImagingLevel3Channels
Sub Cycle Number,Sub Cycle Number,SubCycleNumber,Sub cycle number,False,,,,ImagingLevel3Channels
RRID identifier,RRID identifier,RRIDidentifier,Research Resource Identifier (eg “RRID: AB_394606”),True,,,,ImagingLevel3Channels
Metal Isotope Element,Metal Isotope Element,MetalIsotopeElement,Element abbreviation. eg “La” or “Nd”,False,,"['Sr', 'Lr', 'Sm', 'Rh', 'Fr', 'Zr', 'Ac', 'Te', 'Ta', 'H', 'Ge', 'Be', 'Gd', 'Ag', 'Hg', 'I', 'Li', 'Ti', 'Er', 'Rb', 'Np', 'no', 'Rg', 'Lu', 'Y', 'Lv', 'B', 'Ni', 'Sn', 'C', 'Ne', 'Fm', 'Pd', 'Hf', 'Pm', 'Tb', 'Md', 'Dy', 'Cs', 'V', 'Nb', 'Kr', 'Cd', 'W', 'Zn', 'Bh', 'Ba', 'Nd', 'Ga', 'Pt', 'Re', 'U', 'Cn', 'Cr', 'Ts', 'Mo', 'Br', 'He', 'Cu', 'Sg', 'Am', 'Mt', 'Eu', 'Al', 'Rf', 'Sb', 'Db', 'Ra', 'Co', 'Os', 'Th', 'Ir', 'Ar', 'Tl', 'Au', 'Hs', 'Bk', 'Si', 'Rn', 'K', 'Yb', 'Og', 'Pa', 'Fe', 'Ds', 'Se', 'Po', 'Na', 'Es', 'Bi', 'La', 'In', 'Pr', 'Mn', 'Pb', 'Tm', 'Ru', 'P', 'As', 'Ca', 'F', 'Mc', 'Pu', 'Mg', 'Ho', 'Cl', 'S', 'Fl', 'N', 'Tc', 'O', 'Sc', 'Xe', 'Cf', 'Nh', 'Ce', 'At', '']",,ImagingLevel3Channels
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
Target Name,Target Name,TargetName,Short descriptive name (abbreviation) for this target (antigen),True,,,,ImagingLevel3Channels
Lot,Lot,Lot,Lot number from vendor,False,,,,ImagingLevel3Channels
Channel QC Failure Type,Channel QC Failure Type,ChannelQCFailureType,Reason the channel failed QC,False,True,"['Auto-fluoresence', 'Staining artefacet', 'Other/multiple channel QC faliure types', 'Off-target staining', 'Imaging artefact', '']","['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
Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel4
Imaging Summary Statistic,Imaging Summary Statistic,ImagingSummaryStatistic,Function used to summarize object/feature intensity,False,,"['Not Specified', 'Median', 'Mean', '']",,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
Number of Objects,Number of Objects,NumberofObjects,The number of objects (eg cells) described,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
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
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
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel4
Number of Features,Number of Features,NumberofFeatures,The number of features (eg channels) described,True,,,,ImagingLevel4
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ImagingLevel4
Filename,Filename,Filename,Name of a file,True,,,,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
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,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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,,"['FALSE', '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,,"['3 Prime', '5 Prime', 'Full Length Transcript']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,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,,"['V4', 'V1', 'V2', 'V3', '']",,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
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,,"['Nextera XT', 'Drop-seq', '10xV2', '10xV1.1', 'inDropsV2', '10xV3', 'Smart-seq2', '10xV1.0', 'TruDrop', 'inDropsV3', '10xV3.1', 'Smart-SeqV4']",,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
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
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,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,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,,"['Poly-dT', 'Feature barcoding', 'Oligo-dT', 'Random']",,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
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
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
Spatial Read1,Spatial Read1,SpatialRead1,Read 1 content description,True,,"['cDNA', 'Spatial Barcode and UMI']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Spatial Read2,Spatial Read2,SpatialRead2,Read 2 content description,True,,"['cDNA', 'Spatial Barcode and UMI']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,,,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,,"['A1', 'B', 'A', 'D1', 'B1', 'C', 'C1', 'D', '']",,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
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
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
Spatial Barcode and UMI,Spatial Barcode and UMI,SpatialBarcodeandUMI,Spot and transcript identifiers,True,,,,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
cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1
cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",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 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
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
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,,"['A1', 'B', 'A', 'D1', 'B1', 'C', 'C1', 'D', '']",,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
Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,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-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
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
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
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
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
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
Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,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
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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
Checksum,Checksum,Checksum,MD5 checksum of the BAM file,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
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,,"['A1', 'B', 'A', 'D1', 'B1', 'C', 'C1', 'D', '']",,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
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
Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,,"['low res image', 'qc result html', 'unfiltered mex', 'detected jpg', 'tissue_positions', 'high res image', 'filtered mex', 'json scale factors', 'fiducial image jpg', 'features', 'detected image png', 'fiducial image png', 'reference png', 'probe dataset csv', 'barcodes', 'reference jpg']",,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-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
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
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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
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
Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,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
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,,"['A1', 'B', 'A', 'D1', 'B1', 'C', 'C1', 'D', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,,"['low res image', 'qc result html', 'unfiltered mex', 'detected jpg', 'tissue_positions', 'high res image', 'filtered mex', 'json scale factors', 'fiducial image jpg', 'features', 'detected image png', 'fiducial image png', 'reference png', 'probe dataset csv', 'barcodes', 'reference jpg']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
Spots under tissue,Spots under tissue,Spotsundertissue,The number of barcodes associated with a spot under tissue.,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-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
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
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
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 UMI Counts per Spot,Median UMI Counts per Spot,MedianUMICountsperSpot,The median number of UMI counts per tissue covered spot.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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
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
Visium Workflow Type,Visium Workflow Type,VisiumWorkflowType,Generic name for the workflow used to analyze the visium data set.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
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 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
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
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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
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
GeoMx DSP Library Preparation Kit Version,GeoMx DSP Library Preparation Kit Version,GeoMxDSPLibraryPreparationKitVersion,Version 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
GeoMx DSP NGS Library Selection Method,GeoMx DSP NGS Library Selection Method,GeoMxDSPNGSLibrarySelectionMethod,How RNA molecules are isolated.,False,,,,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 Preparation Kit Name,GeoMx DSP NGS Library Preparation Kit Name,GeoMxDSPNGSLibraryPreparationKitName,Name of Library Preparation Kit. String,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
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,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
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
Filename,Filename,Filename,Name of a file,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 Vendor,GeoMx DSP Library Preparation Kit Vendor,GeoMxDSPLibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
Segment name,Segment name,Segmentname,Name given to segment at time of generation,True,,,,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
Scan Offset X,Scan Offset X,ScanOffsetX,Offset X of the scan for GeoMx Analysis,True,,,,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
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
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
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
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
Scan Offset Y,Scan Offset Y,ScanOffsetY,Offset Y of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Tags,Tags,Tags,Unique descriptor of a variable group (ie. MAPK+),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
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
ROI Y Coordinate,ROI Y Coordinate,ROIYCoordinate,Y location within the image,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,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
Scan Height,Scan Height,ScanHeight,Height of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
Scan Width,Scan Width,ScanWidth,Width of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata
ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,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
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
Scan Width,Scan Width,ScanWidth,Width of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
ROI X Coordinate,ROI X Coordinate,ROIXCoordinate,X location within the image,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,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Nuclei count,Nuclei count,Nucleicount,Number of nuclei detected in the segment (if applicable),True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Scan Offset Y,Scan Offset Y,ScanOffsetY,Offset Y of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Tags,Tags,Tags,Unique descriptor of a variable group (ie. MAPK+),True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Segment name,Segment name,Segmentname,Name given to segment at time of generation,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Positive norm factor,Positive norm factor,Positivenormfactor,The Positive Control Normalization factor calculated using pos-hyb controls,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Scan Height,Scan Height,ScanHeight,Height of the scan for GeoMx Analysis,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
Binding Density,Binding Density,BindingDensity,The binding density as reported by the application,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Scan Offset X,Scan Offset X,ScanOffsetX,Offset X of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Tissue Stain,Tissue Stain,TissueStain,e.g. CD45 or PanCK (if masking was performed),False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
Scan name,Scan name,Scanname,GeoMx Scan name (as appears in Segment Summary),True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
QC status,QC status,QCstatus,ROI quality control flag as reported by the application,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
ROI Y Coordinate,ROI Y Coordinate,ROIYCoordinate,Y location within the image,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata
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', 'Protein nCounter', 'RNA nCounter']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
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', 'Batch Corrected Counts', 'Normalized Counts']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
GeoMx DSP Workflow Parameter Description,GeoMx DSP Workflow Parameter Description,GeoMxDSPWorkflowParameterDescription,Parameters used to run the GeoMx DSP workflow.,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 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
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
GeoMx DSP Unique Target Count,GeoMx DSP Unique Target Count,GeoMxDSPUniqueTargetCount,Total number of unique genes reported.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
GeoMx DSP Unique Probe Count,GeoMx DSP Unique Probe Count,GeoMxDSPUniqueProbeCount,Total number of unique probes reported.,False,,,,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
GeoMx DSP Workflow Link,GeoMx DSP Workflow Link,GeoMxDSPWorkflowLink,Link to workflow or command. DockStore.org recommended. URL,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3
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
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,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,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
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
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
Biotin Enrichment,Biotin Enrichment,BiotinEnrichment,Whether biotin is used for enriching ligation product,True,,"['no', 'yes']",,HI-C-seqLevel1
Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,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
Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,HI-C-seqLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,HI-C-seqLevel1
Crosslinking Condtion,Crosslinking Condtion,CrosslinkingCondtion,Detailed condition for DNA crosslinking,True,,,,HI-C-seqLevel1
Filename,Filename,Filename,Name of a file,True,,,,HI-C-seqLevel1
DNA Input Amount,DNA Input Amount,DNAInputAmount,"Amount of DNA for library construction, in nanograms.",True,,,,HI-C-seqLevel1
DNA Digestion Condition,DNA Digestion Condition,DNADigestionCondition,Enzymes and treatment length/temperature for genome digestion,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
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
Transposition Reaction,Transposition Reaction,TranspositionReaction,"Name of the transposase, transposon sequences",True,,"['Nextera Tn5', 'Tn5-059', 'In-House', 'Diagenode-unloaded Apex-Bio', 'Tn5', 'EZ-Tn5', 'Diagenode-loaded Apex-Bio']",,HI-C-seqLevel1
Resolution,Resolution,Resolution,"Binning size used for generating contact matrix, in basepair.",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
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
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
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,HI-C-seqLevel2
Filename,Filename,Filename,Name of a file,True,,,,HI-C-seqLevel2
Tool,Tool,Tool,Were any software or computational tools generated for this content,True,,"['no', 'yes']",,HI-C-seqLevel2
Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,HI-C-seqLevel2
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
Loop Window,Loop Window,LoopWindow,Binning size used for calling significant dot interactions (loops),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
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
Loop Calling,Loop Calling,LoopCalling,Tool used for identifying loop interactions,True,,"['HiCCUPS', 'Other', 'Cooltools']",,HI-C-seqLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,HI-C-seqLevel3
Filename,Filename,Filename,Name of a file,True,,,,HI-C-seqLevel3
Stripe Calling,Stripe Calling,StripeCalling,"Tool used for identifying architectural stripe-forming, interaction hotspots.",True,,"['MACS2', 'Other']",,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,,,,SRRSImagingLevel2
Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['no', 'yes']",,SRRSImagingLevel2
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,SRRSImagingLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,SRRSImagingLevel2
Objective,Objective,Objective,Objective,False,,,,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
Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['no', 'yes']",,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
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),True,,"['nm', 'mm', 'cm', 'Å', 'µm']",,SRRSImagingLevel2
SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,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
PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['uint32', 'int32', 'bit', 'uint16', 'double', 'uint8', 'float', 'int8', 'int16']",,SRRSImagingLevel2
PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. 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),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,SRRSImagingLevel2
SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2
Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'yes']",,SRRSImagingLevel2
Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,SRRSImagingLevel2
PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,SRRSImagingLevel2
SizeT,SizeT,SizeT,Number of time points. Integer >= 1,True,,,,SRRSImagingLevel2
SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,SRRSImagingLevel2
SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2
Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 'MxIF', 'IMC', 'Not Applicable', 'ExSeq', 'H&E', 'SABER', 'mIHC', 't-CyCIF', 'CODEX', 'MIBI', 'GeoMX-DSP', 'MERFISH', 'RareCyte Orion', 'IHC']",,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
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
Filename,Filename,Filename,Name of a file,True,,,,SRRSImagingLevel2
Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,SRRSImagingLevel2
PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,SRRSImagingLevel2
DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['ZYX', 'XYCTZ', 'XYZTC', 'XYCZT', 'XYZCT', 'XYTZC']",,SRRSImagingLevel2
Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['no', 'yes']",,SRRSImagingLevel2
Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['true', 'false']",,SRRSImagingLevel2
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,SRRSImagingLevel2
Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,SRRSImagingLevel2
Comment,Comment,Comment,Free text field (generally for QC comment),False,True,,"['Passed QC is ""No - Channels QC""']",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,,,,10XGenomicsXeniumISSExperiment
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,10XGenomicsXeniumISSExperiment
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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
Total Number of Cells,Total Number of Cells,TotalNumberofCells,The total number of cells analyzed on the flow cell,True,,,,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
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
Xenium Bundle Contents,Xenium Bundle Contents,XeniumBundleContents,A comma separated list of filenames within the Xenium bundle zip file,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
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
Percent of Transcripts within Cells,Percent of Transcripts within Cells,PercentofTranscriptswithinCells,The percentage of transcripts assigned to assayed cells,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
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
Filename,Filename,Filename,Name of a file,True,,,,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
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
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
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
Transcripts per Cell,Transcripts per Cell,TranscriptsperCell,Mean or Median transcript count per cell analyzed on the flow cell or slide,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
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
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
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,RPPALevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,RPPALevel3
Filename,Filename,Filename,Name of a file,True,,,,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
Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,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
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
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
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,RPPALevel4
Filename,Filename,Filename,Name of a file,True,,,,RPPALevel4
Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,RPPALevel4
Batch Correction Method,Batch Correction Method,BatchCorrectionMethod,Method that was used to batch correct Level 3 data,False,,,,RPPALevel4
HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,RPPALevel4
Unique Genes,Unique Genes,UniqueGenes,The total unique genes detected above background,False,,,,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
CosMx Bundle Contents,CosMx Bundle Contents,CosMxBundleContents,A comma separated list of filenames within the CosMx bundle zip file,True,,,,NanostringCosMxSMIExperiment
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,NanostringCosMxSMIExperiment
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,NanostringCosMxSMIExperiment
Mean Total Transcripts per Area,Mean Total Transcripts per Area,MeanTotalTranscriptsperArea,The mean total transcripts per um3,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,,"['protein', 'RNA']",,NanostringCosMxSMIExperiment
Total Number of Cells,Total Number of Cells,TotalNumberofCells,The total number of cells analyzed on the flow cell,True,,,,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
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
Total Number of Targets,Total Number of Targets,TotalNumberofTargets,Refers to the target of an assay. Can be genes/transcripts or probes,True,,,,NanostringCosMxSMIExperiment
Total Negative Probe Counts,Total Negative Probe Counts,TotalNegativeProbeCounts,Mean Total Negative probe counts/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
Percent of Transcripts within Cells,Percent of Transcripts within Cells,PercentofTranscriptswithinCells,The percentage of transcripts assigned to assayed cells,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
Number of FOVs,Number of FOVs,NumberofFOVs,The total number of FOVs recorded for the sample on a single flow cell,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
Filename,Filename,Filename,Name of a file,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
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
Transcripts per Cell,Transcripts per Cell,TranscriptsperCell,Mean or Median transcript count per cell analyzed on the flow cell or slide,True,,,,NanostringCosMxSMIExperiment
Polarity,Polarity,Polarity,The polarity of the mass analysis (positive or negative ion modes),True,,"['negative', 'positive']",,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
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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
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
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,,"['cDNA Libraries Analyte', 'Total RNA Analyte', 'Tissue Block Analyte', 'cfDNA Analyte', 'Plasma', 'DNA Analyte', 'PBMCs or Plasma or Serum Analyte', 'Serum Analyte', 'protein', 'PBMCs', 'lipid', 'metabolite', 'RNA Analyte', 'Tissue Section Analyte']",,MassSpectrometryLevel1
MS-based Assay Type,MS-based Assay Type,MS-basedAssayType,Analytes are the target molecules being measured with the assay.,True,,"['LC-MS', 'LC-MS/MS', 'TMT', 'MS']",,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
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 Mobile Phase A,LC Mobile Phase A,LCMobilePhaseA,Composition of mobile phase A,True,,,,MassSpectrometryLevel1
MS Scan Mode,MS Scan Mode,MSScanMode,"Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)",True,,"['MS', 'Other', 'MS3', 'MS/MS']",,MassSpectrometryLevel1
MS Labeling,MS Labeling,MSLabeling,"Indicates whether samples were labeled prior to MS analysis (e.g., TMT)",True,,,,MassSpectrometryLevel1
LC Instrument Vendor and Model,LC Instrument Vendor and Model,LCInstrumentVendorandModel,The manufacturer of the instrument used for LC.,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,,"['DIA', 'DDA', 'Other']",,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
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
MS Batch ID,MS Batch ID,MSBatchID,Batch ID indicating a set of samples that were run together.,True,,,,MassSpectrometryLevel1
LC Flow Rate,LC Flow Rate,LCFlowRate,LC flow rate in nL/min.,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
LC Temp Value,LC Temp Value,LCTempValue,LC temperature in C.,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
LC ID Value,LC ID Value,LCIDValue,LC column inner diameter in microns.,True,,,,MassSpectrometryLevel1
Filename,Filename,Filename,Name of a file,True,,,,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
LC Resin,LC Resin,LCResin,"Details of the resin used for lc, including vendor, particle size, pore size",True,,,,MassSpectrometryLevel1
LC Mobile Phase B,LC Mobile Phase B,LCMobilePhaseB,Composition of mobile phase B,True,,,,MassSpectrometryLevel1
LC Gradient,LC Gradient,LCGradient,The program dictates the mobile phase solvent composition over the course of the chromatographic run.,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,,"['Other', 'MALDI', 'DESI', 'SIMS', 'MALDI-2', 'nESI']",,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
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
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
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel2
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MassSpectrometryLevel2
MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel2
Filename,Filename,Filename,Name of a file,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
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
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
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
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MassSpectrometryLevel3
MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel3
Filename,Filename,Filename,Name of a file,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
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
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
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
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel4
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MassSpectrometryLevel4
MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel4
Filename,Filename,Filename,Name of a file,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
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 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
Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ElectronMicroscopyLevel1
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ElectronMicroscopyLevel1
EM spot size,EM spot size,EMspotsize,Beam spot size in micrometers (µm),False,,,,ElectronMicroscopyLevel1
EM voltage,EM voltage,EMvoltage,Accelerating voltage in kiloelectronvolts (keV),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
SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,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
PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,ElectronMicroscopyLevel1
SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,ElectronMicroscopyLevel1
EM stage tilt,EM stage tilt,EMstagetilt,Physical stage tilt in degrees with respect to the electron beam,False,,,,ElectronMicroscopyLevel1
PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. 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,,"['phase', 'SE', 'BSE', 'dark-field', 'bright-field']",,ElectronMicroscopyLevel1
SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,ElectronMicroscopyLevel1
EM signal processing,EM signal processing,EMsignalprocessing,SNR improvement strategies used,False,,"['line integration', 'None', 'frame integration', 'frame averaging', '']",,ElectronMicroscopyLevel1
EM contrast type,EM contrast type,EMcontrasttype,Does the image use standard SEM contrast or TEM contrast,False,,"['SEM', 'TEM', '']",,ElectronMicroscopyLevel1
EM method,EM method,EMmethod,Electron microscopy method used,True,,"['FIB-SEM', 'TEM', 'SBF-SEM', 'AT', 'SEM', 'ET', 'cryo ET', 'ssTEM']",,ElectronMicroscopyLevel1
EM instrument,EM instrument,EMinstrument,Make and model of the EM instrument used,True,,,,ElectronMicroscopyLevel1
SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,ElectronMicroscopyLevel1
EM beam current,EM beam current,EMbeamcurrent,Beam current in nanoamps (nA),False,,,,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
Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel1
PhysicalSizeZ,PhysicalSizeZ,PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,True,,,,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,,"['nm', 'mm', 'cm', 'Å', '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,,"['nm', 'mm', 'cm', 'Å', '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,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ElectronMicroscopyLevel1
EM contrast type,EM contrast type,EMcontrasttype,Does the image use standard SEM contrast or TEM contrast,False,,"['SEM', 'TEM', '']",,ElectronMicroscopyLevel2
Tile overlap X,Tile overlap X,TileoverlapX,Percentage of image overlap to allow tile stitching in x direction,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
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
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,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,,,,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
Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,,,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,,,,ElectronMicroscopyLevel3
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ElectronMicroscopyLevel3
Filename,Filename,Filename,Name of a file,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
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
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
File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ElectronMicroscopyLevel4
Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel4