mc2.model.csv

Attribute,Description,Valid Values,DependsOn,Required,Properties,Validation Rules,columnType,Format,Pattern,Minimum,Maximum,IsTemplate,Source
Biospecimen,Metadata attributes for describing a tissue or tumor sample,,"Biospecimen_id, Study Key, Individual Key, Model Key, Parent Biospecimen Key, Biospecimen Type Category, Biospecimen Type, Biospecimen Tumor Status, Biospecimen Acquisition Method, Biospecimen Incidence Type, Biospecimen Stain, Species, Sex, Biospecimen Age at Collection, Biospecimen Age at Collection Unit, Disease Type, Primary Site, Primary Diagnosis, Site of Origin, Tumor Subtype, Tumor Grade, Known Metastasis Sites, Biospecimen Tumor Morphology, Biospecimen Composition, Biospecimen Preservation Method, Biospecimen Preservation Medium, Biospecimen Embedding Medium, Biospecimen Anatomic Site, Biospecimen Site of Resection or Biopsy, Biospecimen Timepoint Type, Biospecimen Timepoint Offset, Biospecimen Collection Site, Treatment Type, Therapeutic Agent, Treatment Response, Last Known Disease Status, Biospecimen BioSample Identifier, Biospecimen Description, ICD-10-CM Disease Code, Biospecimen Treatment Prior to Specimen Collection Indicator, Biospecimen Aliquot Mass, Biospecimen Aliquot Volume, Biospecimen Days from Diagnosis to Specimen Collection, Biospecimen Days from First Subject Visit to Specimen Collection, Biospecimen Days from First Treatment to Specimen Collection, Biospecimen Days from Initial Genomic Sequencing to Specimen Collection, Biospecimen Days from Recurrence to Specimen Collection, Biospecimen Days from Specimen Collection to Initial Pathologic Diagnosis, Biospecimen Preservation Temperature, Biospecimen Taxonomy ID",,,,,,,,,True,
Biospecimen_id,"Unique row identifier, used as a primary key for record updates. This should terminate in ModelKey-Bxxx or IndividualKey-Bxxx format, unless directed otherwise.",,,True,"CDE:15100774, primary_key",,string,,"B\d{1,9}$",,,,
Biospecimen Type Category,"The general category of material that forms the biospecimen sample, per NCI caDSR CDE 12445832 (Specimen Material Category). See Biospecimen Type for finer-grained specimen classification (e.g. specific analyte types).","Ascites, Blood, Bone Marrow, Cells, Body Fluid or Substance, Cell Line, Central Nervous System, Mouth Rinse, Saliva, Skin, Sputum, Stool, Tissue, Urine, RNA, DNA, Xenograft, Not Reported, Unknown",,True,CRDC_CDE:12445832,,string,,,,,,
Biospecimen Type,The type of biospecimen,"Additional - New Primary, Additional Metastatic, Analyte, Benign Neoplasms, Blood Buffy Coat, Blood Clot, Blood Derived Cancer - Bone Marrow, Blood Derived Cancer - Bone Marrow; Post-treatment, Blood Derived Cancer - Peripheral Blood, Blood Derived Cancer - Peripheral Blood; Post-treatment, Blood Derived Liquid Biopsy, Blood Derived Normal, Body Fluid, Bone Marrow Normal, Buccal Cell Normal, Cell, Cell Line Derived Xenograft Tissue, Cell Lines, Control Analyte, DNA, EBV Immortalized Normal, Expanded Next Generation Cancer Model, FFPE Recurrent, FFPE Scrolls, Fibroblasts from Bone Marrow Normal, GenomePlex (Rubicon) Amplified DNA, Granulocytes, Human Tumor Original Cells, In Situ Neoplasms, Lymphoid Normal, Metastatic, Mixed Adherent Suspension, Mononuclear Cells from Bone Marrow Normal, Neoplasms of Uncertain and Unknown Behavior, Next Generation Cancer Model, Next Generation Cancer Model Expanded Under Non-conforming Conditions, Not Allowed To Collect, Pleural Effusion, Post neo-adjuvant therapy, Primary Blood Derived Cancer - Bone Marrow, Primary Blood Derived Cancer - Peripheral Blood, Primary Tumor, Primary Xenograft Tissue, Recurrent Blood Derived Cancer - Bone Marrow, Recurrent Blood Derived Cancer - Peripheral Blood, Recurrent Tumor, Repli-G (Qiagen) DNA, Repli-G X (Qiagen) DNA, RNA, Saliva, Slides, Solid Tissue Normal, Tissue, Total RNA, Tumor, Tumor Adjacent Normal - Post Neo-adjuvant Therapy, Whole Animal, Whole Blood, Xenograft Tissue, Unknown, Not Reported",,,,,string,,,,,,
Biospecimen Age at Collection,Age at the time the biospecimen was collected. Please provide the unit in field Biospecimen Age at Collection Unit.,,,,CDE:14473376,,number,,,,,,
Biospecimen Age at Collection Unit,Unit associated with age at the time the biospecimen was collected.,,,,,,string,,,,,,
Biospecimen Composition,"The text term used to describe the type(s) of tissue contained in the biospecimen. Multiple values permitted, comma separated.","Metastatic, Not Applicable, Not Reported, Premalignant, Primary, Prior Primary, Progression, Recurrent, Synchronous Primary, Unknown, Xenograft",,,"CDE:12922545, CRDC_CDE:12922545",,string_list,,,,,,
Biospecimen Tumor Status,Normal or Tumor Sample Pathology Indicator,"Tumor, Normal, Not Reported, Peritumoral, Unknown",,True,"CDE:14688604, CRDC_CDE:14688604",,string,,,,,,
Biospecimen Preservation Method,Text term that represents the method used to preserve the sample.,"Cryopreserved, Cytospin Slide, Fixation, Fresh, Fresh Dissociated, Fresh Dissociated and Single Cell Sorted, Fresh Dissociated and Single Cell Sorted into Plates, Frozen, Not Applicable, Not Reported, Refrigerated, Refrigerated Vacuum Chamber, Snap Frozen, Unknown",,,"CDE:8028962, CRDC_CDE:8028962",,string,,,,,,
Biospecimen Anatomic Site,"The UBERON identifier of the primary disease site of the submitted tumor sample (see https://www.ebi.ac.uk/ols4/ontologies/uberon). Reference-validated, not a fixed list.",,,,CDE:14156279,,string,,^UBERON:\d+$,,,,
Biospecimen Site of Resection or Biopsy,The UBERON identifier of the anatomic site of the resection or biopsy of the patient's malignant disease (see https://www.ebi.ac.uk/ols4/ontologies/uberon).,,,,"CDE:14883054, CRDC_CDE:14883054, CRDC_CDE:12083894",,string,,^UBERON:\d+$,,,,
Biospecimen Timepoint Type,"Label to identify an event associated with the collection of the biospecimen (e.g. Baseline, End of Treatment, Overall survival, Final). Use Biospecimen Timepoint Offset to indicate the number of post-event days that elapsed before the biospecimen was collected. NO PHI/PII INFORMATION IS ALLOWED.","Diagnosis, First Visit, First Treatment, Initial Genomic Sequencing, Recurrence, Initial Pathologic Diagnosis",,,,,string,,,,,,
Biospecimen Collection Site,The health care site at which the biospecimen sample was collected.,,,,,,string,,,,,,
Biospecimen Tumor Morphology,"Morphology code from the third edition of the International Classification of Diseases for Oncology, published in 2000, and used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms.","8000/0, 8000/1, 8000/3, 8000/6, 8000/9, 8001/0, 8001/1, 8001/3, 8002/3, 8003/3, 8004/3, 8005/0, 8005/3, 8010/0, 8010/2, 8010/3, 8010/6, 8010/9, 8011/0, 8011/3, 8012/3, 8013/3, 8014/3, 8015/3, 8020/3, 8020/6, 8021/3, 8022/3, 8023/3, 8030/3, 8031/3, 8032/3, 8033/3, 8034/3, 8035/3, 8040/0, 8040/1, 8040/3, 8041/3, 8041/34, 8041/6, 8042/3, 8043/3, 8044/3, 8045/3, 8046/3, 8046/6, 8050/0, 8050/2, 8050/3, 8051/0, 8051/3, 8052/0, 8052/2, 8052/3, 8053/0, 8060/0, 8070/2, 8070/3, 8070/33, 8070/6, 8071/2, 8071/3, 8072/3, 8073/3, 8074/3, 8075/3, 8076/2, 8076/3, 8077/0, 8077/2, 8078/3, 8080/2, 8081/2, 8082/3, 8083/3, 8084/3, 8085/3, 8086/3, 8090/1, 8090/3, 8091/3, 8092/3, 8093/3, 8094/3, 8095/3, 8096/0, 8097/3, 8098/3, 8100/0, 8101/0, 8102/0, 8102/3, 8103/0, 8110/0, 8110/3, 8120/0, 8120/1, 8120/2, 8120/3, 8121/0, 8121/1, 8121/3, 8122/3, 8123/3, 8124/3, 8130/1, 8130/2, 8130/3, 8131/3, 8140/0, 8140/1, 8140/2, 8140/3, 8140/33, 8140/6, 8141/3, 8142/3, 8143/3, 8144/3, 8145/3, 8146/0, 8147/0, 8147/3, 8148/0, 8148/2, 8149/0, 8150/0, 8150/1, 8150/3, 8151/0, 8151/3, 8152/1, 8152/3, 8153/1, 8153/3, 8154/3, 8155/1, 8155/3, 8156/1, 8156/3, 8158/1, 8160/0, 8160/3, 8161/0, 8161/3, 8162/3, 8163/0, 8163/2, 8163/3, 8170/0, 8170/3, 8171/3, 8172/3, 8173/3, 8174/3, 8175/3, 8180/3, 8190/0, 8190/3, 8191/0, 8200/0, 8200/3, 8201/2, 8201/3, 8202/0, 8204/0, 8210/0, 8210/2, 8210/3, 8211/0, 8211/3, 8212/0, 8213/0, 8213/3, 8214/3, 8215/3, 8220/0, 8220/3, 8221/0, 8221/3, 8230/2, 8230/3, 8231/3, 8240/1, 8240/3, 8240/6, 8241/3, 8242/1, 8242/3, 8243/3, 8244/3, 8245/1, 8245/3, 8246/3, 8246/6, 8247/3, 8248/1, 8249/3, 8249/6, 8250/1, 8250/2, 8250/3, 8251/0, 8251/3, 8252/3, 8253/3, 8254/3, 8255/3, 8256/3, 8257/3, 8260/0, 8260/3, 8261/0, 8261/2, 8261/3, 8262/3, 8263/0, 8263/2, 8263/3, 8264/0, 8265/3, 8270/0, 8270/3, 8271/0, 8272/0, 8272/3, 8280/0, 8280/3, 8281/0, 8281/3, 8290/0, 8290/3, 8300/0, 8300/3, 8310/0, 8310/3, 8310/6, 8311/1, 8311/3, 8311/6, 8312/3, 8313/0, 8313/1, 8313/3, 8314/3, 8315/3, 8316/3, 8317/3, 8318/3, 8319/3, 8320/3, 8321/0, 8322/0, 8322/3, 8323/0, 8323/3, 8324/0, 8325/0, 8330/0, 8330/1, 8330/3, 8331/3, 8332/3, 8333/0, 8333/3, 8334/0, 8335/3, 8336/0, 8337/3, 8339/3, 8340/3, 8341/3, 8342/3, 8343/2, 8343/3, 8344/3, 8345/3, 8346/3, 8347/3, 8350/3, 8360/1, 8361/0, 8370/0, 8370/1, 8370/3, 8371/0, 8372/0, 8373/0, 8374/0, 8375/0, 8380/0, 8380/1, 8380/2, 8380/3, 8380/6, 8381/0, 8381/1, 8381/3, 8382/3, 8383/3, 8384/3, 8390/0, 8390/3, 8391/0, 8392/0, 8400/0, 8400/1, 8400/3, 8401/0, 8401/3, 8402/0, 8402/3, 8403/0, 8403/3, 8404/0, 8405/0, 8406/0, 8407/0, 8407/3, 8408/0, 8408/1, 8408/3, 8409/0, 8409/3, 8410/0, 8410/3, 8413/3, 8420/0, 8420/3, 8430/1, 8430/3, 8440/0, 8440/3, 8441/0, 8441/2, 8441/3, 8441/6, 8442/1, 8443/0, 8444/1, 8450/0, 8450/3, 8451/1, 8452/1, 8452/3, 8453/0, 8453/2, 8453/3, 8454/0, 8460/0, 8460/2, 8460/3, 8461/0, 8461/3, 8461/6, 8462/1, 8463/1, 8470/0, 8470/2, 8470/3, 8471/0, 8471/1, 8471/3, 8472/1, 8473/1, 8474/1, 8474/3, 8480/0, 8480/1, 8480/3, 8480/6, 8481/3, 8482/3, 8482/6, 8490/3, 8490/6, 8500/2, 8500/3, 8500/6, 8501/2, 8501/3, 8502/3, 8503/0, 8503/2, 8503/3, 8504/0, 8504/2, 8504/3, 8505/0, 8506/0, 8507/2, 8507/3, 8508/3, 8509/2, 8509/3, 8510/3, 8512/3, 8513/3, 8514/3, 8519/2, 8520/2, 8520/3, 8521/1, 8521/3, 8522/1, 8522/2, 8522/3, 8522/6, 8523/3, 8524/3, 8525/3, 8530/3, 8540/3, 8541/3, 8542/3, 8543/3, 8550/0, 8550/1, 8550/3, 8551/3, 8552/3, 8560/0, 8560/3, 8561/0, 8562/3, 8570/3, 8571/3, 8572/3, 8573/3, 8574/3, 8575/3, 8576/3, 8580/0, 8580/1, 8580/3, 8581/1, 8581/3, 8582/1, 8582/3, 8583/1, 8583/3, 8584/1, 8584/3, 8585/1, 8585/3, 8586/3, 8587/0, 8588/3, 8589/3, 8590/1, 8591/1, 8592/1, 8593/1, 8594/1, 8600/0, 8600/3, 8601/0, 8602/0, 8610/0, 8620/1, 8620/3, 8621/1, 8622/1, 8623/1, 8630/0, 8630/1, 8630/3, 8631/0, 8631/1, 8631/3, 8632/1, 8633/1, 8634/1, 8634/3, 8640/1, 8640/3, 8641/0, 8642/1, 8650/0, 8650/1, 8650/3, 8660/0, 8670/0, 8670/3, 8671/0, 8680/0, 8680/1, 8680/3, 8681/1, 8682/1, 8683/0, 8690/1, 8691/1, 8692/1, 8693/1, 8693/3, 8700/0, 8700/3, 8710/3, 8711/0, 8711/3, 8712/0, 8713/0, 8714/3, 8720/0, 8720/2, 8720/3, 8720/6, 8721/3, 8722/0, 8722/3, 8723/0, 8723/3, 8725/0, 8726/0, 8727/0, 8728/0, 8728/1, 8728/3, 8730/0, 8730/3, 8740/0, 8740/3, 8741/2, 8741/3, 8742/2, 8742/3, 8743/3, 8744/3, 8745/3, 8746/3, 8750/0, 8760/0, 8761/0, 8761/1, 8761/3, 8762/1, 8770/0, 8770/3, 8771/0, 8771/3, 8772/0, 8772/3, 8773/3, 8774/3, 8780/0, 8780/3, 8790/0, 8800/0, 8800/3, 8800/6, 8800/9, 8801/3, 8801/6, 8802/3, 8803/3, 8804/3, 8804/6, 8805/3, 8806/3, 8806/6, 8810/0, 8810/1, 8810/3, 8811/0, 8811/1, 8811/3, 8812/0, 8812/3, 8813/0, 8813/3, 8814/3, 8815/0, 8815/1, 8815/3, 8820/0, 8821/1, 8822/1, 8823/0, 8824/0, 8824/1, 8825/0, 8825/1, 8825/3, 8826/0, 8827/1, 8830/0, 8830/1, 8830/3, 8831/0, 8832/0, 8832/3, 8833/3, 8834/1, 8835/1, 8836/1, 8840/0, 8840/3, 8841/1, 8842/0, 8842/3, 8850/0, 8850/1, 8850/3, 8851/0, 8851/3, 8852/0, 8852/3, 8853/3, 8854/0, 8854/3, 8855/3, 8856/0, 8857/0, 8857/3, 8858/3, 8860/0, 8861/0, 8862/0, 8870/0, 8880/0, 8881/0, 8890/0, 8890/1, 8890/3, 8891/0, 8891/3, 8892/0, 8893/0, 8894/0, 8894/3, 8895/0, 8895/3, 8896/3, 8897/1, 8898/1, 8900/0, 8900/3, 8901/3, 8902/3, 8903/0, 8904/0, 8905/0, 8910/3, 8912/3, 8920/3, 8920/6, 8921/3, 8930/0, 8930/3, 8931/3, 8932/0, 8933/3, 8934/3, 8935/0, 8935/1, 8935/3, 8936/0, 8936/1, 8936/3, 8940/0, 8940/3, 8941/3, 8950/3, 8950/6, 8951/3, 8959/0, 8959/1, 8959/3, 8960/1, 8960/3, 8963/3, 8964/3, 8965/0, 8966/0, 8967/0, 8970/3, 8971/3, 8972/3, 8973/3, 8974/1, 8975/1, 8980/3, 8981/3, 8982/0, 8982/3, 8983/0, 8983/3, 8990/0, 8990/1, 8990/3, 8991/3, 9000/0, 9000/1, 9000/3, 9010/0, 9011/0, 9012/0, 9013/0, 9014/0, 9014/1, 9014/3, 9015/0, 9015/1, 9015/3, 9016/0, 9020/0, 9020/1, 9020/3, 9030/0, 9040/0, 9040/3, 9041/3, 9042/3, 9043/3, 9044/3, 9045/3, 9050/0, 9050/3, 9051/0, 9051/3, 9052/0, 9052/3, 9053/3, 9054/0, 9055/0, 9055/1, 9060/3, 9061/3, 9062/3, 9063/3, 9064/2, 9064/3, 9065/3, 9070/3, 9071/3, 9072/3, 9073/1, 9080/0, 9080/1, 9080/3, 9081/3, 9082/3, 9083/3, 9084/0, 9084/3, 9085/3, 9086/3, 9090/0, 9090/3, 9091/1, 9100/0, 9100/1, 9100/3, 9101/3, 9102/3, 9103/0, 9104/1, 9105/3, 9110/0, 9110/1, 9110/3, 9120/0, 9120/3, 9121/0, 9122/0, 9123/0, 9124/3, 9125/0, 9130/0, 9130/1, 9130/3, 9131/0, 9132/0, 9133/1, 9133/3, 9135/1, 9136/1, 9137/3, 9140/3, 9141/0, 9142/0, 9150/0, 9150/1, 9150/3, 9160/0, 9161/0, 9161/1, 9170/0, 9170/3, 9171/0, 9172/0, 9173/0, 9174/0, 9174/1, 9175/0, 9180/0, 9180/3, 9180/6, 9181/3, 9182/3, 9183/3, 9184/3, 9185/3, 9186/3, 9187/3, 9191/0, 9192/3, 9193/3, 9194/3, 9195/3, 9200/0, 9200/1, 9210/0, 9210/1, 9220/0, 9220/1, 9220/3, 9221/0, 9221/3, 9230/0, 9230/3, 9231/3, 9240/3, 9241/0, 9242/3, 9243/3, 9250/1, 9250/3, 9251/1, 9251/3, 9252/0, 9252/3, 9260/3, 9261/3, 9262/0, 9270/0, 9270/1, 9270/3, 9271/0, 9272/0, 9273/0, 9274/0, 9275/0, 9280/0, 9281/0, 9282/0, 9290/0, 9290/3, 9300/0, 9301/0, 9302/0, 9302/3, 9310/0, 9310/3, 9311/0, 9312/0, 9320/0, 9321/0, 9322/0, 9330/0, 9330/3, 9340/0, 9341/1, 9341/3, 9342/3, 9350/1, 9351/1, 9352/1, 9360/1, 9361/1, 9362/3, 9363/0, 9364/3, 9365/3, 9370/3, 9371/3, 9372/3, 9373/0, 9380/3, 9381/3, 9382/3, 9383/1, 9384/1, 9385/3, 9390/0, 9390/1, 9390/3, 9391/3, 9392/3, 9393/3, 9394/1, 9395/3, 9396/3, 9400/3, 9401/3, 9410/3, 9411/3, 9412/1, 9413/0, 9420/3, 9421/1, 9423/3, 9424/3, 9425/3, 9430/3, 9431/1, 9432/1, 9440/3, 9440/6, 9441/3, 9442/1, 9442/3, 9444/1, 9445/3, 9450/3, 9451/3, 9460/3, 9470/3, 9471/3, 9472/3, 9473/3, 9474/3, 9475/3, 9476/3, 9477/3, 9478/3, 9480/3, 9490/0, 9490/3, 9491/0, 9492/0, 9493/0, 9500/3, 9501/0, 9501/3, 9502/0, 9502/3, 9503/3, 9504/3, 9505/1, 9505/3, 9506/1, 9507/0, 9508/3, 9509/1, 9510/0, 9510/3, 9511/3, 9512/3, 9513/3, 9514/1, 9520/3, 9521/3, 9522/3, 9523/3, 9530/0, 9530/1, 9530/3, 9531/0, 9532/0, 9533/0, 9534/0, 9535/0, 9537/0, 9538/1, 9538/3, 9539/1, 9539/3, 9540/0, 9540/1, 9540/3, 9541/0, 9542/3, 9550/0, 9560/0, 9560/1, 9560/3, 9561/3, 9562/0, 9570/0, 9571/0, 9571/3, 9580/0, 9580/3, 9581/3, 9582/0, 9590/3, 9591/3, 9596/3, 9597/3, 9650/3, 9651/3, 9652/3, 9653/3, 9654/3, 9655/3, 9659/3, 9661/3, 9662/3, 9663/3, 9664/3, 9665/3, 9667/3, 9670/3, 9671/3, 9673/3, 9675/3, 9678/3, 9679/3, 9680/3, 9684/3, 9687/3, 9688/3, 9689/3, 9690/3, 9691/3, 9695/3, 9698/3, 9699/3, 9700/3, 9701/3, 9702/3, 9705/3, 9708/3, 9709/3, 9712/3, 9714/3, 9716/3, 9717/3, 9718/3, 9719/3, 9724/3, 9725/3, 9726/3, 9727/3, 9728/3, 9729/3, 9731/3, 9732/3, 9733/3, 9734/3, 9735/3, 9737/3, 9738/3, 9740/1, 9740/3, 9741/1, 9741/3, 9742/3, 9750/3, 9751/1, 9751/3, 9752/1, 9753/1, 9754/3, 9755/3, 9756/3, 9757/3, 9758/3, 9759/3, 9760/3, 9761/3, 9762/3, 9764/3, 9765/1, 9766/1, 9767/1, 9768/1, 9769/1, 9800/3, 9801/3, 9805/3, 9806/3, 9807/3, 9808/3, 9809/3, 9811/3, 9812/3, 9813/3, 9814/3, 9815/3, 9816/3, 9817/3, 9818/3, 9820/3, 9823/3, 9826/3, 9827/3, 9831/3, 9832/3, 9833/3, 9834/3, 9835/3, 9836/3, 9837/3, 9840/3, 9860/3, 9861/3, 9863/3, 9865/3, 9866/3, 9867/3, 9869/3, 9870/3, 9871/3, 9872/3, 9873/3, 9874/3, 9875/3, 9876/3, 9891/3, 9895/3, 9896/3, 9897/3, 9898/1, 9898/3, 9910/3, 9911/3, 9920/3, 9930/3, 9931/3, 9940/3, 9945/3, 9946/3, 9948/3, 9950/3, 9960/3, 9961/3, 9962/3, 9963/3, 9964/3, 9965/3, 9966/3, 9967/3, 9970/1, 9971/1, 9971/3, 9975/3, 9980/3, 9982/3, 9983/3, 9984/3, 9985/3, 9986/3, 9987/3, 9989/3, 9991/3, 9992/3, Unknown, Not Reported",,,"CDE:11326261, CRDC_CDE:11326261",,string,,,,,,
Biospecimen Preservation Medium,"The kind of substance holding another substance in solution or suspension to maintain a specimen in a viable state, such as a fixative compound used to preserve tissues and cells for microscopic study (renamed from 'Fixative' to align with the CRDC required-CDE terminology).","Desiccant, EDTA, FFPE, Formalin Fixed - Buffered, Formalin Fixed - Unbuffered, Formalin Fixed Tissue, Glutaraldehyde, RNALater, TRIzol, OCT, Paraffin Block, Isopentane, Not Applicable, Not Reported, Unknown, Liquid Nitrogen Vapor, Liquid Nitrogen",,True,"CDE:0065078, CRDC_CDE:16323957",,string_list,,,,,,
Biospecimen Embedding Medium,The name of the material that infiltrates and supports the specimen and preserves its shape and structure for sectioning and microscopy.,"Paraffin wax, Carbowax, Methacrylate, Epoxy Resin (Araldite), Agar embedding, Celloidin media, Gelatin, Other, None, Unknown",,True,,,string_list,,,,,,
Biospecimen Acquisition Method,Records the method of acquisition or source for the specimen under consideration.,"Aspiration, Blood Draw, Bone Marrow Aspiration, Excisional Biopsy, Incisional Biopsy, Needle Biopsy, Not Reported, Other, Surgical Resection, Tumor Resection",,,"CDE:6626651, CRDC_CDE:15115495",,string,,,,,,
Biospecimen Description,A description of the biospecimen.,,,,,,string,,,,,,
Biospecimen Pathology,The pathology identifier associated with the biospecimen. Not currently in use.,"Metastatic Neoplasm, Not Applicable, Not Otherwise Specified, Not Reported, Premalignant Neoplasm, Primary Neoplasm, Recurrent Neoplasm, Unknown, Xenograft",,,,,string,,,,,,
Biospecimen BioSample Identifier,BioSample (SAMN) accession number corresponding to the source of this biospecimen.,,,,,,string,,,,,,
Parent Biospecimen Key,Biospecimen Key identifer of a biospecimen from which this sample was derived. Do not use this field to reference the source model or individual.,,,,,,string,,,,,,
Biospecimen Stain,"Any of the various methods that use a dye, reagent, or other material for producing coloration in tissues or microorganisms for microscopic examination.","H&E, IHC, In situ hybridization, mIHC, Other, Wright-Giemsa",,True,CDE:8120269,,string,,,,,,
Biospecimen Timepoint Offset,"The number of days that elapsed before the biospecimen was collected, relative to the event described by Biospecimen Timepoint Type. Floating point values are allowed.",,,,,,number,,,,,,
Biospecimen Incidence Type,Text term describing a change in disease status associated with the collection of this specimen.  ,"Primary, Progression, Recurrence, Metastasis, Remission, No Disease",,,CDE:62997,,string,,,,,,
Biospecimen Treatment Prior to Specimen Collection Indicator,An indication of whether the administration of therapeutic agents was received before the body specimen was collected.,"Not Reported, Yes, No, Unknown",,,CRDC_CDE:15157426,,string,,,,,,
Biospecimen Aliquot Mass,"The quantity in micrograms (mcg, ug) of the aliquots derived from the analyte.",,,,CRDC_CDE:15745091,,number,,,,,,
Biospecimen Aliquot Volume,The volume in microliters (uL) of the aliquot(s) derived from the analyte.,,,,CRDC_CDE:15745088,,number,,,,,,
Biospecimen Days from Diagnosis to Specimen Collection,The number of days from the date the diagnosis was made to the date a sample was collected.,,,,CRDC_CDE:11248865,,number,,,,,,
Biospecimen Days from First Subject Visit to Specimen Collection,The number of days from the date the subject first visited to the date a sample was collected.,,,,CRDC_CDE:11248874,,number,,,,,,
Biospecimen Days from First Treatment to Specimen Collection,The number of days from the date the first treatment was administered to the date a sample was collected.,,,,CRDC_CDE:11250807,,number,,,,,,
Biospecimen Days from Initial Genomic Sequencing to Specimen Collection,The number of days from the date the initial genomic sequencing was done to the date a sample was collected.,,,,CRDC_CDE:11251130,,number,,,,,,
Biospecimen Days from Recurrence to Specimen Collection,The number of days from the date the disease recurrence was identified to the date a sample was collected.,,,,CRDC_CDE:11251133,,number,,,,,,
Biospecimen Days from Specimen Collection to Initial Pathologic Diagnosis,The number of days from the date a sample was collected to the date of the initial pathologic diagnosis.,,,,CRDC_CDE:11253404,,number,,,,,,
Biospecimen Preservation Temperature,The term which describes the temperature used to maintain the specimen in a viable state.,"25 Degrees C, 4 Degrees C, -80 Degrees C, -20 Degrees C, Ambient Temperature, -150 degrees C, -70 degrees C, Not Applicable, Not Reported, Unknown",,,CRDC_CDE:16306751,,string,,,,,,
Biospecimen Taxonomy ID,"A label provided by the NCBI Taxonomy Database (https://www.ncbi.nlm.nih.gov/taxonomy/) that uniquely identifies the species or other taxonomic group from which the biospecimen originates (e.g. 9606 for Homo sapiens). Companion formal identifier to Biospecimen Species; reference-validated, not a fixed list.",,,,CRDC_CDE:10543100,,string,,^\d+$,,,,
Collection,The set of metadata entries associated with a Study. A collection defines which resources should be grouped for sharing and reuse.,,"Collection_id, GrantView Key, Study Key, PublicationView Key, DatasetView Key, ToolView Key, EducationalResource Key, Biospecimen Table Id, Model Table Id, Individual Table Id, Imaging Channel Table Id, GeoMx ROI Table Id",,,,,,,,,True,
Collection_id,"Unique ID associated with a collection, used as a key for record linking and updates.",,,True,primary_key,,string,,"^C-\d{2,9}$",,,,
Biospecimen Table Id,The Synapse Id corresponding to a Biospecimen metadata table associated with the Dataset(s),,,,,,string,,"^syn\d{7,8}$",,,,
Model Table Id,The Synapse Id corresponding to a Model metadata table associated with the Dataset(s),,,,,,string,,"^syn\d{7,8}$",,,,
Individual Table Id,The Synapse Id corresponding to a Individual metadata table associated with the Dataset(s),,,,,,string,,"^syn\d{7,8}$",,,,
Imaging Channel Table Id,The Synapse Id corresponding to a Imaging Channel metadata table associated with the Dataset(s),,,,,,string,,"^syn\d{7,8}$",,,,
GeoMx ROI Table Id,The Synapse Id corresponding to a GeoMx ROI/Segment Annotations metadata table associated with the Dataset(s),,,,,,string,,"^syn\d{7,8}$",,,,
Consortium,Consortium information,,"Consortium_id, Consortium Name, Consortium Display Name, Consortium Full Name, Consortium Description, Consortium Funding Agency, Website",,,,,,,,,True,
Consortium Name,"Machine readable name of the research consortium. (e.g. sage_bionetworks, csbc_pson, etc.)",,,True,,,string,,,,,,
Consortium Display Name,"Human readable display name of research consortium (e.g. Sage Bionetworks, CSBC, PS-ON, etc.)",,,True,,,string,,,,,,
Consortium Full Name,Full name of research consortium. (e.g. Cancer Systems Biology Consortium).,,,True,,,string,,,,,,
Consortium Description,Description of research consortium,,,True,,,string,,,,,,
Consortium Funding Agency,Funding agency of research consortium ,"Division of Cancer Control and Population Sciences, Department of Defense, Food and Drug Administration, Foundation Medicine Inc, National Cancer Institute, National Institutes of Health, National Library of Medicine, NCI Center for Cancer Research, Purdue University Center for Cancer Research, UNC Lineberger Comprehensive Cancer Center, Georgetown Lombardi Comprehensive Cancer Center, National Clinical Trials Network, Proteogenomic Translational Research Centers, Evelyn H. Lauder Founder’s Fund for Metastatic Breast Cancer Research, Center for Inherited Disease Research, Transplant Recipients International Organization, Multiple Myeloma Research Foundation, Leukemia and Lymphoma Society, Center for Biomedical Informatics and Information Technology, Knight Cancer Institute, Broad Institute",,True,CRDC_CDE:16002760,,string,,,,,,
Website,Website of research consortium,,,True,,,string,uri,,,,,
Consortium_id,"Unique ID associated with a consortium, used as a key for record linking and updates.","program.ccbir, program.csbc, program.htan, program.icbp, program.metnet, program.nci, program.nci-clinical-and-translational-exploratory-developmental-studies, program.pdmc, program.ps-on, program.sage-bionetworks, program.tec",,True,primary_key,,string,,,,,,
community,The Sage Bionetworks project or initiative with which the dataset is associated.,,,,,,string,,,,,,
description,A text description of the dataset. Can be identifical to Dataset Description.,,,,,,string,,,,,,
dataCatalogContributor,"Organization(s), insitution(s), or person(s) that generated and/or deposited the data in Synapse. Can be identical to Grant Institution Name.",,,,,,string_list,,,,,,
keywords,Keywords associated with the dataset. Can be identical to Publication Keywords.,,,True,,,string_list,,,,,,
individualCount,The number of participants or samples associated with the files in the dataset. Can be identical to Study Number of Participants or DSP Number of Participants,,,,,,number,,,,,,
link,"The url where the dataset is displayed, typically on a public-facing data portal. Can be identical to Dataset Url.",,,,,,string,uri,,,,,
croissant_s3_file_object,A Synapse url where the croissant file associated with this dataset is stored.,,,,,,string,uri,,,,,
dataCatalogStudyId,The Synapse ID of the Project associated with this dataset's grant. Populated as a native Synapse annotation directly on the Dataset entity; distinct from this repo's own Study_id/Study Key.,,,,,,string,,"^syn\d{7,8}$",,,,
downloadType,"Hosting type for the dataset's files, as annotated directly on the Synapse Dataset entity (distinct from the CCKP portal's own DatasetView.downloadType column).","Synapse Hosted, Synapse Indexed",,,,,string,,,,,,
externalRepositoryUri,"External repository identifier(s) for the dataset, as CURIE-shaped references (e.g. geo:GSE12345, sra:SRP12345, bioproject:PRJNA12345).",,,,,,string_list,,,,,,
authors,"Author list for the dataset's associated publication. Distinct from creator, which captures the person(s)/organization(s) that generated or deposited the data itself.",,,,,,string_list,,,,,,
ageGroup,Age group of the individual(s)/subject(s) the dataset's data were generated from (e.g. Adult). Free text pending a confident controlled vocabulary - too few real values observed to seed one yet.,,,,,,string,,,,,,
diseaseFocus,"Disease area the dataset focuses on, as annotated directly on the Synapse Dataset entity. Not populated in current practice.",,,,,,string,,,,,,
portal,The Sage Bionetworks portal that curated this record (e.g. CCKP). Distinguishes provenance if this vocabulary is ever shared across multiple Sage portals.,,,,,,string,,,,,,
DataCatalog,The manifest used to describe datasets for the Synapse Data Catalog.,,"DataCatalog_id, GrantView Key, Study Key, DatasetView Key, dataCatalogStudyId, portal, community, description, dataCatalogContributor, keywords, individualCount, link, croissant_s3_file_object, accessType, alternateName, conditionsOfAccess, countryOfOrigin, creator, authors, dataCatalogDataUseModifiers, datePublished, funder, includedInDataCatalog, dataCatalogLicense, measurementTechnique, dataType, Species, subject, title, citation, doi, visualizeDataOn, yearProcessed, specimenCount, series, downloadType, externalRepositoryUri, ageGroup, diseaseFocus, manifestation",,,,,,,,,True,
DataCatalog_id,"Unique ID associated with a Data Catalog entry, used as a key for record linking and updates.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
accessType,Access type for the dataset.,"Open Access, Restricted Access",,,,,string,,,,,,
alternateName,An altername name that can be used for search and discovery improvement.,,,,,,string,,,,,,
conditionsOfAccess,"Additional requirements a user may need outside of Data Use Modifiers. This could include additional registration, updating profile information, joining a Synapse Team, or using specific authentication methods like 2FA or RAS. Omit property if not applicable/unknown.",,,,,,string,,,,,,
countryOfOrigin,Origin of individuals from which data were generated. Omit if not applicable/unknown.,"AD, AE, AF, AG, AI, AL, AM, AO, AQ, AR, AS, AT, AU, AW, AX, AZ, BA, BB, BD, BE, BF, BG, BH, BI, BJ, BL, BM, BN, BO, BQ, BR, BS, BT, BV, BW, BY, BZ, CA, CC, CD, CF, CG, CH, CI, CK, CL, CM, CN, CO, CR, CU, CV, CW, CX, CY, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, EH, ER, ES, ET, FI, FJ, FK, FM, FO, FR, GA, GB, GD, GE, GF, GG, GH, GI, GL, GM, GN, GP, GQ, GR, GS, GT, GU, GW, GY, HK, HM, HN, HR, HT, HU, ID, IE, IL, IM, IN, IO, IQ, IR, IS, IT, JE, JM, JO, JP, KE, KG, KH, KI, KM, KN, KP, KR, KW, KY, KZ, LA, LB, LC, LI, LK, LR, LS, LT, LU, LV, LY, MA, MC, MD, ME, MF, MG, MH, MK, ML, MM, MN, MO, MP, MQ, MR, MS, MT, MU, MV, MW, MX, MY, MZ, NA, NC, NE, NF, NG, NI, NL, NO, NP, NR, NU, NZ, OM, PA, PE, PF, PG, PH, PK, PL, PM, PN, PR, PS, PT, PW, PY, QA, RE, RO, RS, RU, RW, SA, SB, SC, SD, SE, SG, SH, SI, SJ, SK, SL, SM, SN, SO, SR, SS, ST, SV, SX, SY, SZ, TC, TD, TF, TG, TH, TJ, TK, TL, TM, TN, TO, TR, TT, TV, TW, TZ, UA, UG, UM, US, UY, UZ, VA, VC, VE, VG, VI, VN, VU, WF, WS, YE, YT, ZA, ZM, ZW",,,,,string_list,,,,,,
creator,Organization or person that is creator of the dataset. Default is the PI of the project and/or the user who created all files in the dataset.,,,True,,,string_list,,,,,,
dataCatalogDataUseModifiers,"List of data use ontology (DUO) terms that are true for dataset, which describes the allowable scope and terms for data use. Omit property if not applicable/unknown.",,,,,,string_list,,^(DUO:\d{7}|DUOPlus\d+|Pending Annotation)$,,,,
datePublished,Date data were published/available on Synapse.,,,,,,number,,,,,,
funder,The entity(ies) responsible for funding the data contributors.,"Division of Cancer Control and Population Sciences, Department of Defense, Food and Drug Administration, Foundation Medicine Inc, National Cancer Institute, National Institutes of Health, National Library of Medicine, NCI Center for Cancer Research, Purdue University Center for Cancer Research, UNC Lineberger Comprehensive Cancer Center, Georgetown Lombardi Comprehensive Cancer Center, National Clinical Trials Network, Proteogenomic Translational Research Centers, Evelyn H. Lauder Founder’s Fund for Metastatic Breast Cancer Research, Center for Inherited Disease Research, Transplant Recipients International Organization, Multiple Myeloma Research Foundation, Leukemia and Lymphoma Society, Center for Biomedical Informatics and Information Technology, Knight Cancer Institute, Broad Institute",,,,,string_list,,,,,,
includedInDataCatalog,Link(s) to known data catalog(s) the dataset is included in.,,,,,,string,,,,,,
dataCatalogLicense,"The terms and conditions underwhich the data are allowed to be accessed and used. Unless information for license is clear, this should default to UNKNOWN.","AAL, ADSL, AFL-1.1, AFL-1.2, AFL-2.0, AFL-2.1, AFL-3.0, AGPL-1.0, AGPL-3.0, AMDPLPA, AML, AMPAS, ANTLR-PD, APAFML, APL-1.0, APSL-1.0, APSL-1.1, APSL-1.2, APSL-2.0, Abstyles, Adobe-2006, Adobe-Glyph, Afmparse, Aladdin, Apache-1.0, Apache-1.1, Apache-2.0, Artistic-1.0, Artistic-1.0-Perl, Artistic-1.0-cl8, Artistic-2.0, BSD-2-Clause, BSD-2-Clause-FreeBSD, BSD-2-Clause-NetBSD, BSD-3-Clause, BSD-3-Clause-Attribution, BSD-3-Clause-Clear, BSD-3-Clause-LBNL, BSD-3-Clause-No-Nuclear-License, BSD-3-Clause-No-Nuclear-License-2014, BSD-3-Clause-No-Nuclear-Warranty, BSD-4-Clause, BSD-4-Clause-UC, BSD-Protection, BSD-Source-Code, BSD-style, BSL-1.0, Bahyph, Barr, Beerware, BitTorrent-1.0, BitTorrent-1.1, Borceux, CATOSL-1.1, CC-BY-1.0, CC-BY-2.0, CC-BY-2.5, CC-BY-3.0, CC-BY-4.0, CC-BY-NC-1.0, CC-BY-NC-2.0, CC-BY-NC-2.5, CC-BY-NC-3.0, CC-BY-NC-4.0, CC-BY-NC-ND-1.0, CC-BY-NC-ND-2.0, CC-BY-NC-ND-2.5, CC-BY-NC-ND-3.0, CC-BY-NC-ND-4.0, CC-BY-NC-SA-1.0, CC-BY-NC-SA-2.0, CC-BY-NC-SA-2.5, CC-BY-NC-SA-3.0, CC-BY-NC-SA-4.0, CC-BY-ND-1.0, CC-BY-ND-2.0, CC-BY-ND-2.5, CC-BY-ND-3.0, CC-BY-ND-4.0, CC-BY-SA-1.0, CC-BY-SA-2.0, CC-BY-SA-2.5, CC-BY-SA-3.0, CC-BY-SA-4.0, CC0-1.0, CDDL-1.0, CDDL-1.1, CECILL-1.0, CECILL-1.1, CECILL-2.0, CECILL-2.1, CECILL-B, CECILL-C, CNRI-Jython, CNRI-Python, CNRI-Python-GPL-Compatible, CPAL-1.0, CPL-1.0, CPOL-1.02, CUA-OPL-1.0, Caldera, ClArtistic, Condor-1.1, Crossword, CrystalStacker, Cube, D-FSL-1.0, DOC, DSDP, Dotseqn, ECL-1.0, ECL-2.0, EFL-1.0, EFL-2.0, EPL-1.0, EUDatagrid, EUPL-1.0, EUPL-1.1, Entessa, ErlPL-1.1, Eurosym, FSFAP, FSFUL, FSFULLR, FTL, Fair, Frameworx-1.0, FreeImage, Freeware, GFDL-1.1, GFDL-1.2, GFDL-1.3, GL2PS, GPL-1.0, GPL-2.0, GPL-3.0, Giftware, Glide, Glulxe, HPND, HaskellReport, IBM-pibs, ICU, IJG, IPA, IPL-1.0, ISC, ImageMagick, Imlib2, Info-ZIP, Intel, Intel-ACPI, Interbase-1.0, JSON, JasPer-2.0, LAL-1.2, LAL-1.3, LGPL-2.0, LGPL-2.1, LGPL-3.0, LGPLLR, LPL-1.0, LPL-1.02, LPPL-1.0, LPPL-1.1, LPPL-1.2, LPPL-1.3a, LPPL-1.3c, Latex2e, Leptonica, LiLiQ-P-1.1, LiLiQ-R-1.1, LiLiQ-Rplus-1.1, Libpng, MIT, MIT-CMU, MIT-advertising, MIT-enna, MIT-feh, MITNFA, MPL-1.0, MPL-1.1, MPL-2.0, MPL-2.0-no-copyleft-exception, MS-PL, MS-RL, MTLL, MakeIndex, MirOS, Motosoto, Multics, Mup, NASA-1.3, NBPL-1.0, NCSA, NGPL, NLOD-1.0, NLPL, NOSL, NPL-1.0, NPL-1.1, NPOSL-3.0, NRL, NTP, Naumen, NetCDF, Newsletr, Nokia, Not licensed, Noweb, Nunit, OCCT-PL, OCLC-2.0, ODbL-1.0, OFL-1.0, OFL-1.1, OGTSL, OLDAP-1.1, OLDAP-1.2, OLDAP-1.3, OLDAP-1.4, OLDAP-2.0, OLDAP-2.0.1, OLDAP-2.1, OLDAP-2.2, OLDAP-2.2.1, OLDAP-2.2.2, OLDAP-2.3, OLDAP-2.4, OLDAP-2.5, OLDAP-2.6, OLDAP-2.7, OLDAP-2.8, OML, OPL-1.0, OSET-PL-2.1, OSL-1.0, OSL-1.1, OSL-2.0, OSL-2.1, OSL-3.0, OpenSSL, Other, PDDL-1.0, PHP-3.0, PHP-3.01, Plexus, PostgreSQL, Proprietary, Python-2.0, QPL-1.0, Qhull, RHeCos-1.1, RPL-1.1, RPL-1.5, RPSL-1.0, RSA-MD, RSCPL, Rdisc, Ruby, SAX-PD, SCEA, SGI-B-1.0, SGI-B-1.1, SGI-B-2.0, SISSL, SISSL-1.2, SMLNJ, SMPPL, SNIA, SPL-1.0, SWL, Saxpath, Sendmail, SimPL-2.0, Sleepycat, Spencer-86, Spencer-94, Spencer-99, SugarCRM-1.1.3, TCL, TMate, TORQUE-1.1, TOSL, UPL-1.0, Unicode-TOU, Unlicense, VOSTROM, VSL-1.0, Vim, W3C, W3C-19980720, WTFPL, Watcom-1.0, Wsuipa, X11, XFree86-1.1, XSkat, Xerox, Xnet, YPL-1.0, YPL-1.1, ZPL-1.1, ZPL-2.0, ZPL-2.1, Zed, Zend-2.0, Zimbra-1.3, Zimbra-1.4, Zlib, bzip2-1.0.5, bzip2-1.0.6, curl, diffmark, dvipdfm, eGenix, gSOAP-1.3b, gnuplot, iMatix, libtiff, mpich2, psfrag, psutils, xinetd, xpp, zlib-acknowledgement",,,,,string,,,,,,
measurementTechnique,Assay used to generate original data. Omit if not applicable (e.g. for curated dataset such as a list compounds from a database or text extracted from Wikipedia). Can be identical to Dataset Assay.,"10-cell RNA Sequencing, 16S Ribosomal Gene Sequencing Assay, 3' RNA-seq, 3C, 3C-qPCR, 3D ATAC-PALM, 3D Bioprinting, 3D Cell Culture, 4C, 5C, ATAC-Seq, ATP Bioluminescence Assay, Affinity Purification Mass Spectrometry, Allograft, Amplicon Sequencing, Angiogenesis Assay, Apoptosis Assay, Atomic Absorption Spectrophotometry, Atomic Absorption Spectroscopy, Atomic Force Microscopy, Autoradiography, Barcode-Seq, Bicinchoninic Acid Assay, Binding Assay, Bio-Layer Interferometry, Bioluminescence Imaging, Bisulfite Sequencing, Brightfield Microscopy, Brillouin Microscopy, CASFISH, CITE-seq, CLIP-qPCR, CRISPR, CUT&RUN, CUT&Tag-Sequencing, Cell Adhesion Assay, Cell Proliferation Assay, Cell Viability Assay, Cell-spreading Assay, CellTiter-Glo Luminescent Cell Viability Assay, Cerenkov Luminescence Imaging, ChIA-PET, ChIP-PCR, ChIP-Seq, ChIP-qPCR assay, Chemiluminescent Assay, Chemotaxis Assay, Circular Dichroism Spectroscopy, Co-Immunoprecipitation, Co-culture Assay, Collision-Induced Dissociation, Colorimetric Cell Viability Assay, Computational Modeling, Computational Tool, Computed Tomography, Confocal Microscopy, Confocal Reflectance Quantitative Phase Microscopy, Cross-Linking Immunoprecipitation High-throughput Sequencing, Cross-Linking Mass Spectrometry, Cyclic Immunofluorescence, Cytochemical Stain, Cytokine Expression Profile, Cytometric Bead Array Assay, Cytotoxicity Assay, DBiT-Seq, DNA Gene-Expression Microarray, DNA Methylation Array, DNA Sequencing, DNase-Seq, DRIP-seq, Dark Field Microscopy, Deep Mutational Scanning, Desorption Electrospray Ionization, Dideoxy Chain Termination DNA Sequencing, Differential Interference Contrast Microscopy, Differential Scanning Fluorimetry, Diffusion Weighted Imaging, Direct Long-Read RNA Sequencing, Drop-Seq, Droplet Digital PCR, Dual-Luciferase Reporter Assay, Dye Endocytosis Assay, Dynamic Contrast-Enhanced Magnetic Resonance Imaging, Dynamic Force Spectroscopy, Dynamic Light Scattering, Dynamic Susceptibility Contrast-Enhanced Magnetic Resonance Imaging, ELISA, Efferocytosis Assay, Electron Diffraction, Electron Microscopy, Electron Paramagnetic Resonance Spectroscopy, Electrophoretic Mobility Shift Assay, Electrospray Ionization Time-of-Flight Mass Spectrometry, Endotoxin Assay, Energy-Dispersive X-Ray Spectroscopy, Enzyme Activity Assay, Enzyme-Linked Immunospot Assay, Epidemiological Method, FAIRE-Seq, FISH, Flow Cytometry, Fluorescence Activated Cell Sorting, Fluorescence Correlation Spectroscopy, Fluorescence Imaging, Fluorescence Lifetime Imaging Microscopy, Fluorescence Microscopy, Fluorescence Recovery After Photo-Bleaching, Fluorescent Antibody Procedure, Fluorescent Cell Barcoding, Fluorescent In Situ Sequencing, Focused Ion Beam Scanning Electron Microscopy, Forster Resonance Energy Transfer, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Fourier-Transform Infrared Spectroscopy, Gas Chromatography Mass Spectrometry, Gelatin Zymography, Genotyping, Global Chromatin Profiling, Global Run-On Sequencing, Graphite Furnace Atomic Absorption Spectrometry, HL-Chip, HPLC-MSMS, Hematoxylin and Eosin Staining Method, Hi-C, HiChIP, High Throughput Screening, High-Content Screen, Hydrogels, Hydrophilic Interaction Chromatography, Image Cytometry, Imaging, Immobilized Metal Affinity Chromatography, ImmunoFISH, Immunoassay, Immunocytochemistry, Immunohistochemistry Staining Method, Immunoprecipitation, In Situ Hybridization, In Vitro Cell Killing Assay, In Vitro Model, In Vitro Selection, In Vitro Translation, In Vivo Bioluminescence, In-Cell Western Assay, Inductively-Coupled Plasma Mass Spectrometry, Interference Reflection Microscopy, Intravital Microscopy, Invasion Assay, Karyotyping, Knife-Edge Scanning Microscopy, L1000 mRNA Profiling Assay, Lattice Light Sheet Microscopy, Liquid Chromatography Mass Spectrometry, Liquid Chromatography/Tandem Mass Spectrometry, Low-Vacuum Scanning Electron Microscopy, Luciferase Reporter Assay, Luminescent Cell Viability Assay, MALDI-TOF Mass Spectrometry, MEMA Cell Growth Assay, MNase-Seq, MULTI-Seq, Macrophage Polarization Assay, Magnetic Resonance Imaging, Magnetic Tweezers, Magnetic Twisting Cytometry, Magnetically Activated Cell Sorting, Mammosphere Formation Assay, Mass Cytometry, Mass Spectrometry, Mathematical Modeling, MeDIP, MeRIP-Seq, Methyl Binding Domain Sequencing, Methylation-Specific PCR, Micro-computed Tomography, MicroRNA Expression Array, MicroRNA Sequencing, Microcontact Printing, Microfluidics, Micropipette Adhesion Assay, Micropipette Aspiration, Microscopy, Migration Assay, Mint-ChIP, Modeling, Molecular Simulations, Monolayer Stress Microscopy, Multi-Angle Light Scattering, Multi-Isotope Mass Spectrometry, Multiparametric Magnetic Resonance Imaging, Multiphoton Microscopy, Multiplexed Error-Robust Fluorescence In Situ Hybridization, Multiplexed Immunofluorescence, Multiplexed Immunohistochemistry, Multiplexed Ion Beam Imaging, Murine Model, Nano-hmC-Seal, NanoString Digital Spatial Profiling, Nanopatterning, Nanopore Sequencing, Nanowire, Nested PCR, Next Generation Sequencing, Nm-seq, Not Applicable, Nuclear Magnetic Resonance, Optical Coherence Tomography, Optical Emission Spectroscopy, Optical Mapping, Optical Stretcher, Optical Tweezers, Optogenetic Assay, Organoid, PCR, PET-CT, Paraquat Survival Assay, Partial Wave Spectroscopy, Patient Derived Xenograft, Pending Annotation, Permeability Assay, Phagocytosis Assay, Photoacoustic Imaging, Photolithography, Plasmid Construction, PlateSeq, Point Accumulation for Imaging in Nanoscale Topography, Positron Emission Tomography, Precision Run-On Sequencing, Proteomics Assay, Proximity Ligation Assay, Pull-Down Assay, QFISH, Quantitative Multiplex Immunofluorescence, Quantitative Point Accumulation for Imaging in Nanoscale Topography, Questionnaire, RAS Protein Family Activation Assay, RIP, RIP-Seq, RNA Sequencing, RNAi Screen, RT-PCR, RT-qPCR, Raman Spectroscopy, Reduced Representation Bisulfite Sequencing, Reverse Phase Protein Array, Reverse-Phase High-Performance liquid Chromatography, Rheometry, Ribo-Seq, Ribosomal P Protein Antibody Measurement, Scanning Angle Interference Microscopy, Scanning Electron Microscopy, Second-Harmonic Imaging Microscopy, Shotgun Mass Spectrometry, Single Cell ATAC-Seq, Single Cell Cytokine Detection Chip Assay, Single Cell DNA Sequencing, Single Cell Gel Electrophoresis, Single Cell RNA-Sequencing, Single Molecule Forster Resonance Energy Transfer, Single Nucleotide Polymorphism Array, Single Nucleus RNA-Sequencing, Single-Cell BCR Sequencing, Single-Cell Barcode Chip, Single-Cell TCR Sequencing, Single-Molecule Tracking, Sirius Red Staining, Size Exclusion Chromatography, Small-Angle X-ray Scattering, Soft Agar Assay, Southern Blotting, Spectroscopy, Statistical Modeling, Stimulated Emission Depletion Microscopy, Stimulated Raman Scattering, Stochastic Optical Reconstruction Microscopy, Super-Resolution Microscopy, Surface Plasmon Resonance, Surveyor Nuclease Assay, Synaptophysin Staining Method, Synthetic Genetic Array, TAB-Seq, TCR Sequencing, TIRF Microscopy, TRAP Staining, TUNEL assay, Tandem Mass Spectrometry, Tandem Mass Tagging, Target Engagement Assay, Targeted Genome Sequencing, Targeted Transcriptome Sequencing, Thermal Shift Assay, Thin-Layer Chromatography, Tiling Array, Time Lapse Microscopy, Time-Correlated Single Photon Counting, Tissue Engineering, Tissue Microarray, Total Internal Reflection Fluorescence Microscopy, Traction Force Microscopy, Transmission Electron Microscopy, Transwell Assay, UPLC-MSMS, UV Photocrosslinking, Unspecified, Vibrational Spectroscopy, Virus Plaque Assay, Von Kossa Staining, Western Blotting, Whole Exome Sequencing, Whole Genome Bisulfite Sequencing, Whole Genome Sequencing, Widefield Fluorescence Microscopy, Wound-Healing Assay, X-Ray Crystallography, X-Ray Diffraction, X-Ray Micro-Computed Tomography, Xenograft, cDNA Array, eCLIP-Seq, mRNA Sequencing, qPCR, scCGI-seq, scNT-Seq, scSLAM-seq, seqFISH, shRNA, siRNA, smFISH, smRNA-seq, snRNA-seq, Isothermal Titration Calorimetry, Suspended Microchannel Resonator, 10x Multiome, Visium Spatial Gene Expression, Antitumor Drug Screening Assay, Bioelectrochemical Analysis, Chimeric Antigen Receptor T-Cell Therapy, Cell Cycle Assay, Clonality Analysis, Comparative Genomic Hybridization, Cryo-Electron Microscopy, Cryo-Electron Tomography, Data Integration, Field-Emission Scanning Electron Microscopy, Label-free Protein Quantification by LC/MS, Metabolite Profiling Assay, Reporter Gene Assay, Single-Molecule Localization Microscopy, Synthesis, Targeted Therapy Agent, Trichrome Staining Method, Ultrasound Imaging, Transcription profiling by NanoString, Alcian Blue Staining Method, Artificial Intelligence, Cell Culture, Clinical Study, Cell-free Circulating Tumor DNA Assay, Co-Immunoprecipitation Mass Spectrometry, Deep Learning, Gene Ontology Enrichment Analysis, Gene Set Enrichment Analysis, Gene Silencing , Human Induced Pluripotent Stem Cell-derived Cardiomyocytes Culture, Imaging Mass Cytometry, Immunofluorescent Staining Method, Immunotherapy, Viral Transduction, Metastatic Colonization Assay, Phylogenetic Analysis, Picrosirius Staining, Scratch Assay, Structural Variant Analysis, Survival Analysis, Targeted Error Correction Sequencing, Tuba-Seq, SDS-PAGE, Cell Fractionation, Multiscale Light Sheet Microscopy, Light Sheet Microscopy, CODEX, in vivo tumor growth, in silico synthesis, RNA array, shRNA-seq, spatial transcriptomics, in vivo PDX viability, histology, proximity extension assay, compound screen, metabolic screening",,,,,string_list,,,,,,
dataType,"Broad data-type category for the dataset (e.g. gene expression, chromatin activity, genomic variants). Aligned with modules/shared/mc2_iconTag_map_3-4-25.csv's label taxonomy.","gene expression, chromatin activity, genomic variants, immunoassay, network, nucleic acid sequence record, image",,,,,string_list,,,,,,
subject,"Applicable subject term(s) for dataset cataloging - in practice, a free-text model-system/specimen descriptor (e.g. C57BL/6, NOD SCID), not a Library of Congress Subject Heading.",,,,,,string_list,,,,,,
title,The name of the dataset.,,,True,,,string,,,,,,
citation,Academic articles that are recommended by the data provider to be cited in addition to the dataset doi itself. Can be identical to DatasetView.PublicationView Key.,,,,,,string,,,,,,
doi,Digital Object Identifier (DOI) for citation and identification. Can be identical to Dataset Doi,,,,,,string,uri,,,,,
visualizeDataOn,Links to external visualization platforms.,,,,,,string,uri,,,,,
yearProcessed,Year the data were processed (used with specific series only).,,,,,,number,,,,,,
specimenCount,Number of unique specimens in the dataset. Can be identical to DSP Number of Samples.,,,,,,number,,,,,,
series,"Data series designation (e.g., NF-OSI Processed Data).",,,,,,string,,,,,,
manifestation,Tumor type or other clinical manifestation associated with the dataset. Can be identical to Dataset Tumor Type.,"Cutaneous Melanoma, Acinar Cell Carcinoma, Acute Lymphoblastic Leukemia, Acute Monocytic Leukemia, Acute Myeloid Leukemia, Acute Promyelocytic Leukemia, Adenocarcinoma, Angiosarcoma, Astrocytoma, Atypical Teratoid/Rhabdoid Tumor, B Acute Lymphoblastic Leukemia, B-Cell Non-Hodgkin Lymphoma, Barrett Esophagus, Basal Cell Neoplasm, Basal-Like Breast Carcinoma, Biliary Tract Carcinoma, Bladder Carcinoma, Bladder Neoplasm, Bone Neoplasm, Brain Neoplasm, Breast Adenocarcinoma, Breast Carcinoma, Breast Neoplasm, Carcinoma, Carcinoma In Situ, Castration-Resistant Prostate Carcinoma, Cellular Schwannoma, Central Nervous System Cavernous Hemangioma, Central Nervous System Neoplasm, Cerebellar Neoplasm, Cervical Carcinoma, Cervical Neoplasm, Cervical Small Cell Carcinoma, Cholangiocarcinoma, Chondroblastoma, Choriocarcinoma, Chronic Lymphocytic Leukemia, Chronic Myeloid Leukemia, Clear Cell Renal Cell Carcinoma, Colon Adenocarcinoma, Colon Carcinoma, Colorectal Adenocarcinoma, Colorectal Adenoma, Colorectal Carcinoma, Colorectal Neoplasm, Combined Hepatocellular Carcinoma and Cholangiocarcinoma, Craniopharyngioma, Cutaneous T Cell Lymphoma, Diffuse Large B-Cell Lymphoma, Ductal Breast Carcinoma In Situ, Dysembryoplastic Neuroepithelial Neoplasm, Endometrial Carcinoma, Endometrial Neoplasm, Ependymoma, Esophageal Adenocarcinoma, Esophageal Carcinoma, Esophageal Squamous Cell Carcinoma, Ewing Sarcoma, Extraventricular Neurocytoma, Fibroepithelial Polyp, Fibrolamellar Carcinoma, Fibrosarcoma, Follicular Lymphoma, Gallbladder Carcinoma, Gastric Adenocarcinoma, Gastric Carcinoma, Gastric Neoplasm, Gastroesophageal Adenocarcinoma, Gastroesophageal Junction Adenocarcinoma, Gastrointestinal Stromal Neoplasm, Giant Cell Tumor, Glioblastoma, Glioma, Head and Neck Carcinoma, Head and Neck Neoplasm, Head and Neck Squamous Cell Carcinoma, Hepatocellular Carcinoma, High Grade Ovarian Serous Adenocarcinoma, Histiocytic Sarcoma, Hodgkin Lymphoma, Intestinal Neoplasm, Intrahepatic Cholangiocarcinoma, Invasive Ductal Breast Carcinoma, Kaposi Sarcoma, Leiomyoma, Leukemia, Liver and Intrahepatic Bile Duct Carcinoma, Liver and Intrahepatic Bile Duct Neoplasm, Low Grade Glioma, Luminal A Breast Carcinoma, Lung Adenocarcinoma, Lung Carcinoma, Lung Neoplasm, Lung Non-Small Cell Carcinoma, Lung Small Cell Carcinoma, Lung Squamous Cell Carcinoma, Lymphoid Leukemia, Lymphoma, Malignant Brain Neoplasm, Malignant Digestive System Neoplasm, Malignant Genitourinary System Neoplasm, Malignant Glioma, Malignant Neoplasm, Malignant Ovarian Neoplasm, Malignant Pancreatic Neoplasm, Malignant Peripheral Nerve Sheath Tumor, Malignant Peritoneal Neoplasm, Malignant Skin Neoplasm, Mantle Cell Lymphoma, Marginal Zone Lymphoma, Medulloblastoma, Melanoma, Meningioma, Mesothelioma, Multiple Myeloma, Mycosis Fungoides, Myeloid Leukemia, Myeloid Neoplasm, Myeloproliferative Neoplasm, Myoepithelioma, Nasopharyngeal Carcinoma, Neuroblastoma, Neuroendocrine Neoplasm, Neuroepithelial Neoplasm, Neurofibroma, Non-Functioning Pituitary Gland Adenoma, Non-Hodgkin Lymphoma, Not Applicable, Oral Cavity Neoplasm, Oral Cavity Squamous Cell Carcinoma, Oropharyngeal Neoplasm, Osteosarcoma, Ovarian Adenosarcoma, Ovarian Carcinoma, Ovarian Neoplasm, Ovarian Serous Adenocarcinoma, Pan-cancer, Pancreatic Adenocarcinoma, Pancreatic Carcinoma, Pancreatic Ductal Adenocarcinoma, Pancreatic Neoplasm, Pancreatic Neuroendocrine Carcinoma, Pending Annotation, Penile Carcinoma, Pheochromocytoma, Pilocytic Astrocytoma, Pituitary Gland Adenoma, Plasmablastic Lymphoma, Plasmacytoma, Plexiform Schwannoma, Precursor B-cell lymphoblastic leukemia, Primary Central Nervous System Lymphoma, Primary Myelofibrosis, Prostate Adenocarcinoma, Prostate Carcinoma, Prostate Neoplasm, Rectal Adenocarcinoma, Renal Cell Carcinoma, Retinoblastoma, Rhabdomyosarcoma, Rosette-Forming Glioneuronal Tumor, Salivary Gland Adenoid Cystic Carcinoma, Sarcoma, Schwannoma, Serous Tubal Intraepithelial Carcinoma, Sinonasal Squamous Cell Carcinoma, Skin Carcinoma, Skin Neoplasm, Soft Tissue Sarcoma, Squamous Cell Carcinoma, Synovial Sarcoma, T Acute Lymphoblastic Leukemia, T-Cell Lymphoma, Teratoma, Testicular Embryonal Carcinoma, Thyroid Gland Anaplastic Carcinoma, Thyroid Gland Carcinoma, Thyroid Gland Noninvasive Follicular Neoplasm with Papillary-Like Nuclear Features, Triple-Negative Breast Carcinoma, Urothelial Carcinoma, Uterine Adenosarcoma, Uveal Melanoma, Uveal Neoplasm, Vascular Neoplasm, Not-Applicable, Plexiform Neurofibroma",,,,,string,,,,,,
Dataset Name,Name of the dataset,,,True,,,string,,,,,,
Dataset Alias,"Alias of the dataset. Must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters.",,,True,,,string,,,,,,
Dataset Description,Description of the dataset.,,,,,,string,,,,,,
Dataset Design,The overall design of the dataset.,,,,,,string,,,,,,
Dataset Url,The url of where the dataset is stored.,,,True,,,string,uri,,,,,
Dataset Doi,The Digital Object Identifier (DOI) associated with the dataset.,,,True,,,string,uri,,,,,
Dataset File Formats,"A list of file formats associated with the dataset. Multiple values permitted, comma separated.","AVI, BAI, BAM, BED, CDS, CHP, COOL, CSV, DAE, DB, DCC, DS_Store, FASTA, FASTQ, FCS, FIG, FREQ, GCG, GCT, GCTx, GFF3, GTF, GZIP Format, HDF, HDF5, HTML, IDAT, JPG, JSON, LIF, MAP, MAT, MATLAB script, MSF, MTX, PDF, PNG, PZFX, Python Script, R File Format, RAW, RDS, ROUT, RPROJ, RTF, SGI, SRA, STAT, TAR Format, TDF, TIFF, TSV, TXT, VCF, WIG, XML, ZIP, bed12, bedgraph, cel, cloupe, docx, mzIdentML, mzXML, pptx, rcc, xls, xlsx, MGF, BIGWIG, H5AD, H5, SF, PKL, BPM, Unspecified, Pending Annotation, maf, CLS, SCN, SVS",,,,,string_list,,,,,,
Dataset View,The denormalized manifest for dataset submission.,,"DatasetView_id, GrantView Key, Study Key, PublicationView Key, Dataset Name, Dataset Alias, Dataset Description, Dataset Design, Assay, Species, Tumor Type, Tissue, Dataset Url, Dataset Doi, Dataset File Formats, Dataset Data Use Codes",,,,,,,,,True,
Dataset Data Use Codes,"DUO code(s) describing the consent permissions for the dataset, i.e. the purposes for which its data may be used. Provide multiple values as a comma-separated list. Code definitions: https://mc2-center.github.io/data-models/valid_values/shared/#attribute-data-use-codes",,,,,,string_list,,^(DUO:\d{7}|DUOPlus\d+|Pending Annotation)$,,,,
DatasetView_id,"Unique ID associated with this Dataset View entry, used as a key for record linking and updates. Unless otherwise directed, this value should be equivalent to Dataset Alias. For externally hosted datasets with a corresponding Synapse Dataset containing indexed data, this should be the Synapse Id of the Dataset.",,,True,primary_key,,string,,,,,,
Educational Resource,Manifest for describing educational resources.,,"EducationalResource_id, GrantView Key, Study Key, DatasetView Key, PublicationView Key, ToolView Key, Resource Title, Resource Link, Resource Doi, Resource Topic, Resource Activity Type, Resource Primary Format, Resource Intended Use, Resource Primary Audience, Resource Educational Level, Resource Description, Resource Origin Institution, Resource Language, Resource Contributors, Resource Secondary Topic, License, Resource Use Requirements, Resource Alias, Resource Internal Identifier, Resource Media Accessibility, Resource Access Hazard, Resource Tool Link, Resource Dataset Alias",,,,,,,,,True,
Resource Title,Title of the item.,,,True,,,string,,,,,,
Resource Link,The URL that links to the item.,,,True,,,string,uri,,,,,
Resource Doi,The Digital Object Identifier (DOI) associated with the educational resource.,,,True,,,string,uri,,,,,
Resource Topic,"General topic or research context of the item. If 'other' is selected, please provide additional topics in the 'Resource Secondary Topic' field. Multiple values should be provided as a comma separated list.","Computational Model Development, Computational Resource, Diversity/Equity/Inclusion, Drug Resistance/Sensitivity, Epigenetics, Evolution, Experimental Model Development, Heterogeneity, Immunotherapy, Mechano-genetics, Mechano-resistance, Metabolism, Metastasis, Method/Assay Development, Microenvironment, Oncogenic Stress, Other, Outreach, Platform Development, Training Material, Tumor Progression, Tumor-Immune, Computer Science, Environmental Science, Information Science, Educational Technology, Anatomy/Physiology, Biology, Ecology, Genetics, Nutrition, Measurement and Data, Statistics and Probability, Chemistry, Physics, Systems Biology, Patient Advocacy",,True,,,string_list,,,,,,
Resource Activity Type,The type(s) of activities for which the item is intended to be used. Multiple values should be provided as a comma separated list.,"Activity/Lab, Assessment, Case Study, Data Set, Diagram/Illustration, Full Course, Game, Homework/Assignment, Interactive, Lecture, Lecture Notes, Lesson, Lesson Plan, Module, Primary Source, Reading, Simulation, Student Guide, Syllabus, Teaching/Learning Strategy, Textbook, Unit of Study",,True,,,string_list,,,,,,
Resource Primary Format,"The media type(s) of the item (video, audio, text, etc.) Multiple values should be provided as a comma separated list.","Audio, Braille/BNF, Downloadable docs, eBook, Graphics/Photos, Interactive, Mobile, Text/HTML, Video, Other",,True,,,string_list,,,,,,
Resource Intended Use,The purpose of the material for education. Multiple values should be provided as a comma separated list.,"Curriculum/Instruction, Assessment, Professional Development, Other",,True,,,string_list,,,,,,
Resource Primary Audience,The intended end user audience for the resource. Multiple values should be provided as a comma separated list.,"Student, Teacher, Administrator, Parent, Professor, General Audience, Other",,True,,,string_list,,,,,,
Resource Educational Level,"Educational context (pre-school, lower-primary, upper-primary…) in which the item was intended to be used. Multiple values should be provided as a comma separated list.","Preschool, Lower Primary, Upper Primary, Middle School, High School, Community College / Lower Division, College / Upper Division, Graduate / Profession, Career / Technical, Adult Education",,True,,,string_list,,,,,,
Resource Description,Abstract or summary of the item.,,,True,,,string,,,,,,
Resource Origin Institution,Institution(s) of origin for this item. Multiple values should be provided as a comma separated list.,,,True,,,string_list,,,,,,
Resource Language,Language of the item (not of the metadata). Multiple values should be provided as a comma separated list.,"aa, ab, ae, af, ak, am, an, ar, as, av, ay, az, ba, be, bg, bh, bi, bm, bn, bo, br, bs, ca, ca, ce, ch, co, cr, cs, cu, cv, cy, da, de, dv, dv, dz, ee, el, en, eo, es, et, eu, fa, ff, fi, fj, fo, fr, fy, ga, gd, gl, gn, gu, gv, ha, he, hi, ho, hr, ht, hu, hy, hz, ia, id, ie, ig, ii, ik, io, is, it, iu, ja, jv, ka, kg, ki, kj, kk, kl, km, kn, ko, kr, ks, ku, kv, kw, ky, la, lb, lg, li, ln, lo, lt, lu, lv, mg, mh, mi, mk, ml, mn, mr, ms, mt, my, na, nb, nd, ne, ng, nl, nn, no, nr, nv, ny, oc, oj, om, or, os, pa, pi, pl, ps, pt, qu, rm, rn, ro, ru, rw, sa, sc, sd, se, sg, si, sk, sl, sm, sn, so, sq, sr, ss, st, su, sv, sw, ta, te, tg, th, ti, tk, tl, tn, to, tr, ts, tt, tw, ty, ug, uk, ur, uz, ve, vi, vo, wa, wo, xh, yi, yo, za, zh, zu",,True,,,string_list,,[a-z]{2},,,,
Resource Contributors,The name(s) of the contributor(s) to the item. Multiple contributor names should be provided as a comma-separated list.,,,True,,,string_list,,,,,,
Resource Secondary Topic,"Additional topics or keywords to describe the content of the item, in addition to the primary topic. Multiple values should be provided as a comma-separated list.",,,,,,string_list,,,,,,
Resource Use Requirements,"A list of materials, hardware, software, computing power, and network requirements that the end user would need to satisfy before using the resource, if applicable. Multiple values should be provided as a comma separated list.",,,,,,string,,,,,,
Resource Alias,"A unique identifier (DOI, Synapse ID) for the item, if it exists.",,,,,,string,,,,,,
Resource Internal Identifier,"The institution-specific ID for the item, if applicable. May be non-unique. Multiple values should be provided as a comma separated list.",,,,,,string_list,,,,,,
Resource Media Accessibility,"Accessibility features (Alternative Text, Audio Description, etc.) incorporated into the item. Multiple values should be provided as a comma separated list.","Alternative Text, Audio Description, Braille, Captions, ChemML, Described Math, Display Transformability, Haptic, High Contrast, Large Print, Latex, Long Description, MathML, Nemeth Braille, Sign Language, Structural Navigation, Tactile Graphics, Text Transcript",,,,,string_list,,,,,,
Resource Access Hazard,"Sensory hazards (Flashing, Motion, etc.) applicable to the item. Multiple values should be provided as a comma separated list.","Flashing, Motion, Simulation, Sound",,,,,string_list,,,,,,
Resource Tool Link,"URL or persistent identifier (DOI, Synapse ID) for any software or tool that is intended to be used with the item. Multiple values should be provided as a comma separated list.",,,,,,string_list,,,,,,
EducationalResource_id,"Unique ID associated with a Educational Resource entry, used as a key for record linking and updates.",,,True,primary_key,,string,,,,,,
Resource Dataset Alias,"URL or persistent identifier (DOI, Synapse ID) for any dataset(s) that is intended to be used with the item. Multiple values should be provided as a comma separated list.",,,,,,string_list,,,,,,
File Description,Description of the file.,,,,"CDE:11280338, CRDC_CDE:11280338",,string,,,,,,
File Design,The overall design of the file.,,,,,,string,,,,,,
File Batch Identifier,"An identifier for the batch or group of files processed together (e.g. an extract batch, library prep batch, or sequencing run), used to support downstream analysis of batch effects. Free text, not a fixed list.",,,,MIXS:0001382,,string,,,,,,
File Url,The url of where the file is stored.,,,True,CDE:11556141,,string,uri,,,,,
File Level,The processing level the file can be mapped to. ,"Level 1, Level 2, Level 3, Level 4, Auxiliary, Not Applicable, Metadata",,True,,,string,,,,,,
File View,The denormalized manifest for file submission.,,"FileView_id, Biospecimen Key, Study Key, DatasetView Key, Filename, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, File Data Category, File Data Checksum Type, File Data Checksum Value, File Data Compression Status, File Data Size",,,,,,,,,True,
FileView_id,"Unique ID associated with a File entry, used as a key for record linking and updates. This should be equivalent to File Alias unless otherwise directed.",,,True,"CDE:14528010, primary_key",,string,,"^syn\d{7,8}$",,,,
File Longitudinal Group,A label that can be used to identify groups of files from the same longitudinal/time-resolved experiment,,,,,,string,,,,,,
File Longitudinal Event Type,"The type of event to which File Longitudinal Total Time Elapsed is related (e.g. Enrollment, Baseline). Free text, not a fixed list.",,,,,,string,,,,,,
File Longitudinal Sequence Identifier,"The order in which this file was collected with respect to the longitudinal experiment (e.g., 1, 2, etc.).",,,,,,string,,,,,,
File Longitudinal Time Elapsed Unit,The unit of time associated with Sequential and Total Time Elapsed attributes.,,,,,,string,,,,,,
File Longitudinal Sequential Time Elapsed,The time elapsed between collecting the current and previous files in this longitudinal group. ,,,,,,number,,,,,,
File Longitudinal Total Time Elapsed,The total time elapsed between the first and current files contained this longitudinal group. ,,,,,,number,,,,,,
File Format,The format of the file described by this entry.,"ADF, AVI, BAI, BAM, BAS, BCR Biotab, BED, bedgraph, BEDPE Format, bigBed, bigWig, Binary Format, BIOM, cdf, CEL, CNS, CRAI, CRAM, CSV, DICOM, DICT, DOC, DOCX, DSV, EMF, FASTA, FASTQ, GCT/Res Format, GenBank Format, GFF3, GIF, GPR, GTF, gVCF, GZIP Format, HDF5, HIC, HTML, HTSeq Count, IDAT, IDF, idpDB, im3, JPEG, JPEG 2000, JSON, MAF, MAGE-TAB, MAT, MATLAB Script, MCD, MEX, MPEG-4, mtx, mzIdentML, mzML, mzXML, NIFTI Format, ODS, ODT, OME-TIFF, Parquet, PDF, PDT, PED, Plain Text Data Format, PNG, PRISM, Python Script Format, PZFX, QPTIFF, R File Format, R Markdown, rdata, rds, RTF, SAS, SAS binary, SDRF, SEG, Sequence Record Format, SPSS, STATA, SVG, SVS, TAR, TBI, Thermo RAW, TIFF, TSV, TXT, VCF, XLS, XLSX, XML, YAML, ZIP",,True,"CDE:11416926, CRDC_CDE:11416926",,string,,,,,,
File Alias,"A string identifier associated with the file. Must be unique. Can be the repository accesssion number (e.g., Synapse ID, GEO identifier such as GSE12345). No Greek Letters or DOIs.",,,True,,,string,,,,,,
File Anatomic Site,"The UBERON identifier of the anatomic site associated with the data contained in this file (see https://www.ebi.ac.uk/ols4/ontologies/uberon). Reference-validated, not a fixed list.",,,True,CDE:14156279,,string,,^UBERON:\d+$,,,,
File Data Category,A broad classification of the contents of a data file generated from an experiment or a study.,"Clinical, Biospecimen, Genomic Structural Variation, Archive, Not Reported, Quality Control, Proteomic Profile, Protein Expression, Population Science, Microarray, Methylation Analysis, Mass Spectrometry, Copy Number Variation, Clinical Measure Instrument, Chromatin, Transcriptome Profiling, Radiology Imaging, Pathology Imaging, Sequence Data, Supplemental, Publication, Image Annotation, Proteomics, Imaging, Genomics, Gene Expression Analysis, Nanotechnology",,,CRDC_CDE:14824731,,string,,,,,,
File Data Checksum Type,The method by which the file checksum was calculated.,"md5sum, sha1, sha256",,,CRDC_CDE:11475057,,string,,,,,,
File Data Checksum Value,A small-sized block of data derived from a file for the purpose of detecting errors that may have been introduced during file transmission and/or storage and used to verify data integrity.,,,,CRDC_CDE:11480133,,string,,,,,,
File Data Compression Status,The state of data when saved to storage space or during data transmission.,"Unknown, Compressed, Uncompressed",,,CRDC_CDE:11387114,,string,,,,,,
File Data Size,The measure (in bytes) of how much space a data file takes up on a storage medium.,,,,CRDC_CDE:11479876,,number,,,,,,
NanoString GeoMx Auxiliary Files,Contains identifiers for auxiliary files associated with Nanostring GeoMx Spatial Profiling experiments.,,"NanoStringGeoMxAuxiliaryFiles_id, Synapse ID of GeoMx DSP ROI Segment Annotation File, Synapse ID of GeoMx DSP PKC File, Synapse ID of GeoMx Lab Worksheet File, Synapse ID of GeoMx DSP Config File",,,,,,,,,True,
NanoStringGeoMxAuxiliaryFiles_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
Synapse ID of GeoMx Lab Worksheet File,Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.,,,,,,string_list,,"^syn\d{7,8}$",,,,
Synapse ID of GeoMx DSP PKC File,The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.,,,,,,string_list,,"^syn\d{7,8}$",,,,
Synapse ID of GeoMx DSP ROI Segment Annotation File,Synapse ID(s) for ROI/AOI/Segmentation annotations in the GeoMx DSP experiment.,,,,,,string_list,,"^syn\d{7,8}$",,,,
Synapse ID of GeoMx DSP Config File,Synapse ID of config.ini file generated by the GeoMx DSP workflow.,,,,,,string_list,,"^syn\d{7,8}$",,,,
NanoString GeoMx DSP Imaging,Images acquired by the GeoMx instrument,,"NanoStringGeoMxDSPImaging_id, Filename, NanoStringGeoMxDSPLevel1 Key, NanoStringGeoMxDSPLevel2 Key, NanoStringGeoMxAuxiliaryFiles Key, NanoStringGeoMXROISegmentAnnotation Key, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, GeoMx Imaging Channel Names, GeoMx Imaging AOI Coordinates, ImagingChannel Key, Image Assay Type, Image Protocol Link, Image Platform Model, Image Platform Manufacturer, Image Software, Image Objective, Image Nominal Magnification, Image Lense Aperture, Image Working Distance, Image Working Distance Unit, Image Immersion Type, Image Pyramidal, Image Z stack, Image Timeseries, Image FOV Index, Image FOV Size X, Image FOV Size X Unit, Image FOV Size Y, Image FOV Size Y Unit, Image Frame Averaging, Image Identifier, Image Dimension Order, Image Physical Size X, Image Physical Size X Unit, Image Physical Size Y, Image Physical Size Y Unit, Image Physical Size Z, Image Physical Size Z Unit, Image Pixels BigEndian, Image Plane Count, Image Channel Size, Image Number of Timepoints, Image X Pixels, Image Y Pixels, Image Z Pixels, Image Pixel Type",,,,,,,,,True,
NanoStringGeoMxDSPImaging_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
GeoMx Imaging Channel Names,Name(s) of imaging channel(s) associated with the image; multiple values should be provided as a comma-separated list.,,,,,,string_list,,,,,,
GeoMx Imaging AOI Coordinates,Synapse Id(s) of tabular file(s) containing coordinate points for AOIs found in the image; multiple values should be provided as a comma-separated list.,,,,,,string_list,,,,,,
NanoString GeoMx DSP Level 1,Raw sequencing files from GeoMX experiments,,"NanoStringGeoMxDSPLevel1_id, Filename, NanoStringGeoMxAuxiliaryFiles Key, NanoStringGeoMXROISegmentAnnotation Key, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, GeoMx DSP Assay Type, NGS Library Strategy, NGS Library Source Material, NGS Library Source Molecule, NGS Library Selection Method, NGS Library Layout, NGS Sequencing Platform, NGS Sequencing Design Description, NGS Read Length, NGS Raw Reads, NGS Unique Bases, NGS Sequencing Coverage, NGS Library Preparation Kit Name, NGS Library Preparation Kit Vendor, NGS Library Preparation Kit Version, NGS Read Indicator, NGS Library Preparation Days from Index, NGS Sequencing Library Construction Days from Index",,,,,,,,,True,
NanoStringGeoMxDSPLevel1_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
GeoMx DSP Assay Type,The assay type which was used for the GeoMx DSP pipeline.,"RNA nCounter, Protein nCounter, Protein NGS, RNA NGS",,,,,string,,,,,,
NanoString GeoMx DSP Level 2,Processed count conversion (DCC/RCC) files from GeoMX experiments,,"NanoStringGeoMxDSPLevel2_id, Filename, NanoStringGeoMxDSPLevel1 Key, NanoStringGeoMxAuxiliaryFiles Key, NanoStringGeoMXROISegmentAnnotation Key, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, GeoMx DSP Assay Type, NGS Library Strategy, NGS Library Source Material, NGS Library Source Molecule, NGS Library Selection Method, NGS Library Layout, NGS Sequencing Platform, NGS Sequencing Design Description, NGS Raw Reads, NGS Stitched Reads, NGS Aligned Reads, NGS Deduplicated Reads, NGS Trimmed Reads, NGS MapQ30, NGS Unique Bases, NGS Read Length, NGS Sequencing Coverage, Genomic Reference, Software and Version",,,,,,,,,True,
NanoStringGeoMxDSPLevel2_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
NanoString GeoMx DSP Level 3,Files contain processed count data from the NanoString GeoMx DSP Pipeline.,,"NanoStringGeoMxDSPLevel3_id, Filename, NanoStringGeoMxDSPLevel1 Key, NanoStringGeoMxDSPLevel2 Key, NanoStringGeoMxAuxiliaryFiles Key, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, NGS Unique Probe Count, NGS Unique Target Count, NGS Matrix Type, Software and Version, Workflow Type, Workflow Parameter Description, Workflow Link",,,,,,,,,True,
NanoStringGeoMxDSPLevel3_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
NanoString GeoMX ROI Segment Annotation,"GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI and AOI coordinates. ",,"NanoStringGeoMXROISegmentAnnotation_id, Biospecimen Key, GeoMx Scan name, GeoMx ROI Name, GeoMx AOI Name, GeoMx Tags, GeoMx ROI X Coordinate, GeoMx ROI Y Coordinate, GeoMx AOI X Coordinate, GeoMx AOI Y Coordinate, GeoMx QC status, GeoMx Scan Height, GeoMx Scan Width, GeoMx Scan Offset X, GeoMx Scan Offset Y, GeoMx Binding Density, GeoMx Positive norm factor, GeoMx Surface area, GeoMx Nuclei count, GeoMx Tissue Stain, GeoMx Slide name, NGS Raw Reads, NGS Stitched Reads, NGS Aligned Reads, NGS Deduplicated Reads, NGS Trimmed Reads, NGS Sequencing Coverage, NGS MapQ30, GeoMx Negative count mean, GeoMx No Template Control count, GeoMx Excluded Outlier Probes, GeoMx Limit of Quantification",,,,,,,,,True,
NanoStringGeoMXROISegmentAnnotation_id,"Unique row identifier, used as a primary key for record updates",,,True,primary_key,,string,,,,,,
GeoMx Scan name,GeoMx Scan name (as appears in Segment Summary),,,True,,,string,,,,,,
GeoMx ROI Name,Name of Region of Interest corresponding to file. Multiple names should be comma-separated,,,True,,,string_list,,,,,,
GeoMx AOI Name,Name of Area of Illumination corresponding to file. Multiple names should be comma-separated,,,True,,,string_list,,,,,,
GeoMx ROI X Coordinate,Region of Interest X location within the image,,,,,,number,,,,,,
GeoMx ROI Y Coordinate,Region of Interest Y location within the image,,,,,,number,,,,,,
GeoMx AOI X Coordinate,Area of Illumination X location within the image,,,,,,number,,,,,,
GeoMx AOI Y Coordinate,Area of Illumination Y location within the image,,,,,,number,,,,,,
GeoMx QC status,ROI quality control flag as reported by the application,,,,,,string_list,,,,,,
GeoMx Scan Height,Height of the scan for GeoMx Analysis,,,,,,number,,,,,,
GeoMx Scan Width,Width of the scan for GeoMx Analysis,,,,,,number,,,,,,
GeoMx Scan Offset X,Offset X of the scan for GeoMx Analysis,,,,,,number,,,,,,
GeoMx Scan Offset Y,Offset Y of the scan for GeoMx Analysis,,,,,,number,,,,,,
GeoMx Binding Density,The binding density as reported by the application,,,,,,number,,,,,,
GeoMx Positive norm factor,The Positive Control Normalization factor calculated using pos-hyb controls,,,,,,number,,,,,,
GeoMx Surface area,Surface area of the ROI in square microns (µm2),,,,,,number,,,,,,
GeoMx Nuclei count,Number of nuclei detected in the segment (if applicable),,,,,,number,,,,,,
GeoMx Slide name,"Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).",,,,,,string,,,,,,
GeoMx In Situ Negative median,Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.,,,,,,number,,,,,,
GeoMx Biological probe median,Is the median count from all probes except the negative control probes. A measure of signal to background for each segment,,,,,,number,,,,,,
GeoMx Negative count mean,The geometric mean of the unique negative probes in a GeoMx panel that do not target mRNA and establish the background count level per segment,,,,,,number,,,,,,
GeoMx No Template Control count,The number of reads detected by the GeoMx probe panel in the control associated with this ROI.,,,,,,number,,,,,,
GeoMx Excluded Outlier Probes,The list of probes excluded from analysis.,,,,,,number,,,,,,
GeoMx Limit of Quantification,The calculated limit of quantification associated with the segment.,,,,,,number,,,,,,
GeoMx Sequencing Saturation,"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).",,,,,,number,,,,,,
GeoMx Tags,"The basename(s) or unique identifier(s) for FASTQ, RCC, or DCC file(s) associated with this ROI.",,,,,,string,,,,,,
GeoMx Tissue Stain,"Text description of the stain, fluorescent reporter, or channel used to select the boundaries of the ROI.",,,,,,string,,,,,,
Grant Name,Name of the grant,,,True,,,string,,,,,,
Grant Number,"Number of the grant (i.e. ""CA------"" format)",,,True,CRDC_CDE:16002823,,string,,^(CA\d{6}|Affiliated/Non-Grant Associated)$,,,,
Grant Abstract,Abstract for the grant,,,True,,,string,,,,,,
Grant Type,Type of grant,"R01, R21, R37, U01, U24, U54",,True,,,string,,,,,,
Grant View,The denormalized manifest for grant submission.,,"GrantView_id, Grant Name, Grant Number, Grant Abstract, Grant Type, Grant Theme Name, Grant Institution Name, Grant Institution Alias, Institution Key, Investigator, PersonView Key, Consortium Key, Grant Start Date, Grant End Date, NIH RePORTER Link, Duration of Funding, Embargo End Date, Grant Synapse Team, Grant Synapse Project",,,,,,,,,True,
Grant Theme Name,Theme(s) associated with the grant. 1...*,"Computational Model Development, Computational Resource, Drug Resistance/Sensitivity, Epigenetics, Evolution, Experimental Model Development, Heterogeneity, Immunotherapy, Mechano-genetics, Mechano-resistance, Metabolism, Metastasis, Method/Assay Development, Microenvironment, Oncogenic Stress, Platform Development, Tumor Progression, Tumor-Immune",,True,,,string_list,,,,,,
Grant Institution Name,The full name of the institution(s) associated with the grant. (e.g. Harvard University). 1...*,"Albert Einstein College of Medicine, Arizona State University, Auburn University, Barrow Neurological Institute, Baylor College Of Medicine, Beckman Research Institute of City of Hope, Beth Israel Deaconess Hospital, Boston Medical Center, Boston University, Brigham and Womens Hospital, California Institute of Technology, Childrens Hospital of Philadelphia, City Of Hope, Clemson University, Cleveland Clinic, Cold Spring Harbor Laboratory, Columbia University, Cornell University, Dana-Farber Cancer Institute, Dartmouth College, Duke University, Emory University, Georgia Institute of Technology, Harvard Medical School, Harvard University, Hebrew University of Jerusalem, Houston Methodist, Indiana University, Indiana University - Purdue University Indianapolis, Institute for Systems Biology, Jackson Laboratory, Johns Hopkins University, Lurie Children's Hospital, Massachusetts General Hospital, Massachusetts Institute of Technology, Mayo Clinic, Memorial Sloan Kettering Cancer Center, Moffitt Cancer Center, Northeastern University, New York University, Northwestern University, Oregon Health & Science University, Pacific Northwest National Laboratory, Purdue University, Rockefeller University, Sage Bionetworks, Salk Institute for Biological Studies, St. Jude Children's Research Hospital, Stanford University, Stony Brook University, The University of Texas Health Science Center at San Antonio, Tufts University Medford, University of Alabama at Birmingham, University of Arizona, University of Arkansas at Fayetteville, University of California; Berkeley, University of California; Irvine, University of California; Los Angeles, University of California; San Diego, University of California; San Francisco, University of Chicago, University of Chicago Medical Center, University of Colorado Denver, University of Delaware, University of Florida, University of Illinois, University of Illinois at Chicago, University of Massachusetts Medical School, University of Miami, University of Michigan, University of Nevada Reno, University of Minnesota, University of New South Wales, University of North Carolina at Chapel Hill, University of Pennsylvania, University of Pittsburgh, University of Southern California, University of Texas MD Anderson Cancer Center, University of Texas Southwestern Medical Center, University of Texas at Austin, University of Utah, University of Virginia, University of Washington, University of Wisconsin-Madison, Vanderbilt University, Virginia Polytechnic Institute, Washington University in St. Louis, Wake Forest, Weill Cornell Medicine, Wistar Institute, Yale University",,True,,,string_list,,,,,,
Grant Institution Alias,The alias of the institution(s) associated with the grant (e.g. UCSD). 1...*,"AECM, ASU, AU, BCM, BIDMC, BMC, BRI, BU, BWH, Barrow, CHOP, COH, CSHL, Caltech, Clemson, Cleveland Clinic, Columbia, Cornell, DFCI, Dartmouth, Duke, Emory, GTech, HMS, HUJI, Harvard, Houston Methodist, ISB, IU, IUPUI, JHU, Jackson Laboratory, Lurie Children's Hospital, MGH, MIT, MSKCC, Mayo, Moffitt, NEU, NU, NYU, OHSU, PNNL, Pitt, Purdue, Rockefeller University, SBU, Sage, Salk, StJude, Stanford, TUM, U Miami, UA, UARK, UAB, UCBerkeley, UCD, UCI, UCLA, UCMC, UCSD, UCSF, UChicago, UD, UFL, UIC, UMMS, UMichigan, UMinn, UNC, UNR, UNSW, UPenn, USC, UT Austin, UT Southwestern, UTHSCSA, UUtah, UVA, UW, UWM, University of Illinois, University of Texas MD Anderson Cancer Center, Vanderbilt, VT, WUSTL, WCM, Wake Forest, Wistar, Yale",,True,,,string_list,,,,,,
GrantView_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the grant number in CAxxxxxx format unless otherwise indicated.",,,True,primary_key,,string,,,,,,
Grant Synapse Team,"The Synapse team associated with the grant, created by the MC2 Center",,,,,,string,uri,,,,,
Grant Synapse Project,"The Synapse project associated with the grant, created by the MC2 Center",,,,,,string,uri,,,,,
Grant Start Date,The start date of the grant YYYY-MM-DD format,,,True,,,string,date,,,,,
NIH RePORTER Link,Link to the search results for this grant number on the NIH Reporter website,,,True,,,string,uri,,,,,
Duration of Funding,"Duration of the funding period, in years",,,,,,number,,,,,,
Embargo End Date,Date at which an embargo on related resources had lifted,,,,,,string,date,,,,,
Grant End Date,The end date of the grant YYYY-MM-DD format,,,True,,,string,date,,,,,
Imaging Channel,Channel-level Metadata Attributes,,"ImagingChannel_id, Study Key, Channel Identifier, Channel Name, Channel Passed QC, Channel Cycle Number, Channel Sub-cycle Number, Channel Antibody Role, Channel Target Name, Channel Antibody Name, Channel Resource ID, Channel Fluorophore, Channel Antibody Clone, Channel Antibody Lot, Channel Antibody Vendor, Channel Antibody Catalog Number, Channel Excitation Wavelength, Channel Emission Wavelength, Channel Excitation Bandwidth, Channel Emission Bandwidth, Channel Metal Symbol, Channel Metal Isotope, Channel Oligo Barcode Upper Strand, Channel Oligo Barcode Lower Strand, Channel Probe Dilution Ratio, Channel Probe Concentration",,,,,,,,,True,
ImagingChannel_id,"Unique row identifier, used as a primary key for record updates.",,,True,primary_key,,string,,,,,,
Channel Identifier,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1'),,,True,,,string,,,,,,
Channel Name,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin'),,,True,,,string,,,,,,
Channel Passed QC,Identify stains that did not pass QC but are included in the dataset.,"Yes, No - Channel Failed QC",,,,,string,,,,,,
Channel Cycle Number,The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles),,,,,,number,,,,,,
Channel Sub-cycle Number,Sub cycle number,,,,,,number,,,,,,
Channel Antibody Role,Is this antibody acting as a primary or secondary antibody?,"Primary, Secondary",,,,,string,,,,,,
Channel Target Name,Short descriptive name (abbreviation) for this target (antigen),,,True,,,string,,,,,,
Channel Antibody Name,"Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))",,,,CDE:2004006,,string,,,,,,
Channel Resource ID,Research Resource Identifier (eg “RRID: AB_394606”),,,,,,string,,,,,,
Channel Fluorophore,Fluorescent dye label (eg Alexa Fluor 488),,,,,,string,,,,,,
Channel Antibody Clone,Clone,,,,CDE:14767258,,string,,,,,,
Channel Antibody Lot,Lot number from vendor,,,,CDE:6390920,,string,,,,,,
Channel Antibody Vendor,Vendor,,,,CDE:2866141,,string,,,,,,
Channel Antibody Catalog Number,Catalog Number,,,,CDE:2192897,,string,,,,,,
Channel Excitation Wavelength,Center/peak of the excitation spectrum (nm),,,,,,number,,,,,,
Channel Emission Wavelength,Center/peak of the emission spectrum (nm),,,,,,number,,,,,,
Channel Excitation Bandwidth,Nominal width of excitation spectrum (nm),,,,,,number,,,,,,
Channel Emission Bandwidth,Nominal width of emission spectrum (nm),,,,,,number,,,,,,
Channel Metal Symbol,Element abbreviation. eg “La” or “Nd”,"H, He, Li, Be, B, C, N, O, F, Ne, Na, Mg, Al, Si, P, S, Cl, Ar, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ga, Ge, As, Se, Br, Kr, Rb, Sr, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I, Xe, Cs, Ba, La, Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au, Hg, Tl, Pb, Bi, Po, At, Rn, Fr, Ra, Ac, Th, Pa, U, Np, Pu, Am, Bk, Cf, Es, Fm, Md, No, Lr, Rf, Db, Sg, Bh, Hs, Mt, Ds, Rg, Cn, Nh, Fl, Mc, Lv, Ts, Og",,,,,string,,,,,,
Channel Metal Isotope,Element mass number,,,,,,number,,,,,,
Channel Oligo Barcode Upper Strand,Oligo Barcode - Upper Strand,,,,,,string,,,,,,
Channel Oligo Barcode Lower Strand,Oligo Barcode - Lower Strand,,,,,,string,,,,,,
Channel Probe Dilution Ratio,Dilution (eg 1:1000),,,,,,string,,,,,,
Channel Probe Concentration,Concentration (eg 10ug/mL),,,,,,string,,,,,,
Imaging Level 1,Raw imaging data,,"ImagingLevel1_id, Filename, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, Image Assay Type, Image Protocol Link, Image Platform Model, Image Platform Manufacturer, Image Software, ImagingChannel Key, Image Platform Model Version, Image DICOM Modality Type",,,,,,,,,True,
ImagingLevel1_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
Image Assay Type,Type of imaging assay,"CODEX, CyCIF, ExSeq, GeoMX-DSP, H and E, IHC, IMC, MERFISH, MIBI, mIF, mIHC, Not Applicable, t-CyCIF, ELISA, CyTOF, ctdDNA, ATAC-Seq, NULISA, RNA-Seq, WES, TCR-Seq, scRNA-Seq, Olink PEA",,True,CDE:7789196,,string,,,,,,
Image Protocol Link,"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.",,,,,,string,uri,,,,,
Image Platform Model,The specific model of the instrument used to carry out an imaging experiment.,,,,CRDC_CDE:16072578,,string,,,,,,
Image Platform Manufacturer,Producer of the imaging equipment that was used to generate the digital image,,,,CRDC_CDE:16065939,,string,,,,,,
Image Software,"The name of the software package that was used to capture, generate, and process the image.",,,,,,string,,,,,,
Image Platform Model Version,A string of characters used to identify the equipment model version.,,,,CRDC_CDE:16065945,,string,,,,,,
Image DICOM Modality Type,"The specific manner, characteristic, pattern or function, method or process, or devices that created the data.","OP, OT, PR, PT, PX, RF, RG, RTDOSE, RTIMAGE, RTPLAN, RTRECORD, RTSTRUCT, SM, SMR, SR, ST, TG, BI, AS, AU, CD, CF, CP, CR, US, VF, XA, XC, CS, CT, DD, DF, DG, DM, DS, DX, EC, EPS, ES, FA, FS, GM, HC, HD, IO, IVUS, KO, LP, LS, MA, MG, MR, MS, AR, ASMT, BDUS, BMD, CTPROTOCOL, DMS, DOC, EEG, EMG, EOG, FID, IOL, IVOCT, KER, LEN, M3D, OAM, OCT, OPM, OPT, OPTBSV, OPTENF, OPV, OSS, PLAN, POS, REG, RESP, RWV, SEG, SRF, STAIN, TEXTUREMAP, VA, ECG, NM",,,CRDC_CDE:12137353,,string,,,,,,
Imaging Level 2,Raw and pre-processed image data,,"ImagingLevel2_id, Filename, ImagingLevel1 Key, ImagingChannel Key, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, Image Assay Type, Image Protocol Link, Image Platform Model, Image Platform Manufacturer, Image Software, Image Objective, Image Nominal Magnification, Image Lense Aperture, Image Working Distance, Image Working Distance Unit, Image Immersion Type, Image Pyramidal, Image Z stack, Image Timeseries, Image FOV Index, Image FOV Size X, Image FOV Size X Unit, Image FOV Size Y, Image FOV Size Y Unit, Image Frame Averaging, Image Identifier, Image Dimension Order, Image Physical Size X, Image Physical Size X Unit, Image Physical Size Y, Image Physical Size Y Unit, Image Physical Size Z, Image Physical Size Z Unit, Image Pixels BigEndian, Image Plane Count, Image Channel Size, Image Number of Timepoints, Image X Pixels, Image Y Pixels, Image Z Pixels, Image Pixel Type",,,,,,,,,True,
ImagingLevel2_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
Image Objective,Objective lens identifier,,,,,,string,,,,,,
Image Nominal Magnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),,,,CDE:7788940,,number,,,,,,
Image Lense Aperture,The numerical aperture of the lens. Floating point value > 0.,,,,,,number,,,,,,
Image Working Distance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",,,,,,number,,,,,,
Image Working Distance Unit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,,,string,,,,,,
Image Immersion Type,Immersion medium,"Air, Oil, Water, Other, Multi, Glycerol",,,CDE:8058286,,string,,,,,,
Image Pyramidal,Does data file contain pyramid of images,"True, False",,,CDE:7788945,,boolean,,,,,,
Image Z stack,Does data file contain a Z-stack of images,,,,,,boolean,,,,,,
Image Timeseries,Does data file contain a time-series of images,,,,,,boolean,,,,,,
Image FOV Index,Index of FOV (as it pertains to its sequence order). Integer >= 1,,,,,,number,,,,,,
Image FOV Size X,Field of view X dimension. Floating point,,,,,,number,,,,,,
Image FOV Size X Unit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),,,,,,string,,,,,,
Image FOV Size Y,Field  of view Y dimension. Floating point value,,,,,,number,,,,,,
Image FOV Size Y Unit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),,,,,,string,,,,,,
Image Frame Averaging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",,,,,,number,,,,,,
Image Identifier,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",,,,,,string,,,,,,
Image Dimension Order,The order in which the individual planes of data are interleaved.,,,,,,string,,,,,,
Image Physical Size X,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,,,,,,number,,,,,,
Image Physical Size X Unit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),,,,,,string,,,,,,
Image Physical Size Y,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,,,,,,number,,,,,,
Image Physical Size Y Unit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),,,,,,string,,,,,,
Image Physical Size Z,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,,,,,,number,,,,,,
Image Physical Size Z Unit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),,,,,,string,,,,,,
Image Pixels BigEndian,Boolean (True/False),"True, False",,,,,boolean,,,,,,
Image Plane Count,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",,,,,,number,,,,,,
Image Channel Size,Number of channels. Integer >= 1,,,,,,number,,,,,,
Image Number of Timepoints,Number of time points. Integer >= 1,,,,,,number,,,,,,
Image X Pixels,Size of image: X dimension (in pixels). Integer >= 1,,,,,,number,,,,,,
Image Y Pixels,Size of image: Y dimension (in pixels). Integer >= 1,,,,,,number,,,,,,
Image Z Pixels,Size of image: Z dimension (in pixels). Integer >= 1,,,,,,number,,,,,,
Image Pixel Type,"Data type for each pixel value. E.g. ""uint16""",,,,,,string,,,,,,
Imaging Level 3 Image,Quality controlled or co-registered image data,,"ImagingLevel3Image_id, Filename, ImagingChannel Key, ImagingLevel2 Key, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, Image Assay Type, Image Protocol Link, Image Platform Model, Image Platform Manufacturer, Image Software, Image Objective, Image Nominal Magnification, Image Lense Aperture, Image Working Distance, Image Working Distance Unit, Image Immersion Type, Image Pyramidal, Image Z stack, Image Timeseries, Image FOV Index, Image FOV Size X, Image FOV Size X Unit, Image FOV Size Y, Image FOV Size Y Unit, Image Frame Averaging, Image Identifier, Image Dimension Order, Image Physical Size X, Image Physical Size X Unit, Image Physical Size Y, Image Physical Size Y Unit, Image Physical Size Z, Image Physical Size Z Unit, Image Pixels BigEndian, Image Plane Count, Image Channel Size, Image Number of Timepoints, Image X Pixels, Image Y Pixels, Image Z Pixels, Image Pixel Type",,,,,,,,,True,
ImagingLevel3Image_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
Imaging Level 3 Segments,Image segmentation mask information,,"ImagingLevel3Segments_id, Filename, ImagingLevel2 Key, ImagingLevel3Image Key, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, Image Segmentation Data Type, Image Parameter file, Software and Version, Image Object Class, Image Object Class Description, Image Number of Objects",,,,,,,,,True,
ImagingLevel3Segments_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
Image Segmentation Data Type,Specifies how the segmentation is stored,"Mask, Outline, Polygon, Probability Map, Point",,True,,,string,,,,,,
Image Parameter file,Path in Synapse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis,,,,,,string,,,,,,
Image Object Class,Defines the structure that the mask delineates,"Nucleus, Cytoplasm, Plasma Membrane, Whole Cell, Spot, Other",,,,,string,,,,,,
Image Number of Objects,The number of objects (eg cells) described,,,,,,number,,,,,,
Image Object Class Description,"If Imaging Object Class is ""Other"", please use this field to provide a text description of the imaging object class associated with the segmentation data",,,,,,string,,,,,,
Imaging Level 4,Derived imaging data or object by feature array,,"ImagingLevel4_id, Filename, ImagingLevel2 Key, ImagingLevel3Image Key, ImagingLevel3Segments Key, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, Image Parameter file, Image Software, Image Number of Objects, Image Number of Features, Image Object Class, Image Summary Statistic",,,,,,,,,True,
ImagingLevel4_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
Image Number of Features,The number of features (eg channels) described,,,True,,,number,,,,,,
Image Summary Statistic,Function used to summarize object/feature intensity,"Mean, Median, Not Specified",,True,,,string,,,,,,
Individual,Information about models and individuals from which biospecimen(s) were collected.,,"Individual_id, Study Key, Individual dbGaP Subject Id, Sex, Individual Gender, Individual Age at Diagnosis, Disease Type, Primary Diagnosis, Primary Site, Individual Primary Tumor Stage, Site of Origin, Tumor Subtype, Tumor Grade, Individual Tumor Lymph Node Stage, Known Metastasis Sites, Individual Metastasis Stage, Treatment Type, Therapeutic Agent, Days to Treatment, Treatment Response, Individual Days to Last Followup, Individual Recurrence Status, Individual Days To Recurrence, Individual Days to Last Known Disease Status, Last Known Disease Status, Individual Vital Status, Individual Residual Disease Status, Individual Age 90 or Older, Individual Year of Birth, Individual Year of Death, Individual Year of Diagnosis, Individual Disease Progression or Recurrence Type, ICD-10-CM Disease Code, Individual Lymph Node Involvement Anatomic Site Uberon Identifier, Individual Progression or Recurrence Anatomic Site Uberon Identifier, Treatment Anatomic Site, Individual Treatment Intent Type, Individual Treatment or Therapy Indicator",,,,,,,,,True,
Individual_id,"Unique row identifier, used as a primary key for record updates. This should follow the GrantNumber-INDxxx convention unless otherwise indicated.",,,True,"CDE:12220014, primary_key",,string,,"^CA\d{6}-IND\d{1,9}$",,,,
Individual Age at Diagnosis,"Age at the time the individual was diagnosed, expressed in years. Note: the CRDC-required CDE for this concept (Subject Age At Diagnosis, CDE 10609539) expresses this value in days rather than years; a documented days<->years derivation is implemented at the mapping/ETL layer for CRDC submission, not as a separate stored field.",,,,"CDE:15019300, CRDC_CDE:10609539",,number,,,,,,
Individual Gender,"Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.","Female, Male, Intersex, Unknown, Unspecified, Not Reported",,,,,string,,,,,,
Individual dbGaP Subject Id,The identifer assigned to the participant by dbGap,,,,,,string,,,,,,
Individual Days to Last Followup,Number of days between the dates used for index and last follow-up,,,,,,number,,,,,,
Individual Primary Tumor Stage,Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,"Not Reported, T0, T1, T1a, T1a1, T1a2, T1b, T1b1, T1b2, T1c, T1mi, T2, T2a, T2a1, T2a2, T2b, T2c, T2d, T3, T3a, T3b, T3c, T3d, T4, T4a, T4b, T4c, T4d, T4e, T5, Ta, Tis, Tis (DCIS), Tis (LCIS), Tis (Paget's), TX, Unknown",,,CDE:3440328,,string,,,,,,
Individual Tumor Lymph Node Stage,Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,"N0, N0 (i+), N0 (i-), N0 (mol+), N0 (mol-), N1, N1a, N1b, N1bI, N1bII, N1bIII, N1bIV, N1c, N1mi, N2, N2a, N2b, N2c, N3, N3a, N3b, N3c, N4, NX, Unknown, Not Reported",,,CDE:3440330,,string,,,,,,
Individual Days To Recurrence,Number of days between the date used for index and the date the patient's disease recurred,,,,,,number,,,,,,
Individual Days to Last Known Disease Status,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.",,,,,,number,,,,,,
Individual Metastasis Stage,Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,"M0, M1, M1a, M1b, M1c, MX, cM0 (i+), Unknown, Not Reported",,,CDE:3440331,,string,,,,,,
Individual Recurrence Status,Yes/No/Unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,"Yes, Unknown, Not Reported, Not Applicable, Not Allowed to Collect, No, Censored",,,"CDE:13529783, CRDC_CDE:13529783",,string,,,,,,
Individual Vital Status,Text term that describes the patient's current vital status.,"Unspecified, Unknown, Dead, Alive, Not reported",,,"CDE:2847330, CRDC_CDE:2847330",,string,,,,,,
Individual Residual Disease Status,A text term describing the assessment of the presence of tumor cells remaining in the body following cancer treatment.,"R0, RX, R2, R1, Not Reported",,,CRDC_CDE:15157297,,string,,,,,,
Individual Age 90 or Older,The response to indicate whether an individual is age 90 or older.,"No, Yes",,,CRDC_CDE:15354920,,string,,,,,,
Individual Year of Birth,The 4-digit year of the subject's birth.,,,,CRDC_CDE:16032218,,number,,,,,,
Individual Year of Death,The year of a subject's death.,,,,CRDC_CDE:15112166,,number,,,,,,
Individual Year of Diagnosis,Numeric value to represent the year of an individual's diagnosis of cancer.,,,,CRDC_CDE:15157224,,number,,,,,,
Individual Disease Progression or Recurrence Type,A term describing the kind of worsening or return of disease that a subject is experiencing.,"Not Reported, Unknown, Regional, Local, Biochemical, Distant, Locoregional",,,CRDC_CDE:14742451,,string,,,,,,
Individual Lymph Node Involvement Anatomic Site Uberon Identifier,The UBERON identifier of the organ or part of the body describing lymph node involvement in disease (see https://www.ebi.ac.uk/ols4/ontologies/uberon).,,,,CRDC_CDE:14883075,,string,,^UBERON:\d+$,,,,
Individual Progression or Recurrence Anatomic Site Uberon Identifier,The UBERON identifier of the organ or part of the body related to the progressive or recurrent disease (see https://www.ebi.ac.uk/ols4/ontologies/uberon).,,,,CRDC_CDE:14883061,,string,,^UBERON:\d+$,,,,
Individual Treatment Intent Type,Text term to identify the reason for the administration of a treatment regimen.,"Unknown, Prevention, Palliative, Neoadjuvant, Maintenance, Curative, Adjuvant",,,CRDC_CDE:15157467,,string,,,,,,
Individual Treatment or Therapy Indicator,An indicator that describes whether therapy was administered.,"Not Reported, Yes, No, Unknown",,,CRDC_CDE:14713318,,string,,,,,,
Institution,Institutions participating in consortia activities,,"Institution_id, Institution Name, Institution Full Name, Institution Alias, Institution Location State, Institution Location City, Rorid",,,,,,,,,True,
Institution Name,"Machine readable name of the institution. (e.g. ArizonaStatUniversity, BostonUniversity, etc.)",,,True,,,string,,,,,,
Institution Full Name,"Human readable, full name of the institution. (e.g. Arizona State University, Boston University, etc.)",,,True,,,string,,,,,,
Institution Alias,"Alias of the institution (e.g. ASU, BU, etc.)",,,True,,,string,,,,,,
Institution Location State,"The US state the institution is located in. Use Not Applicable, if not applicable. ","Alabama, Alaska, American Samoa, Arizona, Arkansas, California, Colorado, Connecticut, Delaware, District of Columbia, Florida, Georgia, Guam, Hawaii, Idaho, Illinois, Indiana, Iowa, Kansas, Kentucky, Louisiana, Maine, Maryland, Massachusetts, Michigan, Minnesota, Minor Outlying Islands, Mississippi, Missouri, Montana, Nebraska, Nevada, New Hampshire, New Jersey, New Mexico, New York, North Carolina, North Dakota, Northern Mariana Islands, Not Applicable, Ohio, Oklahoma, Oregon, Pennsylvania, Puerto Rico, Rhode Island, South Carolina, South Dakota, Tennessee, Texas, U.S. Virgin Islands, Utah, Vermont, Virginia, Washington, West Virginia, Wisconsin, Wyoming",,True,,,string,,,,,,
Institution Location City,The City the institution is located in. ,,,True,,,string,,,,,,
Rorid,Unique identifier (ROR ID) of an the institution,,,True,,,string,,,,,,
Institution_id,"Unique, stable, cross-portal identifier for the institution (see Sage Common Data Model's ORGANIZATION entity), used as a key for record linking and updates. Curated only for institutions with a well-formed ROR id.","org.albert-einstein-college-of-medicine, org.arizona-state-university, org.auburn-university, org.barrow-neurological-institute, org.baylor-college-of-medicine, org.beckman-research-institute-of-city-of-hope, org.beth-israel-deaconess-hospital, org.boston-medical-center, org.boston-university, org.brigham-and-womens-hospital, org.california-institute-of-technology, org.childrens-hospital-of-philadelphia, org.city-of-hope, org.clemson-university, org.cleveland-clinic, org.cold-spring-harbor-laboratory, org.columbia-university, org.cornell-university, org.dana-farber-cancer-institute, org.dartmouth-college, org.duke-university, org.emory-university, org.georgia-institute-of-technology, org.harvard-medical-school, org.harvard-university, org.hebrew-university-of-jerusalem, org.houston-methodist, org.indiana-university, org.institute-for-systems-biology, org.jackson-laboratory, org.johns-hopkins-university, org.lurie-children-s-hospital, org.massachusetts-general-hospital, org.massachusetts-institute-of-technology, org.mayo-clinic, org.memorial-sloan-kettering-cancer-center, org.moffitt-cancer-center, org.northeastern-university, org.new-york-university, org.northwestern-university, org.oregon-health-science-university, org.pacific-northwest-national-laboratory, org.purdue-university, org.rockefeller-university, org.sage-bionetworks, org.salk-institute-for-biological-studies, org.st-jude-children-s-research-hospital, org.stanford-university, org.stony-brook-university, org.the-university-of-texas-health-science-center-at-san-antonio, org.tufts-university-medford, org.university-of-alabama-at-birmingham, org.university-of-arizona, org.university-of-arkansas-at-fayetteville, org.university-of-california-berkeley, org.university-of-california-irvine, org.university-of-california-los-angeles, org.university-of-california-san-diego, org.university-of-california-san-francisco, org.university-of-chicago, org.university-of-chicago-medical-center, org.university-of-colorado-denver, org.university-of-delaware, org.university-of-florida, org.university-of-illinois, org.university-of-illinois-at-chicago, org.university-of-massachusetts-medical-school, org.university-of-miami, org.university-of-michigan, org.university-of-nevada-reno, org.university-of-minnesota, org.university-of-new-south-wales, org.university-of-north-carolina-at-chapel-hill, org.university-of-pennsylvania, org.university-of-pittsburgh, org.university-of-southern-california, org.university-of-texas-md-anderson-cancer-center, org.university-of-texas-southwestern-medical-center, org.university-of-texas-at-austin, org.university-of-utah, org.university-of-virginia, org.university-of-washington, org.university-of-wisconsin-madison, org.vanderbilt-university, org.virginia-polytechnic-institute, org.washington-university-in-st-louis, org.wake-forest, org.weill-cornell-medicine, org.wistar-institute, org.yale-university",,True,primary_key,,string,,,,,,
Model,Information about a non-human organism or any cell line from which experimental data is derived.,,"Model_id, Study Key, Individual Key, Model Age, Model Age Unit, Sex, Disease Type, Primary Diagnosis, Primary Site, Site of Origin, Tumor Subtype, Species, Model Type, Model Method, Model Source, Model Acquisition Type, Model Graft Source, Model Genotype, Treatment Type, Therapeutic Agent, Days to Treatment, Treatment Response, Treatment Anatomic Site",,,,,,,,,True,
Model_id,"Unique row identifier, used as a primary key for record updates. This should use the GrantNumber-Mxxx format unless directed otherwise.",,,True,"CDE:12220014, primary_key",,string,,"^CA\d{6}-M\d{1,9}$",,,,
Model Age,"The age of the model when used for an experiment (mice, zebrafish, etc.) or model source (cell lines, organoids, etc.)",,,,,,number,,,,,,
Model Age Unit,The unit corresponding to the age provided for this model.,,,,,,string,,,,,,
Model Type,The general label used to identify the model type.,,,True,,,string,,,,,,
Model Method,The term that describes the general method used to create the model.,,,,,,string,,,,,,
Model Source,"The reference organism from which the model was derived, if applicable. This could be a specific Biospecimen Key, Model Key, mouse type, cell line, or other reference. Provide RRID if available, to link to existing cell line information. Do not use this field to designate an Individual as the source of the model.",,,,,,string,,,,,,
Model Acquisition Type,"The method by which the model was obtained. If applicable, please provide a link to the supplier of the model source.",,,,,,string,,,,,,
Model Graft Source,"If the model is an allograft or xenograft, as indicated by Model Type, please provide a unique identifier associated with the source of the graft material (e.g., RRID, Individual Key, Model Key, Biospecimen Key)",,,,,,string,,,,,,
Model Genotype,"The relevant genotype information associated with the model, including markers, background, etc.",,,,,,string,,,,,,
Name,Name of the individual,,,True,,,string,,,,,,
Alternative Names,"Other ways the individual's name is displayed. Multiple values permitted, comma separated.",,,,,,string_list,,,,,,
Email,Email address of the individual,,,,CRDC_CDE:2517550,,string,,,,,,
Url,"URL, e.g., individual's home page address",,,,,,string,uri,,,,,
Orcid Id,Unique identifier (ORCID ID) of the individual,,,,CRDC_CDE:10624734,,string,,\d{4}\-\d{4}\-\d{4}\-\d{3}(\d|X),,,,
Synapse Profile Id,Unique identifier (Synapse Profile ID) of the individual. See identifer in the url of the synapse profile page. ,,,,,,string,,,,,,
Last Known Institution,Last known institutional affiliation of the individual.,,,True,,,string,,,,,,
Working Group Participation,"CSBC/PSON working group(s) of which the individual is a member (current and former). Multiple values permitted, comma separated.","Cancer Metabolism, Cell and Tissue Mechanics, Education and Outreach, Image Analysis, Navigating Cancer with Science and Art, None, Patient Advocacy Working Group, Protein-Protein Interactions, Resource and Data Sharing",,True,,,string_list,,,,,,
Chair Roles,"Committee or working group chair role(s) the individual fulfilled (current and former). Multiple values permitted, comma separated.","Annual Meeting, None, Steering Committee, Working Group",,True,,,string_list,,,,,,
Consent For Portal Display,Consent from individual to display Person information in the CCKP,"No, Yes",,True,,,string,,,,,,
Portal Display,Display content in CCKP,"FALSE, TRUE",,True,,,boolean,,,,,,
Person View,The denormalized manifest for person submission.,,"PersonView_id, GrantView Key, Consortium Key, Name, Alternative Names, Email, Url, Orcid Id, Synapse Profile Id, Last Known Institution, Institution Key, Working Group Participation, Chair Roles, Consent For Portal Display, Portal Display, Person Publications, Person Datasets, Person Tools, Person Educational Resources",,,,,,,,,True,
Person Publications,"A list of the pubmed Ids associated with the person. Multiple values permitted, comma separated.",,,,,,string_list,,,,,,
Person Datasets,"A list of the dataset aliases (An alias of the dataset must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters) associated with the person. Multiple values permitted, comma separated.",,,,,,string_list,,,,,,
Person Tools,"A list of the tool names associated with the person. Multiple values permitted, comma separated.",,,,,,string_list,,,,,,
Person Educational Resources,"A list of educational resource identifiers associated with the person. Multiple values permitted, comma separated.",,,,,,string_list,,,,,,
PersonView_id,A unique primary key that enables record updates using schematic.,,,True,primary_key,,string,,,,,,
Project Name,Name of the project,,,True,CRDC_CDE:11459804,,string,,,,,,
Project Type,Type of project,"Core, Project",,True,,,string,,,,,,
Project Description,Description of the project,,,True,,,string,,,,,,
Project View,The denormalized manifest for project submission.,,"ProjectView_id, GrantView Key, Project Name, Project Type, Project Description, Investigator, PersonView Key, Consortium Key, Project Short Name",,,,,,,,,True,
ProjectView_id,"Unique row identifier, used as a primary key for record updates.",,,True,primary_key,,string,,,,,,
Project Short Name,"An acronym or abbreviated form of the title used to refer to an organ-, site- or disease-specific data collection within a broad framework of goals under which related studies or other research activities are grouped.",,,,CRDC_CDE:11459806,,string,,,,,,
Publication Doi,The digital object identifier associated with the publication in the form of https://www.doi.org/{doi} to comply with CrossRef DOI display guidelines.,,,,,,string,uri,,,,,
Publication Journal,The name of the periodical publication in which the publication was published.,,,True,,,string,,,,,,
Pubmed Id,The PubMed identifier associated with the publication.,,,True,CDE:3443453,,string,,,,,,
Pubmed Url,Pubmed URL for the publication,,,True,,,string,uri,,,,,
Publication Title,Title of the publication,,,True,,,string,,,,,,
Publication Year,Year of the publication,,,True,,,number,,,,,,
Publication Keywords,"Keywords associated with the publication. Multiple values permitted, comma separated.",,,,,,string_list,,,,,,
Publication Authors,"Authors of the publication. Multiple values permitted, comma separated.",,,True,,,string_list,,,,,,
Publication Abstract,The abstract of the publication.,,,True,,,string,,,,,,
Publication Accessibility,Whether there are non-monetary restrictions on accessing an the publication.,"Open Access, Restricted Access",,True,,,string,,,,,,
Publication View,The denormalized manifest for publication submission.,,"PublicationView_id, Study Key, GrantView Key, Publication Doi, Publication Journal, Pubmed Id, Pubmed Url, Publication Title, Publication Year, Publication Keywords, Publication Authors, Publication Abstract, Assay, Tumor Type, Tissue, Publication Accessibility, Publication Dataset Alias",,,,,,,,,True,
Publication Dataset Alias,"A list of the dataset aliases (An alias of the dataset must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters) associated with the publication. Multiple values permitted, comma separated.",,,,,,string_list,,,,,,
PublicationView_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the PubMed Id, unless directed otherwise.",,,True,primary_key,,string,,,,,,
Sequencing Level 1,Unaligned/unprocessed sequencing data ,,"SequencingLevel1_id, Filename, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, NGS Library Strategy, NGS Library Source Material, NGS Library Source Molecule, NGS Library Selection Method, NGS Library Layout, NGS Sequencing Platform, NGS Sequencing Design Description, NGS Read Length, NGS Raw Reads, NGS Unique Bases, NGS Sequencing Coverage, NGS Library Preparation Kit Name, NGS Library Preparation Kit Vendor, NGS Library Preparation Kit Version, NGS Read Indicator, NGS Library Preparation Days from Index, NGS Sequencing Library Construction Days from Index",,,,,,,,,True,
SequencingLevel1_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
NGS Sequencing Coverage,Depth of coverage on assembly used. Found by (Unique Aligned Basecalls)/(Reference Length),,,,CDE:11556322,,number,,,,,,
NGS Read Length,"The average length of the sequencing reads. Can be integer, null",,,True,CDE:12426615,,number,,,,,,
NGS Library Selection Method,How nucleic acid molecules are isolated.,"5-methylcytidine antibody, CAGE, rRNA Depletion, cDNA, cDNA oligo_dT, cDNA random priming, CF-H, CF-M, CF-S, CF-T, Poly-T Enrichment, ChIP, DNAse, HMPR, Hybrid Selection, Not applicable, Inverse rRNA, MBD2 protein methyl-CpG binding domain, miRNA Size Fractionation, MDA, MF, MNase, MSLL, Oligo-dT, Other, Padlock probes capture method, PCR, PolyA, RACE, Random, Random PCR, Reduced Representation, Repeat fractionation, Restriction Digest, RT-PCR, Size fractionation, Affinity Enrichment, Unspecified",,,CDE:6347743,,string,,,,,,
NGS Library Strategy,"The assay associated with the nucleic acid library (e.g., RNA-Seq, ChIP-Seq)","AMPLICON, ATAC-seq, Bisulfite-Seq, ChIA-PET, ChIP-Seq, CLONE, CLONEEND, CTS, Spatial-tx, snATAC-Seq, DNase-Hypersensitivity, scMultiome, EST, FAIRE-seq, FINISHING, FL-cDNA, Hi-C, MBD-Seq, MeDIP-Seq, miRNA-Seq, MNase-Seq, MRE-Seq, ncRNA-Seq, Other, POOLCLONE, RAD-Seq, RIP-Seq, RNA-Seq, mRNA-Seq, Bulk RNA-Seq, scRNA-Seq, SELEX, DNA-Seq, scDNA-Seq, ssRNA-seq, Synthetic-Long-Read, Targeted-Capture, Tethered Chromatin Conformation Capture, Tn-Seq, WCS, WGA, WGS, WXS",,True,"CDE:6273393, CRDC_CDE:6273393",,string,,,,,,
NGS Library Source Material,The type of source material being sequenced.,"Bulk Cells, Bulk Tissue, Bulk Nuclei, Single-nuclei, Single-cells, Not Reported",,True,CDE:15235975,,string,,,,,,
NGS Library Layout,"Text description of the library layout, one of Paired-end or Single.","Paired-end, Single-indexed",,True,CDE:11527735,,string,,,,,,
NGS Library Preparation Kit Name,Name of Library Preparation Kit. String,,,,,,string,,,,,,
NGS Library Preparation Kit Vendor,Vendor of Library Preparation Kit. String,,,,,,string,,,,,,
NGS Library Preparation Kit Version,Version of Library Preparation Kit. String,,,,,,string,,,,,,
NGS Sequencing Platform,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.,"454 GS, 454 GS 20, 454 GS FLX, 454 GS FLX Titanium, 454 GS FLX+, 454 GS Junior, AB 310 Genetic Analyzer, AB 3130 Genetic Analyzer, AB 3130xL Genetic Analyzer, AB 3500 Genetic Analyzer, AB 3500xL Genetic Analyzer, AB 3730 Genetic Analyzer, AB 3730xL Genetic Analyzer, AB 5500 Genetic Analyzer, AB 5500x-Wl Genetic Analyzer, AB 5500xl Genetic Analyzer, AB SOLiD 2, AB SOLiD 3, AB SOLiD 3 Plus System, AB SOLiD 4, AB SOLiD 4hq System, AB SOLiD PI System, AB SOLiD System, BGISEQ-500, Complete Genomics, DNBSEQ-G400, DNBSEQ-G50, DNBSEQ-T7, Affymetrix SNP 6.0, GeneChip U133 Plus 2.0, GeneChip U133A, GridION, Helicos HeliScope, Illumina Human Methylation 27, Illumina Human Methylation 450, Illumina Genome Analyzer, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiScanSQ, Illumina HiSeq 1000, Illumina HiSeq 1500, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 3000, Illumina HiSeq 4000, Illumina HiSeq X Five, Illumina HiSeq X Ten, Illumina iSeq 100, Illumina Methylation Epic, Illumina Methylation Epic v2, Illumina MiniSeq, Illumina MiSeq, Illumina NextSeq, Illumina NextSeq 1000, Illumina NextSeq 2000, Illumina NextSeq 2500, Illumina NextSeq 500, Illumina NextSeq 550, Illumina NovaSeq, Illumina NovaSeq 6000, Illumina NovaSeq S4, Illumina NovaSeq X Plus, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, Ion Torrent S5 XL, MGISEQ-2000RS, MinION, Not Reported, Other, PacBio RS, PacBio RS II, PacBio Sequel, PacBio Sequel II, PromethION, Ultima Genomics UG100, Unknown",,True,"CDE:6352164, CRDC_CDE:6352164",,string,,,,,,
NGS Sequencing Design Description,Free-form description of the methods used to create the sequencing library; a brief 'materials and methods' section.,,,True,CDE:11529028,,string,,,,,,
NGS Read Indicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other","R1, R2, R1&R2, I1, Other",,True,,,string,,,,,,
NGS Library Preparation Days from Index,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',,,,,,string,,\d+$|Not\sApplicable$|unknown$,,,,
NGS Sequencing Library Construction Days from Index,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',,,True,,,string,,\d+$|Not\sApplicable$|unknown$,,,,
NGS Unique Bases,Count of unique basecalls present in the data.,,,,,,number,,,,,,
NGS Raw Reads,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. ,,,,CDE:11529035,,number,,,,,,
NGS Library Source Molecule,The source of nucleic acids represented in the sequencing library. ,"Genomic DNA, Metagenomic, Metatranscriptomic, Not Reported, Transcriptome, Viral RNA",,True,CDE:15235981,,string,,,,,,
Sequencing Level 2,Sequencing data that has been aligned with a reference genome.,,"SequencingLevel2_id, SequencingLevel1 Key, Filename, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, NGS Library Strategy, NGS Library Source Material, NGS Library Source Molecule, NGS Library Selection Method, NGS Library Layout, NGS Sequencing Platform, NGS Sequencing Design Description, NGS Raw Reads, NGS Stitched Reads, NGS Aligned Reads, NGS Deduplicated Reads, NGS Trimmed Reads, NGS MapQ30, NGS Unique Bases, NGS Read Length, NGS Sequencing Coverage, Genomic Reference, Software and Version",,,,,,,,,True,
SequencingLevel2_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
NGS Stitched Reads,"Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads",,,,,,number,,,,,,
NGS Aligned Reads,Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.,,,,,,number,,,,,,
NGS Deduplicated Reads,Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.,,,,,,number,,,,,,
NGS Trimmed Reads,Number of the reads remaining after trimming has been applied.,,,,,,number,,,,,,
NGS MapQ30,Number of reads with Quality >= 30.,,,,,,number,,,,,,
Sequencing Level 3,Sequencing data that has been aligned with a reference genome.,,"SequencingLevel3_id, SequencingLevel2 Key, Filename, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, NGS Unique Probe Count, NGS Unique Target Count, NGS Matrix Type, Software and Version, Workflow Type, Workflow Parameter Description, Workflow Link",,,,,,,,,True,
SequencingLevel3_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
NGS Unique Probe Count,Total number of unique probes reported.,,,,,,number,,,,,,
NGS Unique Target Count,Total number of unique genes reported.,,,,,,number,,,,,,
NGS Matrix Type,Type of count data stored in matrix.,"Raw Counts, Normalized Counts, Scaled Counts, Batch Corrected Counts",,,,,string,,,,,,
Sequencing RNA Level 1,Unaligned/unprocessed RNA sequencing data,,"SequencingRNALevel1_id, Filename, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, NGS Library Strategy, NGS Library Source Material, NGS Library Source Molecule, NGS Library Selection Method, NGS Library Layout, NGS Sequencing Platform, NGS Sequencing Design Description, NGS Read Length, NGS Raw Reads, NGS Unique Bases, NGS Sequencing Coverage, NGS Library Preparation Kit Name, NGS Library Preparation Kit Vendor, NGS Library Preparation Kit Version, NGS Read Indicator, NGS Library Preparation Days from Index, NGS Sequencing Library Construction Days from Index, NGS RNA End Bias, NGS RNA Reverse Transcription Primer, NGS RNA RIN, NGS RNA DV200",,,,,,,,,True,
SequencingRNALevel1_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
NGS RNA End Bias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript","3 Prime, 5 Prime, Full Length Transcript",,True,,,string,,,,,,
NGS RNA Reverse Transcription Primer,"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","Oligo-dT, Poly-dT, Feature barcoding, Random",,True,,,string,,,,,,
NGS RNA 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,,,,,,number,,,,,,
NGS RNA DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,,,,,,number,,,,,,
Data Use Codes,"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. Available DUO code definitions can be found here: https://mc2-center.github.io/data-models/valid_values/shared/#attribute-data-use-codes","Pending Annotation, DUO:0000042, DUO:0000027, DUO:0000016, DUO:0000029, DUO:0000043, DUO:0000015, DUO:0000004, DUO:0000045, DUO:0000017, DUO:0000011, DUO:0000046, DUO:0000018, DUO:0000044, DUO:0000021, DUO:0000006, DUO:0000019, DUO:0000026, DUO:0000020, DUO:0000012, DUO:0000025, DUO:0000024, DUO:0000028, DUO:0000022, DUO:0000007, DUOPlus1, DUOPlus2, DUOPlus3, DUOPlus4, DUOPlus5, DUOPlus6, DUOPlus7",,,CDE:0002001,,string_list,,,,,,
ProjectView Key,"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.",,,,foreign_key,,string,,,,,,
Study Key,"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.",,,,foreign_key,,string,,,,,,
PersonView Key,"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.",,,,foreign_key,,string,,,,,,
Consortium Key,"Unique Consortium_id foreign key(s) that group the resource with other components, as part of the same consortium-associated grants. Please provide multiple values as a comma-separated list.",,,,foreign_key,,string,,,,,,
Institution Key,"Unique Institution_id foreign key(s) that group the resource with other components, as part of the same institution-associated grants. Please provide multiple values as a comma-separated list.",,,,foreign_key,,string,,,,,,
GrantView Key,"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.",,,,foreign_key,,string,,(CA\d{6}|Affiliated/Non-Grant Associated),,,,
DatasetView Key,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.,,,,foreign_key,,string,,,,,,
Biospecimen Key,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.,,,,foreign_key,,string,,"-B\d{1,9}",,,,
Individual Key,Unique Individual_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,,,,foreign_key,,string,,"CA\d{6}-IND\d{1,9}",,,,
PublicationView Key,Unique PublicationView_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,,,,foreign_key,,string,,,,,,
ToolView Key,Unique ToolView_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,,,,foreign_key,,string,,,,,,
EducationalResource Key,Unique EducationalResource_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,,,,foreign_key,,string,,,,,,
DataDSP Key,Unique DataDSP_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.,,,,foreign_key,,string,,,,,,
Model Key,Unique Model_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,"CA\d{6}-M\d{1,9}",,,,
NanoStringGeoMxAuxiliaryFiles Key,Unique NanoStringGeoMxAuxiliaryFiles_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
NanoStringGeoMxDSPImaging Key,Unique NanoStringGeoMxDSPImaging_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
NanoStringGeoMxDSPLevel1 Key,Unique NanoStringGeoMxDSPLevel1_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
NanoStringGeoMxDSPLevel2 Key,Unique NanoStringGeoMxDSPLevel2_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
NanoStringGeoMxDSPLevel3 Key,Unique NanoStringGeoMxDSPLevel3_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
NanoStringGeoMXROISegmentAnnotation Key,Unique NanoStringGeoMXROISegmentAnnotation_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
ImagingChannel Key,Unique ImagingChannel_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
ImagingLevel1 Key,Unique ImagingLevel1_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
ImagingLevel2 Key,Unique ImagingLevel2_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
ImagingLevel3Image Key,Unique ImagingLevel3Image_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
ImagingLevel3Segments Key,Unique ImagingLevel3Segments_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
ImagingLevel4 Key,Unique ImagingLevel4_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
SequencingLevel1 Key,Unique SequencingLevel1_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
SequencingLevel2 Key,Unique SequencingLevel2_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
SequencingLevel3 Key,Unique SequencingLevel3_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
SequencingRNALevel1 Key,Unique SequencingRNALevel1_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
VisiumRNALevel1 Key,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.,,,,foreign_key,,string,,,,,,
VisiumRNALevel2 Key,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.,,,,foreign_key,,string,,,,,,
VisiumRNALevel3 Key,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.,,,,foreign_key,,string,,,,,,
VisiumRNALevel4 Key,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.,,,,foreign_key,,string,,,,,,
VisiumAuxiliaryFiles Key,Unique VisiumAuxiliaryFiles_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list.,,,,foreign_key,,string,,,,,,
Filename,"The path of a file in Synapse, relative to the project. The file associated with the path will be annotated with attributes contained in this sheet.",,,,"CDE:11284037, CRDC_CDE:11284037",,string,,,,,,
Workflow Type,Type of computational workflow used to generate the file.,,,,,,string,,,,,,
Workflow Link,Link to documentation or webpage associated with the computational workflow used to generate the file.,,,,,,string,uri,,,,,
Workflow Parameter Description,Link or text description of flags or options provided to the workflow used to generate the file.,,,,,,string,,,,,,
Software and Version,Name of software used to generate the information contained in the file. String,,,,CDE:11529072,,string,,,,,,
Workflow Version,Major version of the workflow (e.g. Cell Ranger v3.1),,,,,,string,,,,,,
Genomic Reference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),,,,CDE:11529031,,string,,,,,,
Genomic Reference URL,Link to human genome sequence; ftp or reference URL will be accepted.,,,,,,string,uri,,,,,
Genome Annotation URL,Link to the human genome annotation (GTF) file; ftp or reference URL will be accepted.,,,,,,string,uri,,,,,
AccessRequirementKey,The Access Requirement id(s) associated with this object. Provide multiple values as a comma-separated list.,,,,,,string,,,,,,
dataUseModifiers,"A list of data use modifiers that apply to the access requirement. Examples include GRU, IRB, etc.","Pending Annotation, DUO:0000042, DUO:0000027, DUO:0000016, DUO:0000029, DUO:0000043, DUO:0000015, DUO:0000004, DUO:0000045, DUO:0000017, DUO:0000011, DUO:0000046, DUO:0000018, DUO:0000044, DUO:0000021, DUO:0000006, DUO:0000019, DUO:0000026, DUO:0000020, DUO:0000012, DUO:0000025, DUO:0000024, DUO:0000028, DUO:0000022, DUO:0000007, DUOPlus1, DUOPlus2, DUOPlus3, DUOPlus4, DUOPlus5, DUOPlus6, DUOPlus7",,,CDE:00002002,,string_list,,,,,,
collaborationRequired,"If collaboration is required for the access requirement, provide the PI email address. Provide multiple as a comma-separated list.",,,,,,string,,,,,,
diseaseSpecificResearch,The type(s) of disease research allowed by this access requirement. Provide the MONDO ID in format MONDO:id. Provide multiple values as a comma-separated list. MONDO terms can be found here: https://ols.monarchinitiative.org/ontologies/mondo,,,,,,string,,MONDO:\d{7},,,,
geographicalRestriction,The specific geographic region(s) to which use is limited by the access requirement.,"AD, AE, AF, AG, AI, AL, AM, AO, AQ, AR, AS, AT, AU, AW, AX, AZ, BA, BB, BD, BE, BF, BG, BH, BI, BJ, BL, BM, BN, BO, BQ, BR, BS, BT, BV, BW, BY, BZ, CA, CC, CD, CF, CG, CH, CI, CK, CL, CM, CN, CO, CR, CU, CV, CW, CX, CY, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, EH, ER, ES, ET, FI, FJ, FK, FM, FO, FR, GA, GB, GD, GE, GF, GG, GH, GI, GL, GM, GN, GP, GQ, GR, GS, GT, GU, GW, GY, HK, HM, HN, HR, HT, HU, ID, IE, IL, IM, IN, IO, IQ, IR, IS, IT, JE, JM, JO, JP, KE, KG, KH, KI, KM, KN, KP, KR, KW, KY, KZ, LA, LB, LC, LI, LK, LR, LS, LT, LU, LV, LY, MA, MC, MD, ME, MF, MG, MH, MK, ML, MM, MN, MO, MP, MQ, MR, MS, MT, MU, MV, MW, MX, MY, MZ, NA, NC, NE, NF, NG, NI, NL, NO, NP, NR, NU, NZ, OM, PA, PE, PF, PG, PH, PK, PL, PM, PN, PR, PS, PT, PW, PY, QA, RE, RO, RS, RU, RW, SA, SB, SC, SD, SE, SG, SH, SI, SJ, SK, SL, SM, SN, SO, SR, SS, ST, SV, SX, SY, SZ, TC, TD, TF, TG, TH, TJ, TK, TL, TM, TN, TO, TR, TT, TV, TW, TZ, UA, UG, UM, US, UY, UZ, VA, VC, VE, VG, VI, VN, VU, WF, WS, YE, YT, ZA, ZM, ZW",,,,,string_list,,,,,,
institutionSpecificRestriction,Institutions with specific restrictions associated with the access requirement. Provide the institution ROR ID in format ROR:id. Provide multiple entries as a comma-separated list. ROR IDs can be found here: https://ror.org/search,,,,,,string,,ROR:[a-z0-9]{9},,,,
publicationMoratorium,End date of the publication moratorium associated with the access requirement.,,,,,,string,date,,,,,
researchSpecificRestrictions,Research-specific restrictions associated with the access requirement.,,,,,,string,,,,,,
timeLimitOnUse,Time limit on the use of the data associated with the access requirement.,,,,,,number,,,,,,
userSpecificRestriction,The user-specific restrictions associated with the access requirement.,,,,,,string,,,,,,
sourceGeography,The geographical source of the data associated with the access requirement. Equivalent to DUOPlus1.,"AD, AE, AF, AG, AI, AL, AM, AO, AQ, AR, AS, AT, AU, AW, AX, AZ, BA, BB, BD, BE, BF, BG, BH, BI, BJ, BL, BM, BN, BO, BQ, BR, BS, BT, BV, BW, BY, BZ, CA, CC, CD, CF, CG, CH, CI, CK, CL, CM, CN, CO, CR, CU, CV, CW, CX, CY, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, EH, ER, ES, ET, FI, FJ, FK, FM, FO, FR, GA, GB, GD, GE, GF, GG, GH, GI, GL, GM, GN, GP, GQ, GR, GS, GT, GU, GW, GY, HK, HM, HN, HR, HT, HU, ID, IE, IL, IM, IN, IO, IQ, IR, IS, IT, JE, JM, JO, JP, KE, KG, KH, KI, KM, KN, KP, KR, KW, KY, KZ, LA, LB, LC, LI, LK, LR, LS, LT, LU, LV, LY, MA, MC, MD, ME, MF, MG, MH, MK, ML, MM, MN, MO, MP, MQ, MR, MS, MT, MU, MV, MW, MX, MY, MZ, NA, NC, NE, NF, NG, NI, NL, NO, NP, NR, NU, NZ, OM, PA, PE, PF, PG, PH, PK, PL, PM, PN, PR, PS, PT, PW, PY, QA, RE, RO, RS, RU, RW, SA, SB, SC, SD, SE, SG, SH, SI, SJ, SK, SL, SM, SN, SO, SR, SS, ST, SV, SX, SY, SZ, TC, TD, TF, TG, TH, TJ, TK, TL, TM, TN, TO, TR, TT, TV, TW, TZ, UA, UG, UM, US, UY, UZ, VA, VC, VE, VG, VI, VN, VU, WF, WS, YE, YT, ZA, ZM, ZW",,,,,string_list,,,,,,
populationType,The population studied in the research associated with the access requirement. Equivalent to DUOPlus2,,,,,,string,,,,,,
deidentificationType,The type of de-identification applied to the data associated with the access requirement. Equivalent to DUOPlus3.,"Manual, Semiautomatic, Automatic, Not Applicable",,,,,string_list,,,,,,
dataPermission,The permissions associated with the data under the access requirement. Equivalent to DUOPlus4.,"Agreement, Attestation, Award, Other",,,,,string_list,,,,,,
dataTier,The tier of data access associated with the access requirement. Equivalent to DUOPlus5.,"Anonymous, Open, Controlled, Private",,,,,string_list,,,,,,
attribution,The attribution statement for the data associated with the access requirement. Equivalent to DUOPlus7.,,,,,,string,,,,,,
DUO:0000026,This data use modifier indicates that use is limited to use by approved users.,,userSpecificRestriction,,DUO:0000026,,string,,,,,,
DUO:0000020,This data use modifier indicates that the requestor must agree to collaboration with the primary study investigator(s).,,collaborationRequired,,DUO:0000020,,string,,,,,,
DUO:0000012,This data use modifier indicates that use is limited to studies of a certain research type.,,researchSpecificRestrictions,,DUO:0000012,,string,,,,,,
DUO:0000025,This data use modifier indicates that use is approved for a specific number of months.,,timeLimitOnUse,,DUO:0000025,,string,,,,,,
DUO:0000024,This data use modifier indicates that requestor agrees not to publish results of studies until a specific date.,,publicationMoratorium,,DUO:0000024,,string,,,,,,
DUO:0000028,This data use modifier indicates that use is limited to use within an approved institution.,,institutionSpecificRestriction,,DUO:0000028,,string,,,,,,
DUO:0000022,This data use modifier indicates that use is limited to within a specific geographic region.,,geographicalRestriction,,DUO:0000022,,string,,,,,,
DUO:0000007,This data use permission indicates that use is allowed provided it is related to the specified disease.,,diseaseSpecificResearch,,DUO:0000007,,string,,,,,,
DUOPlus1,Source geography is relevant to governance decisions.,,sourceGeography,,,,string,,,,,,
DUOPlus2,Study population is relevant to governance decisions.,,populationType,,,,string,,,,,,
DUOPlus3,Data deidentification is relevant to governance decisions.,,deidentificationType,,,,string,,,,,,
DUOPlus4,A data permission designation is associated with the Study.,,dataPermission,,,,string,,,,,,
DUOPlus5,A data tier designation is associated with the Study.,,dataTier,,,,string,,,,,,
DUOPlus6,A license is associated with the Study.,,License,,,,string,,,,,,
DUOPlus7,Attribution conditions are associated with this Study.,,attribution,,,,string,,,,,,
Sex,"Biological sex associated with the individual, biospecimen donor, or model.","Female, Male, Unknown",,True,"CDE:7572817, CRDC_CDE:7572817",,string,,,,,,
Tumor Grade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.","GB Borderline, GX Grade Cannot Be Assessed, Not Applicable, Not Reported, Unknown, G3 High Grade, G2 Intermediate Grade, G1 Low Grade, G4 Anaplastic",,,"CDE:11325685, CRDC_CDE:11325685",,string,,,,,,
Last Known Disease Status,"Text term that describes the last known disease status of the individual, biospecimen donor, or model.","Biochemical evidence of disease without structural correlate, Tumor Free, Unknown, With Tumor, Not Reported, Not Applicable, Not Allowed To Collect, Distant Metastasis, Localized Disease, Regional Disease, New Tumor Event",,,"CDE:12447172, CRDC_CDE:12447172",,string,,,,,,
Treatment Type,"Text term that describes the kind of treatment administered to the individual, biospecimen donor, or model.","3-Dimensional Conformal Radiation Therapy, Allogeneic Hematopoietic Stem Cell Transplantation, Autologous Stem Cell Transplantation, Brachytherapy, Cellular Therapy, Chemotherapy, Concurrent Chemoradiation, Conditioning Therapy, Ablation Therapy, Control, Conventional Radiotherapy, Electron Beam Radiation Therapy, External Beam Radiation Therapy, High-Dose Rate Brachytherapy, Hormone Therapy, Immunosuppressive Therapy/GVHD Prophylaxis for Transplant, Immunotherapy, Intensity-Modulated Radiation Therapy, Low-Dose Rate Brachytherapy, Not Reported, Oncolytic Virus Therapy, Organ Transplantation, Palliative Care, Pharmacotherapy, Photon Beam Radiation Therapy, Post-Transplant Salvage Therapy, Proton Beam Radiation Therapy, Radiation Therapy, Radiofrequency Ablation, Radiopharmaceutical, Stem Cell Transplant, Stereotactic Body Radiation Therapy, Stereotactic Radiosurgery, Surgical Procedure, Targeted Molecular Therapy, Targeted Therapy, Unknown, Vaccine Therapy",,,"CDE:14737565, CRDC_CDE:14737565",,string_list,,,,,,
Treatment Response,"Text term that describes the final outcome after a treatment was administered to the individual, biospecimen donor, or model.","Complete Response, No Evidence of Disease, No Response, Not Applicable, Not Evaluable, Not Reported, Partial Response, Persistent Disease, Progressive Disease, Stable Disease, Unknown, Less than Partial Response, Too Early, Not Assessed",,,"CDE:13383448, CRDC_CDE:13383448, CRDC_CDE:15179918",,string,,,,,,
Therapeutic Agent,"The name of the individual agent(s) used as part of a treatment regimen or experimental protocol (NCI Thesaurus concept name -- reference-validated, not a fixed list; see https://ncithesaurus.nci.nih.gov/).",,,,CRDC_CDE:14913015,,string_list,,,,,,
Primary Diagnosis,"Text term used to describe the histologic diagnosis of the patient, biospecimen donor, or model (NCI Thesaurus concept name -- reference-validated, not a fixed list; see https://ncithesaurus.nci.nih.gov/).",,,True,CRDC_CDE:14905532,,string,,,,,,
Primary Site,"The UBERON identifier of the organ or part of the body where the disease began, i.e. the primary/original disease site (see https://www.ebi.ac.uk/ols4/ontologies/uberon). Reference-validated, not a fixed list.",,,,"CDE:14883047, CRDC_CDE:14883047",,string,,^UBERON:\d+$,,,,
Site of Origin,"The UBERON identifier of the anatomic site of origin of the patient's, biospecimen donor's, or model's malignant disease (see https://www.ebi.ac.uk/ols4/ontologies/uberon).",,,,"CDE:14156279, CRDC_CDE:14883072",,string,,^UBERON:\d+$,,,,
Known Metastasis Sites,The UBERON identifier(s) of the anatomic site(s) of metastasis associated with the malignant disease of the individual or biospecimen donor (see https://www.ebi.ac.uk/ols4/ontologies/uberon). Provide multiple values as a comma-separated list.,,,,"CDE:2856440, CRDC_CDE:15114457",,string_list,,^UBERON:\d+$,,,,
Disease Type,"The type of tumor associated with the individual, biospecimen, or model. Multiple values permitted, comma separated.","Acinar Cell Neoplasms, Adenomas and Adenocarcinomas, Adnexal and Skin Appendage Neoplasms, Basal Cell Neoplasms, Blood Vessel Tumors, Complex Mixed and Stromal Neoplasms, Cystic; Mucinous and Serous Neoplasms, Ductal and Lobular Neoplasms, Epithelial Neoplasms; NOS, Fibroepithelial Neoplasms, Fibromatous Neoplasms, Germ Cell Neoplasms, Giant Cell Tumors, Gliomas, Granular Cell Tumors and Alveolar Soft Part Sarcomas, Immunoproliferative Diseases, Leukemias, Lipomatous Neoplasms, Lymphatic Vessel Tumors, Mast Cell Neoplasm, Meningiomas, Mesothelial Neoplasms, Miscellaneous Bone Tumors, Miscellaneous Tumors, Mucoepidermoid Neoplasms, Myelodysplastic Syndromes, Myomatous Neoplasms, Myxomatous Neoplasms, Neoplasms; NOS, Nerve Sheath Tumors, Neuroepitheliomatous Neoplasms, Nevi and Melanomas, Not Applicable, Not Otherwise Specified, Not Reported, Odontogenic Tumors, Osseous and Chondromatous Neoplasms, Paragangliomas and Glomus Tumors, Plasma Cell Neoplasm, Soft Tissue Tumors and Sarcomas; NOS, Squamous Cell Neoplasms, Synovial-like Neoplasms, Thymic Epithelial Neoplasms, Transitional Cell Papillomas and Carcinomas, Trophoblastic neoplasms, Unknown",,,CDE:13471160,,string_list,,,,,,
Tumor Subtype,"The molecular or histologic subtype of the tumor associated with the individual, biospecimen, or model.",,,,,,string_list,,,,,,
Species,"The species of origin corresponding to the model, or from which the biospecimen originates.","African Bush Elephant, Armadillo, Asian Elephant, Boar, Cat, Chicken, Candida albicans, Cow, Dog, Escherichia coli, Guinea Pig, Horse, Human, Human Patient, Human Cell Line, Macaca nemestrina, Mouse, Multispecies, Not Applicable, Opossum, Rabbit, Rat, Rhesus monkey, Schizosaccharomyces pombe, Sheep, Trichoplax adhaerens, Unknown, Unspecified, Worm, Yeast, Fruit Fly, Zebrafish",,True,,,string_list,,,,,,
Days to Treatment,Number of days between the date used for index and the date the treatment started.,,,,,,number,,,,,,
ICD-10-CM Disease Code,"An alphanumeric value from the tenth version of the International Classification of Disease (ICD-10-CM) used to identify the diagnosis (e.g. C80.1). Reference-validated against the ICD-10-CM code system, not a fixed list.",,,,CRDC_CDE:11479873,,string,,"^[A-Z][0-9]{2}(\.[0-9A-Z]{1,4})?-?$",,,,
Treatment Anatomic Site,The UBERON identifier of the organ or part of the body targeted by a therapeutic procedure (see https://www.ebi.ac.uk/ols4/ontologies/uberon).,,,,CRDC_CDE:14461856,,string,,^UBERON:\d+$,,,,
Assay,"The assay the dataset, file, or publication is representative of. Multiple values permitted, comma separated.","10-cell RNA Sequencing, 16S Ribosomal Gene Sequencing Assay, 3' RNA-seq, 3C, 3C-qPCR, 3D ATAC-PALM, 3D Bioprinting, 3D Cell Culture, 4C, 5C, ATAC-Seq, ATP Bioluminescence Assay, Affinity Purification Mass Spectrometry, Allograft, Amplicon Sequencing, Angiogenesis Assay, Apoptosis Assay, Atomic Absorption Spectrophotometry, Atomic Absorption Spectroscopy, Atomic Force Microscopy, Autoradiography, Barcode-Seq, Bicinchoninic Acid Assay, Binding Assay, Bio-Layer Interferometry, Bioluminescence Imaging, Bisulfite Sequencing, Brightfield Microscopy, Brillouin Microscopy, CASFISH, CITE-seq, CLIP-qPCR, CRISPR, CUT&RUN, CUT&Tag-Sequencing, Cell Adhesion Assay, Cell Proliferation Assay, Cell Viability Assay, Cell-spreading Assay, CellTiter-Glo Luminescent Cell Viability Assay, Cerenkov Luminescence Imaging, ChIA-PET, ChIP-PCR, ChIP-Seq, ChIP-qPCR assay, Chemiluminescent Assay, Chemotaxis Assay, Circular Dichroism Spectroscopy, Co-Immunoprecipitation, Co-culture Assay, Collision-Induced Dissociation, Colorimetric Cell Viability Assay, Computational Modeling, Computational Tool, Computed Tomography, Confocal Microscopy, Confocal Reflectance Quantitative Phase Microscopy, Cross-Linking Immunoprecipitation High-throughput Sequencing, Cross-Linking Mass Spectrometry, Cyclic Immunofluorescence, Cytochemical Stain, Cytokine Expression Profile, Cytometric Bead Array Assay, Cytotoxicity Assay, DBiT-Seq, DNA Gene-Expression Microarray, DNA Methylation Array, DNA Sequencing, DNase-Seq, DRIP-seq, Dark Field Microscopy, Deep Mutational Scanning, Desorption Electrospray Ionization, Dideoxy Chain Termination DNA Sequencing, Differential Interference Contrast Microscopy, Differential Scanning Fluorimetry, Diffusion Weighted Imaging, Direct Long-Read RNA Sequencing, Drop-Seq, Droplet Digital PCR, Dual-Luciferase Reporter Assay, Dye Endocytosis Assay, Dynamic Contrast-Enhanced Magnetic Resonance Imaging, Dynamic Force Spectroscopy, Dynamic Light Scattering, Dynamic Susceptibility Contrast-Enhanced Magnetic Resonance Imaging, ELISA, Efferocytosis Assay, Electron Diffraction, Electron Microscopy, Electron Paramagnetic Resonance Spectroscopy, Electrophoretic Mobility Shift Assay, Electrospray Ionization Time-of-Flight Mass Spectrometry, Endotoxin Assay, Energy-Dispersive X-Ray Spectroscopy, Enzyme Activity Assay, Enzyme-Linked Immunospot Assay, Epidemiological Method, FAIRE-Seq, FISH, Flow Cytometry, Fluorescence Activated Cell Sorting, Fluorescence Correlation Spectroscopy, Fluorescence Imaging, Fluorescence Lifetime Imaging Microscopy, Fluorescence Microscopy, Fluorescence Recovery After Photo-Bleaching, Fluorescent Antibody Procedure, Fluorescent Cell Barcoding, Fluorescent In Situ Sequencing, Focused Ion Beam Scanning Electron Microscopy, Forster Resonance Energy Transfer, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Fourier-Transform Infrared Spectroscopy, Gas Chromatography Mass Spectrometry, Gelatin Zymography, Genotyping, Global Chromatin Profiling, Global Run-On Sequencing, Graphite Furnace Atomic Absorption Spectrometry, HL-Chip, HPLC-MSMS, Hematoxylin and Eosin Staining Method, Hi-C, HiChIP, High Throughput Screening, High-Content Screen, Hydrogels, Hydrophilic Interaction Chromatography, Image Cytometry, Imaging, Immobilized Metal Affinity Chromatography, ImmunoFISH, Immunoassay, Immunocytochemistry, Immunohistochemistry Staining Method, Immunoprecipitation, In Situ Hybridization, In Vitro Cell Killing Assay, In Vitro Model, In Vitro Selection, In Vitro Translation, In Vivo Bioluminescence, In-Cell Western Assay, Inductively-Coupled Plasma Mass Spectrometry, Interference Reflection Microscopy, Intravital Microscopy, Invasion Assay, Karyotyping, Knife-Edge Scanning Microscopy, L1000 mRNA Profiling Assay, Lattice Light Sheet Microscopy, Liquid Chromatography Mass Spectrometry, Liquid Chromatography/Tandem Mass Spectrometry, Low-Vacuum Scanning Electron Microscopy, Luciferase Reporter Assay, Luminescent Cell Viability Assay, MALDI-TOF Mass Spectrometry, MEMA Cell Growth Assay, MNase-Seq, MULTI-Seq, Macrophage Polarization Assay, Magnetic Resonance Imaging, Magnetic Tweezers, Magnetic Twisting Cytometry, Magnetically Activated Cell Sorting, Mammosphere Formation Assay, Mass Cytometry, Mass Spectrometry, Mathematical Modeling, MeDIP, MeRIP-Seq, Methyl Binding Domain Sequencing, Methylation-Specific PCR, Micro-computed Tomography, MicroRNA Expression Array, MicroRNA Sequencing, Microcontact Printing, Microfluidics, Micropipette Adhesion Assay, Micropipette Aspiration, Microscopy, Migration Assay, Mint-ChIP, Modeling, Molecular Simulations, Monolayer Stress Microscopy, Multi-Angle Light Scattering, Multi-Isotope Mass Spectrometry, Multiparametric Magnetic Resonance Imaging, Multiphoton Microscopy, Multiplexed Error-Robust Fluorescence In Situ Hybridization, Multiplexed Immunofluorescence, Multiplexed Immunohistochemistry, Multiplexed Ion Beam Imaging, Murine Model, Nano-hmC-Seal, NanoString Digital Spatial Profiling, Nanopatterning, Nanopore Sequencing, Nanowire, Nested PCR, Next Generation Sequencing, Nm-seq, Not Applicable, Nuclear Magnetic Resonance, Optical Coherence Tomography, Optical Emission Spectroscopy, Optical Mapping, Optical Stretcher, Optical Tweezers, Optogenetic Assay, Organoid, PCR, PET-CT, Paraquat Survival Assay, Partial Wave Spectroscopy, Patient Derived Xenograft, Pending Annotation, Permeability Assay, Phagocytosis Assay, Photoacoustic Imaging, Photolithography, Plasmid Construction, PlateSeq, Point Accumulation for Imaging in Nanoscale Topography, Positron Emission Tomography, Precision Run-On Sequencing, Proteomics Assay, Proximity Ligation Assay, Pull-Down Assay, QFISH, Quantitative Multiplex Immunofluorescence, Quantitative Point Accumulation for Imaging in Nanoscale Topography, Questionnaire, RAS Protein Family Activation Assay, RIP, RIP-Seq, RNA Sequencing, RNAi Screen, RT-PCR, RT-qPCR, Raman Spectroscopy, Reduced Representation Bisulfite Sequencing, Reverse Phase Protein Array, Reverse-Phase High-Performance liquid Chromatography, Rheometry, Ribo-Seq, Ribosomal P Protein Antibody Measurement, Scanning Angle Interference Microscopy, Scanning Electron Microscopy, Second-Harmonic Imaging Microscopy, Shotgun Mass Spectrometry, Single Cell ATAC-Seq, Single Cell Cytokine Detection Chip Assay, Single Cell DNA Sequencing, Single Cell Gel Electrophoresis, Single Cell RNA-Sequencing, Single Molecule Forster Resonance Energy Transfer, Single Nucleotide Polymorphism Array, Single Nucleus RNA-Sequencing, Single-Cell BCR Sequencing, Single-Cell Barcode Chip, Single-Cell TCR Sequencing, Single-Molecule Tracking, Sirius Red Staining, Size Exclusion Chromatography, Small-Angle X-ray Scattering, Soft Agar Assay, Southern Blotting, Spectroscopy, Statistical Modeling, Stimulated Emission Depletion Microscopy, Stimulated Raman Scattering, Stochastic Optical Reconstruction Microscopy, Super-Resolution Microscopy, Surface Plasmon Resonance, Surveyor Nuclease Assay, Synaptophysin Staining Method, Synthetic Genetic Array, TAB-Seq, TCR Sequencing, TIRF Microscopy, TRAP Staining, TUNEL assay, Tandem Mass Spectrometry, Tandem Mass Tagging, Target Engagement Assay, Targeted Genome Sequencing, Targeted Transcriptome Sequencing, Thermal Shift Assay, Thin-Layer Chromatography, Tiling Array, Time Lapse Microscopy, Time-Correlated Single Photon Counting, Tissue Engineering, Tissue Microarray, Total Internal Reflection Fluorescence Microscopy, Traction Force Microscopy, Transmission Electron Microscopy, Transwell Assay, UPLC-MSMS, UV Photocrosslinking, Unspecified, Vibrational Spectroscopy, Virus Plaque Assay, Von Kossa Staining, Western Blotting, Whole Exome Sequencing, Whole Genome Bisulfite Sequencing, Whole Genome Sequencing, Widefield Fluorescence Microscopy, Wound-Healing Assay, X-Ray Crystallography, X-Ray Diffraction, X-Ray Micro-Computed Tomography, Xenograft, cDNA Array, eCLIP-Seq, mRNA Sequencing, qPCR, scCGI-seq, scNT-Seq, scSLAM-seq, seqFISH, shRNA, siRNA, smFISH, smRNA-seq, snRNA-seq, Isothermal Titration Calorimetry, Suspended Microchannel Resonator, 10x Multiome, Visium Spatial Gene Expression, Antitumor Drug Screening Assay, Bioelectrochemical Analysis, Chimeric Antigen Receptor T-Cell Therapy, Cell Cycle Assay, Clonality Analysis, Comparative Genomic Hybridization, Cryo-Electron Microscopy, Cryo-Electron Tomography, Data Integration, Field-Emission Scanning Electron Microscopy, Label-free Protein Quantification by LC/MS, Metabolite Profiling Assay, Reporter Gene Assay, Single-Molecule Localization Microscopy, Synthesis, Targeted Therapy Agent, Trichrome Staining Method, Ultrasound Imaging, Transcription profiling by NanoString, Alcian Blue Staining Method, Artificial Intelligence, Cell Culture, Clinical Study, Cell-free Circulating Tumor DNA Assay, Co-Immunoprecipitation Mass Spectrometry, Deep Learning, Gene Ontology Enrichment Analysis, Gene Set Enrichment Analysis, Gene Silencing , Human Induced Pluripotent Stem Cell-derived Cardiomyocytes Culture, Imaging Mass Cytometry, Immunofluorescent Staining Method, Immunotherapy, Viral Transduction, Metastatic Colonization Assay, Phylogenetic Analysis, Picrosirius Staining, Scratch Assay, Structural Variant Analysis, Survival Analysis, Targeted Error Correction Sequencing, Tuba-Seq, SDS-PAGE, Cell Fractionation, Multiscale Light Sheet Microscopy, Light Sheet Microscopy, CODEX, in vivo tumor growth, in silico synthesis, RNA array, shRNA-seq, spatial transcriptomics, in vivo PDX viability, histology, proximity extension assay, compound screen, metabolic screening",,True,,,string_list,,,,,,
File Assay Category,"The broad category of experimental method used to generate the file, per NCI caDSR CDE 12373576 (Research Activity Experimental Method Type).","DNA Sequencing, Immunofluorescence, LC-MS/MS, Methylation Analysis, Multigene Expression Assay, Pathology, Quantitative Immunofluorescence, Radiology, RNA Sequencing",,FALSE,CRDC_CDE:12373576,,string,,,,,,
Tissue,"Tissue type(s) associated with the dataset, file, or publication. Multiple values permitted, comma separated.","Gonad, Abdominal Esophagus, Adipose Tissue, Adrenal Gland, Alveolus, Aorta, Artery, Ascending Colon, Bile Duct, Bladder, Blood, Blood Vessel, Bone, Bone Marrow, Brain, Breast, Caecum, Cancer-Associated Fibroblast, Cardia, Cartilage, Cervix Uteri, Choroid, Colon, Connective and Soft Tissue, Cornea, Duodenum, Ear, Embryo, Embryonic Heart, Endocervix, Endometrium, Endothelium, Epithelium, Esophagus, Eye, Fallopian Tube, Foreskin, Frontal Lobe, Gastroesophageal Junction, Gastrointestinal Tract, Genitourinary, Hair Follicle, Head and Neck, Heart, Heart Muscle, Hematopoietic System, Hippocampus, Intestine, Intra-Abdominal Lymph Nodes, Intrathoracic Lymph Nodes, Joint, Kidney, Larynx, Ligament, Liver, Lung, Lymph, Lymph Node, Lymph Nodes of Axilla or Arm, Lymph Nodes of Inguinal Region or Leg, Lymphatic System, Lymphoid Tissue, Main Bronchus, Mammary Gland, Meninges, Mesenchyme, Mucosa, Muscle, Nasal Cavity, Nervous System, Not Applicable, Olfactory Mucosa, Omentum, Oral Cavity, Oral Mucosa, Ovary, Pancreas, Pelvic Lymph Nodes, Pending Annotation, Periodontal Ligament, Peripheral Nerves, Peritoneum, Pharynx, Pituitary Gland, Placenta, Pleura, Prostate Gland, Rectum, Reproductive System, Respiratory System, Salivary Gland, Sclera, Sinonasal Tract, Skin, Small Intestine, Spinal Cord, Spleen, Stomach, Synovial Membrane, Tendon, Testis, Thymus, Thyroid Gland, Tongue, Tonsil, Trachea, Umbilical Cord, Unspecified, Uterus, Vagina, Vascular Endothelium, Vein, Vertebra, Peripheral Blood Mononuclear Cell",,,,,string_list,,,,,,
Tumor Type,"The tumor type(s), if applicable, associated with the dataset, file, or publication. Multiple values permitted, comma separated.","Cutaneous Melanoma, Acinar Cell Carcinoma, Acute Lymphoblastic Leukemia, Acute Monocytic Leukemia, Acute Myeloid Leukemia, Acute Promyelocytic Leukemia, Adenocarcinoma, Angiosarcoma, Astrocytoma, Atypical Teratoid/Rhabdoid Tumor, B Acute Lymphoblastic Leukemia, B-Cell Non-Hodgkin Lymphoma, Barrett Esophagus, Basal Cell Neoplasm, Basal-Like Breast Carcinoma, Biliary Tract Carcinoma, Bladder Carcinoma, Bladder Neoplasm, Bone Neoplasm, Brain Neoplasm, Breast Adenocarcinoma, Breast Carcinoma, Breast Neoplasm, Carcinoma, Carcinoma In Situ, Castration-Resistant Prostate Carcinoma, Cellular Schwannoma, Central Nervous System Cavernous Hemangioma, Central Nervous System Neoplasm, Cerebellar Neoplasm, Cervical Carcinoma, Cervical Neoplasm, Cervical Small Cell Carcinoma, Cholangiocarcinoma, Chondroblastoma, Choriocarcinoma, Chronic Lymphocytic Leukemia, Chronic Myeloid Leukemia, Clear Cell Renal Cell Carcinoma, Colon Adenocarcinoma, Colon Carcinoma, Colorectal Adenocarcinoma, Colorectal Adenoma, Colorectal Carcinoma, Colorectal Neoplasm, Combined Hepatocellular Carcinoma and Cholangiocarcinoma, Craniopharyngioma, Cutaneous T Cell Lymphoma, Diffuse Large B-Cell Lymphoma, Ductal Breast Carcinoma In Situ, Dysembryoplastic Neuroepithelial Neoplasm, Endometrial Carcinoma, Endometrial Neoplasm, Ependymoma, Esophageal Adenocarcinoma, Esophageal Carcinoma, Esophageal Squamous Cell Carcinoma, Ewing Sarcoma, Extraventricular Neurocytoma, Fibroepithelial Polyp, Fibrolamellar Carcinoma, Fibrosarcoma, Follicular Lymphoma, Gallbladder Carcinoma, Gastric Adenocarcinoma, Gastric Carcinoma, Gastric Neoplasm, Gastroesophageal Adenocarcinoma, Gastroesophageal Junction Adenocarcinoma, Gastrointestinal Stromal Neoplasm, Giant Cell Tumor, Glioblastoma, Glioma, Head and Neck Carcinoma, Head and Neck Neoplasm, Head and Neck Squamous Cell Carcinoma, Hepatocellular Carcinoma, High Grade Ovarian Serous Adenocarcinoma, Histiocytic Sarcoma, Hodgkin Lymphoma, Intestinal Neoplasm, Intrahepatic Cholangiocarcinoma, Invasive Ductal Breast Carcinoma, Kaposi Sarcoma, Leiomyoma, Leukemia, Liver and Intrahepatic Bile Duct Carcinoma, Liver and Intrahepatic Bile Duct Neoplasm, Low Grade Glioma, Luminal A Breast Carcinoma, Lung Adenocarcinoma, Lung Carcinoma, Lung Neoplasm, Lung Non-Small Cell Carcinoma, Lung Small Cell Carcinoma, Lung Squamous Cell Carcinoma, Lymphoid Leukemia, Lymphoma, Malignant Brain Neoplasm, Malignant Digestive System Neoplasm, Malignant Genitourinary System Neoplasm, Malignant Glioma, Malignant Neoplasm, Malignant Ovarian Neoplasm, Malignant Pancreatic Neoplasm, Malignant Peripheral Nerve Sheath Tumor, Malignant Peritoneal Neoplasm, Malignant Skin Neoplasm, Mantle Cell Lymphoma, Marginal Zone Lymphoma, Medulloblastoma, Melanoma, Meningioma, Mesothelioma, Multiple Myeloma, Mycosis Fungoides, Myeloid Leukemia, Myeloid Neoplasm, Myeloproliferative Neoplasm, Myoepithelioma, Nasopharyngeal Carcinoma, Neuroblastoma, Neuroendocrine Neoplasm, Neuroepithelial Neoplasm, Neurofibroma, Non-Functioning Pituitary Gland Adenoma, Non-Hodgkin Lymphoma, Not Applicable, Oral Cavity Neoplasm, Oral Cavity Squamous Cell Carcinoma, Oropharyngeal Neoplasm, Osteosarcoma, Ovarian Adenosarcoma, Ovarian Carcinoma, Ovarian Neoplasm, Ovarian Serous Adenocarcinoma, Pan-cancer, Pancreatic Adenocarcinoma, Pancreatic Carcinoma, Pancreatic Ductal Adenocarcinoma, Pancreatic Neoplasm, Pancreatic Neuroendocrine Carcinoma, Pending Annotation, Penile Carcinoma, Pheochromocytoma, Pilocytic Astrocytoma, Pituitary Gland Adenoma, Plasmablastic Lymphoma, Plasmacytoma, Plexiform Schwannoma, Precursor B-cell lymphoblastic leukemia, Primary Central Nervous System Lymphoma, Primary Myelofibrosis, Prostate Adenocarcinoma, Prostate Carcinoma, Prostate Neoplasm, Rectal Adenocarcinoma, Renal Cell Carcinoma, Retinoblastoma, Rhabdomyosarcoma, Rosette-Forming Glioneuronal Tumor, Salivary Gland Adenoid Cystic Carcinoma, Sarcoma, Schwannoma, Serous Tubal Intraepithelial Carcinoma, Sinonasal Squamous Cell Carcinoma, Skin Carcinoma, Skin Neoplasm, Soft Tissue Sarcoma, Squamous Cell Carcinoma, Synovial Sarcoma, T Acute Lymphoblastic Leukemia, T-Cell Lymphoma, Teratoma, Testicular Embryonal Carcinoma, Thyroid Gland Anaplastic Carcinoma, Thyroid Gland Carcinoma, Thyroid Gland Noninvasive Follicular Neoplasm with Papillary-Like Nuclear Features, Triple-Negative Breast Carcinoma, Urothelial Carcinoma, Uterine Adenosarcoma, Uveal Melanoma, Uveal Neoplasm, Vascular Neoplasm, Not-Applicable, Plexiform Neurofibroma",,,,,string_list,,,,,,
License,"The license(s) applied to this item, if applicable. Multiple values permitted, comma separated. Studies with data submitted to CDS are required to provide a license (maps to DUOplus6).","AAL, ADSL, AFL-1.1, AFL-1.2, AFL-2.0, AFL-2.1, AFL-3.0, AGPL-1.0, AGPL-3.0, AMDPLPA, AML, AMPAS, ANTLR-PD, APAFML, APL-1.0, APSL-1.0, APSL-1.1, APSL-1.2, APSL-2.0, Abstyles, Adobe-2006, Adobe-Glyph, Afmparse, Aladdin, Apache-1.0, Apache-1.1, Apache-2.0, Artistic-1.0, Artistic-1.0-Perl, Artistic-1.0-cl8, Artistic-2.0, BSD-2-Clause, BSD-2-Clause-FreeBSD, BSD-2-Clause-NetBSD, BSD-3-Clause, BSD-3-Clause-Attribution, BSD-3-Clause-Clear, BSD-3-Clause-LBNL, BSD-3-Clause-No-Nuclear-License, BSD-3-Clause-No-Nuclear-License-2014, BSD-3-Clause-No-Nuclear-Warranty, BSD-4-Clause, BSD-4-Clause-UC, BSD-Protection, BSD-Source-Code, BSD-style, BSL-1.0, Bahyph, Barr, Beerware, BitTorrent-1.0, BitTorrent-1.1, Borceux, CATOSL-1.1, CC-BY-1.0, CC-BY-2.0, CC-BY-2.5, CC-BY-3.0, CC-BY-4.0, CC-BY-NC-1.0, CC-BY-NC-2.0, CC-BY-NC-2.5, CC-BY-NC-3.0, CC-BY-NC-4.0, CC-BY-NC-ND-1.0, CC-BY-NC-ND-2.0, CC-BY-NC-ND-2.5, CC-BY-NC-ND-3.0, CC-BY-NC-ND-4.0, CC-BY-NC-SA-1.0, CC-BY-NC-SA-2.0, CC-BY-NC-SA-2.5, CC-BY-NC-SA-3.0, CC-BY-NC-SA-4.0, CC-BY-ND-1.0, CC-BY-ND-2.0, CC-BY-ND-2.5, CC-BY-ND-3.0, CC-BY-ND-4.0, CC-BY-SA-1.0, CC-BY-SA-2.0, CC-BY-SA-2.5, CC-BY-SA-3.0, CC-BY-SA-4.0, CC0-1.0, CDDL-1.0, CDDL-1.1, CECILL-1.0, CECILL-1.1, CECILL-2.0, CECILL-2.1, CECILL-B, CECILL-C, CNRI-Jython, CNRI-Python, CNRI-Python-GPL-Compatible, CPAL-1.0, CPL-1.0, CPOL-1.02, CUA-OPL-1.0, Caldera, ClArtistic, Condor-1.1, Crossword, CrystalStacker, Cube, D-FSL-1.0, DOC, DSDP, Dotseqn, ECL-1.0, ECL-2.0, EFL-1.0, EFL-2.0, EPL-1.0, EUDatagrid, EUPL-1.0, EUPL-1.1, Entessa, ErlPL-1.1, Eurosym, FSFAP, FSFUL, FSFULLR, FTL, Fair, Frameworx-1.0, FreeImage, Freeware, GFDL-1.1, GFDL-1.2, GFDL-1.3, GL2PS, GPL-1.0, GPL-2.0, GPL-3.0, Giftware, Glide, Glulxe, HPND, HaskellReport, IBM-pibs, ICU, IJG, IPA, IPL-1.0, ISC, ImageMagick, Imlib2, Info-ZIP, Intel, Intel-ACPI, Interbase-1.0, JSON, JasPer-2.0, LAL-1.2, LAL-1.3, LGPL-2.0, LGPL-2.1, LGPL-3.0, LGPLLR, LPL-1.0, LPL-1.02, LPPL-1.0, LPPL-1.1, LPPL-1.2, LPPL-1.3a, LPPL-1.3c, Latex2e, Leptonica, LiLiQ-P-1.1, LiLiQ-R-1.1, LiLiQ-Rplus-1.1, Libpng, MIT, MIT-CMU, MIT-advertising, MIT-enna, MIT-feh, MITNFA, MPL-1.0, MPL-1.1, MPL-2.0, MPL-2.0-no-copyleft-exception, MS-PL, MS-RL, MTLL, MakeIndex, MirOS, Motosoto, Multics, Mup, NASA-1.3, NBPL-1.0, NCSA, NGPL, NLOD-1.0, NLPL, NOSL, NPL-1.0, NPL-1.1, NPOSL-3.0, NRL, NTP, Naumen, NetCDF, Newsletr, Nokia, Not licensed, Noweb, Nunit, OCCT-PL, OCLC-2.0, ODbL-1.0, OFL-1.0, OFL-1.1, OGTSL, OLDAP-1.1, OLDAP-1.2, OLDAP-1.3, OLDAP-1.4, OLDAP-2.0, OLDAP-2.0.1, OLDAP-2.1, OLDAP-2.2, OLDAP-2.2.1, OLDAP-2.2.2, OLDAP-2.3, OLDAP-2.4, OLDAP-2.5, OLDAP-2.6, OLDAP-2.7, OLDAP-2.8, OML, OPL-1.0, OSET-PL-2.1, OSL-1.0, OSL-1.1, OSL-2.0, OSL-2.1, OSL-3.0, OpenSSL, Other, PDDL-1.0, PHP-3.0, PHP-3.01, Plexus, PostgreSQL, Proprietary, Python-2.0, QPL-1.0, Qhull, RHeCos-1.1, RPL-1.1, RPL-1.5, RPSL-1.0, RSA-MD, RSCPL, Rdisc, Ruby, SAX-PD, SCEA, SGI-B-1.0, SGI-B-1.1, SGI-B-2.0, SISSL, SISSL-1.2, SMLNJ, SMPPL, SNIA, SPL-1.0, SWL, Saxpath, Sendmail, SimPL-2.0, Sleepycat, Spencer-86, Spencer-94, Spencer-99, SugarCRM-1.1.3, TCL, TMate, TORQUE-1.1, TOSL, UPL-1.0, Unicode-TOU, Unlicense, VOSTROM, VSL-1.0, Vim, W3C, W3C-19980720, WTFPL, Watcom-1.0, Wsuipa, X11, XFree86-1.1, XSkat, Xerox, Xnet, YPL-1.0, YPL-1.1, ZPL-1.1, ZPL-2.0, ZPL-2.1, Zed, Zend-2.0, Zimbra-1.3, Zimbra-1.4, Zlib, bzip2-1.0.5, bzip2-1.0.6, curl, diffmark, dvipdfm, eGenix, gSOAP-1.3b, gnuplot, iMatix, libtiff, mpich2, psfrag, psutils, xinetd, xpp, zlib-acknowledgement",,,CDE:14902606,,string_list,,,,,,
Investigator,"Investigator(s) associated with this record. Provide either the investigator's free-text name or a PersonView_id reference (see PersonView Key) -- both forms are acceptable. Multiple values permitted, comma separated.",,,True,,,string_list,,,,,,
DataDSP,Dataset sharing plan information. Used to indicate planned usage of MC2 Center supported Synapse projects.,,"DataDSP_id, GrantView Key, Study Key, DatasetView Key, DSP Dataset Alias, DSP Dataset Name, DSP Dataset Url, DSP Dataset Assay, DSP Dataset Level, DSP Dataset Species, DSP Dataset Tumor Type, DSP Dataset Tissue, DSP Dataset File Formats, DSP Number of Files, DSP Number of Samples, DSP Number of Participants, DSP Storage Size, DSP Dataset Description, DSP Planned Upload Date, DSP Planned Release Date, DSP Data Use Codes, DSP IRB Form, DSP Dataset Destination, DSP Dataset Metadata",,,,,,,,,True,
DSP Dataset Name,Name of the dataset,,,True,,,string,,,,,,
DSP Dataset Alias,"Alias of the dataset. For Synapse storage, the Synapse id associated with the storage folder should be used. Must be unique.",,,,,,string,,,,,,
DSP Dataset File Formats,"The list of extensions (e.g., csv, fastq, geojson, qpath, etc.) associated with files that should be included in the dataset. Multiple values permitted, comma separated.",,,,,,string_list,,,,,,
DataDSP_id,"Unique row identifier, used as a primary key for record updates. This should be in CAxxxxxx-DSPxxx format unless otherwise directed.",,,True,primary_key,,string,,"^CA\d{6}-DSP-\d{2,9}$",,,,
DSP Dataset Level,The level of processing associated with the dataset.,"Level 1, Level 2, Level 3, Level 4, Auxiliary, Not Applicable, Metadata",,,,,string,,,,,,
DSP Number of Files,The number of files that will be uploaded as part of this dataset.,,,,,,number,,,,,,
DSP Number of Samples,The number of biospecimens associated with the files included in the dataset,,,,,,number,,,,,,
DSP Number of Participants,The number of individuals or model organisms from which samples were collected to generate the dataset.,,,,,,number,,,,,,
DSP Storage Size,The expected total storage space required for the dataset in gigabytes (GB),,,,,,number,,,,,,
DSP Planned Upload Date,"A non-binding, estimated date by which the files are expected to be uploaded to a repository.",,,True,,,string,date,,,,,
DSP Planned Release Date,The projected date that marks the end of any requested or required sharing embargo for the dataset.,,,,,,string,date,,,,,
DSP Dataset Grant Number,"Grant number(s) associated with the dataset's development. Multiple values permitted, comma separated.","Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808, CA279408, CA279560, CA280984, CA280849, CA280829, CA284090, CA284086, CA274504, CA283114, CA274507, CA274506, CA274511, CA282451, CA284085, CA283749, CA289564, CA293470, CA279722, CA290115, CA279948, CA281216, CA292382, CA290442, CA293853",,True,,,string_list,,,,,,
DSP Dataset Url,"The url where the dataset is or will be stored. For Synapse storage, the Synapse url or doi associated with the dataset storage folder should be used.",,,,,,string,uri,,,,,
DSP IRB Form,The Synapse Id for the executed IRB protocol or exemption document that was uploaded to Synapse. Required if human-derived data was generated for this study and will be uploaded as part of this dataset,,,,,,string,,syn\d+,,,,
DSP Dataset Description,A text description of the files contained in this dataset.,,,,,,string,,,,,,
DSP Dataset Destination,An identifier representing the repository in which this dataset is intended to be held for long term preservation.,,,,,,string,,,,,,
DSP Dataset Metadata,The link(s) corresponding to metadata templates that should be used to record information about this data. This field will be populated by the MC2 Center after plan submission.,,,,,,string_list,,,,,,
DSP Dataset Species,"The species the data was collected on. Multiple values permitted, comma separated.","African Bush Elephant, Armadillo, Asian Elephant, Boar, Cat, Chicken, Candida albicans, Cow, Dog, Escherichia coli, Guinea Pig, Horse, Human, Human Patient, Human Cell Line, Macaca nemestrina, Mouse, Multispecies, Not Applicable, Opossum, Rabbit, Rat, Rhesus monkey, Schizosaccharomyces pombe, Sheep, Trichoplax adhaerens, Unknown, Unspecified, Worm, Yeast, Fruit Fly, Zebrafish",,True,,,string_list,,,,,,
DSP Dataset Assay,"The assay the dataset is representative of. Multiple values permitted, comma separated.","10-cell RNA Sequencing, 16S Ribosomal Gene Sequencing Assay, 3' RNA-seq, 3C, 3C-qPCR, 3D ATAC-PALM, 3D Bioprinting, 3D Cell Culture, 4C, 5C, ATAC-Seq, ATP Bioluminescence Assay, Affinity Purification Mass Spectrometry, Allograft, Amplicon Sequencing, Angiogenesis Assay, Apoptosis Assay, Atomic Absorption Spectrophotometry, Atomic Absorption Spectroscopy, Atomic Force Microscopy, Autoradiography, Barcode-Seq, Bicinchoninic Acid Assay, Binding Assay, Bio-Layer Interferometry, Bioluminescence Imaging, Bisulfite Sequencing, Brightfield Microscopy, Brillouin Microscopy, CASFISH, CITE-seq, CLIP-qPCR, CRISPR, CUT&RUN, CUT&Tag-Sequencing, Cell Adhesion Assay, Cell Proliferation Assay, Cell Viability Assay, Cell-spreading Assay, CellTiter-Glo Luminescent Cell Viability Assay, Cerenkov Luminescence Imaging, ChIA-PET, ChIP-PCR, ChIP-Seq, ChIP-qPCR assay, Chemiluminescent Assay, Chemotaxis Assay, Circular Dichroism Spectroscopy, Co-Immunoprecipitation, Co-culture Assay, Collision-Induced Dissociation, Colorimetric Cell Viability Assay, Computational Modeling, Computational Tool, Computed Tomography, Confocal Microscopy, Confocal Reflectance Quantitative Phase Microscopy, Cross-Linking Immunoprecipitation High-throughput Sequencing, Cross-Linking Mass Spectrometry, Cyclic Immunofluorescence, Cytochemical Stain, Cytokine Expression Profile, Cytometric Bead Array Assay, Cytotoxicity Assay, DBiT-Seq, DNA Gene-Expression Microarray, DNA Methylation Array, DNA Sequencing, DNase-Seq, DRIP-seq, Dark Field Microscopy, Deep Mutational Scanning, Desorption Electrospray Ionization, Dideoxy Chain Termination DNA Sequencing, Differential Interference Contrast Microscopy, Differential Scanning Fluorimetry, Diffusion Weighted Imaging, Direct Long-Read RNA Sequencing, Drop-Seq, Droplet Digital PCR, Dual-Luciferase Reporter Assay, Dye Endocytosis Assay, Dynamic Contrast-Enhanced Magnetic Resonance Imaging, Dynamic Force Spectroscopy, Dynamic Light Scattering, Dynamic Susceptibility Contrast-Enhanced Magnetic Resonance Imaging, ELISA, Efferocytosis Assay, Electron Diffraction, Electron Microscopy, Electron Paramagnetic Resonance Spectroscopy, Electrophoretic Mobility Shift Assay, Electrospray Ionization Time-of-Flight Mass Spectrometry, Endotoxin Assay, Energy-Dispersive X-Ray Spectroscopy, Enzyme Activity Assay, Enzyme-Linked Immunospot Assay, Epidemiological Method, FAIRE-Seq, FISH, Flow Cytometry, Fluorescence Activated Cell Sorting, Fluorescence Correlation Spectroscopy, Fluorescence Imaging, Fluorescence Lifetime Imaging Microscopy, Fluorescence Microscopy, Fluorescence Recovery After Photo-Bleaching, Fluorescent Antibody Procedure, Fluorescent Cell Barcoding, Fluorescent In Situ Sequencing, Focused Ion Beam Scanning Electron Microscopy, Forster Resonance Energy Transfer, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Fourier-Transform Infrared Spectroscopy, Gas Chromatography Mass Spectrometry, Gelatin Zymography, Genotyping, Global Chromatin Profiling, Global Run-On Sequencing, Graphite Furnace Atomic Absorption Spectrometry, HL-Chip, HPLC-MSMS, Hematoxylin and Eosin Staining Method, Hi-C, HiChIP, High Throughput Screening, High-Content Screen, Hydrogels, Hydrophilic Interaction Chromatography, Image Cytometry, Imaging, Immobilized Metal Affinity Chromatography, ImmunoFISH, Immunoassay, Immunocytochemistry, Immunohistochemistry Staining Method, Immunoprecipitation, In Situ Hybridization, In Vitro Cell Killing Assay, In Vitro Model, In Vitro Selection, In Vitro Translation, In Vivo Bioluminescence, In-Cell Western Assay, Inductively-Coupled Plasma Mass Spectrometry, Interference Reflection Microscopy, Intravital Microscopy, Invasion Assay, Karyotyping, Knife-Edge Scanning Microscopy, L1000 mRNA Profiling Assay, Lattice Light Sheet Microscopy, Liquid Chromatography Mass Spectrometry, Liquid Chromatography/Tandem Mass Spectrometry, Low-Vacuum Scanning Electron Microscopy, Luciferase Reporter Assay, Luminescent Cell Viability Assay, MALDI-TOF Mass Spectrometry, MEMA Cell Growth Assay, MNase-Seq, MULTI-Seq, Macrophage Polarization Assay, Magnetic Resonance Imaging, Magnetic Tweezers, Magnetic Twisting Cytometry, Magnetically Activated Cell Sorting, Mammosphere Formation Assay, Mass Cytometry, Mass Spectrometry, Mathematical Modeling, MeDIP, MeRIP-Seq, Methyl Binding Domain Sequencing, Methylation-Specific PCR, Micro-computed Tomography, MicroRNA Expression Array, MicroRNA Sequencing, Microcontact Printing, Microfluidics, Micropipette Adhesion Assay, Micropipette Aspiration, Microscopy, Migration Assay, Mint-ChIP, Modeling, Molecular Simulations, Monolayer Stress Microscopy, Multi-Angle Light Scattering, Multi-Isotope Mass Spectrometry, Multiparametric Magnetic Resonance Imaging, Multiphoton Microscopy, Multiplexed Error-Robust Fluorescence In Situ Hybridization, Multiplexed Immunofluorescence, Multiplexed Immunohistochemistry, Multiplexed Ion Beam Imaging, Murine Model, Nano-hmC-Seal, NanoString Digital Spatial Profiling, Nanopatterning, Nanopore Sequencing, Nanowire, Nested PCR, Next Generation Sequencing, Nm-seq, Not Applicable, Nuclear Magnetic Resonance, Optical Coherence Tomography, Optical Emission Spectroscopy, Optical Mapping, Optical Stretcher, Optical Tweezers, Optogenetic Assay, Organoid, PCR, PET-CT, Paraquat Survival Assay, Partial Wave Spectroscopy, Patient Derived Xenograft, Pending Annotation, Permeability Assay, Phagocytosis Assay, Photoacoustic Imaging, Photolithography, Plasmid Construction, PlateSeq, Point Accumulation for Imaging in Nanoscale Topography, Positron Emission Tomography, Precision Run-On Sequencing, Proteomics Assay, Proximity Ligation Assay, Pull-Down Assay, QFISH, Quantitative Multiplex Immunofluorescence, Quantitative Point Accumulation for Imaging in Nanoscale Topography, Questionnaire, RAS Protein Family Activation Assay, RIP, RIP-Seq, RNA Sequencing, RNAi Screen, RT-PCR, RT-qPCR, Raman Spectroscopy, Reduced Representation Bisulfite Sequencing, Reverse Phase Protein Array, Reverse-Phase High-Performance liquid Chromatography, Rheometry, Ribo-Seq, Ribosomal P Protein Antibody Measurement, Scanning Angle Interference Microscopy, Scanning Electron Microscopy, Second-Harmonic Imaging Microscopy, Shotgun Mass Spectrometry, Single Cell ATAC-Seq, Single Cell Cytokine Detection Chip Assay, Single Cell DNA Sequencing, Single Cell Gel Electrophoresis, Single Cell RNA-Sequencing, Single Molecule Forster Resonance Energy Transfer, Single Nucleotide Polymorphism Array, Single Nucleus RNA-Sequencing, Single-Cell BCR Sequencing, Single-Cell Barcode Chip, Single-Cell TCR Sequencing, Single-Molecule Tracking, Sirius Red Staining, Size Exclusion Chromatography, Small-Angle X-ray Scattering, Soft Agar Assay, Southern Blotting, Spectroscopy, Statistical Modeling, Stimulated Emission Depletion Microscopy, Stimulated Raman Scattering, Stochastic Optical Reconstruction Microscopy, Super-Resolution Microscopy, Surface Plasmon Resonance, Surveyor Nuclease Assay, Synaptophysin Staining Method, Synthetic Genetic Array, TAB-Seq, TCR Sequencing, TIRF Microscopy, TRAP Staining, TUNEL assay, Tandem Mass Spectrometry, Tandem Mass Tagging, Target Engagement Assay, Targeted Genome Sequencing, Targeted Transcriptome Sequencing, Thermal Shift Assay, Thin-Layer Chromatography, Tiling Array, Time Lapse Microscopy, Time-Correlated Single Photon Counting, Tissue Engineering, Tissue Microarray, Total Internal Reflection Fluorescence Microscopy, Traction Force Microscopy, Transmission Electron Microscopy, Transwell Assay, UPLC-MSMS, UV Photocrosslinking, Unspecified, Vibrational Spectroscopy, Virus Plaque Assay, Von Kossa Staining, Western Blotting, Whole Exome Sequencing, Whole Genome Bisulfite Sequencing, Whole Genome Sequencing, Widefield Fluorescence Microscopy, Wound-Healing Assay, X-Ray Crystallography, X-Ray Diffraction, X-Ray Micro-Computed Tomography, Xenograft, cDNA Array, eCLIP-Seq, mRNA Sequencing, qPCR, scCGI-seq, scNT-Seq, scSLAM-seq, seqFISH, shRNA, siRNA, smFISH, smRNA-seq, snRNA-seq, Isothermal Titration Calorimetry, Suspended Microchannel Resonator, 10x Multiome, Visium Spatial Gene Expression, Antitumor Drug Screening Assay, Bioelectrochemical Analysis, Chimeric Antigen Receptor T-Cell Therapy, Cell Cycle Assay, Clonality Analysis, Comparative Genomic Hybridization, Cryo-Electron Microscopy, Cryo-Electron Tomography, Data Integration, Field-Emission Scanning Electron Microscopy, Label-free Protein Quantification by LC/MS, Metabolite Profiling Assay, Reporter Gene Assay, Single-Molecule Localization Microscopy, Synthesis, Targeted Therapy Agent, Trichrome Staining Method, Ultrasound Imaging, Transcription profiling by NanoString, Alcian Blue Staining Method, Artificial Intelligence, Cell Culture, Clinical Study, Cell-free Circulating Tumor DNA Assay, Co-Immunoprecipitation Mass Spectrometry, Deep Learning, Gene Ontology Enrichment Analysis, Gene Set Enrichment Analysis, Gene Silencing , Human Induced Pluripotent Stem Cell-derived Cardiomyocytes Culture, Imaging Mass Cytometry, Immunofluorescent Staining Method, Immunotherapy, Viral Transduction, Metastatic Colonization Assay, Phylogenetic Analysis, Picrosirius Staining, Scratch Assay, Structural Variant Analysis, Survival Analysis, Targeted Error Correction Sequencing, Tuba-Seq, SDS-PAGE, Cell Fractionation, Multiscale Light Sheet Microscopy, Light Sheet Microscopy, CODEX, in vivo tumor growth, in silico synthesis, RNA array, shRNA-seq, spatial transcriptomics, in vivo PDX viability, histology, proximity extension assay, compound screen, metabolic screening",,True,,,string_list,,,,,,
DSP Dataset Tissue,"Tissue type(s) associated with the dataset. Multiple values permitted, comma separated.","Gonad, Abdominal Esophagus, Adipose Tissue, Adrenal Gland, Alveolus, Aorta, Artery, Ascending Colon, Bile Duct, Bladder, Blood, Blood Vessel, Bone, Bone Marrow, Brain, Breast, Caecum, Cancer-Associated Fibroblast, Cardia, Cartilage, Cervix Uteri, Choroid, Colon, Connective and Soft Tissue, Cornea, Duodenum, Ear, Embryo, Embryonic Heart, Endocervix, Endometrium, Endothelium, Epithelium, Esophagus, Eye, Fallopian Tube, Foreskin, Frontal Lobe, Gastroesophageal Junction, Gastrointestinal Tract, Genitourinary, Hair Follicle, Head and Neck, Heart, Heart Muscle, Hematopoietic System, Hippocampus, Intestine, Intra-Abdominal Lymph Nodes, Intrathoracic Lymph Nodes, Joint, Kidney, Larynx, Ligament, Liver, Lung, Lymph, Lymph Node, Lymph Nodes of Axilla or Arm, Lymph Nodes of Inguinal Region or Leg, Lymphatic System, Lymphoid Tissue, Main Bronchus, Mammary Gland, Meninges, Mesenchyme, Mucosa, Muscle, Nasal Cavity, Nervous System, Not Applicable, Olfactory Mucosa, Omentum, Oral Cavity, Oral Mucosa, Ovary, Pancreas, Pelvic Lymph Nodes, Pending Annotation, Periodontal Ligament, Peripheral Nerves, Peritoneum, Pharynx, Pituitary Gland, Placenta, Pleura, Prostate Gland, Rectum, Reproductive System, Respiratory System, Salivary Gland, Sclera, Sinonasal Tract, Skin, Small Intestine, Spinal Cord, Spleen, Stomach, Synovial Membrane, Tendon, Testis, Thymus, Thyroid Gland, Tongue, Tonsil, Trachea, Umbilical Cord, Unspecified, Uterus, Vagina, Vascular Endothelium, Vein, Vertebra, Peripheral Blood Mononuclear Cell",,,,,string_list,,,,,,
DSP Dataset Tumor Type,"The tumor type(s), if applicable, associated with the dataset. Multiple values permitted, comma separated.","Cutaneous Melanoma, Acinar Cell Carcinoma, Acute Lymphoblastic Leukemia, Acute Monocytic Leukemia, Acute Myeloid Leukemia, Acute Promyelocytic Leukemia, Adenocarcinoma, Angiosarcoma, Astrocytoma, Atypical Teratoid/Rhabdoid Tumor, B Acute Lymphoblastic Leukemia, B-Cell Non-Hodgkin Lymphoma, Barrett Esophagus, Basal Cell Neoplasm, Basal-Like Breast Carcinoma, Biliary Tract Carcinoma, Bladder Carcinoma, Bladder Neoplasm, Bone Neoplasm, Brain Neoplasm, Breast Adenocarcinoma, Breast Carcinoma, Breast Neoplasm, Carcinoma, Carcinoma In Situ, Castration-Resistant Prostate Carcinoma, Cellular Schwannoma, Central Nervous System Cavernous Hemangioma, Central Nervous System Neoplasm, Cerebellar Neoplasm, Cervical Carcinoma, Cervical Neoplasm, Cervical Small Cell Carcinoma, Cholangiocarcinoma, Chondroblastoma, Choriocarcinoma, Chronic Lymphocytic Leukemia, Chronic Myeloid Leukemia, Clear Cell Renal Cell Carcinoma, Colon Adenocarcinoma, Colon Carcinoma, Colorectal Adenocarcinoma, Colorectal Adenoma, Colorectal Carcinoma, Colorectal Neoplasm, Combined Hepatocellular Carcinoma and Cholangiocarcinoma, Craniopharyngioma, Cutaneous T Cell Lymphoma, Diffuse Large B-Cell Lymphoma, Ductal Breast Carcinoma In Situ, Dysembryoplastic Neuroepithelial Neoplasm, Endometrial Carcinoma, Endometrial Neoplasm, Ependymoma, Esophageal Adenocarcinoma, Esophageal Carcinoma, Esophageal Squamous Cell Carcinoma, Ewing Sarcoma, Extraventricular Neurocytoma, Fibroepithelial Polyp, Fibrolamellar Carcinoma, Fibrosarcoma, Follicular Lymphoma, Gallbladder Carcinoma, Gastric Adenocarcinoma, Gastric Carcinoma, Gastric Neoplasm, Gastroesophageal Adenocarcinoma, Gastroesophageal Junction Adenocarcinoma, Gastrointestinal Stromal Neoplasm, Giant Cell Tumor, Glioblastoma, Glioma, Head and Neck Carcinoma, Head and Neck Neoplasm, Head and Neck Squamous Cell Carcinoma, Hepatocellular Carcinoma, High Grade Ovarian Serous Adenocarcinoma, Histiocytic Sarcoma, Hodgkin Lymphoma, Intestinal Neoplasm, Intrahepatic Cholangiocarcinoma, Invasive Ductal Breast Carcinoma, Kaposi Sarcoma, Leiomyoma, Leukemia, Liver and Intrahepatic Bile Duct Carcinoma, Liver and Intrahepatic Bile Duct Neoplasm, Low Grade Glioma, Luminal A Breast Carcinoma, Lung Adenocarcinoma, Lung Carcinoma, Lung Neoplasm, Lung Non-Small Cell Carcinoma, Lung Small Cell Carcinoma, Lung Squamous Cell Carcinoma, Lymphoid Leukemia, Lymphoma, Malignant Brain Neoplasm, Malignant Digestive System Neoplasm, Malignant Genitourinary System Neoplasm, Malignant Glioma, Malignant Neoplasm, Malignant Ovarian Neoplasm, Malignant Pancreatic Neoplasm, Malignant Peripheral Nerve Sheath Tumor, Malignant Peritoneal Neoplasm, Malignant Skin Neoplasm, Mantle Cell Lymphoma, Marginal Zone Lymphoma, Medulloblastoma, Melanoma, Meningioma, Mesothelioma, Multiple Myeloma, Mycosis Fungoides, Myeloid Leukemia, Myeloid Neoplasm, Myeloproliferative Neoplasm, Myoepithelioma, Nasopharyngeal Carcinoma, Neuroblastoma, Neuroendocrine Neoplasm, Neuroepithelial Neoplasm, Neurofibroma, Non-Functioning Pituitary Gland Adenoma, Non-Hodgkin Lymphoma, Not Applicable, Oral Cavity Neoplasm, Oral Cavity Squamous Cell Carcinoma, Oropharyngeal Neoplasm, Osteosarcoma, Ovarian Adenosarcoma, Ovarian Carcinoma, Ovarian Neoplasm, Ovarian Serous Adenocarcinoma, Pan-cancer, Pancreatic Adenocarcinoma, Pancreatic Carcinoma, Pancreatic Ductal Adenocarcinoma, Pancreatic Neoplasm, Pancreatic Neuroendocrine Carcinoma, Pending Annotation, Penile Carcinoma, Pheochromocytoma, Pilocytic Astrocytoma, Pituitary Gland Adenoma, Plasmablastic Lymphoma, Plasmacytoma, Plexiform Schwannoma, Precursor B-cell lymphoblastic leukemia, Primary Central Nervous System Lymphoma, Primary Myelofibrosis, Prostate Adenocarcinoma, Prostate Carcinoma, Prostate Neoplasm, Rectal Adenocarcinoma, Renal Cell Carcinoma, Retinoblastoma, Rhabdomyosarcoma, Rosette-Forming Glioneuronal Tumor, Salivary Gland Adenoid Cystic Carcinoma, Sarcoma, Schwannoma, Serous Tubal Intraepithelial Carcinoma, Sinonasal Squamous Cell Carcinoma, Skin Carcinoma, Skin Neoplasm, Soft Tissue Sarcoma, Squamous Cell Carcinoma, Synovial Sarcoma, T Acute Lymphoblastic Leukemia, T-Cell Lymphoma, Teratoma, Testicular Embryonal Carcinoma, Thyroid Gland Anaplastic Carcinoma, Thyroid Gland Carcinoma, Thyroid Gland Noninvasive Follicular Neoplasm with Papillary-Like Nuclear Features, Triple-Negative Breast Carcinoma, Urothelial Carcinoma, Uterine Adenosarcoma, Uveal Melanoma, Uveal Neoplasm, Vascular Neoplasm, Not-Applicable, Plexiform Neurofibroma",,,,,string_list,,,,,,
DSP Data Use Codes,"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. Available DUO code definitions can be found here: https://mc2-center.github.io/data-models/valid_values/shared/#attribute-data-use-codes","Pending Annotation, DUO:0000042, DUO:0000027, DUO:0000016, DUO:0000029, DUO:0000043, DUO:0000015, DUO:0000004, DUO:0000045, DUO:0000017, DUO:0000011, DUO:0000046, DUO:0000018, DUO:0000044, DUO:0000021, DUO:0000006, DUO:0000019, DUO:0000026, DUO:0000020, DUO:0000012, DUO:0000025, DUO:0000024, DUO:0000028, DUO:0000022, DUO:0000007, DUOPlus1, DUOPlus2, DUOPlus3, DUOPlus4, DUOPlus5, DUOPlus6, DUOPlus7",,,,,string_list,,,,,,
Study,Studies associated with a grant,,"Study_id, GrantView Key, ProjectView Key, Study dbGaP Accession Id, Study Name, Study Description, Investigator, PersonView Key, Study Number of Participants, Study Number of Samples, Study Deidentification Method Type, Study Deidentification Method Description, Study Deidentification Method Software, Study Index Date, Study Project Identifier, Data Use Codes, Study Short Name, License",,,,,,,,,True,
Study Name,Name of the study,,,True,"CDE:11459810, CRDC_CDE:11459810",,string,,,,,,
Study Description,"Description of the study, including the types of experimental assays, model systems, types of analysis, description of cohort, associated vulnerable populations, special categories of data, rare diseases, etc. Maps to DUOplus2.",,,True,CDE:03444002,,string,,,,,,
Study_id,"Unique row identifier, used as a primary key for record updates.",,,True,primary_key,,string,,,,,,
Study Number of Participants,The number of participant instances associated with systematic investigation into a subject.,,,True,CDE:11555662,,number,,,,,,
Study Deidentification Method Type,General description of the de-identification method. Maps to DUOplus3.,"Manual, Semiautomatic, Automatic, Not Applicable",,True,CDE:14576319,,string,,,,,,
Study Deidentification Method Description,Description of the process of removing potentially identifying data or data elements to render data into a form that does not identify individuals and where identification is not likely to take place.,,,,,,string,,,,,,
Study Deidentification Method Software,Software that was used to de-identify the data (if used),,,,,,string,,,,,,
Study dbGaP Accession Id,A stable unique alphanumeric identifier assigned to a study and any objects by the database of Genotypes and Phenotypes (dbGaP). Required for controlled access data being submitted to CDS/CRDC.,,,,"CDE:11524544, CRDC_CDE:11524544",,string,,,,,,
Study Index Date,"The reference event associated with timepoints in this study. One of Diagnosis Date, Enrollment Date, Collection Date, or Birth Date.","Diagnosis Date , Enrollment Date, Collection Date, Birth Date",,,,,string,,,,,,
Study Project Identifier,The Synapse Project identifier (synID) with which this Study is related.,,,,,,string_list,,syn[0-9]+,,,,
Study Short Name,The acronym or abbreviated form of the title for a research data collection (e.g. GLIOMA01).,,,,CRDC_CDE:11459812,,string,,,,,,
Study Number of Samples,The number of specimens associated with systematic investigation into a subject.,,,True,CDE:11555663,,number,,,,,,
Theme,Themes associated with resources derived from consortia activities,,"Theme Name, Theme Display Name, Theme Description",,,,,,,,,True,
Theme Name,"Machine readable name of the research theme. (e.g. compuational_resource, drug_resistance_sensitivity).",,,True,,,string,,,,,,
Theme Display Name,"Human readable display name of the research theme. (e.g. Computational Resource, Drug Resistance/Sensitivity)",,,True,,,string,,,,,,
Theme Description,Description of the research theme.,,,True,,,string,,,,,,
Tool Accessibility,Whether there are non-monetary restrictions on accessing an online service.,"Open Access, Open Access (With Restrictions), Restricted Access",,,,,string,,,,,,biotoolsschema
Tool Cmd,"Relevant command, command-line fragment, or option for executing this function/running the tool in this mode.",,,,,,string,,,,,,biotoolsschema
Tool Compute Requirements,"Component dependency requirements for application. This includes runtime environments and shared libraries that are not included in the application distribution package, but required to run the application (examples: DirectX, Java or .NET runtime).",,,,,,string_list,,,,,,schema.org
Tool Cost,Monetary cost of acquiring the software.,"Commercial, Free of Charge, Free of Charge (With Restrictions)",,,,,string,,,,,,biotoolsschema
Tool Date Last Modified,"The date indicating when the tool's entry was most recently modified or updated, providing a timestamp of the latest changes made to the tool's information.",,,,,,string,date,,,,,schema.org
Tool Description,Textual description of the tool.,,,True,,,string,,,,,,biotoolsschema
Tool Documentation Note,Comment about the documentation.,,,,,,string,,,,,,biotoolsschema
Tool Documentation Type,"Type of documentation that is linked to. Multiple values permitted, comma separated.","API Documentation, Citation Instructions, Code of Conduct, Command-Line Options, Contributions Policy, FAQ, General, Governance, Installation Instructions, Other, Quick Start Guide, Release Notes, Terms of Use, Training Material, User Manual",,,,,string_list,,,,,,biotoolsschema
Tool Documentation Url,Link to documentation on the web for the tool.,,,,,,string,uri,,,,,biotoolsschema
Tool Download Note,Comment about the download.,,,,,,string,,,,,,biotoolsschema
Tool Download Type,"The type of data, information, or system that is obtained when the link is resolved.","API Specification, Binaries, Biological Data, Command-Line Specification, Container File, Downloads Page, Icon, Other, Screenshot, Software Package, Source Code, Test Data, Test Script, Tool Wrapper (CWL), Tool Wrapper (Galaxy), Tool Wrapper (Taverna), Tool wrapper (Other), VM Image",,,,,string,,,,,,biotoolsschema
Tool Download Url,Link to download (or repo providing a download) for the software.,,,,,,string,uri,,,,,biotoolsschema
Tool Download Version,Version information (typically a version number) of the software applicable to this download.,,,,,,string,,,,,,biotoolsschema
Tool Entity Name,Name of the entities that may be credited,,,,,,string_list,,,,,,
Tool Entity Role,"Role performed by entity that is credited, e.g. “Developer”","Developer, Maintainer, Provider, Documentor, Contributor, Support, Primary Contact",,True,,,string_list,,,,,,biotoolsschema
Tool Entity Type,"Types of entities that may be credited, e.g. ‘Person’.","Person, Project, Division, Institute, Research Consortium, Funding Agency",,True,,,string_list,,,,,,biotoolsschema
Tool Function Note,"Concise comment about this function, if not apparent from the software description and EDAM annotations.",,,,,,string,,,,,,biotoolsschema
Tool Homepage,"Homepage of the software, or some URL that best serves this purpose.",,,True,,,string,uri,,,,,biotoolsschema
Tool Input Data,"Type of primary input data. Multiple values permitted, comma separated.","Accession, Alignment, Biological Model ID, Biological Model Name, Cell Line Name, Cell Migration Track Image, Cell Type Identifier, Cell Type Name, Cell Type Ontology ID, Chromosome Name, Chromosome Report, Clustered Expression Profiles, Codon Number, Comparison Matrix, Compound Identifier, Compound Name, Concentration, Count Matrix, DNA Sequence, Data Index, Data Reference, Database Search Results, Drug Identifier, Drug Name, Drug Report, Electronic Health Record, Enzyme Kinetics Data, Experimental Measurement, Expression Data, GO-Term Enrichment Data, Gene Expression Matrix, Gene Expression Profile, Gene ID, Gene ID (NCBI), Gene Identifier, Gene Name, Gene Report, Gene Symbol, Gene Tree, Genetic Map, Genotype/Phenotype Report, Heat Map, Hidden Markov Model, Hierarchy, Histogram, Identifier, Image, Image Metadata, Kinetic Model, MRI Image, Map, Map Data, Mass Spectrometry Data, Mass Spectrum, Mathematical Model, Matrix, Molecular Property, Molecular Simulation Data, Molecule Identifier, Molecule Name, Morphology Parameter, Mutation ID, Not Applicable, Nucleic Acid Identifier, Nucleic Acid Report, Nucleic Acid Sequence, Ontology, Ontology Concept Data, Ontology Data, Ontology Identifier, Ontology Mapping, Ontology Name, Ontology Term, Organism Identifier, Organism Name, Over-Represesntation Data, P-Value, Pair Sequence Alignment, Pathway Or Network, Pathway Or Network Report, Pathway Overrepresentation Data, Peptide Identification, Peptide Property, Phenotype Name, Phylogenetic Data, Phylogenetic Tree, Plain Text, Plot, Position Weight Matrix, Position-Specific Scoring Matrix, Protein Contact Map, Protein Identifier, Protein Interaction Data, Protein Name, Protein Property, Protein Report, Protein Sequence, Protein Structure Report, Quality Control Report, RNA Sequence, Raw Image, Reaction Data, RefSeq Accession, Report, Resource Metadata, Sample Annotation, Sample ID, Score, Sequence, Sequence Alignment, Sequence Attribute, Sequence Cluster, Sequence Composition Plot, Sequence Composition Report, Sequence Coordinates, Sequence Features, Sequence Image, Sequence Motif, Sequence Position, Sequence Property, Sequence Range, Sequence Record, Sequence Report, Sequence Search Results, Sequence Set, Sequence Signature Data, Sequence Similarity, Sequence Similarity Score, Sequence Variations, Simulation, Small Molecule Report, Spectrum, Statistical Estimate Score, Strain Identifier, Strain Name, Structure, Structure Report, Taxonomy, Text Data, Text Mining Report, Topology Data, Training Material, Trajectory Data, Transcription Factor Identifier, Transcription Factor Name, Vmax, dbSNP ID",,True,,,string_list,,,,,,biotoolsschema
Tool Input Format,"Allowed format(s) of the input data. Multiple values permitted, comma separated.","Alignment Format, Alignment Format (Pair Only), Alignment Format (Text), Annotated Text Format, Antimony, BAM, BCF, BED, BLAST Results, BNGL, Binary Format, Biological Model Format, Biological Pathway Or Network Format, CSV, Chemical Data Format, Cytoband Format, Cytoscape Input File Format, DCC, DCD, DSV, Database Hits (Sequence) Format , Docker Image Format, Document Format, Dot-Bracket Format, FASTA, FASTQ, FASTQ-Illumina, FCS, GCT/Res Format, GFF, GFF3, GIF, GML, GTF, Gene Annotation Format, Gene Cluster Format, Gene Expression Report Format, Genotype And Phenotype Annotation Format, Graph Format, H5AD, HDF, HDF5, HTML, Hidden Markov Model Format, Image Format, Individual Genetic Data Format, JPG, JSON, LSM, MAF, MAGE-ML, MAGE-TAB, MAT, MATLAB Script, MSF, Map Format, Mass Spectrometry Data Format, Matrix Format, NIFTI Format, Nexus Format, Not Applicable, NumPy Format, OME-TIFF, Ontology Format, PDF, PNG, PS, PSF, Phylip Format, Phylip Format Variant, Phylogenetic Tree Format, Phylogenetic Tree Format (Text), Protein Interaction Format, Python Script, R File Format, R Script, RDS, RNA Annotation Format, RNA Secondary Structure Format, RPKM, Raw Sequence Format, SAM, SBML, SQLite Format, SVG, Scores Format, Sequence Annotation Track Format, Sequence Cluster Format, Sequence Cluster Format (Protein), Sequence Feature Annotation Format, Sequence Feature Table Format, Sequence Feature Table Format (Text), Sequence Profile Format, Sequence Range Format, Sequence Record Format, Sequence Trace Format, Sequence Variation Annotation Format, TIFF, TSV, TXT, Tertiary Structure Format, Textual Format, Topology Format, Trajectory Format, VCF, Workflow Format, XML, YAML, bedgraph, bigWig, cel, imzML Metadata File, mzML, nii, pkl, sif, xls, xlsx, PDB, HED, MRC, Unspecified",,True,,,string_list,,,,,,biotoolsschema
Tool Language,"Name of programming language the software source code was written in. Multiple values permitted, comma separated.","AWK, ActionScript, Ada, AppleScript, Assembly Language, Bash, C, C#, C++, COBOL, CSS, CWL, ColdFusion, D, Delphi, Dockerfile, Dylan, Eiffel, Elm, Forth, Fortran, Go, Groovy, HTML, Haskell, Icarus, JSP, Java, JavaScript, Julia, LabVIEW, Lisp, Lua, MATLAB, MLXTRAN, Maple, Mathematica, NMTRAN, Netlogo, Nextflow, Ocaml, OpenEdge ABL, Other, PHP, Pascal, Perl, PostScript, PowerShell, Prolog, PyMOL, Python, R, REXX, Racket, Ruby, SAS, SQL, Scala, Scheme, Shell, TeX, Turing, VHDL, Verilog, Visual Basic, WDL, XAML",,,,,string_list,,,,,,biotoolsschema
Tool Link Note,Comment about the link.,,,,,,string,,,,,,biotoolsschema
Tool Link Type,"The type of data, information or system that is obtained when the link is resolved. Multiple values permitted, comma separated.","Discussion Forum, Galaxy Service, Helpdesk, Issue Tracker, Mailing list, Mirror, Other, Repository, Service, Social Media, Software Catalogue, Technical Monitoring",,,,,string_list,,,,,,biotoolsschema
Tool Link Url,A link of some relevance to the software (URL).,,,,,,string,uri,,,,,biotoolsschema
Tool Name,Canonical tool name provided by the tool developer or service provider.,,,True,,,string,,,,,,biotoolsschema
Tool Operating System,"The operating system supported by a downloadable software package. Multiple values permitted, comma separated.","Linux, Mac, Windows",,,,,string_list,,,,,,biotoolsschema
Tool Operation,"The basic operation(s) performed by this software function. Multiple values permitted, comma separated.","Aggregation, Allele Frequency Distribution Analysis, Analysis, Annotation, Box-Whisker Plot Plotting, Calculation, Cell Migration Analysis, Cell Modelling, Cell Number Quantification, Cell Type Enrichment Analysis, Classification, Clustering, Clustering Profile Plotting, Comparison, Conversion, Copy Number Variation Detection, Correlation, DNA Barcoding, Data Handling, Data Retrieval, Database Search, De Novo Sequencing, Demultiplexing, Differential Gene Expression Profiling, Differential Protein Expression Profiling, Dimensionality Reduction, Editing, Enrichment Analysis, Expression Analysis, Expression Correlation Analysis, Expression Data Visualisation, Expression Profile Clustering, Expression Profile Comparison, Functional Clustering, Gene Expression Profiling, Gene Methylation Analysis, Gene Regulatory Network Analysis, Gene Regulatory Network Prediction, Gene-Set Enrichment Analysis, Generation, Genetic Mapping, Genetic Variation Analysis, Genome Analysis, Genome Annotation, Genome Visualisation, Genotyping, Heat Map Generation, Image Analysis, Imputation, Incident Curve Plotting, Information Retrieval, Linkage Analysis, Mapping, Metabolic Pathway Prediction, Methylation Analysis, Microscope Image Visualisation, Modelling and Simulation, Molecular Dynamics, Network Analysis, Network Visualisation, Nucleic Acid Feature Detection, Nucleic Acid Sequence Analysis, Nucleosome Position Prediction, Ontology Visualisation, Pathway Analysis, Pathway Modelling, Peak Calling, Phylogenetic Analysis, Prediction and Recognition, Principal Component Analysis, Protein Comparison, Protein Function Comparison, Protein Function Prediction, Protein Identification, Protein Interaction Network Analysis, Protein Quantification, Protein-Protein Interaction Analysis, Quantification, Query and Retrieval, RNA Secondary Structure Prediction, RNA-Seq Analysis, RNA-Seq Quantification, Regression Analysis, SNP Annotation, SNP Detection, Scatter Plot Plotting, Sequence Alignment Analysis, Sequence Alignment Comparison, Sequence Analysis, Sequence Annotation, Sequence Classification, Sequence Cluster Visualisation, Sequence Clustering, Sequence Comparison, Sequence Composition Calculation, Sequence Editing, Sequence File Editing, Sequence Read Processing, Sequencing Quality Control, Simulated Gene Expression Data Generation, Sorting, Spectral Analysis, Standardisation and Normalisation, Statistical Calculation, Statistical Inference, Statistical Modelling, Structural Variation Detection, Structure Analysis, Text Mining, Tissue Modelling, Validation, Variant Calling, Variant Classification, Variant Effect Prediction, Visualisation, scRNA-Seq Analysis, Agent-Based Cell Modelling, Not Applicable",,True,,,string_list,,,,,,biotoolsschema
Tool Output Data,"Type of primary output data. Multiple values permitted, comma separated.","Accession, Alignment, Biological Model ID, Biological Model Name, Cell Line Name, Cell Migration Track Image, Cell Type Identifier, Cell Type Name, Cell Type Ontology ID, Chromosome Name, Chromosome Report, Clustered Expression Profiles, Codon Number, Comparison Matrix, Compound Identifier, Compound Name, Concentration, Count Matrix, DNA Sequence, Data Index, Data Reference, Database Search Results, Drug Identifier, Drug Name, Drug Report, Electronic Health Record, Enzyme Kinetics Data, Experimental Measurement, Expression Data, GO-Term Enrichment Data, Gene Expression Matrix, Gene Expression Profile, Gene ID, Gene ID (NCBI), Gene Identifier, Gene Name, Gene Report, Gene Symbol, Gene Tree, Genetic Map, Genotype/Phenotype Report, Heat Map, Hidden Markov Model, Hierarchy, Histogram, Identifier, Image, Image Metadata, Kinetic Model, MRI Image, Map, Map Data, Mass Spectrometry Data, Mass Spectrum, Mathematical Model, Matrix, Molecular Property, Molecular Simulation Data, Molecule Identifier, Molecule Name, Morphology Parameter, Mutation ID, Not Applicable, Nucleic Acid Identifier, Nucleic Acid Report, Nucleic Acid Sequence, Ontology, Ontology Concept Data, Ontology Data, Ontology Identifier, Ontology Mapping, Ontology Name, Ontology Term, Organism Identifier, Organism Name, Over-Represesntation Data, P-Value, Pair Sequence Alignment, Pathway Or Network, Pathway Or Network Report, Pathway Overrepresentation Data, Peptide Identification, Peptide Property, Phenotype Name, Phylogenetic Data, Phylogenetic Tree, Plain Text, Plot, Position Weight Matrix, Position-Specific Scoring Matrix, Protein Contact Map, Protein Identifier, Protein Interaction Data, Protein Name, Protein Property, Protein Report, Protein Sequence, Protein Structure Report, Quality Control Report, RNA Sequence, Raw Image, Reaction Data, RefSeq Accession, Report, Resource Metadata, Sample Annotation, Sample ID, Score, Sequence, Sequence Alignment, Sequence Attribute, Sequence Cluster, Sequence Composition Plot, Sequence Composition Report, Sequence Coordinates, Sequence Features, Sequence Image, Sequence Motif, Sequence Position, Sequence Property, Sequence Range, Sequence Record, Sequence Report, Sequence Search Results, Sequence Set, Sequence Signature Data, Sequence Similarity, Sequence Similarity Score, Sequence Variations, Simulation, Small Molecule Report, Spectrum, Statistical Estimate Score, Strain Identifier, Strain Name, Structure, Structure Report, Taxonomy, Text Data, Text Mining Report, Topology Data, Training Material, Trajectory Data, Transcription Factor Identifier, Transcription Factor Name, Vmax, dbSNP ID",,True,,,string_list,,,,,,biotoolsschema
Tool Output Format,"Allowed format(s) of the output data. Multiple values permitted, comma separated.","Alignment Format, Alignment Format (Pair Only), Alignment Format (Text), Annotated Text Format, Antimony, BAM, BCF, BED, BLAST Results, BNGL, Binary Format, Biological Model Format, Biological Pathway Or Network Format, CSV, Chemical Data Format, Cytoband Format, Cytoscape Input File Format, DCC, DCD, DSV, Database Hits (Sequence) Format , Docker Image Format, Document Format, Dot-Bracket Format, FASTA, FASTQ, FASTQ-Illumina, FCS, GCT/Res Format, GFF, GFF3, GIF, GML, GTF, Gene Annotation Format, Gene Cluster Format, Gene Expression Report Format, Genotype And Phenotype Annotation Format, Graph Format, H5AD, HDF, HDF5, HTML, Hidden Markov Model Format, Image Format, Individual Genetic Data Format, JPG, JSON, LSM, MAF, MAGE-ML, MAGE-TAB, MAT, MATLAB Script, MSF, Map Format, Mass Spectrometry Data Format, Matrix Format, NIFTI Format, Nexus Format, Not Applicable, NumPy Format, OME-TIFF, Ontology Format, PDF, PNG, PS, PSF, Phylip Format, Phylip Format Variant, Phylogenetic Tree Format, Phylogenetic Tree Format (Text), Protein Interaction Format, Python Script, R File Format, R Script, RDS, RNA Annotation Format, RNA Secondary Structure Format, RPKM, Raw Sequence Format, SAM, SBML, SQLite Format, SVG, Scores Format, Sequence Annotation Track Format, Sequence Cluster Format, Sequence Cluster Format (Protein), Sequence Feature Annotation Format, Sequence Feature Table Format, Sequence Feature Table Format (Text), Sequence Profile Format, Sequence Range Format, Sequence Record Format, Sequence Trace Format, Sequence Variation Annotation Format, TIFF, TSV, TXT, Tertiary Structure Format, Textual Format, Topology Format, Trajectory Format, VCF, Workflow Format, XML, YAML, bedgraph, bigWig, cel, imzML Metadata File, mzML, nii, pkl, sif, xls, xlsx, PDB, HED, MRC, Unspecified",,True,,,string_list,,,,,,biotoolsschema
Tool Package Dependencies,"Specifies the software libraries, frameworks, or other components that a tool or package relies on for its proper functioning. This attribute helps users understand the prerequisites needed for installation and usage of the tool within a given computational environment",,,,,,string_list,,,,,,CWL
Tool Package Dependencies Present,Indicates whether the required package dependencies for tool are present.,"True, False",,True,,,boolean,,,,,,CWL
Tool Release Date,The release date of a product or product model. This can be used to distinguish the exact variant of a product.,,,True,,,string,date,,,,,schema.org
Tool Topic,"General scientific domain the software serves, or other general category. Multiple values permitted, comma separated.","Allergy Clinical Immunology and Immunotherapeutics, Biochemistry, Bioimaging, Bioinformatics, Biological Databases, Biology, Biomedical Science, Biomolecular Simulation, Biophysics, Biotechnology, Biotherapeutics, Cell Biology, Cell Culture Collection, Chemistry, Chip-Seq, Chromosome Conformation Capture, Comparative Genomics, Compound Libraries and Screening, Computational Biology, Computer Science, Cytogenetics, Cytometry, DNA, DNA Mutation, DNA Packaging, DNA Polymorphism, Data Architecture Analysis and Design, Data Identity and Mapping, Data Mining, Data Submission Annotation and Curation, Data Visualisation, Developmental Biology, Drug Development, Drug Discovery, Drug Metabolism, Electron Microscopy, Epigenetics, Evolutionary Biology, Exome Sequencing, Experimental Design and Studies, Function Analysis, Functional Genomics, Functional Regulatory and Non-Coding RNA, GWAS Study, Gene Expression, Gene Regulation, Gene Structure, Gene Transcripts, Gene and Protein Families, Genetic Engineering, Genetic Variation, Genetics, Genomics, Genotype and Phenotype, Imaging, Immunoinformatics, Immunology, Immunomics, Immunoprecipitation Experiment, Immunoproteins and Antigens, Infectious Disease, Informatics, Laboratory Techniques, Light Microscopy, Lipids, Machine Learning, Mapping, Mathematics, Medical Imaging, Medical Informatics, Medicine, Medicines Research and Development, Membrane and Lipoproteins, Metagenomics, Molecular Biology, Molecular Genetics, Molecular Interactions Pathways and Networks, Nucleic Acid Structure Analysis, Nucleic Acids, Omics, Oncology, Ontology and Terminology, Pathology, Pharmacogenomics, Pharmacology, Pharmacovigilance, Phylogenetics, Phylogenomics, Phylogeny, Preclinical and Clinical Studies, Probes and Primers, Protein Expression, Protein Modifications, Protein Properties, Proteins, Proteomics, Proteomics Experiment, RNA, RNA-Seq, Safety Sciences, Sample Collections, Sequence Analysis, Sequencing, Simulation Experiment, Software Engineering, Statistics and Probability, Structural Analysis, Structural Biology, Systems Biology, Transcription Factors and Regulatory Sites, Transcriptomics, Virology, Whole Genome Sequencing, Workflows, scRNA-Seq",,,,,string_list,,,,,,biotoolsschema
Tool Type,"A type of application software: a discrete software entity can have more than one type. Multiple values permitted, comma separated.","Bioinformatics Portal, Command-Line Tool, Database Portal, Desktop Application, Library, Notebook, Ontology, Other, Plug-In, SPARQL Endpoint, Script, Serialized Model, Suite, Web API, Web Application, Web Service, Workbench, Workflow",,,,,string_list,,,,,,biotoolsschema
Tool Version,Version information (typically a version number) of the software applicable to this entry.,,,,,,string,,,,,,biotoolsschema
Tool View,The denormalized manifest for tool submission.,,"ToolView_id, GrantView Key, Study Key, DatasetView Key, PublicationView Key, Tool Name, Tool Description, Tool Homepage, Tool Version, Tool Operation, Tool Input Data, Tool Output Data, Tool Input Format, Tool Output Format, Tool Function Note, Tool Cmd, Tool Type, Tool Topic, Tool Operating System, Tool Language, License, Tool Cost, Tool Accessibility, Tool Download Url, Tool Download Type, Tool Download Note, Tool Download Version, Tool Documentation Url, Tool Documentation Type, Tool Documentation Note, Tool Link Url, Tool Link Type, Tool Link Note, Tool Doi, Tool Date Last Modified, Tool Release Date, Tool Package Dependencies, Tool Package Dependencies Present, Tool Compute Requirements, Tool Entity Name, Tool Entity Type, Tool Entity Role",,,,,,,,,True,
ToolView_id,"Unique row identifier, used as a primary key for record updates.",,,True,primary_key,,string,,,,,,
Tool Doi,The Digital Object Identifier (DOI) associated with the computational tool.,,,True,,,string,uri,,,,,
Visium Auxiliary Files,"Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc)  from Spatial Transcriptomics.",,"VisiumAuxiliaryFiles_id, Filename, VisiumRNALevel1 Key, VisiumRNALevel2 Key, VisiumRNALevel3 Key, VisiumRNALevel4 Key, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, Visium Run ID, Visium File Type, Visium Slide ID, Visium Capture Area, Workflow Version, Workflow Link",,,,,,,,,True,
VisiumAuxiliaryFiles_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
Visium RNA Level 1,Files contain raw RNA-seq data associated with spot/slide data.,,"VisiumRNALevel1_id, Filename, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, Visium Run ID, NGS Read Indicator, Visium Spatial Read1, Visium Spatial Read2, Visium Spatial Library Construction Method, NGS Library Preparation Days from Index, NGS Sequencing Library Construction Days from Index, NGS RNA End Bias, NGS RNA Reverse Transcription Primer, NGS Sequencing Platform, Visium Capture Area, Image Protocol Link, Visium Slide Version, Visium Slide ID, Visium Image Re-orientation, Visium Permeabilization Time, NGS RNA RIN, NGS RNA DV200",,,,,,,,,True,
VisiumRNALevel1_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
Visium Run ID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,,,True,,,string,,,,,,HTAN
Visium Capture Area,"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.","A, B, C, D, A1, B1, C1, D1",,,,,string,,,,,,HTAN
Visium Slide Version,Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.,"V1, V2, V3, V4",,True,,,string,,,,,,HTAN
Visium Spatial Read1,Read 1 content description,"cDNA, Spatial Barcode and UMI",,True,,,string,,,,,,HTAN
Visium Spatial Read2,Read 2 content description,"cDNA, Spatial Barcode and UMI",,True,,,string,,,,,,HTAN
Visium Spatial Library Construction Method,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],"Smart-seq2, Smart-SeqV4, 10xV1.0, 10xV1.1, 10xV2, 10xV3, 10xV3.1, Drop-seq, inDropsV2, inDropsV3, TruDrop, Nextera XT",,True,,,string,,,,,,HTAN
Visium Slide ID,"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,,,string,,,,,,HTAN
Visium Image Re-orientation,"To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.","True, False",,,,,boolean,,,,,,HTAN
Visium Permeabilization Time,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.,,,,,,number,,,,,,HTAN
Visium RNA Level 2,Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.,,"VisiumRNALevel2_id, Filename, VisiumRNALevel1 Key, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, Visium UMI Tag, Visium Whitelist Spatial Barcode File Link, Visium Spatial Barcode Tag, Visium Applied Hard Trimming, Workflow Version, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Visium Run ID, Visium Capture Area",,,,,,,,,True,HTAN
VisiumRNALevel2_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
Visium UMI Tag,"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,,,string,,,,,,HTAN
Visium Whitelist Spatial Barcode File Link,Link to file listing all possible spatial barcodes. URL,,,True,,,string,,,,,,HTAN
Visium Spatial Barcode Tag,"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,,,string,,,,,,HTAN
Visium Applied Hard Trimming,Was Hard Trimming applied,"True, False",,True,,,boolean,,,,,,HTAN
Visium RNA Level 3,Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.,,"VisiumRNALevel3_id, Filename, VisiumRNALevel2 Key, VisiumAuxiliaryFiles Key, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, Visium Run ID, Visium File Type, Workflow Version, Workflow Link, Visium Capture Area, Visium Spots under tissue, Visium Mean Reads per Spatial Spot, Visium Median Number Genes per Spatial Spot, NGS Sequencing Coverage, Visium Proportion Reads Mapped, Visium Proportion Reads Mapped to Transcriptome, Visium Median UMI Counts per Spot",,,,,,,,,True,HTAN
VisiumRNALevel3_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
Visium File Type,The file type generated for the visium experiment.,"reference png, reference jpg, json scale factors, probe dataset csv, qc result html, filtered mex, unfiltered mex, tissue_positions, barcodes, features, fiducial image png, fiducial image jpg, detected image png, detected jpg, high res image, low res image, json scale factors, probe dataset csv",,True,,,string,,,,,,HTAN
Visium Spots under tissue,The number of barcodes associated with a spot under tissue.,,,True,,,number,,,,,,HTAN
Visium Mean Reads per Spatial Spot,"The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.",,,True,,,number,,,,,,HTAN
Visium Median Number Genes per Spatial Spot,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,,,number,,,,,,HTAN
Visium Proportion Reads Mapped,Proportion of mapped reads collected from samtools. Number,,,,,,number,,,,,,HTAN
Visium Proportion Reads Mapped to Transcriptome,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,,,number,,,,,,HTAN
Visium Median UMI Counts per Spot,The median number of UMI counts per tissue covered spot.,,,True,,,number,,,,,,HTAN
Visium RNA Level 4,Processed data files based on Spatial Transcriptomics RNA-seq Level 3.,,"VisiumRNALevel4_id, Filename, VisiumRNALevel3 Key, Biospecimen Key, Study Key, DatasetView Key, File Alias, File Description, File Design, File Batch Identifier, File Level, Assay, Species, Tissue, Tumor Type, File Url, File Format, File Assay Category, Data Use Codes, File Longitudinal Group, File Longitudinal Event Type, File Longitudinal Sequence Identifier, File Longitudinal Time Elapsed Unit, File Longitudinal Total Time Elapsed, Visium Run ID, Workflow Version, Workflow Link, Visium Workflow Type, Visium Workflow Parameters Description",,,,,,,,,True,HTAN
VisiumRNALevel4_id,"Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated.",,,True,primary_key,,string,,"^syn\d{7,8}$",,,,
Visium Workflow Type,Generic name for the workflow used to analyze the visium data set.,,,True,,,string,,,,,,HTAN
Visium Workflow Parameters Description,Parameters used to run the workflow.,,,True,,,string,,,,,,HTAN