From 669d371916e1f343bf1842c5b0911fe59357e4c4 Mon Sep 17 00:00:00 2001
From: Orion Banks <49208907+Bankso@users.noreply.github.com>
Date: Fri, 30 Aug 2024 15:27:20 -0700
Subject: [PATCH] Add files via upload

---
 files/JSON/mc2_rfc_test_8.30.24.json | 152 +++++++++++++++++++++++++++
 1 file changed, 152 insertions(+)
 create mode 100644 files/JSON/mc2_rfc_test_8.30.24.json

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+,Attribute,Label,Description,Required,Valid Values,Component
+Survival Outcome,Survival Outcome,SurvivalOutcome,Text term that describes the last known status of an individual.,False,"['Distant met recurrence/progression', 'unknown tumor status', 'Tumor free', 'Deceased', 'With tumor', 'Loco-regional recurrence/progression', 'Not Applicable', 'Not Reported', 'Not Allowed To Collect', 'Biochemical evidence of disease without structural correlate', '']",Biospecimen
+Tumor Grade,Tumor Grade,TumorGrade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.",False,"['G2', 'G4', 'unknown', 'G1', 'Intermediate Grade', 'G3', 'Not Applicable', 'High Grade', 'GB', 'Not Reported', 'GX', 'Low Grade', '']",Biospecimen
+Biospecimen Tumor Type,Biospecimen Tumor Type,BiospecimenTumorType,"The type of tumor associated with the specimen. Multiple values permitted, comma separated.",False,"['Non-Functioning Pituitary Gland Adenoma', 'Soft Tissue Sarcoma', 'Myeloproliferative Neoplasm', 'Ewing Sarcoma', 'High Grade Ovarian Serous Adenocarcinoma', 'Histiocytic Sarcoma', 'Central Nervous System Neoplasm', 'Myeloid Leukemia', 'Uveal Neoplasm', 'Atypical Teratoid/Rhabdoid Tumor', 'T-Cell Lymphoma', 'Meningioma', 'Sinonasal Squamous Cell Carcinoma', 'Leiomyoma', 'Cerebellar Neoplasm', 'Neurofibroma', 'Cervical Small Cell Carcinoma', 'Castration-Resistant Prostate Carcinoma', 'Pan-cancer', 'Medulloblastoma', 'Rhabdomyosarcoma', 'Pituitary Gland Adenoma', 'Pancreatic Adenocarcinoma', 'Lung Small Cell Carcinoma', 'Schwannoma', 'Combined Hepatocellular Carcinoma and Cholangiocarcinoma', 'Invasive Ductal Breast Carcinoma', 'T Acute Lymphoblastic Leukemia', 'Malignant Skin Neoplasm', 'Acute Myeloid Leukemia', 'Thyroid Gland Anaplastic Carcinoma', 'Lymphoma', 'Breast Adenocarcinoma', 'Colorectal Adenocarcinoma', 'Pending Annotation', 'Leukemia', 'Rosette-Forming Glioneuronal Tumor', 'Dysembryoplastic Neuroepithelial Neoplasm', 'Multiple Myeloma', 'Breast Carcinoma', 'Malignant Ovarian Neoplasm', 'Glioblastoma', 'Skin Carcinoma', 'Skin Neoplasm', 'Pancreatic Neuroendocrine Carcinoma', 'Lung Neoplasm', 'Plasmacytoma', 'Lung Adenocarcinoma', 'Testicular Embryonal Carcinoma', 'Non-Hodgkin Lymphoma', 'Biliary Tract Carcinoma', 'Acute Monocytic Leukemia', 'Follicular Lymphoma', 'Precursor B-cell lymphoblastic leukemia', 'Not Applicable', 'Urothelial Carcinoma', 'Ovarian Neoplasm', 'Primary Myelofibrosis', 'Synovial Sarcoma', 'Neuroendocrine Neoplasm', 'Uterine Adenosarcoma', 'Plexiform Neurofibroma', 'Head and Neck Carcinoma', 'Cervical Neoplasm', 'Bone Neoplasm', 'Chronic Myeloid Leukemia', 'Liver and Intrahepatic Bile Duct Carcinoma', 'Intrahepatic Cholangiocarcinoma', 'Choriocarcinoma', 'Central Nervous System Cavernous Hemangioma', 'B-Cell Non-Hodgkin Lymphoma', 'Primary Central Nervous System Lymphoma', 'Prostate Carcinoma', 'Breast Neoplasm', 'Fibrosarcoma', 'Cholangiocarcinoma', 'Mesothelioma', 'Hodgkin Lymphoma', 'Renal Cell Carcinoma', 'Gastric Neoplasm', 'Triple-Negative Breast Carcinoma', 'Intestinal Neoplasm', 'Colorectal Carcinoma', 'Lung Squamous Cell Carcinoma', 'Malignant Peripheral Nerve Sheath Tumor', 'Pancreatic Carcinoma', 'Uveal Melanoma', 'Gastrointestinal Stromal Neoplasm', 'Cutaneous Melanoma', 'Head and Neck Squamous Cell Carcinoma', 'Barrett Esophagus', 'Ovarian Adenosarcoma', 'Angiosarcoma', 'Malignant Digestive System Neoplasm', 'Acinar Cell Carcinoma', 'B Acute Lymphoblastic Leukemia', 'Craniopharyngioma', 'Gallbladder Carcinoma', 'Pheochromocytoma', 'Malignant Peritoneal Neoplasm', 'Sarcoma', 'Serous Tubal Intraepithelial Carcinoma', 'Chronic Lymphocytic Leukemia', 'Cutaneous T Cell Lymphoma', 'Acute Lymphoblastic Leukemia', 'Esophageal Adenocarcinoma', 'Colorectal Neoplasm', 'Fibroepithelial Polyp', 'Glioma', 'Esophageal Squamous Cell Carcinoma', 'Carcinoma In Situ', 'Low Grade Glioma', 'Myoepithelioma', 'Malignant Glioma', 'Malignant Neoplasm', 'Esophageal Carcinoma', 'Retinoblastoma', 'Chondroblastoma', 'Plasmablastic Lymphoma', 'Hepatocellular Carcinoma', 'Cervical Carcinoma', 'Rectal Adenocarcinoma', 'Colorectal Adenoma', 'Bladder Neoplasm', 'Gastric Carcinoma', 'Pancreatic Ductal Adenocarcinoma', 'Plexiform Schwannoma', 'Luminal A Breast Carcinoma', 'Ductal Breast Carcinoma In Situ', 'Mantle Cell Lymphoma', 'Thyroid Gland Noninvasive Follicular Neoplasm with Papillary-Like Nuclear Features', 'Giant Cell Tumor', 'Basal Cell Neoplasm', 'Kaposi Sarcoma', 'Bladder Carcinoma', 'Teratoma', 'Carcinoma', 'Cellular Schwannoma', 'Ovarian Carcinoma', 'Endometrial Neoplasm', 'Prostate Adenocarcinoma', 'Astrocytoma', 'Oral Cavity Squamous Cell Carcinoma', 'Malignant Genitourinary System Neoplasm', 'Ovarian Serous Adenocarcinoma', 'Penile Carcinoma', 'Gastroesophageal Adenocarcinoma', 'Squamous Cell Carcinoma', 'Liver and Intrahepatic Bile Duct Neoplasm', 'Thyroid Gland Carcinoma', 'Lymphoid Leukemia', 'Extraventricular Neurocytoma', 'Neuroblastoma', 'Lung Non-Small Cell Carcinoma', 'Diffuse Large B-Cell Lymphoma', 'Nasopharyngeal Carcinoma', 'Myeloid Neoplasm', 'Acute Promyelocytic Leukemia', 'Clear Cell Renal Cell Carcinoma', 'Oral Cavity Neoplasm', 'Lung Carcinoma', 'Osteosarcoma', 'Colon Carcinoma', 'Malignant Brain Neoplasm', 'Adenocarcinoma', 'Brain Neoplasm', 'Prostate Neoplasm', 'Ependymoma', 'Fibrolamellar Carcinoma', 'Pilocytic Astrocytoma', 'Mycosis Fungoides', 'Colon Adenocarcinoma', 'Vascular Neoplasm', 'Basal-Like Breast Carcinoma', 'Gastroesophageal Junction Adenocarcinoma', 'Endometrial Carcinoma', 'Malignant Pancreatic Neoplasm', 'Oropharyngeal Neoplasm', 'Salivary Gland Adenoid Cystic Carcinoma', 'Melanoma', 'Head and Neck Neoplasm', 'Not-Applicable', 'Pancreatic Neoplasm', 'Marginal Zone Lymphoma', 'Gastric Adenocarcinoma', 'Neuroepithelial Neoplasm', '']",Biospecimen
+Health Care Site,Health Care Site,HealthCareSite,The health care site at which the biospecimen sample was collected.,False,,Biospecimen
+Biospecimen_id,Biospecimen_id,BiospecimenId,"Unique row identifier, used as a primary key for record updates",True,,Biospecimen
+Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,Biospecimen
+Biospecimen Species,Biospecimen Species,BiospecimenSpecies,The species from which the biospecimen originates,True,"['Human', 'Chicken', 'Yeast', 'Trichoplax adhaerens', 'Boar', 'Rhesus monkey', 'Rat', 'Armadillo', 'African Bush Elephant', 'unknown', 'Escherichia coli', 'Cow', 'Dog', 'Multispecies', 'Cat', 'Asian Elephant', 'Opossum', 'Horse', 'Fruit Fly', 'Rabbit', 'Guinea Pig', 'Zebrafish', 'Worm', 'Sheep', 'Mouse', 'Unspecified']",Biospecimen
+Age at Sample Collection,Age at Sample Collection,AgeatSampleCollection,"Age at the time the biospecimen was collected, expressed in number of years since birth.",False,,Biospecimen
+Tumor Subtype,Tumor Subtype,TumorSubtype,"The subtype related to the scientific determination and investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms of tissue growth resulting from uncontrolled cell proliferation.",False,"['LumB', 'TNBC', 'LumA', 'Not Applicable', 'HER2', '']",Biospecimen
+Known Metastasis Sites,Known Metastasis Sites,KnownMetastasisSites,The text term(s) used to describe the anatomic site(s) of metastasis associated with the patient's malignant disease.,False,,Biospecimen
+Timepoint,Timepoint,Timepoint,"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.",False,,Biospecimen
+Biospecimen ID,Biospecimen ID,BiospecimenID,ID associated with a biosample,True,,Biospecimen
+Individual ID,Individual ID,IndividualID,ID associated with a study participant,True,,Biospecimen
+Biospecimen Type,Biospecimen Type,BiospecimenType,The type of biospecimen,True,"['Urine', 'Tissue', 'Blood', 'Analyte', 'Mouth Rinse', 'Sputum', 'Stool', 'Bone Marrow', 'Cells', 'Fluids', 'Ascites']",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.,False,"['Artery', 'Trachea', 'Tongue', 'Intestine', 'Lymphoid Tissue', 'Blood', 'Eye', 'Gastroesophageal Junction', 'Cervix Uteri', 'Lymphatic System', 'Endocervix', 'Thymus', 'Omentum', 'Olfactory Mucosa', 'Adrenal Gland', 'Kidney', 'Ovary', 'Vascular Endothelium', 'Placenta', 'Pending Annotation', 'Epithelium', 'Salivary Gland', 'Lung', 'Ear', 'Hippocampus', 'Pituitary Gland', 'Duodenum', 'Lymph Node', 'Pharynx', 'Foreskin', 'Adipose Tissue', 'Hematopoietic System', 'Genitourinary', 'Synovial Membrane', 'Not Applicable', 'Fallopian Tube', 'Aorta', 'Vertebra', 'Blood Vessel', 'Spinal Cord', 'Stomach', 'Cancer-Associated Fibroblast', 'Endothelium', 'Testis', 'Mammary Gland', 'Pleura', 'Gastrointestinal Tract', 'Joint', 'Periodontal Ligament', 'Vagina', 'Frontal Lobe', 'Breast', 'Bile Duct', 'Hair Follicle', 'Skin', 'Cardia', 'Ligament', 'Rectum', 'Caecum', 'Main Bronchus', 'Respiratory System', 'Embryonic Heart', 'Meninges', 'Brain', 'Alveolus', 'Intra-Abdominal Lymph Nodes', 'Uterus', 'Liver', 'Bone', 'Mesenchyme', 'Head and Neck', 'Heart Muscle', 'Embryo', 'Thyroid Gland', 'Cartilage', 'Abdominal Esophagus', 'Nervous System', 'Reproductive System', 'Intrathoracic Lymph Nodes', 'Peritoneum', 'Heart', 'Peripheral Blood Mononuclear Cell', 'Muscle', 'Prostate Gland', 'Mucosa', 'Connective and Soft Tissue', 'Larynx', 'Sclera', 'Unspecified', 'Nasal Cavity', 'Small Intestine', 'Endometrium', 'Esophagus', 'Tonsil', 'Gonad', 'Choroid', 'Sinonasal Tract', 'Lymph Nodes of Axilla or Arm', 'Pelvic Lymph Nodes', 'Oral Cavity', 'Colon', 'Lymph', 'Ascending Colon', 'Bladder', 'Spleen', 'Umbilical Cord', 'Peripheral Nerves', 'Lymph Nodes of Inguinal Region or Leg', 'Vein', 'Pancreas', 'Oral Mucosa', 'Bone Marrow', 'Cornea', 'Tendon', '']",Biospecimen
+Biospecimen Composition,Biospecimen Composition,BiospecimenComposition,"The text term used to describe the type(s) of tissue contained in the biospecimen. Multiple values permitted, comma separated.",False,,Biospecimen
+Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,False,"['Cryopreservation in liquid nitrogen - live cells', 'Frozen', 'Liquid Nitrogen', 'Fresh dissociated and single cell sorted', 'unknown', 'Cryopreservation in dry ice - dead tissue', 'Fresh dissociated', 'Snap Frozen', 'Fresh', 'Cryopreserved', 'Cryopreservation in liquid nitrogen - dead tissue', 'Formalin fixed paraffin embedded - FFPE', 'Formalin fixed-buffered', 'Fresh dissociated and single cell sorted into plates', 'Negative 80 Deg C', 'Methacarn fixed paraffin embedded - MFPE', 'Not Reported', 'Formalin fixed-unbuffered', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'OCT', '']",Biospecimen
+Site of Origin,Site of Origin,SiteofOrigin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease.",False,"['Artery', 'Trachea', 'Tongue', 'Intestine', 'Lymphoid Tissue', 'Blood', 'Eye', 'Gastroesophageal Junction', 'Cervix Uteri', 'Lymphatic System', 'Endocervix', 'Thymus', 'Omentum', 'Olfactory Mucosa', 'Adrenal Gland', 'Kidney', 'Ovary', 'Vascular Endothelium', 'Placenta', 'Pending Annotation', 'Epithelium', 'Salivary Gland', 'Lung', 'Ear', 'Hippocampus', 'Pituitary Gland', 'Duodenum', 'Lymph Node', 'Pharynx', 'Foreskin', 'Adipose Tissue', 'Hematopoietic System', 'Genitourinary', 'Synovial Membrane', 'Not Applicable', 'Fallopian Tube', 'Aorta', 'Vertebra', 'Blood Vessel', 'Spinal Cord', 'Stomach', 'Cancer-Associated Fibroblast', 'Endothelium', 'Testis', 'Mammary Gland', 'Pleura', 'Gastrointestinal Tract', 'Joint', 'Periodontal Ligament', 'Vagina', 'Frontal Lobe', 'Breast', 'Bile Duct', 'Hair Follicle', 'Skin', 'Cardia', 'Ligament', 'Rectum', 'Caecum', 'Main Bronchus', 'Respiratory System', 'Embryonic Heart', 'Meninges', 'Brain', 'Alveolus', 'Intra-Abdominal Lymph Nodes', 'Uterus', 'Liver', 'Bone', 'Mesenchyme', 'Head and Neck', 'Heart Muscle', 'Embryo', 'Thyroid Gland', 'Cartilage', 'Abdominal Esophagus', 'Nervous System', 'Reproductive System', 'Intrathoracic Lymph Nodes', 'Peritoneum', 'Heart', 'Peripheral Blood Mononuclear Cell', 'Muscle', 'Prostate Gland', 'Mucosa', 'Connective and Soft Tissue', 'Larynx', 'Sclera', 'Unspecified', 'Nasal Cavity', 'Small Intestine', 'Endometrium', 'Esophagus', 'Tonsil', 'Gonad', 'Choroid', 'Sinonasal Tract', 'Lymph Nodes of Axilla or Arm', 'Pelvic Lymph Nodes', 'Oral Cavity', 'Colon', 'Lymph', 'Ascending Colon', 'Bladder', 'Spleen', 'Umbilical Cord', 'Peripheral Nerves', 'Lymph Nodes of Inguinal Region or Leg', 'Vein', 'Pancreas', 'Oral Mucosa', 'Bone Marrow', 'Cornea', 'Tendon', '']",Biospecimen
+Sex,Sex,Sex,Biological sex associated with the specimen donor,False,"['Other', 'M', 'unknown', 'F', '']",Biospecimen
+Study Investigator,Study Investigator,StudyInvestigator,Investigator(s) associated with the project. Multiple names should be provided as a comma-separated list.,True,,Study
+PersonView Key,PersonView Key,PersonViewKey,"Unique PersonView_id foreign key(s) that group the resource with other components, as part of the same person-associated studies. Please provide multiple values as a comma-separated list.",False,,Study
+GrantView Key,GrantView Key,GrantViewKey,"Unique GrantView_id foreign key(s) that group the resource with other components, as part of the same grant-associated collection. Please provide multiple values as a comma-separated list.",False,,Study
+ProjectView Key,ProjectView Key,ProjectViewKey,"Unique ProjectView_id foreign key(s) that group the resource with other components, as part of the same grant-associated studies. Please provide multiple values as a comma-separated list.",False,,Study
+Study_id,Study_id,StudyId,A unique primary key that enables record updates using schematic.,True,,Study
+Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,Study
+Study Name,Study Name,StudyName,Name of the study,True,,Study
+Study Reuse Statement,Study Reuse Statement,StudyReuseStatement,"The funder-, contributor-, patient-, etc., derived content that includes terms, conditions, or statements associated with accessing and reusing the resource(s).",False,,Study
+Study Description,Study Description,StudyDescription,"Description of the study, including the types of experimental assays, model systems, types of analysis, etc.",True,,Study
+Grant Theme Name,Grant Theme Name,GrantThemeName,Theme(s) associated with the grant. 1...*,True,,GrantView
+Embargo End Date,Embargo End Date,EmbargoEndDate,Date at which an embargo on related resources had lifted,False,,GrantView
+NIH RePORTER Link,NIH RePORTER Link,NIHRePORTERLink,Link to the search results for this grant number on the NIH Reporter website,True,,GrantView
+Duration of Funding,Duration of Funding,DurationofFunding,"Duration of the funding period, in years",False,,GrantView
+Grant Name,Grant Name,GrantName,Name of the grant,True,,GrantView
+Grant Institution Name,Grant Institution Name,GrantInstitutionName,The full name of the institution(s) associated with the grant. (e.g. Harvard University). 1...*,True,,GrantView
+Grant Number,Grant Number,GrantNumber,"Number of the grant (i.e. ""CA------"" format)",True,,GrantView
+Grant Type,Grant Type,GrantType,Type of grant,True,"['R21', 'R37', 'U54', 'R01', 'U01', 'U24']",GrantView
+Grant Synapse Team,Grant Synapse Team,GrantSynapseTeam,"The Synapse team associated with the grant, created by the MC2 Center",False,,GrantView
+Grant Abstract,Grant Abstract,GrantAbstract,Abstract for the grant,True,,GrantView
+Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,GrantView
+Grant Institution Alias,Grant Institution Alias,GrantInstitutionAlias,The alias of the institution(s) associated with the grant (e.g. UCSD). 1...*,True,,GrantView
+Grant Consortium Name,Grant Consortium Name,GrantConsortiumName,Consortium(s) associated with the grant. 1...1,True,"['CCBIR', 'CSBC', 'PS-ON', 'TEC', 'PDMC', 'Sage Bionetworks', 'ICBP', 'MetNet', 'NCI Clinical and Translational Exploratory/Developmental Studies', 'HTAN', 'NCI']",GrantView
+Grant Investigator,Grant Investigator,GrantInvestigator,Investigator(s) associated witht the grant. 1...*,True,,GrantView
+Grant Start Date,Grant Start Date,GrantStartDate,The start date of the grant YYYY-MM-DD format,True,,GrantView
+Grant Synapse Project,Grant Synapse Project,GrantSynapseProject,"The Synapse project associated with the grant, created by the MC2 Center",False,,GrantView
+GrantView_id,GrantView_id,GrantViewId,A unique primary key that enables record updates using schematic.,True,,GrantView
+File Description,File Description,FileDescription,Description of the file.,False,,FileView
+File Species,File Species,FileSpecies,"The species the data was collected on. Multiple values permitted, comma separated.",True,,FileView
+Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,FileView
+FileView_id,FileView_id,FileViewId,A unique primary key that enables record updates using schematic.,True,,FileView
+DatasetView Key,DatasetView Key,DatasetViewKey,Unique DatasetView_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,FileView
+Data Use Codes,Data Use Codes,DataUseCodes,"DUO code - A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used.",False,,FileView
+File Assay,File Assay,FileAssay,The assay the file is representative of.,True,"['Deep Mutational Scanning', 'Multiplexed Immunofluorescence', 'Micropipette Aspiration', 'Electron Diffraction', 'QFISH', 'Multi-Angle Light Scattering', 'Gene Silencing', 'Whole Exome Sequencing', 'Vibrational Spectroscopy', 'Bioluminescence Imaging', 'Confocal Reflectance Quantitative Phase Microscopy', 'Global Chromatin Profiling', 'Comparative Genomic Hybridization', 'Hydrophilic Interaction Chromatography', 'Intravital Microscopy', 'siRNA', 'SDS-PAGE', 'In Situ Hybridization', 'Allograft', 'PlateSeq', 'Surveyor Nuclease Assay', 'Computed Tomography', 'Not Applicable', 'ImmunoFISH', 'Gas Chromatography Mass Spectrometry', 'Wound-Healing Assay', 'Magnetic Tweezers', 'Antitumor Drug Screening Assay', 'Virus Plaque Assay', 'TUNEL assay', 'Barcode-Seq', 'Optogenetic Assay', 'Forster Resonance Energy Transfer', 'Cell Adhesion Assay', 'Enzyme Activity Assay', 'Cytometric Bead Array Assay', 'Optical Stretcher', 'Plasmid Construction', 'Dynamic Contrast-Enhanced Magnetic Resonance Imaging', 'DNA Gene-Expression Microarray', 'High Throughput Screening', 'Synthesis', 'Tiling Array', 'Modeling', 'Bioelectrochemical Analysis', 'Mint-ChIP', 'Magnetic Twisting Cytometry', 'Phylogenetic Analysis', 'DBiT-Seq', 'Scanning Angle Interference Microscopy', 'Reverse-Phase High-Performance liquid Chromatography', '3C', 'Fluorescent Cell Barcoding', 'Fluorescence Activated Cell Sorting', 'Luciferase Reporter Assay', 'Field-Emission Scanning Electron Microscopy', 'Single-Molecule Localization Microscopy', 'Circular Dichroism Spectroscopy', 'DNase-Seq', 'Gene Set Enrichment Analysis', 'TIRF Microscopy', 'Patient Derived Xenograft', 'Mammosphere Formation Assay', 'Fluorescence Imaging', 'Immunohistochemistry Staining Method', 'Computational Modeling', 'Target Engagement Assay', 'MeRIP-Seq', 'Reduced Representation Bisulfite Sequencing', 'NanoString Digital Spatial Profiling', 'Transwell Assay', 'Reverse Phase Protein Array', 'ATAC-Seq', 'Whole Genome Sequencing', 'Suspended Microchannel Resonator', 'Cell Cycle Assay', 'Small-Angle X-ray Scattering', 'cDNA Array', 'RAS Protein Family Activation Assay', 'Tissue Microarray', 'Differential Scanning Fluorimetry', 'Computational Tool', 'Autoradiography', 'Surface Plasmon Resonance', 'Global Run-On Sequencing', 'Southern Blotting', 'Gene Ontology Enrichment Analysis', 'Unspecified', 'Von Kossa Staining', 'Electron Paramagnetic Resonance Spectroscopy', 'Mass Cytometry', 'Nm-seq', 'Proteomics Assay', 'Nuclear Magnetic Resonance', 'Atomic Force Microscopy', 'Hi-C', 'Cell Viability Assay', 'Scratch Assay', 'Fluorescence Lifetime Imaging Microscopy', 'Fourier-Transform Infrared Spectroscopy', 'Single-Molecule Tracking', '16S Ribosomal Gene Sequencing Assay', '5C', 'Photolithography', 'Bio-Layer Interferometry', 'MEMA Cell Growth Assay', 'Luminescent Cell Viability Assay', 'Colorimetric Cell Viability Assay', 'Clonality Analysis', 'Nanopore Sequencing', 'RNA Sequencing', 'Western Blotting', 'Survival Analysis', 'Shotgun Mass Spectrometry', 'Paraquat Survival Assay', 'Tandem Mass Tagging', 'Optical Tweezers', 'Microscopy', 'Deep Learning', 'Picrosirius Staining', 'Phagocytosis Assay', 'Nanopatterning', 'Transmission Electron Microscopy', 'Clinical Study', 'mRNA Sequencing', 'Thin-Layer Chromatography', 'Lattice Light Sheet Microscopy', 'Visium Spatial Gene Expression', 'Co-culture Assay', 'Imaging Mass Cytometry', 'eCLIP-Seq', 'Inductively-Coupled Plasma Mass Spectrometry', 'MicroRNA Expression Array', 'Nested PCR', 'Differential Interference Contrast Microscopy', 'Metabolite Profiling Assay', 'scSLAM-seq', 'DRIP-seq', 'Traction Force Microscopy', 'Quantitative Multiplex Immunofluorescence', 'Atomic Absorption Spectrophotometry', 'Stimulated Raman Scattering', 'qPCR', 'X-Ray Micro-Computed Tomography', 'Angiogenesis Assay', 'Optical Mapping', 'PET-CT', 'Artificial Intelligence', 'ChIP-qPCR assay', 'Bicinchoninic Acid Assay', 'MULTI-Seq', 'Immobilized Metal Affinity Chromatography', 'Microfluidics', 'Dye Endocytosis Assay', 'L1000 mRNA Profiling Assay', 'Fourier Transform Ion Cyclotron Resonance Mass Spectrometry', 'MicroRNA Sequencing', 'Tandem Mass Spectrometry', 'Immunofluorescent Staining Method', 'Image Cytometry', 'ChIP-Seq', 'Cell-spreading Assay', 'Scanning Electron Microscopy', '10x Multiome', 'Soft Agar Assay', 'Second-Harmonic Imaging Microscopy', 'Dideoxy Chain Termination DNA Sequencing', 'CRISPR', 'X-Ray Diffraction', 'Tissue Engineering', 'Next Generation Sequencing', 'Multiplexed Ion Beam Imaging', 'Fluorescence Correlation Spectroscopy', 'Hydrogels', 'Statistical Modeling', 'DNA Sequencing', 'Methylation-Specific PCR', 'High-Content Screen', 'Single Nucleus RNA-Sequencing', 'Methyl Binding Domain Sequencing', 'HL-Chip', 'ChIA-PET', 'Optical Coherence Tomography', 'Epidemiological Method', 'Nano-hmC-Seal', 'Ribosomal P Protein Antibody Measurement', 'UV Photocrosslinking', 'Targeted Transcriptome Sequencing', 'In Vivo Bioluminescence', 'Isothermal Titration Calorimetry', 'Immunoprecipitation', 'Gelatin Zymography', 'Synthetic Genetic Array', '3C-qPCR', 'Binding Assay', 'Fluorescent In Situ Sequencing', 'Chimeric Antigen Receptor T-Cell Therapy', 'Murine Model', 'Immunoassay', 'Flow Cytometry', 'ATP Bioluminescence Assay', 'Drop-Seq', 'Magnetic Resonance Imaging', 'Permeability Assay', 'Stochastic Optical Reconstruction Microscopy', 'Thermal Shift Assay', 'Affinity Purification Mass Spectrometry', 'Dynamic Light Scattering', 'Single Cell Gel Electrophoresis', 'Knife-Edge Scanning Microscopy', 'RIP-Seq', 'RT-PCR', 'Pending Annotation', 'Magnetically Activated Cell Sorting', 'Raman Spectroscopy', 'CUT&RUN', 'Dynamic Susceptibility Contrast-Enhanced Magnetic Resonance Imaging', 'Data Integration', '3D Cell Culture', 'Cerenkov Luminescence Imaging', 'Cell Proliferation Assay', 'Targeted Error Correction Sequencing', 'Fluorescence Recovery After Photo-Bleaching', 'TCR Sequencing', 'Immunocytochemistry', 'Cross-Linking Immunoprecipitation High-throughput Sequencing', 'Chemotaxis Assay', 'Microcontact Printing', 'Quantitative Point Accumulation for Imaging in Nanoscale Topography', 'RNAi Screen', 'UPLC-MSMS', 'scCGI-seq', 'Spectroscopy', 'Electrospray Ionization Time-of-Flight Mass Spectrometry', 'Diffusion Weighted Imaging', 'Immunotherapy', '3D Bioprinting', 'In Vitro Selection', 'Time-Correlated Single Photon Counting', 'Dark Field Microscopy', 'Direct Long-Read RNA Sequencing', 'Hematoxylin and Eosin Staining Method', 'Cell Fractionation', 'FAIRE-Seq', 'Tuba-Seq', 'Brightfield Microscopy', 'In Vitro Cell Killing Assay', 'Brillouin Microscopy', 'smFISH', 'Imaging', 'Chemiluminescent Assay', 'Fluorescent Antibody Procedure', 'Liquid Chromatography Mass Spectrometry', 'Organoid', 'Electron Microscopy', 'TRAP Staining', 'Monolayer Stress Microscopy', 'Xenograft', 'Questionnaire', 'Cryo-Electron Tomography', ""3' RNA-seq"", 'Targeted Therapy Agent', 'HiChIP', 'Micropipette Adhesion Assay', 'TAB-Seq', 'CITE-seq', 'Ultrasound Imaging', 'Photoacoustic Imaging', 'Label-free Protein Quantification by LC/MS', 'Precision Run-On Sequencing', 'Metastatic Colonization Assay', 'Cell Culture', 'Desorption Electrospray Ionization', 'Atomic Absorption Spectroscopy', 'Size Exclusion Chromatography', 'Total Internal Reflection Fluorescence Microscopy', 'Migration Assay', 'Co-Immunoprecipitation', 'FISH', 'Karyotyping', 'Collision-Induced Dissociation', 'Viral Transduction', 'Multiplexed Error-Robust Fluorescence In Situ Hybridization', 'Cyclic Immunofluorescence', 'Micro-computed Tomography', 'Single Cell ATAC-Seq', 'Invasion Assay', 'RIP', 'Positron Emission Tomography', 'Dual-Luciferase Reporter Assay', 'Low-Vacuum Scanning Electron Microscopy', 'Multi-Isotope Mass Spectrometry', 'Transcription profiling by NanoString', 'Stimulated Emission Depletion Microscopy', 'Co-Immunoprecipitation Mass Spectrometry', 'DNA Methylation Array', 'Targeted Genome Sequencing', 'Mass Spectrometry', 'Point Accumulation for Imaging in Nanoscale Topography', 'Reporter Gene Assay', 'Multiscale Light Sheet Microscopy', 'Partial Wave Spectroscopy', 'HPLC-MSMS', 'Molecular Simulations', 'Cytokine Expression Profile', 'Rheometry', 'Cell-free Circulating Tumor DNA Assay', 'Multiphoton Microscopy', 'scNT-Seq', 'Genotyping', 'Trichrome Staining Method', 'Dynamic Force Spectroscopy', 'Human Induced Pluripotent Stem Cell-derived Cardiomyocytes Culture', 'CASFISH', 'Structural Variant Analysis', 'CLIP-qPCR', 'Cryo-Electron Microscopy', 'Bisulfite Sequencing', 'Single-Cell BCR Sequencing', '4C', 'Cross-Linking Mass Spectrometry', 'Multiparametric Magnetic Resonance Imaging', 'Multiplexed Immunohistochemistry', 'Interference Reflection Microscopy', 'Widefield Fluorescence Microscopy', 'MeDIP', 'Single-Cell TCR Sequencing', 'In Vitro Model', 'Amplicon Sequencing', 'Single-Cell Barcode Chip', 'Whole Genome Bisulfite Sequencing', 'CellTiter-Glo Luminescent Cell Viability Assay', 'Liquid Chromatography/Tandem Mass Spectrometry', 'Nanowire', 'RT-qPCR', 'Proximity Ligation Assay', 'CUT&Tag-Sequencing', 'Enzyme-Linked Immunospot Assay', 'MNase-Seq', 'Endotoxin Assay', 'PCR', 'Sirius Red Staining', 'Time Lapse Microscopy', 'Alcian Blue Staining Method', 'Ribo-Seq', 'Graphite Furnace Atomic Absorption Spectrometry', 'Electrophoretic Mobility Shift Assay', 'seqFISH', 'Optical Emission Spectroscopy', 'In-Cell Western Assay', 'Droplet Digital PCR', 'Pull-Down Assay', 'In Vitro Translation', 'Focused Ion Beam Scanning Electron Microscopy', 'Single Molecule Forster Resonance Energy Transfer', 'Single Cell RNA-Sequencing', 'Efferocytosis Assay', 'Synaptophysin Staining Method', 'Apoptosis Assay', 'snRNA-seq', 'shRNA', 'Confocal Microscopy', 'X-Ray Crystallography', 'Energy-Dispersive X-Ray Spectroscopy', 'Mathematical Modeling', 'Single Cell Cytokine Detection Chip Assay', 'Single Cell DNA Sequencing', 'Macrophage Polarization Assay', 'smRNA-seq', '10-cell RNA Sequencing', 'Fluorescence Microscopy', 'ELISA', 'MALDI-TOF Mass Spectrometry', 'ChIP-PCR', 'Super-Resolution Microscopy', 'Single Nucleotide Polymorphism Array', 'Cytochemical Stain', 'Cytotoxicity Assay']",FileView
+File Design,File Design,FileDesign,The overall design of the dataset or file.,False,,FileView
+File Alias,File Alias,FileAlias,"Alias of the file. Must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters.",True,,FileView
+File Tumor Type,File Tumor Type,FileTumorType,"The tumor type(s), if applicable, of the data collected. Multiple values permitted, comma separated.",False,,FileView
+File Level,File Level,FileLevel,The processing level the file can be mapped to.,True,"['Level 3', 'Level 1', 'Auxilliary', 'Not Applicable', 'Level 4', 'Level 2']",FileView
+Filename,Filename,Filename,Name of a file,True,,FileView
+File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,FileView
+Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,FileView
+Study Key,Study Key,StudyKey,"The unique Study_id foreign keys associated with the resource, found in the grant Study information. Used to group the resource with other components. Please provide multiple values as a comma-separated list.",False,,FileView
+File Tissue,File Tissue,FileTissue,"Tissue type(s) associated with the file. Multiple values permitted, comma separated.",False,,FileView
+File Url,File Url,FileUrl,The url of where the file is stored.,True,,FileView
+Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,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.",True,,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
+VisiumRNALevel3 Key,VisiumRNALevel3 Key,VisiumRNALevel3Key,Unique VisiumRNALevel3_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
+Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,"['json scale factors', 'probe dataset csv', 'features', 'high res image', 'fiducial image jpg', 'reference png', 'detected jpg', 'low res image', 'filtered mex', 'detected image png', 'reference jpg', 'barcodes', 'qc result html', 'tissue_positions', 'fiducial image png', 'unfiltered mex']",10xVisiumSpatialTranscriptomics-AuxiliaryFiles
+VisiumRNALevel2 Key,VisiumRNALevel2 Key,VisiumRNALevel2Key,Unique VisiumRNALevel2_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
+VisiumAux_id,VisiumAux_id,VisiumAuxId,"Unique row identifier, used as a primary key for record updates",True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
+Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,"['D', 'A', 'D1', 'B1', 'A1', 'C1', 'C', 'B', '']",10xVisiumSpatialTranscriptomics-AuxiliaryFiles
+VisiumRNALevel4 Key,VisiumRNALevel4 Key,VisiumRNALevel4Key,Unique VisiumRNALevel4_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
+Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. URL,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
+File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
+Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
+VisiumRNALevel1 Key,VisiumRNALevel1 Key,VisiumRNALevel1Key,Unique VisiumRNALevel1_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
+Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),False,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
+Filename,Filename,Filename,Name of a file,True,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles
+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
+Spatial Read1,Spatial Read1,SpatialRead1,Read 1 content description,True,"['Spatial Barcode and UMI', 'cDNA']",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.,True,"['V3', 'V1', 'V4', 'V2']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1
+Spatial Read2,Spatial Read2,SpatialRead2,Read 2 content description,True,"['Spatial Barcode and UMI', 'cDNA']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1
+Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",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,"['Smart-seq2', '10xV1.1', 'Drop-seq', 'inDropsV3', 'TruDrop', 'inDropsV2', '10xV1.0', '10xV3', 'Nextera XT', 'Smart-SeqV4', '10xV2', '10xV3.1']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1
+Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
+File Alias,File Alias,FileAlias,"Alias of the file. Must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
+File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,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
+Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,"['R2', 'R1', 'R1&R2', 'I1', 'Other']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1
+VisiumRNALevel1_id,VisiumRNALevel1_id,VisiumRNALevel1Id,"Unique row identifier, used as a primary key for record updates",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
+Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",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
+DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,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', 'Full Length Transcript', '5 Prime']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1
+RIN,RIN,RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
+Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1
+Filename,Filename,Filename,Name of a file,True,,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,"['Oligo-dT', 'Random', 'Feature barcoding', 'Poly-dT']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1
+Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,"['Illumina NextSeq', 'Illumina Genome Analyzer II', 'Illumina HiSeq X Ten', 'PacBio RS', 'GridION', 'Revio', 'Other', 'Illumina Next Seq 500', 'Illumina Genome Analyzer IIx', 'Illumina Next Seq 550', 'unknown', 'NovaSeq 6000', 'Illumina HiSeq 4000', 'Ion Torrent Proton', 'AB SOLiD 2', 'Complete Genomics', 'NovaSeqS4', 'Ion Torrent S5', 'Illumina HiSeq 2000', 'Illumina NextSeq 1000', 'Illumina HiSeq 2500', 'Illumina Next Seq 2500', 'Ultima Genomics UG100', 'Illumina MiSeq', 'PacBio Sequel2', 'Not Reported', 'Illumina NovaSeq 6000', 'AB SOLiD 3', 'Oxford Nanopore minION', 'Illumina HiSeq X Five', '454 GS FLX Titanium', 'Ion Torrent PGM', 'Illumina NextSeq 2000', 'AB SOLiD 4', 'PromethION']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1
+Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,"['D', 'A', 'D1', 'B1', 'A1', 'C1', 'C', 'B', '']",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
+Whitelist Spatial Barcode File Link,Whitelist Spatial Barcode File Link,WhitelistSpatialBarcodeFileLink,Link to file listing all possible spatial barcodes. URL,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
+Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence; ftp or reference URL will be accepted.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
+Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
+Spatial Barcode Tag,Spatial Barcode Tag,SpatialBarcodeTag,"SAM tag for spot barcode field; please provide a valid tag-type pair, consisting of a tag (e.g. CB or CR) and type (e.g. Z) separated by a colon.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
+Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
+File Alias,File Alias,FileAlias,"Alias of the file. Must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
+File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
+Checksum,Checksum,Checksum,TBD,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
+VisiumRNALevel1 Key,VisiumRNALevel1 Key,VisiumRNALevel1Key,Unique VisiumRNALevel1_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
+VisiumRNALevel2_id,VisiumRNALevel2_id,VisiumRNALevel2Id,"Unique row identifier, used as a primary key for record updates",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
+UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid tag-type pair, consisting of a tag (e.g. UB or UR) and type (e.g. Z) separated by a colon.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
+Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,"['False', '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
+Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
+Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. URL,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
+Filename,Filename,Filename,Name of a file,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2
+Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file; ftp or reference URL will be accepted.,True,,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,"['D', 'A', 'D1', 'B1', 'A1', 'C1', 'C', 'B', '']",10xVisiumSpatialTranscriptomics-RNA-seqLevel2
+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
+VisiumRNALevel3_id,VisiumRNALevel3_id,VisiumRNALevel3Id,"Unique row identifier, used as a primary key for record updates",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).",False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
+Spots under tissue,Spots under tissue,Spotsundertissue,The number of barcodes associated with a spot under tissue.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
+Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,"['json scale factors', 'probe dataset csv', 'features', 'high res image', 'fiducial image jpg', 'reference png', 'detected jpg', 'low res image', 'filtered mex', 'detected image png', 'reference jpg', 'barcodes', 'qc result html', 'tissue_positions', 'fiducial image png', 'unfiltered mex']",10xVisiumSpatialTranscriptomics-RNA-seqLevel3
+Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
+Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
+VisiumAux Key,VisiumAux Key,VisiumAuxKey,Unique VisiumAux_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
+File Alias,File Alias,FileAlias,"Alias of the file. Must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
+File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
+Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,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
+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
+Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
+Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. URL,False,,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
+Filename,Filename,Filename,Name of a file,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
+Median Number Genes per Spatial Spot,Median Number Genes per Spatial Spot,MedianNumberGenesperSpatialSpot,The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3
+VisiumRNALevel2 Key,VisiumRNALevel2 Key,VisiumRNALevel2Key,Unique VisiumRNALevel2_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,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,"['D', 'A', 'D1', 'B1', 'A1', 'C1', 'C', 'B', '']",10xVisiumSpatialTranscriptomics-RNA-seqLevel3
+Biospecimen Key,Biospecimen Key,BiospecimenKey,Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,False,,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
+VisiumRNALevel3 Key,VisiumRNALevel3 Key,VisiumRNALevel3Key,Unique VisiumRNALevel3_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,False,,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
+Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. URL,False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
+File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
+Component,Component,Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
+VisiumRNALevel4_id,VisiumRNALevel4_id,VisiumRNALevel4Id,"Unique row identifier, used as a primary key for record updates",True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
+Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),False,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
+Visium Workflow Parameters Description,Visium Workflow Parameters Description,VisiumWorkflowParametersDescription,Parameters used to run the workflow.,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4
+Filename,Filename,Filename,Name of a file,True,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4