diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..0772a03 --- /dev/null +++ b/.gitignore @@ -0,0 +1,18 @@ +# Ignore the data_files directory +*node_data_files/ +#*transformed_data_files*/ +*old/ +__pycache__/ +.ipynb_checkpoints/ +cds_config.yaml +*.zip +*.xlsx +!UI-database mappings.xlsx +!UI-database mappings_v2.xlsx +*.rtf +*.tsv +#cds-model* +tmp/ +.gitsecret/keys/random_seed +!*.secret +*.json diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..1685271 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "1-Transformation-Scripts/bento"] + path = 1-Transformation-Scripts/bento + url = https://github.com/CBIIT/bento-common.git diff --git a/0-Raw-Data-Files/cds_raw_data_files/.placeholder b/0-Raw-Data-Files/cds_raw_data_files/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/0-Raw-Data-Files/cds_raw_data_files_v1.2/.placeholder b/0-Raw-Data-Files/cds_raw_data_files_v1.2/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/0-Raw-Data-Files/cds_raw_data_files_v1.2/cds_data_2022-11-17/.placeholder b/0-Raw-Data-Files/cds_raw_data_files_v1.2/cds_data_2022-11-17/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/0-Raw-Data-Files/cds_raw_data_files_v1.3/.placeholder b/0-Raw-Data-Files/cds_raw_data_files_v1.3/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/0-Raw-Data-Files/cds_raw_data_files_v1.3/cds_data_2022-11-22/.placeholder b/0-Raw-Data-Files/cds_raw_data_files_v1.3/cds_data_2022-11-22/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/1-Transformation-Scripts/bento b/1-Transformation-Scripts/bento new file mode 160000 index 0000000..d644aac --- /dev/null +++ b/1-Transformation-Scripts/bento @@ -0,0 +1 @@ +Subproject commit d644aac1198ad56b9dc2a7e95f8173f6eae271e6 diff --git a/1-Transformation-Scripts/cds-transformation.py b/1-Transformation-Scripts/cds-transformation.py new file mode 100644 index 0000000..7655242 --- /dev/null +++ b/1-Transformation-Scripts/cds-transformation.py @@ -0,0 +1,145 @@ +import pandas as pd +import os +import yaml +import argparse + +parser = argparse.ArgumentParser() +parser.add_argument('config_file') +args = parser.parse_args() +config = args.config_file + +def extract_data(df, model, df_list, node): + new_df = pd.DataFrame() + for cds_df in df_list: + for property in model['Nodes'][node]['Props']: + for col in cds_df.columns: + col_name = col.replace(" ", "_").lower() + if col_name in property or property in col_name: + #if len(cds_df) > len(df): + new_df[property] = cds_df[col] + + for property in new_df.keys(): + if property in df.keys(): + df = df.join(new_df.set_index(property), on=property) + df['type'] = [node] * len(df) + return df + df = pd.concat([df, new_df], axis=1) + df['type'] = [node] * len(df) + return df + +#Add acl to file node +def add_properties(file_name, df, cds_df, dataframe_name): + props = [ + {'node':'file', 'new_property':'acl', 'new_value': 'acl', 'dataframe_name': 'CDS_Manifest_df'}, + {'node':'file', 'new_property':'file_id', 'new_value': 'GUID', 'dataframe_name': 'CDS_Manifest_df'}, + {'node':'file', 'new_property':'sample.sample_id', 'new_value': 'sample_id', 'dataframe_name': 'CDS_Manifest_df'}, + {'node':'genomic_info', 'new_property':'library_id', 'new_value': 'library_id', 'dataframe_name': 'CDS_Manifest_df'}, + {'node':'genomic_info', 'new_property':'file.file_id', 'new_value': 'GUID', 'dataframe_name': 'CDS_Manifest_df'}, + {'node':'sample', 'new_property':'sample_id', 'new_value': 'Sample ID', 'dataframe_name': 'CGC_CDS_Explorer_df'}, + {'node':'sample', 'new_property':'participant.participant_id', 'new_value': 'Participant ID', 'dataframe_name': 'CGC_CDS_Explorer_df'}, + {'node':'participant', 'new_property':'study.phs_accession', 'new_value': 'phs_accession', 'dataframe_name': 'Study_df'}, + {'node':'study', 'new_property':'data_access_level', 'new_value': 'acl', 'dataframe_name': 'Study_df'} + + ] + new_df = pd.DataFrame() + for property in props: + if property['node'] == file_name and property['dataframe_name'] == dataframe_name: + new_df[property['new_property']] = cds_df[property['new_value']] + + for property in new_df.keys(): + if property in df.keys(): + df = df.join(new_df.set_index(property), on = property) + df = df.drop_duplicates() + return df + if len(new_df) != len(df): + new_df = new_df[0:len(df)] + df = pd.concat([df, new_df], axis=1) + return df + +#Remove node +def remove_node(df, file_name): + nodes = [ + {'node':'diagnosis'}, + {'node':'participant'} + ] + for node in nodes: + if node['node'] == file_name: + df = pd.DataFrame() + return df +#Print data +def print_data(df, config, file_name): + file_name = config['OUTPUT_FOLDER'] + file_name + '.tsv' + if not os.path.exists(config['OUTPUT_FOLDER']): + os.mkdir(config['OUTPUT_FOLDER']) + df.to_csv(file_name, sep = "\t", index = False) + + +with open(config) as f: + config = yaml.load(f, Loader = yaml.FullLoader) + +CDS_Manifest_df = pd.read_excel(io = config['DATA_FILE1'], + sheet_name = "CDS Manifest", + engine = "openpyxl", + keep_default_na = False) +CGC_CDS_Explorer_df = pd.read_excel(io = config['DATA_FILE1'], + sheet_name = "CGC CDS Explorer", + engine = "openpyxl", + keep_default_na = False) +SRA_Run_Selector_df = pd.read_excel(io = config['DATA_FILE1'], + sheet_name = "SRA Run Selector", + engine = "openpyxl", + keep_default_na = False) +Participant = pd.read_excel(io = config['DATA_FILE2'], + sheet_name = "Participant", + engine = "openpyxl", + keep_default_na = False) +Sample = pd.read_excel(io = config['DATA_FILE2'], + sheet_name = "Sample", + engine = "openpyxl", + keep_default_na = False) +File = pd.read_excel(io = config['DATA_FILE2'], + sheet_name = "File", + engine = "openpyxl", + keep_default_na = False) +Genomic_Info = pd.read_excel(io = config['DATA_FILE2'], + sheet_name = "Genomic Info", + engine = "openpyxl", + keep_default_na = False) +Study = pd.read_excel(io = config['DATA_FILE2'], + sheet_name = "Study", + header = None, + engine = "openpyxl", + keep_default_na = False) + +header_list = Study.values.T[0].tolist() +value_list = Study.values.T[1].tolist() + +Study_df = pd.DataFrame() +for index in range(0, len(header_list)): + if value_list[index] != '': + Study_df[header_list[index]] = [value_list[index]] * len(CDS_Manifest_df) + +with open(config['NODE_FILE']) as f: + model = yaml.load(f, Loader = yaml.FullLoader) +df_dict = {} +for node in model['Nodes']: + #print(node) + df = pd.DataFrame() + df_list = [File, Genomic_Info, CDS_Manifest_df, CGC_CDS_Explorer_df, SRA_Run_Selector_df, Study_df, Sample] + df = extract_data(df, model, df_list, node) + + df = remove_node(df, node) + #participant should only come from Participant sheet + df = extract_data(df, model, [Participant], node) + df = add_properties(node, df, CDS_Manifest_df, 'CDS_Manifest_df') + df = add_properties(node, df, CGC_CDS_Explorer_df, 'CGC_CDS_Explorer_df') + df = add_properties(node, df, Study_df, 'Study_df') + + if len(df) > 0: + df_dict[node] = df +#improve the data after extraction +df_dict['study'] = df_dict['study'].drop(columns = ['size_of_data_being_uploaded', 'study_external_url']) +df_dict['study'] = df_dict['study'].drop_duplicates() +for node in df_dict.keys(): + print_data(df_dict[node], config, node) + print(f'Data node {node} is created') diff --git a/1-Transformation-Scripts/cds-transformation_v1.2.py b/1-Transformation-Scripts/cds-transformation_v1.2.py new file mode 100644 index 0000000..15d13fd --- /dev/null +++ b/1-Transformation-Scripts/cds-transformation_v1.2.py @@ -0,0 +1,255 @@ +import pandas as pd +import os +import yaml +import argparse +from difflib import SequenceMatcher +import numpy as np +import glob +import dateutil.tz +import datetime +from cds_transformation_functions import clean_data, print_data, upload_files +import random +from bento.common.utils import get_logger + +cds_log = get_logger('CDS V1.2 Transformation Script') + +def match_property(model, node, col, limit): + # The function to match the column name from the raw files and the properties from the model file + # The function will create a list of candidate properties for each column name base on the similarity + # The "limit" will decide the minimum similarity for the property to be added into the candidate list + col_name = col.replace(" ", "_").lower() + property_list = [] + for property in model['Nodes'][node]['Props']: + s = SequenceMatcher(None) + s.set_seq1(col_name) + s.set_seq2(property) + ratio = s.ratio() + if ratio >= limit: + property_list.append({'ratio': ratio, 'property': property}) + if len(property_list) == 0: + return None + max_index = max(range(len(property_list)), key=lambda index: property_list[index]['ratio']) + similar_property = property_list[max_index]['property'] + return similar_property + +def extract_raw_data_dict(cds_df, model, node, limit, raw_dict): + # The function to extract raw data dictionary from the raw data files + # "cds_df" is the raw data data frame + # "model" is the data model from the model file + # "node" is the node name of the current node for extracting + # "limit" is the minimum similarity + # "raw_dict" is the raw data dictionary + for col in cds_df.columns: + property = match_property(model, node, col, limit) + if property != None: + if not cds_df[col].isnull().all(): + #new_df[property] = cds_df[col] + if node not in raw_dict.keys(): + raw_dict[node] = {} + raw_dict[node][col] = property + return raw_dict + +def extract_data(cds_df, node, raw_data_dict): + # The function to extract data from the raw data files + # "cds_df" is the raw data data frame + # "raw_data_dict" is the raw data dictionary, this function use the raw data dictionary to locate the corresponding + with open(raw_data_dict) as f: + raw_dict = yaml.load(f, Loader = yaml.FullLoader) + new_df = pd.DataFrame() + for col in cds_df.columns: + if node in raw_dict.keys(): + if col in raw_dict[node].keys() and not cds_df[col].isnull().all(): + new_df[raw_dict[node][col]] = cds_df[col] + #print(property, col, node) + new_df_nulllist = list(new_df.isnull().all(axis=1)) + if False in new_df_nulllist: + if node == 'file' and 'file_id' not in new_df.keys(): + if 'GUID' in cds_df.keys(): + new_df['file_id'] = cds_df['GUID'] + elif 'guid' in cds_df.keys(): + new_df['file_id'] = cds_df['guid'] + else: + file_id = random.sample(range(10**9, 10**10), len(new_df)) + new_df['file_id'] = file_id + # If the extracted dataframe not only consist with NAN values, then add the 'type' property to the dataframe + new_df['type'] = [node] * len(new_df) + #new_df = new_df.drop_duplicates() + return new_df + +parser = argparse.ArgumentParser() +parser.add_argument('--config_file', type=str, help='The path of the config file.', required=True) #Argument about the config file +parser.add_argument('--upload_s3', help='Decide whether or not upload the transformed data to s3', action='store_true') +parser.add_argument('--extract_raw_data_dictionary', help='Decide whether or not extract raw data dictionary instead of transformed raw data', action='store_true') +args = parser.parse_args() +config = args.config_file + +with open(config) as f: + config = yaml.load(f, Loader = yaml.FullLoader) +path = os.path.join(config['DATA_FOLDER'], config['DATA_BATCH_NAME'], '*.xlsx') +ratio_limit = config['RATIO_LIMIT'] +eastern = dateutil.tz.gettz('US/Eastern') +timestamp = datetime.datetime.now(tz=eastern).strftime("%Y-%m-%dT%H%M%S") +if args.extract_raw_data_dictionary == False: + for data_file in glob.glob(path): + # The for loop will grab all the EXCEL files from the raw data folder + cds_log.info(f'Start transforming {os.path.basename(data_file)}') + # 'io' is the path of the excel file + # 'sheet_name' is the sheet's name of the table we are going to read in + # 'engine' is the engine used for reading in the data from excel + # 'openpyxl' needs to install first and it is in the requirement.txt + # 'keep_default_na' is whether or not to include the default NaN values when parsing the data. + Participant = pd.read_excel(io = data_file, + sheet_name = "Participant", + engine = "openpyxl", + keep_default_na = False) + Sample = pd.read_excel(io = data_file, + sheet_name = "Sample", + engine = "openpyxl", + keep_default_na = False) + File = pd.read_excel(io = data_file, + sheet_name = "File", + engine = "openpyxl", + keep_default_na = False) + Genomic_Info = pd.read_excel(io = data_file, + sheet_name = "Genomic Info", + engine = "openpyxl", + keep_default_na = False) + + Study = pd.read_excel(io = data_file, + sheet_name = "Study", + engine = "openpyxl", + keep_default_na = False) + + File_Participant_Sample = pd.read_excel(io = data_file, + sheet_name = "File-Participant-Sample Mapping", + engine = "openpyxl", + keep_default_na = False) + Diagnosis = pd.read_excel(io = data_file, + sheet_name = "Diagnosis (opt)", + engine = "openpyxl", + keep_default_na = False) + + # Replace all the empty string with NAN values + Participant = Participant.replace(r'^\s*$', np.nan, regex=True) + Sample = Sample.replace(r'^\s*$', np.nan, regex=True) + File = File.replace(r'^\s*$', np.nan, regex=True) + Genomic_Info = Genomic_Info.replace(r'^\s*$', np.nan, regex=True) + Study = Study.replace(r'^\s*$', np.nan, regex=True) + File_Participant_Sample = File_Participant_Sample.replace(r'^\s*$', np.nan, regex=True) + Diagnosis = Diagnosis.replace(r'^\s*$', np.nan, regex=True) + + with open(config['NODE_FILE']) as f: + model = yaml.load(f, Loader = yaml.FullLoader) + df_dict = {} + raw_data_dict = config['RAW_DATA_DICTIONARY'] + # Extract dataframe based on different sheet + file_df = extract_data(File, 'file', raw_data_dict) + genomic_info_df = extract_data(Genomic_Info, 'genomic_info', raw_data_dict) + participant_df = extract_data(Participant, 'participant', raw_data_dict) + study_df = extract_data(Study, 'study', raw_data_dict) + sample_df = extract_data(Sample, 'sample', raw_data_dict) + diagnosis_df = extract_data(Diagnosis, 'diagnosis', raw_data_dict) + df_dict['file'] = file_df + df_dict['participant'] = participant_df + df_dict['study'] = study_df + df_dict['sample'] = sample_df + df_dict['genomic_info'] = genomic_info_df + df_dict['diagnosis'] = diagnosis_df + if 'participant_id' in Diagnosis.keys(): + if not Diagnosis['participant_id'].isnull().all(): + df_dict['diagnosis']['participant.participant_id'] = Diagnosis['participant_id'] + participant_nulllist = list(df_dict['participant'].isnull().all(axis=1)) + if len(df_dict['study'] == 1) and 'phs_accession' in df_dict['study'].keys() and False in participant_nulllist: + # If the participant data frame is not null and the study dataframe has only one record and 'phs_accession' is in the study's dataframe + # Then the participant data frame can has it's parent mapping column + if not df_dict['study']['phs_accession'].isnull().values.any(): + df_dict['participant']['study.phs_accession'] = list(df_dict['study']['phs_accession']) * len(df_dict['participant']) + + if not File_Participant_Sample['sample_id'].isnull().values.any() and not File_Participant_Sample['participant_id'].isnull().values.any(): + # If the 'sample_id' column from the sheet File_Participant_Sample is not completely empty + # And if the 'participant_id' from the sheet File_Participant_Sample is not completely empty + # Then start build a parent mapping column for the sample based on 'sample_id' + participant_id_list = [] + for sample_id in df_dict['sample']['sample_id']: + try: + participant_id_list.append(File_Participant_Sample.loc[File_Participant_Sample['sample_id'] == sample_id, 'participant_id'].iloc[0]) + except: + participant_id_list.append(None) + if None not in participant_id_list: + # Parent mapping column can not have none values + df_dict['sample']['participant.participant_id'] = participant_id_list + + if not File_Participant_Sample['file_id'].isnull().values.any() and not File_Participant_Sample['sample_id'].isnull().values.any(): + # If the 'file_id' column from the sheet File_Participant_Sample is not completely empty + # And if the 'sample_id' from the sheet File_Participant_Sample is not completely empty + # Then start build a parent mapping column for the file based on 'file_id' + sample_id_list = [] + for file_id in df_dict['file']['file_id']: + try: + sample_id_list.append(File_Participant_Sample.loc[File_Participant_Sample['file_id'] == file_id, 'sample_id'].iloc[0]) + except: + sample_id_list.append(None) + if None not in participant_id_list: + # Parent mapping column can not have none values + df_dict['file']['sample.sample_id'] = sample_id_list + + df_dict = clean_data(df_dict, config) + prefix = df_dict['study']['phs_accession'][0] + print_data(df_dict, config, cds_log, prefix) + if args.upload_s3 == True: + upload_files(config, timestamp, cds_log) +else: + raw_dict = {} + for data_file in glob.glob(path): + data_file_base = os.path.basename(data_file) + #data_file_sheet_name = os.path.splitext(data_file_base)[0] + cds_log.info(f'Start extracting raw data dictionary from {data_file_base}') + # 'io' is the path of the excel file + # 'sheet_name' is the sheet's name of the table we are going to read in + # 'engine' is the engine used for reading in the data from excel + # 'openpyxl' needs to install first and it is in the requirement.txt + # 'keep_default_na' is whether or not to include the default NaN values when parsing the data. + Participant = pd.read_excel(io = data_file, + sheet_name = "Participant", + engine = "openpyxl", + keep_default_na = False) + Sample = pd.read_excel(io = data_file, + sheet_name = "Sample", + engine = "openpyxl", + keep_default_na = False) + File = pd.read_excel(io = data_file, + sheet_name = "File", + engine = "openpyxl", + keep_default_na = False) + Genomic_Info = pd.read_excel(io = data_file, + sheet_name = "Genomic Info", + engine = "openpyxl", + keep_default_na = False) + + Study = pd.read_excel(io = data_file, + sheet_name = "Study", + engine = "openpyxl", + keep_default_na = False) + Diagnosis = pd.read_excel(io = data_file, + sheet_name = "Diagnosis (opt)", + engine = "openpyxl", + keep_default_na = False) + # Replace all the empty string with NAN values + Participant = Participant.replace(r'^\s*$', np.nan, regex=True) + Sample = Sample.replace(r'^\s*$', np.nan, regex=True) + File = File.replace(r'^\s*$', np.nan, regex=True) + Genomic_Info = Genomic_Info.replace(r'^\s*$', np.nan, regex=True) + Study = Study.replace(r'^\s*$', np.nan, regex=True) + Diagnosis = Diagnosis.replace(r'^\s*$', np.nan, regex=True) + with open(config['NODE_FILE']) as f: + model = yaml.load(f, Loader = yaml.FullLoader) + raw_dict = extract_raw_data_dict(File, model, 'file', ratio_limit, raw_dict) + raw_dict = extract_raw_data_dict(Genomic_Info, model, 'genomic_info', ratio_limit, raw_dict) + raw_dict = extract_raw_data_dict(Participant, model, 'participant', ratio_limit, raw_dict) + raw_dict = extract_raw_data_dict(Study, model, 'study', ratio_limit, raw_dict) + raw_dict = extract_raw_data_dict(Sample, model, 'sample', ratio_limit, raw_dict) + raw_dict = extract_raw_data_dict(Diagnosis, model, 'diagnosis', ratio_limit, raw_dict) + + with open(config['RAW_DATA_DICTIONARY'], 'w') as outfile: + yaml.dump(raw_dict, outfile, default_flow_style=False) + cds_log.info('Raw data dictionary is stored in {}'.format(config['RAW_DATA_DICTIONARY'])) diff --git a/1-Transformation-Scripts/cds-transformation_v1.3.py b/1-Transformation-Scripts/cds-transformation_v1.3.py new file mode 100644 index 0000000..d6f042b --- /dev/null +++ b/1-Transformation-Scripts/cds-transformation_v1.3.py @@ -0,0 +1,355 @@ +import pandas as pd +import warnings +warnings.simplefilter(action='ignore', category=FutureWarning) +import os +import yaml +import json +import argparse +from difflib import SequenceMatcher +import numpy as np +import glob +import dateutil.tz +import datetime +from cds_transformation_functions import clean_data, print_data, upload_files, combine_rows, remove_node, ui_validation, id_validation, download_from_s3, combine_columns, add_secondary_id, ssn_validation #add_historical_value, print_historical_value +from bento.common.utils import get_logger +from openai import OpenAI + +client = OpenAI( + api_key=os.environ['OPENAI_API_KEY'], +) +cds_log = get_logger('CDS V1.3 Transformation Script') + +def embeding_props(model_props): + props_list = list(model_props["PropDefinitions"].keys()) + embeding_props_key = "2-Config-Files/cds_config_v1.3/props_embeding.json" + if os.path.exists(embeding_props_key): + with open(embeding_props_key) as f: + embeding_dict = json.load(f) + dict_props_list = list(embeding_dict.keys()) + different_props_list = [item for item in props_list if item not in dict_props_list] + if len(different_props_list) > 0: + resp = client.embeddings.create( + input=different_props_list, + model="text-embedding-ada-002") + for i in range(0, len(different_props_list)): + embeding_dict[different_props_list[i]] = resp.data[i].embedding + with open(embeding_props_key, "w") as json_file: + json.dump(embeding_dict, json_file, indent=4) + return embeding_dict + else: + embeding_dict = {} + resp = client.embeddings.create( + input=props_list, + model="text-embedding-ada-002") + for i in range(0, len(props_list)): + embeding_dict[props_list[i]] = resp.data[i].embedding + + with open(embeding_props_key, "w") as json_file: + json.dump(embeding_dict, json_file, indent=4) + return embeding_dict +''' +def embeding_raw_data_col(cds_df): + raw_col_dict = {} + col_list = [] + for col in cds_df.columns: + col_list.append(col.replace(" ", "_").lower()) + resp = client.embeddings.create( + input=col_list, + model="text-embedding-ada-002") + for i in range(0, len(col_list)): + raw_col_dict[col_list[i]] = resp.data[i].embedding + return raw_col_dict +''' +def embeding_raw_data_col(cds_df): + raw_cols_key = "2-Config-Files/cds_config_v1.3/cols_embeding.json" + col_list = [] + for col in cds_df.columns: + col_list.append(col.replace(" ", "_").lower()) + if os.path.exists(raw_cols_key): + with open(raw_cols_key) as f: + raw_col_dict = json.load(f) + dict_cols_list = list(raw_col_dict.keys()) + different_cols_list = [item for item in col_list if item not in dict_cols_list] + if len(different_cols_list) > 0: + resp = client.embeddings.create( + input=different_cols_list, + model="text-embedding-ada-002") + for i in range(0, len(different_cols_list)): + raw_col_dict[different_cols_list[i]] = resp.data[i].embedding + with open(raw_cols_key, "w") as json_file: + json.dump(raw_col_dict, json_file, indent=4) + return raw_col_dict + else: + raw_col_dict = {} + + resp = client.embeddings.create( + input=col_list, + model="text-embedding-ada-002") + for i in range(0, len(col_list)): + raw_col_dict[col_list[i]] = resp.data[i].embedding + with open(raw_cols_key, "w") as json_file: + json.dump(raw_col_dict, json_file, indent=4) + return raw_col_dict + +def match_col_cos(cds_df, property, limit, raw_col_dict, embeding_dict): + # The function to match the properties from the model file and the column name from the raw files + # The function will create a list of candidate column names for each property name base on the similarity + # The "limit" will decide the minimum similarity for the column name to be added into the candidate list + col_list = [] + for col in cds_df.columns: + col_name = col.replace(" ", "_").lower() + #s = SequenceMatcher(None) + #s.set_seq1(col_name) + #s.set_seq2(property) + #ratio = s.ratio() + dot_product = np.dot(raw_col_dict[col_name], embeding_dict[property]) + norm_emb1 = np.linalg.norm(raw_col_dict[col_name]) + norm_emb2 = np.linalg.norm(embeding_dict[property]) + similarity_score = dot_product / (norm_emb1 * norm_emb2) + if similarity_score >= limit: + col_list.append({'ratio': similarity_score, 'col': col}) + if len(col_list) == 0: + return None + print(property, col_list) + max_index = max(range(len(col_list)), key=lambda index: col_list[index]['ratio']) + similar_col = col_list[max_index]['col'] + return similar_col + +def match_col(cds_df, property, limit): + # The function to match the properties from the model file and the column name from the raw files + # The function will create a list of candidate column names for each property name base on the similarity + # The "limit" will decide the minimum similarity for the column name to be added into the candidate list + col_list = [] + for col in cds_df.columns: + col_name = col.replace(" ", "_").lower() + s = SequenceMatcher(None) + s.set_seq1(col_name) + s.set_seq2(property) + ratio = s.ratio() + if ratio >= limit: + col_list.append({'ratio': ratio, 'col': col}) + if len(col_list) == 0: + return None + max_index = max(range(len(col_list)), key=lambda index: col_list[index]['ratio']) + similar_col = col_list[max_index]['col'] + return similar_col + +def find_nodes(model, similar_prop): + for node in model['Nodes']: + if similar_prop in model['Nodes'][node]['Props']: + return node + +def extract_raw_data_dict(cds_df, model, limit, raw_dict, raw_col_dict, embeding_dict, data_file, mapping): + for col in cds_df.columns: + col_list = [] + col_name = col.replace(" ", "_").lower() + for property in embeding_dict.keys(): + dot_product = np.dot(raw_col_dict[col_name], embeding_dict[property]) + norm_emb1 = np.linalg.norm(raw_col_dict[col_name]) + norm_emb2 = np.linalg.norm(embeding_dict[property]) + similarity_score = dot_product / (norm_emb1 * norm_emb2) + if similarity_score >= limit: + col_list.append({'similarity_score': similarity_score, 'prop': property}) + if not len(col_list) == 0: + max_index = max(range(len(col_list)), key=lambda index: col_list[index]['similarity_score']) + similar_prop = col_list[max_index]['prop'] + node = find_nodes(model, similar_prop) + if node not in raw_dict.keys(): + raw_dict[node] = {} + raw_dict[node][col] = similar_prop + #if col == "program_description": + # print(col_list, similar_prop) + if data_file not in mapping.keys(): + mapping[data_file] = {} + if node not in mapping[data_file].keys(): + mapping[data_file][node] = {} + mapping[data_file][node][col] = col_list + return raw_dict, mapping + + +''' +def extract_raw_data_dict(cds_df, model, node, limit, raw_dict, raw_col_dict, embeding_dict): + # The function to extract raw data dictionary from the raw data files + #new_df = pd.DataFrame() + # "cds_df" is the raw data data frame + # "model" is the data model from the model file + # "node" is the node name of the current node for extracting + # "limit" is the minimum similarity + # "raw_dict" is the raw data dictionary + for property in model['Nodes'][node]['Props']: + col = match_col_cos(cds_df, property, limit, raw_col_dict, embeding_dict) + if col != None: + if not cds_df[col].isnull().all(): + #new_df[property] = cds_df[col] + if node not in raw_dict.keys(): + raw_dict[node] = {} + raw_dict[node][col] = property + return raw_dict +''' +def match_col_from_raw_dict(raw_dict, node, property, cds_df): + # The function to match the column name from the raw files and the properties from the model file using raw data dictionary + # "node" is the node name of the current node for transforming + # "property" is the property from the model file + # "raw_dict" is the raw data dictionary + col_list = [] + if node in raw_dict.keys(): + for column, prop in raw_dict[node].items(): + if property == prop: + col_list.append(column) + for col in col_list: + if col in cds_df.keys() and not cds_df[col].isnull().all(): + return col + return None + + +def extract_data(cds_df, model, node, raw_data_dict): + with open(raw_data_dict) as f: + raw_dict = yaml.load(f, Loader = yaml.FullLoader) + # The function to extract data from the raw data files + new_df = pd.DataFrame() + for property in model['Nodes'][node]['Props']: + col = match_col_from_raw_dict(raw_dict, node, property, cds_df) + if col != None: + new_df[property] = cds_df[col] + new_df_nulllist = list(new_df.isnull().all(axis=1)) + if False in new_df_nulllist: + new_df['type'] = [node] * len(new_df) + return new_df + +def extract_parent_property(parent_mapping_column_list, df_dict): + # Function to add parent id column to the data node files + # "parent_mapping_column_list" is the parent relationship list from the config file + # "df_dict" is the transformed data frame dictionary + for node in df_dict.keys(): + new_df_nulllist = list(df_dict[node].isnull().all(axis=1)) + if False in new_df_nulllist: + for parent_mapping_column in parent_mapping_column_list: + if node == parent_mapping_column['node']: + parent_mapping_column_name = parent_mapping_column['parent_node'] + '.' + parent_mapping_column['property'] + if parent_mapping_column['property'] in df_dict[parent_mapping_column['parent_node']].keys(): + df_dict[node][parent_mapping_column_name] = df_dict[parent_mapping_column['parent_node']][parent_mapping_column['property']] + return df_dict + + +parser = argparse.ArgumentParser() +parser.add_argument('--config_file', type=str, help='The path of the config file.', required=True) #Argument about the config file +parser.add_argument('--upload_s3', help='Decide whether or not upload the transformed data to s3', action='store_true') #Argument to decide whether or not to upload the transformed data to the s3 bucket +parser.add_argument('--extract_raw_data_dictionary', help='Decide whether or not extract raw data dictionary instead of transformed raw data', action='store_true') +parser.add_argument('--download_s3', help="Decide whether or not download datafiles from s3 bucket.", action='store_true') +args = parser.parse_args() +config = args.config_file +property_validation_df_columns = ['Missing_Properties', 'UI_Related', 'Raw_Data_File'] +property_validation_df = pd.DataFrame(columns=property_validation_df_columns) +filename_validation_df_columns = ['Raw_Data_File', 'File_Name', 'Suspicious_SSN'] +filename_validation_df = pd.DataFrame(columns=filename_validation_df_columns) + +with open(config) as f: + config = yaml.load(f, Loader = yaml.FullLoader) +ratio_limit = config['RATIO_LIMIT'] +path = os.path.join(config['DATA_FOLDER'], config['DATA_BATCH_NAME'], '*.xlsx') +eastern = dateutil.tz.gettz('US/Eastern') +timestamp = datetime.datetime.now(tz=eastern).strftime("%Y-%m-%dT%H%M%S") +if args.download_s3 == True: + download_from_s3(config, cds_log) +if args.extract_raw_data_dictionary == False: + for data_file in glob.glob(path): + data_file_base = os.path.basename(data_file) + #data_file_sheet_name = os.path.splitext(data_file_base)[0] + cds_log.info(f'Start transforming {data_file_base}') + # 'io' is the path of the excel file + # 'sheet_name' is the sheet's name of the table we are going to read in + # 'engine' is the engine used for reading in the data from excel + # 'openpyxl' needs to install first and it is in the requirement.txt + # 'keep_default_na' is whether or not to include the default NaN values when parsing the data. + df_dict = {} + Metadata = pd.read_excel(io = data_file, + sheet_name = "Metadata", + engine = "openpyxl", + keep_default_na = False) + # Replace all the empty string with NAN values + Metadata = Metadata.replace(r'^\s*$', np.nan, regex=True) + # Remove all leading and trailing spaces + Metadata = Metadata.applymap(lambda x: x.strip() if isinstance(x, str) else x) + with open(config['NODE_FILE']) as f: + model = yaml.load(f, Loader = yaml.FullLoader) + for node in model['Nodes']: + raw_data_dict = config['RAW_DATA_DICTIONARY'] + df_dict[node] = extract_data(Metadata, model, node, raw_data_dict) + parent_mapping_column_list = config['PARENT_MAPPING_COLUMNS'] + df_dict = add_secondary_id(df_dict, config, cds_log) + df_dict = combine_columns(df_dict, config, cds_log) + df_dict = extract_parent_property(parent_mapping_column_list, df_dict) + df_dict = remove_node(df_dict, config) + for node in df_dict.keys(): + #remove duplicate reocrd + str_dataframe = df_dict[node].astype(str) + str_dataframe = str_dataframe.drop_duplicates() + index = str_dataframe.index.values.tolist() + df_dict[node] = df_dict[node].loc[index] + df_nulllist = list(df_dict[node].isnull().all(axis=1)) + if False in df_nulllist: + original_property_list = [] + for column_name in df_dict[node].keys(): + if column_name in model['Nodes'][node]['Props'] and column_name != config['NODE_ID_FIELD'][node]: + original_property_list.append(column_name) + df_dict[node] = df_dict[node].dropna(subset = original_property_list, how='all') + df_dict = combine_rows(df_dict, config, cds_log) + df_dict = clean_data(df_dict, config) + df_dict, property_validation_df = ui_validation(df_dict, config, data_file, cds_log, property_validation_df, model, data_file_base) + filename_validation_df = ssn_validation(df_dict, data_file, cds_log, filename_validation_df) + df_dict = id_validation(df_dict, config, data_file, cds_log, model) + #add_historical_value(df_dict, config, cds_log) + prefix = os.path.splitext(data_file_base)[0] + print_data(df_dict, config, cds_log, prefix) + + + sub_folder = os.path.join(config['ID_VALIDATION_RESULT_FOLDER'], config['DATA_BATCH_NAME']) + property_validation_file_name = config['DATA_BATCH_NAME'] + '-' + 'Properties_validation_result' + '.tsv' + property_validation_file_name = os.path.join(sub_folder, property_validation_file_name) + filename_validation_file_name = config['DATA_BATCH_NAME'] + '-' + 'Filename_validation_result' + '.tsv' + filename_validation_file_name = os.path.join(sub_folder,filename_validation_file_name) + if not os.path.exists(sub_folder): + os.makedirs(sub_folder) + if len(property_validation_df) > 0: + property_validation_df.to_csv(property_validation_file_name, sep = "\t", index = False) + cds_log.info(f'Properties validation result file {os.path.basename(property_validation_file_name)} is created and stored in {sub_folder}') + if len(filename_validation_df) > 0: + filename_validation_df.to_csv(filename_validation_file_name, sep = "\t", index = False) + cds_log.info(f'File name validation result file {os.path.basename(filename_validation_file_name)} is created and stored in {sub_folder}') + #print_historical_value(config, cds_log) + if args.upload_s3 == True: + upload_files(config, timestamp, cds_log) + +else: + raw_dict = {} + raw_cols_embeding = {} + mapping = {} + with open(config['MODEL_FILE_PROPS']) as f: + model_props = yaml.load(f, Loader = yaml.FullLoader) + with open(config['NODE_FILE']) as f: + model = yaml.load(f, Loader = yaml.FullLoader) + props_embeding = embeding_props(model_props) + #print(props_embeding['sample_age_at_collection']) + for data_file in glob.glob(path): + data_file_base = os.path.basename(data_file) + #data_file_sheet_name = os.path.splitext(data_file_base)[0] + cds_log.info(f'Start extracting raw data dictionary from {data_file_base}') + # 'io' is the path of the excel file + # 'sheet_name' is the sheet's name of the table we are going to read in + # 'engine' is the engine used for reading in the data from excel + # 'openpyxl' needs to install first and it is in the requirement.txt + # 'keep_default_na' is whether or not to include the default NaN values when parsing the data. + Metadata = pd.read_excel(io = data_file, + sheet_name = "Metadata", + engine = "openpyxl", + keep_default_na = False) + # Replace all the empty string with NAN values + Metadata = Metadata.replace(r'^\s*$', np.nan, regex=True) + raw_cols_embeding = embeding_raw_data_col(Metadata) + #for node in model['Nodes']: + raw_dict, mapping = extract_raw_data_dict(Metadata, model, ratio_limit, raw_dict, raw_cols_embeding, props_embeding, data_file, mapping) + with open(config['RAW_DATA_DICTIONARY'], 'w') as outfile: + yaml.dump(raw_dict, outfile, default_flow_style=False) + with open("2-Config-Files/cds_config_v1.3/mapping.json", "w") as json_file: + json.dump(mapping, json_file, indent=4) + cds_log.info('Raw data dictionary is stored in {}'.format(config['RAW_DATA_DICTIONARY'])) \ No newline at end of file diff --git a/1-Transformation-Scripts/cds_transformation_functions.py b/1-Transformation-Scripts/cds_transformation_functions.py new file mode 100644 index 0000000..ea2aa95 --- /dev/null +++ b/1-Transformation-Scripts/cds_transformation_functions.py @@ -0,0 +1,466 @@ +import yaml +import numpy as np +import boto3 +import os +import pandas as pd +import re +import sys +import glob + +def clean_data(df_dict, config): + # The function to clean the transformed data base on the clean data dictionary + # "df_dict" is the transformed data frame dictionary + # "config" is the config file + # The function will only replace the property's value if the property have "Enum" list value specific in the model props file + # and the "Enum" list value does not have only one "TBD" or "NOT_REPORTED" value inside the list + # and the property's value is not inside the "Enum" list but is record in the raw data dictionary + ENUM = 'Enum' + PROPDEFINITIONS = 'PropDefinitions' + TBD = 'TBD' + NOT_REPORTED = 'not reported' + with open(config['MODEL_FILE_PROPS']) as f: + props = yaml.safe_load(f) + with open(config['CLEAN_DICT']) as f: + clean_dict = yaml.safe_load(f) + for node, df in df_dict.items(): + df.reset_index(inplace = True, drop=True) + for key in list(df.keys()): + if key in list(props[PROPDEFINITIONS]): + if ENUM in props[PROPDEFINITIONS][key]: + if props[PROPDEFINITIONS][key][ENUM][0] != TBD and props[PROPDEFINITIONS][key][ENUM][0] != NOT_REPORTED or len(props[PROPDEFINITIONS][key][ENUM]) > 1: + value_list = [] + for value in df[key]: + if value not in props[PROPDEFINITIONS][key][ENUM]: + if key in clean_dict.keys(): + str_value = str(value) + #print(len(list(clean_dict['primary_diagnosis'].keys()))) + if str_value in clean_dict[key].keys() or value in clean_dict[key].keys(): + try: + value_list.append(clean_dict[key][value]) + except: + value_list.append(clean_dict[str(key)][str_value]) + #print(clean_dict[key][value]) + elif pd.isnull(value) and 'nan_value' in clean_dict[key].keys(): + value_list.append(clean_dict[key]['nan_value']) + elif value in clean_dict["extra_long_values"]: #if the value is too long to be the key of a yaml file + #print(value) + value_list.append("Not specified in data") + else: + #value_list.append(None) + value_list.append(value) + else: + value_list.append(value) + else: + value_list.append(value) + df[key] = value_list + elif "Type" in props[PROPDEFINITIONS][key]: + if props[PROPDEFINITIONS][key]["Type"] == 'integer': + value_list = [] + for value in df[key]: + if not isinstance(value, int) and value is not None and not pd.isna(value): + try: + int_value = int(value) + if value == int_value: + value_list.append(int_value) + else: + value_list.append(value) + except Exception as e: + value_list.append(value) + print(e) + else: + value_list.append(value) + df[key] = pd.Series(value_list, dtype=object) + df_dict[node] = df + return df_dict +""" + if len(value_list) > 0: + print(key) + print(props[PROPDEFINITIONS][key][ENUM]) + print(set(value_list)) +""" + +def upload_files(config, timestamp, cds_log): + # Function to upload the transformed data to the s3 bucket + # The subfolder name of the uploaded data will be timestamp + # "data_file" is the path of the raw data files + # "config" is the config file + local_sub_folder_name = config['DATA_BATCH_NAME'] + s3 = boto3.client('s3') + for file_name in os.listdir(os.path.join(config['OUTPUT_FOLDER'], local_sub_folder_name)): + if file_name.endswith('.tsv'): + # Find every file that end with '.tsv' and upload them to se bucket + file_directory = os.path.join(config['OUTPUT_FOLDER'], local_sub_folder_name, file_name) + s3_file_directory = os.path.join('transformed', config['DATA_BATCH_NAME'], timestamp, file_name) + s3.upload_file(file_directory, config['S3_BUCKET'], s3_file_directory) + for file_name in os.listdir(os.path.join(config['DATA_FOLDER'], local_sub_folder_name)): + if file_name.endswith('.xlsx'): + # Find every file that end with '.tsv' and upload them to se bucket + file_directory = os.path.join(config['DATA_FOLDER'], local_sub_folder_name, file_name) + s3_file_directory = os.path.join('raw', config['DATA_BATCH_NAME'], timestamp, file_name) + s3.upload_file(file_directory, config['S3_BUCKET'], s3_file_directory) + transformed_subfolder = 's3://' + config['S3_BUCKET'] + '/' + 'transformed' + '/' + config['DATA_BATCH_NAME'] + '/' + timestamp + raw_subfolder = 's3://' + config['S3_BUCKET'] + '/' + 'raw' + '/' + config['DATA_BATCH_NAME'] + '/' + timestamp + cds_log.info(f'Transformed data files for {local_sub_folder_name} uploaded to {transformed_subfolder}') + cds_log.info(f'Raw data files for {local_sub_folder_name} uploaded to {raw_subfolder}') + +def print_data(df_dict, config, cds_log, prefix): + # The function to store the transformed data to local file + # The function will create a set of raw folders based on the name of the raw datafiles + # "data_file" is the path of the raw data files + # "config" is the config file + # "prefix" is the prefix of transfomed files + # "cds_log" is the log object + sub_folder = os.path.join(config['OUTPUT_FOLDER'], config['DATA_BATCH_NAME']) + for file_name, df in df_dict.items(): + file_name = prefix + '-' + file_name + '.tsv' + file_name = os.path.join(sub_folder, file_name) + if not os.path.exists(sub_folder): + os.makedirs(sub_folder) + df_nulllist = list(df.isnull().all(axis=1)) + if False in df_nulllist: + df.to_csv(file_name, sep = "\t", index = False) + cds_log.info(f'Data node {os.path.basename(file_name)} is created and stored in {sub_folder}') + + +def combine_rows(df_dict, config, cds_log): + # The function to combine rows base on the config file + # "df_dict" is the transformed data frame dictionary + # "config" is the config file + for combine_node in config['COMBINE_NODE']: + try: + combine_df = pd.DataFrame() + df = df_dict[combine_node['node']] + id_column = combine_node['id_column'] + for id in list(set(list(df[id_column]))): + id_row = pd.DataFrame() + for key in df.keys(): + values = df.loc[df[id_column] == id][key].dropna() + value_list = list(set(values)) + value_list.sort() + if len(value_list) > 1: + value_string = '' + for i in range(0, len(value_list)): + value_item = str(value_list[i]).strip() + if i != 0: + if value_item not in value_string: + value_string = value_string + ', ' + value_item + else: + value_string = value_item + id_row[key] = [value_string] + elif len(value_list) == 1: + id_row[key] = value_list + else: + id_row[key] = [np.nan] + #print(id_row) + combine_df = pd.concat([combine_df, id_row], ignore_index=True) + df_dict[combine_node['node']] = combine_df + except Exception as e: + cds_log.warning('Data node {} dose not exist'.format(combine_node)) + cds_log.error(e) + return df_dict + +def remove_node(df_dict, config): + # The function to remove some extracted data node + # "data_file" is the path of the raw data files + # "config" is the config file + nodes = config['REMOVE_NODES'] + for node in nodes: + df_dict.pop(node) + return df_dict + +def get_parent_list(node, parent_mapping_column_list): + parent_list = [] + for parent_mapping_column in parent_mapping_column_list: + if node == parent_mapping_column['node']: + parent_list.append(parent_mapping_column['parent_node'] + '.' + parent_mapping_column['property']) + return parent_list + +def delete_children(parent_mapping_column_list, delete_list, parent_node, df_dict, config): + for parent_mapping_column in parent_mapping_column_list: + if parent_mapping_column['parent_node'] == parent_node and len(df_dict[parent_mapping_column['node']]) > 0: + parent_id_field = parent_mapping_column['parent_node'] + '.' + parent_mapping_column['property'] + children_node = parent_mapping_column['node'] + parent_list = get_parent_list(children_node, parent_mapping_column_list) + df_dict[children_node].loc[df_dict[children_node][parent_id_field].isin(delete_list), parent_id_field] = np.nan #replace the parent id with nan values + for pc in parent_mapping_column_list: + if pc['parent_node'] == children_node and len(df_dict[pc['node']]) > 0: + #pc_children_node = pc['node'] + #children_delete_list_df = df_dict[children_node][df_dict[children_node][parent_id_field].isna()] + children_delete_list_df = df_dict[children_node][df_dict[children_node][parent_list].isna().all(axis=1)] + children_delete_list = list(children_delete_list_df[config['NODE_ID_FIELD'][children_node]]) + df_dict = delete_children(parent_mapping_column_list, children_delete_list, children_node, df_dict, config) + + df_dict[children_node] = df_dict[children_node].dropna(subset = parent_list, how='all') + #df_dict[children_node] = df_dict[children_node][~df_dict[children_node][parent_id_field].isin(delete_list)] + return df_dict + +def print_id_validation_result(id_validation_df, config, cds_log, prefix, parent): + sub_folder = os.path.join(config['ID_VALIDATION_RESULT_FOLDER'], config['DATA_BATCH_NAME']) + if parent: + file_name = prefix + '-' + 'parent_ID_validation_result' + '.tsv' + else: + file_name = prefix + '-' + 'ID_validation_result' + '.tsv' + file_name = os.path.join(sub_folder, file_name) + if not os.path.exists(sub_folder): + os.makedirs(sub_folder) + id_validation_df.to_csv(file_name, sep = "\t", index = False) + cds_log.info(f'ID data validation result file {os.path.basename(file_name)} is created and stored in {sub_folder}') + +def id_validation(df_dict, config, data_file, cds_log, model): + id_validation_df = pd.DataFrame(columns = ['node name', 'ID', 'conflict property']) + parent_id_validation_df = pd.DataFrame(columns = ['node name', 'ID', 'parent ID field']) + prefix = os.path.splitext(os.path.basename(data_file))[0] + raw_data_name = os.path.basename(data_file) + mul = "many_to_one" + parent_mapping_column_list = config['PARENT_MAPPING_COLUMNS'] + for node in df_dict.keys(): + if len(df_dict[node]) > 0: + df_dict[node] = df_dict[node].drop_duplicates() + df_dict[node] = df_dict[node].dropna(subset = [config['NODE_ID_FIELD'][node]]) + parent_id_validation_result_list = [] + missing_parent_id = False + for parent_column in config['PARENT_MAPPING_COLUMNS']: + if parent_column['node'] == node: + parent_id_field = parent_column['parent_node'] + '.' + parent_column['property'] + relationship = parent_column["relationship"] + if model["Relationships"][relationship]["Mul"] == "many_to_many": + mul = "many_to_many" + if parent_id_field in df_dict[node].keys(): + parent_id_validation_result_df = df_dict[node][df_dict[node][parent_id_field].isna()] + if len(parent_id_validation_result_df) > 0: + #df_dict[node] = df_dict[node].drop(parent_id_validation_result_df.index) + #parent_id_validation_result = list(set(list(parent_id_validation_result_df[config['NODE_ID_FIELD'][node]]))) + parent_id_validation_result_list.append(list(set(list(parent_id_validation_result_df[config['NODE_ID_FIELD'][node]])))) + missing_parent_id = True + else: + parent_id_validation_result_list.append([]) + if missing_parent_id: + parent_id_validation_result = list(set(parent_id_validation_result_list[0]).intersection(*parent_id_validation_result_list[1:])) + if len(parent_id_validation_result) > 0: + cds_log.warning("The ID {}'s all parent_ids are NULL in the node {} from the study {}".format(parent_id_validation_result, node, raw_data_name)) + df_dict[node] = df_dict[node].drop(df_dict[node][df_dict[node][config['NODE_ID_FIELD'][node]].isin(parent_id_validation_result)].index) + df_dict = delete_children(parent_mapping_column_list, parent_id_validation_result, node, df_dict, config) + for deleted_parent_id in parent_id_validation_result: + parent_id_validation_df_row = pd.DataFrame(data = [[node, deleted_parent_id, parent_id_field]], columns = ['node name', 'ID', 'parent ID field']) + parent_id_validation_df = pd.concat([parent_id_validation_df, parent_id_validation_df_row], ignore_index=True) + print_id_validation_result(parent_id_validation_df, config, cds_log, prefix, True) + if node in config['NODE_ID_FIELD'].keys(): + #id_validation_result = [x for x in set(list(df_dict[node][config['NODE_ID_FIELD'][node]])) if list(df_dict[node][config['NODE_ID_FIELD'][node]]).count(x) > 1 or pd.isna(x) or "nan" in x] + id_validation_result = [x for x in set(list(df_dict[node][config['NODE_ID_FIELD'][node]])) if list(df_dict[node][config['NODE_ID_FIELD'][node]]).count(x) > 1 or pd.isna(x)] + new_id_validation_result = [] + many_to_many_id_list = [] + if len(id_validation_result) > 0: + deleted_record = df_dict[node][df_dict[node][config['NODE_ID_FIELD'][node]].isin(id_validation_result)] + for id in id_validation_result: + conflicted_column_names = [] + for column_name in deleted_record.keys(): + conflicted_column = False + deleted_id_df = deleted_record.loc[deleted_record[config['NODE_ID_FIELD'][node]] == id] + if len(set(list(deleted_id_df[column_name]))) > 1: + conflicted_column = True + if conflicted_column and column_name != config['NODE_ID_FIELD'][node]: + conflicted_column_names.append(column_name) + + if mul == "many_to_many" and len(conflicted_column_names) == 1 and conflicted_column_names[0] not in model["Nodes"][node]["Props"]: #if the relationship is many to many and the only comflicted column is parent column, then we do nothing + many_to_many_id_list.append(id) + else: + id_validation_df_row = pd.DataFrame(data = [[node, id, conflicted_column_names]], columns = ['node name', 'ID', 'conflict property']) + id_validation_df = pd.concat([id_validation_df, id_validation_df_row], ignore_index=True) + new_id_validation_result.append(id) + if len(new_id_validation_result) > 0: + df_dict[node] = df_dict[node][~df_dict[node][config['NODE_ID_FIELD'][node]].isin(new_id_validation_result)] + df_dict = delete_children(parent_mapping_column_list, new_id_validation_result, node, df_dict, config) + cds_log.warning('The ID {} is duplicate in the node {} from the study {}'.format(new_id_validation_result, node, raw_data_name)) + cds_log.warning('Removed all data related to the duplicated ID {} from the node {} from the study {}'.format(new_id_validation_result, node, raw_data_name)) + if len(many_to_many_id_list) >0: + cds_log.warning('The ID {} is duplicate in the node {} from the study {} but match the many to many relationship'.format(many_to_many_id_list, node, raw_data_name)) + + if len(id_validation_df) > 0: + #prefix = df_dict['study']['phs_accession'][0] + print_id_validation_result(id_validation_df, config, cds_log, prefix, False) + return df_dict + + +def ssn_validation(df_dict, data_file, cds_log, file_validation_df): + raw_data_name = os.path.basename(data_file) + pattern_list = [r"\d{3}-\d{2}-\d{4}", r"\d{3}_\d{2}_\d{4}", r"(?<=\D)\d{9}(?=\D)"] + df_nulllist = list(df_dict['file'].isnull().all(axis=1)) + if False in df_nulllist: + cds_log.info('Start validating file name for {}'.format(raw_data_name)) + for file_name in df_dict['file']['file_name']: + for pattern in pattern_list: + matches = re.findall(pattern, file_name) + if len(matches) > 0: + file_validation_df_new_row = pd.DataFrame() + file_validation_df_new_row['Raw_Data_File'] = [raw_data_name ] + file_validation_df_new_row['File_Name'] = [file_name] + file_validation_df_new_row['Suspicious_SSN'] = [str(matches)] + file_validation_df = pd.concat([file_validation_df, file_validation_df_new_row], ignore_index=True) + return file_validation_df + + + +def ui_validation(df_dict, config, data_file, cds_log, property_validation_df, model, data_file_base): + # The function to do check if the UI related properties are in the transformed data files + # "data_file" is the path of the raw data files + # "config" is the config file + # "cds_log" is the log object + raw_data_name = os.path.basename(data_file) + validation_df = pd.read_excel(io = config['VALIDATION_FILE'], + sheet_name = "Mapping", + engine = "openpyxl", + keep_default_na = True) + for node in df_dict.keys(): + df_nulllist = list(df_dict[node].isnull().all(axis=1)) + if False in df_nulllist: + ui_properties = list(validation_df.loc[validation_df['Node Name'] == node, 'Property Name']) + ui_properties = list(set([x for x in ui_properties if x != '-' and not pd.isna(x)])) + #properties = model['Nodes'][node]['Props'] + if len(ui_properties) > 0: + #for prop in properties: + for prop in ui_properties: + if prop not in df_dict[node].keys() and prop in ui_properties: + if prop != "experimental_strategy_and_data_subtypes": + df_dict[node][prop] = ['Not specified in data'] * len(df_dict[node]) + property_validation_df_new_row = pd.DataFrame() + property_validation_df_new_row['Missing_Properties'] = [node + '.' +prop] + property_validation_df_new_row['UI_Related'] = [True] + property_validation_df_new_row['Raw_Data_File'] = [data_file_base] + property_validation_df = pd.concat([property_validation_df, property_validation_df_new_row], ignore_index=True) + + cds_log.warning('The data node {} does not have require UI property {} extracted from raw data file {}'.format(node, prop, raw_data_name)) + elif prop in df_dict[node].keys() and prop in ui_properties and df_dict[node][prop].isnull().values.any(): + if prop != "experimental_strategy_and_data_subtypes": + df_dict[node][prop] = df_dict[node][prop].replace(np.nan, 'Not specified in data') + #df_dict[node][prop] = df_dict[node][prop].replace('', 'Not specified in data') + ''' + elif prop not in df_dict[node].keys() and prop not in ui_properties: + property_validation_df_new_row = pd.DataFrame() + property_validation_df_new_row['Missing_Properties'] = [node + '.' +prop] + property_validation_df_new_row['UI_Related'] = [False] + property_validation_df_new_row['Raw_Data_File'] = [data_file_base] + property_validation_df = pd.concat([property_validation_df, property_validation_df_new_row], ignore_index=True) + ''' + return df_dict, property_validation_df + +def download_from_s3(config, cds_log): + # Function to download raw data files from the s3 bucket + # The user can decide use this function to get raw data or just read raw data from local + # 's3' is a boto3 s3 object + s3 = boto3.client('s3') + subfolder_directory = config['S3_RAWDATA_SUBFOLDER'] + cds_log.info('Start downloading file from s3 {}'.format(os.path.join(config['S3_BUCKET'], subfolder_directory))) + for key in s3.list_objects(Bucket = config['S3_BUCKET'], Prefix = subfolder_directory)['Contents']: + download_folder = os.path.join(config['DATA_FOLDER'], config['DATA_BATCH_NAME']) + if not os.path.exists(download_folder): + # If the path does not exist, then create the folder + os.mkdir(download_folder) + file_key = os.path.join(download_folder, os.path.basename(key['Key'])) + if key['Key'].endswith(".xlsx"): + s3.download_file(config['S3_BUCKET'], key['Key'], file_key) + +def combine_columns(df_dict, config, cds_log): + for combine_node in config['COMBINE_COLUMN']: + if combine_node['node'] in df_dict.keys(): + if combine_node['external_node'] == False: + if combine_node['column1'] in df_dict[combine_node['node']].keys() and combine_node['column2'] in df_dict[combine_node['node']].keys(): + #df_dict[combine_node['node']][combine_node['new_column']] = df_dict[combine_node['node']][combine_node['column1']].astype(str) + "_" + df_dict[combine_node['node']][combine_node['column2']].astype(str) + if combine_node['new_column'] not in df_dict[combine_node['node']].keys(): + df_dict[combine_node['node']][combine_node['new_column']] = [np.nan] * len(df_dict[combine_node['node']]) + for i in range(0, len(df_dict[combine_node['node']])): + if not pd.isna(df_dict[combine_node['node']].loc[i, combine_node['column1']]) and not pd.isna(df_dict[combine_node['node']].loc[i, combine_node['column2']]): + string_value_1 = convert_to_string(df_dict[combine_node['node']].loc[i, combine_node['column1']]) + string_value_2 = convert_to_string(df_dict[combine_node['node']].loc[i, combine_node['column2']]) + df_dict[combine_node['node']].loc[i, combine_node['new_column']] = string_value_1 + "_" + string_value_2 + elif combine_node['column1'] not in df_dict[combine_node['node']].keys(): + cds_log.info(f"{combine_node['column1']} not in {combine_node['node']}") + else: + cds_log.info(f"{combine_node['column2']} not in {combine_node['node']}") + else: + #df_dict[combine_node['node']][combine_node['new_column']] = df_dict[combine_node['external_node']][combine_node['column1']].astype(str) + "_" + df_dict[combine_node['node']][combine_node['column2']].astype(str) + if combine_node['column1'] in df_dict[combine_node['external_node']].keys() and combine_node['column2'] in df_dict[combine_node['node']].keys(): + if combine_node['new_column'] not in df_dict[combine_node['node']].keys(): + df_dict[combine_node['node']][combine_node['new_column']] = [np.nan] * len(df_dict[combine_node['node']]) + for i in range(0, len(df_dict[combine_node['node']])): + if not pd.isna(df_dict[combine_node['external_node']].loc[i, combine_node['column1']]) and not pd.isna(df_dict[combine_node['node']].loc[i, combine_node['column2']]): + string_value_1 = convert_to_string(df_dict[combine_node['external_node']].loc[i, combine_node['column1']]) + string_value_2 = convert_to_string(df_dict[combine_node['node']].loc[i, combine_node['column2']]) + df_dict[combine_node['node']].loc[i, combine_node['new_column']] = string_value_1 + "_" + string_value_2 + elif combine_node['column1'] not in df_dict[combine_node['external_node']].keys(): + cds_log.info(f"{combine_node['column1']} not in {combine_node['external_node']}") + else: + cds_log.info(f"{combine_node['column2']} not in {combine_node['node']}") + return df_dict + +def convert_to_string(value): + if isinstance(value, float): + if value.is_integer(): + int_value = int(value) + return str(int_value) + return str(value) + +def add_secondary_id(df_dict, config, cds_log): + try: + for secondary_id_node in config['SECONDARY_ID_COLUMN']: + if secondary_id_node['node'] in df_dict.keys(): + df_nulllist = list(df_dict[secondary_id_node['node']].isnull().all(axis=1)) + if False in df_nulllist: + if secondary_id_node['node_id'] not in df_dict[secondary_id_node['node']].keys(): + cds_log.warning('The ID {} is missing and will be replaced by {} for the node {}'.format(secondary_id_node['node_id'], secondary_id_node['secondary_id'], secondary_id_node['node'])) + parent_node = secondary_id_node['secondary_id'].split('.')[0] + parent_node_id = secondary_id_node['secondary_id'].split('.')[1] + for i in range(0, len(df_dict[secondary_id_node['node']])): + df_dict[secondary_id_node['node']].loc[i, secondary_id_node['node_id']] = df_dict[parent_node].loc[i, parent_node_id] + #df_dict[secondary_id_node['node']][secondary_id_node['node_id']] = df_dict[parent_node][parent_node_id] + except Exception as e: + cds_log.info("Unable to create secondary ID") + cds_log.error(e) + return df_dict + +def add_historical_value(df_dict, config, cds_log): + if 'HISTORICAL_PROPERTIES' in config.keys(): + for historical_property in config['HISTORICAL_PROPERTIES']: + historical_property_value = list(df_dict[historical_property['node']][historical_property['property']])[0] + if historical_property_value is None: + cds_log.error(f"{historical_property['property']} is None, abort transformation") + sys.exit(1) + historical_property_key = list(df_dict[historical_property['node']][config['NODE_ID_FIELD'][historical_property['node']]])[0] + historical_property_value_list = historical_property_value.split(",") + historical_property_value_list = [i.strip() for i in historical_property_value_list] + historical_property_file = historical_property['historical_property_file'] + with open(historical_property_file) as f: + history_value = yaml.safe_load(f) + if history_value is None: + history_value = {} + history_value[historical_property_key] = historical_property_value_list + else: + if historical_property_key not in history_value.keys(): + history_value[historical_property_key] = historical_property_value_list + else: + new_historical_value_list = list(set(historical_property_value_list) - set(history_value[historical_property_key])) + if len(new_historical_value_list) > 0: + history_value[historical_property_key] += new_historical_value_list + history_value[historical_property_key].sort(reverse=True) + with open(historical_property_file, 'w') as yaml_file: + yaml.dump(history_value, yaml_file, default_flow_style=False, width=10000) + +#Update the study version for all study files +def print_historical_value(config, cds_log): + output_folder = os.path.join(config['OUTPUT_FOLDER'], config['DATA_BATCH_NAME']) + for data_file in glob.glob('{}/*.tsv'.format(output_folder)): + for historical_property in config['HISTORICAL_PROPERTIES']: + with open(historical_property['historical_property_file']) as f: + history_value = yaml.safe_load(f) + suffix = "-" + historical_property['node'] + if suffix in os.path.splitext(os.path.basename(data_file))[0]: + cds_log.info(f"Start updating the historical property {historical_property['property']} for transformed file {os.path.basename(data_file)}") + history_df = pd.read_csv(data_file, sep='\t') + new_history_value = "" + historical_property_key = list(history_df[config['NODE_ID_FIELD'][historical_property['node']]])[0] + for i in range(0, len(history_value[historical_property_key])): + if i == 0: + new_history_value = history_value[historical_property_key][i] + else: + new_history_value = new_history_value + "," + history_value[historical_property_key][i] + history_df[historical_property["property"]] = [new_history_value] * len(history_df) + history_df.to_csv(data_file, sep = "\t", index = False) \ No newline at end of file diff --git a/2-Config-Files/cds_config/UI-database mappings.xlsx b/2-Config-Files/cds_config/UI-database mappings.xlsx new file mode 100644 index 0000000..2904247 Binary files /dev/null and b/2-Config-Files/cds_config/UI-database mappings.xlsx differ diff --git a/2-Config-Files/cds_config/UI-database mappings_v2.xlsx b/2-Config-Files/cds_config/UI-database mappings_v2.xlsx new file mode 100644 index 0000000..eefce05 Binary files /dev/null and b/2-Config-Files/cds_config/UI-database mappings_v2.xlsx differ diff --git a/2-Config-Files/cds_config/UI-database mappings_v3.xlsx b/2-Config-Files/cds_config/UI-database mappings_v3.xlsx new file mode 100644 index 0000000..28900fb Binary files /dev/null and b/2-Config-Files/cds_config/UI-database mappings_v3.xlsx differ diff --git a/2-Config-Files/cds_config/cds_config_example.yaml b/2-Config-Files/cds_config/cds_config_example.yaml new file mode 100644 index 0000000..9157958 --- /dev/null +++ b/2-Config-Files/cds_config/cds_config_example.yaml @@ -0,0 +1,4 @@ +NODE_FILE: ./node_file/cds-model.yml +DATA_FILE1: ./cds_raw_data_files/data1.xlsx +DATA_FILE2: ./cds_raw_data_files/data2.xlsx +OUTPUT_FOLDER: ./cds_node_data_files/ \ No newline at end of file diff --git a/2-Config-Files/cds_config_v1.2/cds_config_example_v1.2.yaml b/2-Config-Files/cds_config_v1.2/cds_config_example_v1.2.yaml new file mode 100644 index 0000000..bfd63c4 --- /dev/null +++ b/2-Config-Files/cds_config_v1.2/cds_config_example_v1.2.yaml @@ -0,0 +1,9 @@ +NODE_FILE: ./3-Model-Files/cds-model-wprog.yml +DATA_FOLDER: ./0-Raw-Data-Files/cds_raw_data_files_v1.2/ +OUTPUT_FOLDER: ./4-Transformed-Data-Files/cds_transformed_data_files_v1.2/ +RATIO_LIMIT: 0.75 +S3_BUCKET: bruce-cds +MODEL_FILE_PROPS: ./3-Model-Files/cds-model-props.yml +RAW_DATA_DICTIONARY: ./2-Config-Files/cds_config_v1.2/cds_raw_dict_v1.2.yaml +CLEAN_DICT: ./2-Config-Files/cds_config_v1.3/cds_clean_dict_v1.3.yaml +DATA_BATCH_NAME: cds_data_2022-11-17 \ No newline at end of file diff --git a/2-Config-Files/cds_config_v1.2/cds_raw_dict_v1.2.yaml b/2-Config-Files/cds_config_v1.2/cds_raw_dict_v1.2.yaml new file mode 100644 index 0000000..7001fa7 --- /dev/null +++ b/2-Config-Files/cds_config_v1.2/cds_raw_dict_v1.2.yaml @@ -0,0 +1,48 @@ +diagnosis: + age_at_diagnosis: age_at_diagnosis + diagnosis_id: diagnosis_id + tumor_stage_clinical_m: tumor_stage_clinical_m +file: + file_id: file_id + file_name: file_name + file_size: file_size + file_type: file_type + file_url_in_cds: file_url_in_cds + md5sum: md5sum +genomic_info: + design_description: design_description + instrument_model: instrument_model + library_id: library_id + library_layout: library_layout + library_selection: library_selection + library_source: library_source + library_strategy: library_strategy + platform: platform + reference_genome_assembly: reference_genome_assembly + sequence_alignment_software: sequence_alignment_software +participant: + dbGaP_subject_id: dbGaP_subject_id + ethnicity: ethnicity + gender: gender + participant_id: participant_id + race: race +sample: + biosample_accession: biosample_accession + sample_anatomic_site: sample_anatomic_site + sample_id: sample_id + sample_tumor_status: sample_tumor_status + sample_type: sample_type +study: + bioproject_accession: bioproject_accession + experimental_strategy_and_data_subtype: experimental_strategy_and_data_subtypes + file_types_and_format: file_types_and_format + funding_agency: funding_agency + grant_id: grant_id + number_of_participant: number_of_participants + number_of_samples: number_of_samples + phs_accession: phs_accession + primary_investigator_email: primary_investigator_email + primary_investigator_name: primary_investigator_name + study_data_types: study_data_types + study_description: study_description + study_name: study_name diff --git a/2-Config-Files/cds_config_v1.3/cds_clean_dict_v1.3.yaml b/2-Config-Files/cds_config_v1.3/cds_clean_dict_v1.3.yaml new file mode 100644 index 0000000..343c05d --- /dev/null +++ b/2-Config-Files/cds_config_v1.3/cds_clean_dict_v1.3.yaml @@ -0,0 +1,1268 @@ +adult_or_childhood_study: + pediatric: Pediatric + adult: Adult + Pediatric, pediatric: Pediatric +library_layout: + paired: Paired-end + Single: Single-end + Paired End: Paired-end + Paired-end: Paired-end + Paired end: Paired-end + paired-end: Paired-end + paired_end: Paired-end + single-end: Single-end + single: Single-end + Not specified in data: Not Reported +instrument_model: + HiSeq 3000: Illumina HiSeq 3000 + HiSeq 2500: Illumina HiSeq 2500 + HiSeq 2000: Illumina HiSeq 2000 + Illumina Next Seq 500: NextSeq 500 + Illumina HiSeq X Five: HiSeq X Five + Illumina HiSeq X Ten: HiSeq X Ten + Illumina NextSeq: Illumina NextSeq + HiSeq: Illumina HiSeq +reference_genome_assembly: + hg19 / GRCh37: GRCh37 + hs37d5: GRCh37 + GRCh38.p12: GRCh38 + GRCh38.p13: GRCh38 + GRCh38_ens93filt: GRCh38 + GRCh38_long_polya: GRCh38 + GRCh38_premrna_v3.0.0: GRCh38 + refdata-cellranger-arc-GRCh38-2020-A: GRCh38 + refdata-cellranger-GRCh38-3.0.0: GRCh38 + RefSeq_Build_73: GRCh37 + hg19: GRCh37 + hg19_with_GenBank_Viral_Genomes: GRCh37 + hg19-mm10: GRCh37 + "Blood-derived genomic DNA (100ng - 1µg) was sheared using a Covaris S2 instrument.Ê Libraries were prepared using the NEBNext DNA Library Prep Reagent Set for Illumina (NEB # E6000) according to the manufacturerÕs instructions.Ê Library enrichment for a 34 gene custom panel was done with the Roche SeqCap EZ Choice Library (cat# 06266339001) and the SeqCap EZ Reagent Kit Plus v2 (NimbleGen #06-953-247-001) using the manufacturerÕs protocol. Individual libraries were combined into pools of 6-12 prior to hybridization.": Not specified in data + "DNA samples (1 ug) were sheared using a Covaris S2 Focused-ultrasonicator and libraries were prepared using the Illumina TruSeq DNA PCR-Free Sample Preparation Kit (cat# FC-121-3001 and FC-121-3002) with an average insert size of 350 bp.Ê Adapter-ligated molecules were analyzed by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824) and the molarity of individual libraries were normalized to 10 nM in preparation for Illumina sequence analysis.": Not specified in data +file_type: + fastq: FASTQ + fastq.gz: FASTQ + bai: BAI + bam: BAM + bw: BW + tbi: VCF + tsv: TSV + vcf: VCF + json: JSON + txt: TXT + xlsx: XLSX + vcf_index : VCF + bam_index: BAI + cns: CNS + crai: CRAI + cram: CRAM + csv: CSV + gvcf: GVCF + html: HTML + maf: MAF + pdf: PDF + ped: PED + png: PNG + seg: SEG + tar: TAR + bed: BED + idat: IDAT + nifti: NIFTI + #nan_value: unknown +gender: + female: Female + male: Male + F: Female + FEMALE: Female + M: Male + MALE: male + #nan_value: Not Specified in Data +progression_or_recurrence: + Yes - Progression or Recurrence: "Yes" + "True": "Yes" + Not Reported: Unknown + "no": "No" + not reported: Unknown + unknown: Unknown + "TRUE": "Yes" +primary_site: + Bronchus and lung: Bronchus and Lung +sample_tumor_status: + primary CRC tumor FFPE tissue: tumor + normal blood: normal + normal buccal tissue: normal + adjacent normal colonic FFPE tissue: normal + normal saliva: normal +study_data_types: + Genomics: Genomic + GENOMIC: Genomic + genomic: Genomic + #nan_value: unknown +sample_anatomic_site: + #Blood: Peripheral bloodß + UNKNOWN PRIMARY SITE: Unknowm + Invalid value: Not specified in data + Rare Disease: Not specified in data + Soft Tissue Sarcoma: Not specified in data +library_strategy: + wxs: WXS + RNA-seq: RNA-Seq + Archer_Fusion: Archer Fusion + AMPLICON: Amplicon +experimental_strategy_and_data_subtypes: + wxs: WXS + RNA-seq: RNA-Seq + WXS, Amplicon, Bisulfite-Seq, RNA-seq, WGA: WXS, Amplicon, Bisulfite-Seq, RNA-Seq, WGA + WXS, RNA-seq: WXS, RNA-Seq + Methylation: Methylation Array + Methylation_Array: Methylation Array + Archer_Fusion: Archer Fusion + RNA-seq, Targeted-Capture, WXS: RNA-Seq, Targeted-Capture, WXS + #Targeted-Capture: Targeted Sequencing +sample_tumor_status: + normal: Normal + tumor: Tumor +library_source: + GENOMIC: Genomic + TRANSCRIPTOMIC: Transcriptomic + Single-nuclei: Single Nucleus + GENOMIC SINGLE CELL: Genomic Single Cell + TRANSCRIPTOMIC SINGLE CELL: Transcritomic Single Cell + VIRAL RNA: Viral RNA + Transcritomic Single Cell: Transcriptomic Single Cell +library_selection: + RANDOM: Random +primary_diagnosis: + Acute myeloid leukemia with myelodysplasia-related changes: Acute Myeloid Leukemia + Adrenal cortical carcinoma, conventional, high-grade carcinoma involves the renal vein edge (not true margin): Adrenal Cortical Carcinoma + Adrenalcortical carcinoma: Adrenalcortical Carcinoma + Aggressive fibromatosis: Aggressive Fibromatosis + Anaplastic medulloblastoma (WHO Grade 4): Anaplastic Medulloblastoma WHO Grade 4 + Atypical Choroid Plexus Papilloma (WHO Grade 2): Atypical Choroid Plexus Papilloma WHO Grade 2 + Blue cell tumor, favor medulloblastoma: Blue Cell Tumor + Cellular schwannoma: Cellular Schwannoma + Choroid plexus neoplasm, consistent with choroid plexus carcinoma CNS WHO grade 3: Choroid Plexus Neoplasm + Chronic myelogenous leukemia, BCR/ABL positive: Chronic Myelogenous Leukemia + Combined small cell-adenocarcinoma: Combined Small Cell Adenocarcinoma + Combined small cell-large carcinoma: Combined Small Cell Large Carcinoma + Combined small cell-squamous cell carcinoma: Small Cell Squamous Cell Carcinoma + Compact neoplasm with mesenchymal features: Compact Neoplasm with MesenchymalFfeatures + Consistent with pilocytic astrocytoma, CNS WHO Grade 1: Pilocytic Astrocytoma, CNS WHO Grade 1 + Diffuse midline glioma H3 K27-altered WHO grade 4: Diffuse Midline Glioma H3 K27-altered WHO Grade 4 + Embryonal neoplasm, consistent with Medulloblastoma: Embryonal Neoplasm + Embryonal neoplasm. The tumor histology is consistent with medulloblastoma: Embryonal Neoplasm + Embryonal rhabdomyosarcoma (FNCLCC grade 3): Embryonal Rhabdomyosarcoma + Embryonal rhabdomyosarcoma with anaplasia involving paratesticular soft tissue: Embryonal Rhabdomyosarcoma + Ependymoma, anaplastic: Ependymoma, Anaplastic + Epithelioid hemangioendothelioma, NOS: Epithelioid Hemangioendothelioma, NOS + Fibroblastic/myofibroblastic lesion, consistent with dermatofibrosarcoma protuberans: Fibroblastic/Myofibroblastic Lesion + Ganglioglioma, WHO GRADE I: Ganglioglioma, WHO Grade I + Ganglioma (CNS WHO grade 1): Ganglioma, CNS WHO Grade 1 + Glioma, favor high-grade: Glioma + Glioma; low-grade glial versus glioneuronal tumor, favor pilocytic astrocytoma, CNS WHO Grade 1: Glioma + Hepatocellular carcinoma, NOS: Hepatocellular Carcinoma, NOS + High grade diffuse astrocytic neoplasm, histologically at least CNS WHO grade 3: Diffuse Astrocytic Neoplasm + High grade glial/Glioneuronal neoplasm: Glial/Glioneuronal Neoplasm + High grade mesenchymal neoplasm: High Grade Mesenchymal Neoplasm + High grade neoplasm, round blue cell tumor, CNS WHO grade 4: Round Blue Cell Tumor + "High grade neuroepithelial tumor (HGNET) morphologically most C/W or aligning best with CNS embryonal type tumor, possibly from a medulloblastoma": High Grade Neuroepithelial Tumor + IDH1 mutated diffuse astrocytoma: Diffuse Astrocytoma + INI-1 deficient round to epithelioid cell tumor, malignant, most consistent with INI-1 deficient sarcoma: Epithelioid Cell Tumor + Juvenile myelomonocytic leukemia, NOS: Juvenile Myelomonocytic Leukemia, NOS + Low grade glial tumor favor pilocytic astrocytoma: Glial Tumor + Low grade glioma with piloid features: Glioma + Low grade glioma, morphologically aligning well with classic pilocytic astrocytoma: Glioma + Low grade neuroepithelial tumor with MYB::QKI fusion, most compatible with WHO grade 1 designation: Neuroepithelial Tumor + Low grade neuroglial neoplasm with features of a dysembryoplastic neuroepithelial tumor: Neuroglial Neoplasm + Low-grade Glioneuronal tumor, WHO Grade 1: Glioneuronal Tumor + Low-grade glial/glioneuronal neoplasm, oligodendroglioma-like morphology: Glial/glioneuronal Neoplasm + Low-grade glioma, favor pilocytic astrocytoma, CNS WHO grade 1: Glioma + Low-grade glioneuronal process: Glioneuronal + Lymphoepithelial carcinoma: Lymphoepithelial Carcinoma + Malignant neoplasm with necrosis: Malignant Neoplasm + Malignant neoplasm, worrisome for high grade: Malignant Neoplasm + Malignant spindle cell neoplasm: Malignant Spindle Cell Neoplasm + Medulloblastoma (WHO grade 4): Medulloblastoma + Medulloblastoma CNS WHO grade 4: Medulloblastoma + Medulloblastoma SHH activated favor TP53 wild type WHO grade 4: Medulloblastoma + Medulloblastoma classic histology CNS WHO 4: Medulloblastoma + Medulloblastoma, NON-WNT/NON-SHH CNS WHO GRADE 4: Medulloblastoma + Medulloblastoma, NOS WHO Grade 4: Medulloblastoma + Medulloblastoma, WHO Grade 4, classic histology, molecular subtype NOS: Medulloblastoma + Medulloblastoma, nodular desmoplastic WHO grade 4: Medulloblastoma + Medulloblastoma, non-WNT/non-SHH (CNS WHO grade 4): Medulloblastoma + Meningioma (WHO Grade 1): Meningioma + Mixed malignant germ cell tumor: Mixed Malignant Germ Cell Tumor + Mixed phenotype acute leukemia, B/myeloid, NOS: Acute Leukemia, B/myeloid, NOS + Mixed phenotype acute leukemia, T/myeloid, NOS: Acute Leukemia, T/myeloid, NOS + Morphologically consistent with pilomyxoid astrocytoma: Pilomyxoid Astrocytoma + Morphology aligns with pilocytic astrocytoma: Pilomyxoid Astrocytoma + Mucous adenocarcinoma: Mucous Adenocarcinoma + Myoepithelial carcinoma: Myoepithelial Carcinoma + Nasopharyngeal carcinoma, nonkeratinizing: Nasopharyngeal Carcinoma + Neoplastic process suggestive of a high grade astrocytoma: Astrocytoma + Neuroepithelial tumor with PATZ-1 Fusion by DNA methylation: Neuroepithelial Tumor + Neuroepithelial tumor, favored a high grade glial neoplasm: Neuroepithelial Tumor + Oligodendroglioma IDH mutant,1p 19q codleted CNS WHO grade 2: Oligodendroglioma + Papillary tumor, favor low grade: Papillary Tumor + Parosteal osteosarcoma: Parosteal Osteosarcoma + Periosteal Osteosarcoma: Periosteal osteosarcoma + Periosteal osteosarcoma: Periosteal Osteosarcoma + Pilocytic astrocytoma, CNS WHO Grade 1: Pilocytic Astrocytoma + Pineal parenchymal tumor of intermediate differentiation: Pineal Parenchymal Tumor + Platal lesion, Epithelial - Myoepithelial Carcinoma: Epithelial - Myoepithelial Carcinoma + Pseudomyogenic hemangioendothelioma (epithelioid sarcoma-like hemangioendothelioma): Pseudomyogenic Hemangioendothelioma + Rhabdomyosarcoma of the testis, favor embryonal type: Rhabdomyosarcoma + Rhabdomyosarcoma, FOXO1 fusion negative; suggestive of embryonal sarcoma with a primitive phenotype: Rhabdomyosarcoma + Signet-ring cell carcinoma, poorly differentiated: Signet-ring Cell Carcinoma + Small blue cell tumor. Medulloblastoma most likely.: Small Blue Cell Tumor + Small cell carcinoma: Small Cell Carcinoma + Small round blue cell tumour: Small Round Blue Cell Tumor + Small round cell tumor: Small Round Blue Cell Tumor + Small, round, blue-cell tumor, in favor medulloblastoma, WNT-activated, CNS WHO Grade 4: Small Round Blue Cell Tumor + Subependymal giant cell astrocytoma (CNS WHO grade 1): Subependymal Giant Cell Astrocytoma + Synovial Sarcoma, NOS: Synovial sarcoma, NOS + Synovial sarcoma, NOS: Synovial Sarcoma, NOS + Telangiectatic Osteosarcoma: Telangiectatic osteosarcoma + Telangiectatic osteosarcoma: Telangiectatic Osteosarcoma + Teratoma, Malignant, NOS: Teratoma, malignant, NOS + Teratoma, malignant, NOS: Teratoma, Malignant, NOS + Ulcerated nodular melanoma: Ulcerated Nodular Melanoma + hamartomatous lesion with marked reactive changes versus neoplasm: Hamartomatous Lesion + leomorphic xanthoastrocytoma: Leomorphic Xanthoastrocytoma + Adenocarcinoma, Not Otherwise Specified: Adenocarcinoma, NOS + Aggressive spindle cell neoplasm with myoepithelial features: Aggressive Spindle Cell Neoplasm + Astrocytoma with pilomyxoid features: Astrocytoma with Pilomyxoid Features + Atypical choroid plexus papilloma CNS WHO grade 2: Atypical Choroid Plexus Papilloma + Atypical mixed glioneuronal lesion, favor ganglioglioma: Atypical Mixed Glioneuronal Lesion + Atypical teratoid/rhabdoid tumor involving posterior fossa: Atypical Teratoid/Rhabdoid Tumor + Atypical teratoid/rhabdoid tumor, CNS WHO grade 4: Atypical Teratoid/Rhabdoid Tumor + 'Brain tumor: Myxoid round blue cell tumor': Brain Tumor + CNS Embryonal tumor - small round blue cell tumor: CNS Embryonal Tumor + CPNET: Central Primary Primitive Neuroectodermal Tumor + Cervical spine tumor, Meningioma: Meningioma + Clear cell sarcoma, NOS: Clear Cell Sarcoma, NOS + Compatible with myxopapillary ependymoma: Myxopapillary Ependymoma + Consistent with Pineoblastoma, WHO Grade 4: Pineoblastoma + Dermatofibrosarcoma protuberans (DFSP): Dermatofibrosarcoma Protuberans + Dermatofibrosarcoma protuberans with myxoid changes: Dermatofibrosarcoma Protuberans + Differential may include meningioma or glial neoplasm: Meningioma + Diffuse glioma high-grade: Diffuse Glioma High-grade + Diffuse hemispheric glioma, H3 G34-mutant, WHO grade 4: Diffuse Hemispheric Glioma + Diffuse high-grade glioma, involving cerebral cortex and white matter: Diffuse Glioma High-grade + Diffuse midline glioma, CNS WHO grade 4: Diffuse Midline Glioma + Embryonal rhabdomyosarcoma with anaplasia: Embryonal Rhabdomyosarcoma + Embryonal tumor with multilayered rosettes C19MC-altered: Embryonal Tumor + Endometrioid carcinoma, NOS: Endometrioid Carcinoma, NOS + Ependymoma WHO grade 3 PFA subtype: Ependymoma, NOS + Ependymoma, classification pending molecular analysis, with extensive central necrosis and hemorrhage: Ependymoma, NOS + Fibroblastic spindle cell lesion, favor fibromatosis: Fibroblastic Spindle Cell Lesion + Ganglioglioma WHO grade 1: Ganglioglioma + Ganglioglioma with BRAF V600E immunoreactivity, CNS WHO grade 1: Ganglioglioma + Ganglioglioma, WHO Grade 1: Ganglioglioma + Gastrointestinal stromal tumor (GIST) epithelioid type, low grade: Gastrointestinal Stromal Tumor + Glioblastoma Multiforme (GBM): Glioblastoma Multiforme + Glioma, favor pilocytic astrocytoma: Glioma + Glioma, malignant: Glioma + Glioneuronal tumor NOS with low grade histologic features: Glioneuronal Tumor NOS + High grade glioma, favor astrocytoma, IDH mutant (WHO grade 4): High-grade Glioma + High grade malignant neoplasm, favor high-grade glioma: High-grade Malignant Neoplasm + High grade serous carcinoma: High-grade Serous Carcinoma + High grade small round blue cell tumor with immunoprofile consistent with Alveolar rhabdomyosarcoma: High-grade Small Round Blue Cell Tumor + High-grade carcinoma most suggestive of a high-grade acinic cell carcinoma involving tissue edges: High-grade Carcinoma + High-grade fibrosarcoma with myxoid features: High-grade Fibrosarcoma + High-grade glial or glioneuronal neoplasm: High-grade Glial or Glioneuronal Neoplasm + High-grade malignant neoplasm with desmin expression: High-grade Malignant Neoplasm + IDH mutant glioma; favor IDH mutant astrocytoma: IDH Mutant Gliomaa + Infiltrating glial neoplasm: Infiltrating Glial Neoplasm + Infiltrating glioma with focal high grade features: Infiltrating Glioma + Infiltrative fibromatosis: Infiltrative Fibromatosis + Inflammatory myofibroblastic tumor, ALK positive by IHC: Inflammatory Myofibroblastic Tumor + Inflammatory myofibroblastic tumor, ALK-1 negative: Inflammatory Myofibroblastic Tumor + Invasive Carcinoma With Ductal And Lobular Features: Invasive Carcinoma + Involvement by desmoplastic small round cell tumor: Desmoplastic Small Round Cell Tumor + Lesional tissue obtained consistent with glioma: Glioma + Leydig cell tumor and background seminiferous tubules with spermatogenesis: Leydig Cell Tumor + Lobular and ossifying round cell neoplasm with brisk mitotic activity and necrosis, with morphologic features of malignant ossifying fibromyxoid tumor: Lobular and Ossifying Round Cell Neoplasm + Low cellularity glioma, favor low grade: Low Cellularity Glioma + Low grade glial neoplasm most consistent with pilocytic astrocytoma, WHO Grade 1: Low-grade Glial Neoplasm + Low grade glial/glioneuronal tumor predominantly showing features of a pilocytic astrocytoma, but with fragment showing features of ganglioglioma: Low-grade Glial/Glioneuronal Tumor + Low grade-appearing glioma, morphologically aligns best with pilocytic astrocytoma: Low-grade Glioma + Low-grade glial -neuronal tumor, favor ganglioglioma: Low-grade Glial/Neuronal Tumor + Low-grade glial neoplasm, consistent with pilocytic astrocytoma: Low-grade Glial Neoplasm + Low-grade glial or glioneuronal neoplasm: Low-grade Glial or Glioneuronal neoplasm + Low-grade glioma with features consistent with pilocytic astrocytoma (WHO GRADE I): Low-grade Glioma + Lung Adenocarcinoma- Not Otherwise Specified (NOS): Lung Adenocarcinoma, NOS + Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS): Lung Squamous Cell Carcinoma, NOS + Malignant neoplasm with primitive features: Malignant Meoplasm + Medulloblastoma WNT-Activated(IHC) CNS WHO grade 4: Medulloblastoma + Medulloblastoma, Desmoplastic/nodular histologic type: Medulloblastoma + Medulloblastoma, NOS: Medulloblastoma + Medulloblastoma, WNT activated, WHO Grade 4: Medulloblastoma + Medulloblastoma, anaplastic/large-cell, non-WNT: Medulloblastoma + Medulloblastoma, classic type, CNS WHO grade 4: Medulloblastoma + Medulloblastoma, classic variant: Medulloblastoma + Medulloblastoma, desmoplastic/nodular, SHH activated, CNS WHO Grade 4: Medulloblastoma + Medulloblastoma, nodular/desmoplastic pattern, WHO Grade IV: Medulloblastoma + Medulloblastoma, with extensive nodularity: Medulloblastoma + Meningioma, WHO Grade 1: Meningioma + Metastatic adrenal cortical carcinoma: Metastatic Adrenal Cortical Carcinoma + Morphologically compatible with low grade astrocytic tumor: Low-grade Astrocytic tumor + Multiple myeloma: Multiple Myeloma + Nodular spindle neoplasm with mesenchymal phenotype, focal necrosis, and associated abnormally vascular and calcified neuronal component of uncertain etiology: Nodular Spindle Neoplasm + Not specified in data: Not Specified in Data + Oligodendroglioma IDH mutant,1p 19q codeleted CNS WHO grade 2: Oligodendroglioma + Oncocytic adrenal cortical carcinoma: Oncocytic Adrenal Cortical Carcinoma + Papillary Thyroid carcinoma: Papillary Thyroid Carcinoma + Papillary thyroid carcinoma, classic subtype: Papillary Thyroid Carcinoma + Pilocytic Astrocytoma CNS WHO Grade 1: Pilocytic Astrocytoma + Pilocytic astrocytoma CNS WHO grade 1: Pilocytic Astrocytoma + Pilocytic astrocytoma with focal pilomyxoid morphology: Pilocytic Astrocytoma + Pilocytic astrocytoma, BRAF-rearranged: Pilocytic Astrocytoma + Pilocytic astrocytoma, WHO GRADE 1: Pilocytic Astrocytoma + Pleuropulmonary blastoma, type II/III, DICER1-associated: Pleuropulmonary Blastoma + Posterior fossa group A (PFA) ependymoma, CNS WHO grade 3: Posterior Fossa Ependymoma + Precursor T-cell lymphoblastic leukemia: Precursor T-cell lymphoblastic Leukemia + Primary CNS neoplasm, high grade: Primary CNS Neoplasm + Probable pilocytic astrocytoma: Probable Pilocytic Astrocytoma + Renal cell carcinoma with papillary features: Renal Cell Carcinoma + Residual high-grade glioneuronal tumor: High-grade Glioneuronal Tumor + Rhabdoid tumor, NOS: Rhabdoid Tumor, NOS + Rhabdomyosarcoma with spindle cell features: Rhabdomyosarcoma + SMARCB1-Deficient tumor, consistent with extrarenal rhabdoid tumor or atypical teratoid/rhabdoid tumor: Atypical Teratoid/Rhabdoid Tumor + SMARCB1-deficient tumor NOS (This is most likely atypical teratoid/rhabdoid tumor (ATRT)): Atypical Teratoid/Rhabdoid Tumor + Schwannoma, WHO Grade 1: Schwannoma + Small cell carcinoma of ovary, Hypercalcemic type (SMARCA4 Deficient malignant rhabdoid tumor of ovary): Small Cell Carcinoma of Ovary + Small cell carcinoma, NOS: Small Cell Carcinoma, NOS + Small round blue cell tumor most consistent with embryonal rhabdomyosarcoma: Small Round Blue Cell Tumor + Small round cell sarcoma: Small Round Cell Sarcoma + posterior fossa ependymoma: Posterior Fossa Ependymoma + Thyroid papillary carcinoma: Thyroid Papillary Carcinoma + 'Undifferentiated round cell malignancy, favor EWSR1: Patz1 Sarcoma': Undifferentiated Round Cell Malignancy + Acral lentiginous melanoma, malignant: Melanoma + Adenocarcinoma with mixed subtypes: Adenocarcinoma + Adenocarcinoma, endocervical type: Adenocarcinoma + Adenocarcinoma, intestinal type: Adenocarcinoma + Adenosquamous carcinoma: Adenosquamous Carcinoma + Amelanotic melanoma: Melanoma + Astrocytoma, NOS: Astrocytoma + Astrocytoma, anaplastic: Astrocytoma + Basaloid squamous cell carcinoma: Basaloid Squamous Cell Carcinoma + Bronchio-alveolar carcinoma, mucinous: Bronchio-alveolar Carcinoma + Bronchiolo-alveolar carcinoma, non-mucinous: Bronchio-alveolar Carcinoma + CNS Neoplasm: CNS Neoplasm + Carcinoma, diffuse type: Carcinoma NOS + Carcinoma, undifferentiated, NOS: Carcinoma NOS + Dedifferentiated liposarcoma: Liposarcoma + Ductal carcinoma in situ, NOS: Ductal Carcinoma NOS + Epithelioid cell melanoma: Melanoma + Epithelioid sarcoma: Epithelioid Sarcoma + Follicular adenocarcinoma, NOS: Follicular Carcinoma + Follicular carcinoma, minimally invasive: Follicular Carcinoma + Gastrointestinal Stromal Tumor (GIST): Gastrointestinal Stromal Tumor (GIST) + Hemangioma: Hemangioma + Infiltrating duct mixed with other types of carcinoma: Carcinoma + Leiomyosarcoma, NOS: Leiomyosarcoma, NOS + Lobular carcinoma, NOS: Lobular carcinoma NOS + Malignant melanoma, NOS: Melanoma + Medullary carcinoma, NOS: Medullary Carcinoma + Metaplastic carcinoma, NOS: Metaplastic Carcinoma + Micropapillary carcinoma, NOS: Micropapillary Carcinoma + Mixed epithelioid and spindle cell melanoma: Melanoma + Mixed glioma: Glioma + Mucinous adenocarcinoma: Mucinous Adenocarcinoma + Mucinous adenocarcinoma, endocervical type: Mucinous Adenocarcinoma + Nodular melanoma: Melanoma + Oligodendroglioma, NOS: Oligodendroglioma + Oligodendroglioma, anaplastic: Oligodendroglioma + Oxyphilic adenocarcinoma: Oxyphilic Adenocarcinoma + Papillary adenocarcinoma, NOS: Papillary Carcinoma + Papillary carcinoma, columnar cell: Papillary Carcinoma + Papillary carcinoma, follicular variant: Papillary Carcinoma + Papillary transitional cell carcinoma: Papillary Carcinoma + Serous cystadenocarcinoma, NOS: Serous Cystadenocarcinoma NOS + Spindle cell melanoma, NOS: Melanoma + Spindle cell melanoma, type B: Melanoma + Squamous cell carcinoma, keratinizing, NOS: Squamous Cell Carcinoma Nos + Squamous cell carcinoma, large cell, nonkeratinizing, NOS: Squamous Cell Carcinoma Nos + Thymoma: Thymoma + Thyroid Carcinoma: Thyroid Carcinoma + Tubular adenocarcinoma: Tubular Adenocarcinoma + Atypical Teratoid Rhabdoid Tumor (ATRT): Atypical Teratoid/Rhabdoid Tumor + Brainstem glioma- Diffuse intrinsic pontine glioma: Glioma + Dysembryoplastic neuroepithelial tumor (DNET): Dysembryoplastic Neuroepithelial Tumor + Dysplasia/Gliosis: Dysplasia + Embryonal Tumor with Multilayered Rosettes (ETMR): Embryonal Tumor + Ewings Sarcoma: Ewing Sarcoma + Glial-neuronal tumor NOS: Glial Tumor + Gliomatosis cerebri: Glioma + High-grade glioma/astrocytoma (WHO grade III/IV): Glioma + Langerhans Cell histiocytosis: Langerhans Cell Histiocytosis + Low-grade glioma/astrocytoma (WHO grade I/II): Glioma + Malignant peripheral nerve sheath tumor (MPNST): Malignant Peripheral Nerve Sheath Tumor (Mpnst) + Metastatic secondary tumors: Metastatic Secondary Tumors + Neurofibroma/Plexiform: Neurofibroma + Non-germinomatous germ cell tumor: Non-Germinomatous Germ Cell Tumor + Oligodendroglioma: Oligodendroglioma + Ossifying fibroma: Ossifying Fibroma + Primary CNS lymphoma: Lymphoma, NOS + Subependymal Giant Cell Astrocytoma (SEGA): Astrocytoma + Supratentorial or Spinal Cord PNET: Supratentorial Ependymoma + arteriovenous malformation: Arteriovenous Malformation + atypical lymphoid infiltrate: Atypical Lymphoid Infiltrate + choroid plexus cyst: Choroid Plexus Neoplasm + dermoid cyst: Dermoid Cyst + dermoid inclusion cyst: Dermoid Cyst + embryonal tumor, nos, congenital type: Embryonal Tumor + epidermoid cyst: Dermoid Cyst + epilepsy, chronic rasmussen encephalitis: Rasmussen Encephalitis + fibroma: Fibroma + fibromyxoid lesion: Fibroma + hamartoma: Hamartoma + inclusion cyst: Dermoid Cyst + juvenile xanthogranuloma of the cns: Xanthogranuloma + malignant melanocytic neoplasm: Malignant Melanocytic Neoplasm + meningioangiomatosis: Meningioangiomatosis + myofibroblastic tumor: Myofibroblastic Tumor + myxoid spindle cell tumor: Myxoid Spindle Cell Tumor + osteoblastoma: Osteoblastoma + perineuroma: Perineuroma + reactive connective tissue: Reactive Connective Tissue + rosai-dorfman disease: Glioma + Prostate Cancer: Prostate Cancer + Adamantinomatous craniopharyngioma (WHO grade 1): Adamantinomatous Craniopharyngioma + Adrenal cortical neoplasm, low risk: Adrenal Cortical Neoplasm + Astrocytoma, IDH-mutant, WHO grade 2: Astrocytoma + Atypical choroid plexus papilloma (CNS WHO grade 2): Atypical Choroid Plexus Papilloma + Atypical meningioma, CNS WHO Grade 2: Atypical Meningioma + Atypical teratoid/Rhabdoid tumor (AT/RT), WHO Grade IV: Atypical Teratoid/Rhabdoid Tumor + CNS neuroblastoma, CNS WHO grade 4: CNS Neuroblastoma + Clear cell adenocarcinoma: Clear Cell Adenocarcinoma + Diffuse Astrocytic neoplasm: Diffuse Astrocytic Neoplasm + Diffuse midline glioma, H3K27-altered: Diffuse Glioma + Diffuse pediatric-type high-grade glioma, H3-wildtype and IDH-wildtype (CNS WHO Grade 4), with evidence of DNA mismatch repair deficiency: Diffuse Glioma + Embryonal malignancy with features of embryonal tumor with multilayered rosettes: Embryonal Tumor + Embryonal tumor, favor medulloblastoma: Embryonal Tumor + Embryonal tumor, possible rhabdoid features: Embryonal Tumor + Ependymoma, NOS, CNS WHO grade 3: Ependymoma NOS + Ependymoma, residual/recurrent, WHO Grade 2: Ependymoma NOS + Extra-renal malignant rhabdoid tumor: Rhabdoid Tumor + Follicular Carcinoma: Follicular Carcinoma + Follicular thyroid carcinoma with angioinvasion: Follicular Carcinoma + Gastric mass/Gastrointestinal tumor; Gastrointestinal stromal tumor: Gastrointestinal Stromal Tumor (GIST) + Generally lower grade appearing glioma, morphologically aligning best with piloid/ pilocytic astrocytoma: Glioma + Glial neoplasm, morphologically most consistent with pilocytic astrocytoma: Glial Neoplasm + Glioma with abundant myxoid changes: Glioma + Glioma with piloid features, consistent with pilocytic astrocytoma: Glioma + High grade CNS tumor with embryonal features: CNS Embryonal Tumor + High-grade malignant glioma: Glioma + Low grade glioneuronal tumor (favor Grade 1 ganglioglioma): Glioneuronal Tumor + Low grade neoplasm, favor pilocytic astrocytoma: Pilocytic Astrocytoma + Low-grade, infiltrating glioma (NOS), IDH-1 (R132H) wild type: Glioma + Malignant small round blue cell tumor, consistent with alveolar rhabdomyosarcoma: Small Round Blue Cell Tumor + Malignant spindle cell neoplasm with rhabdomyosarcomatous features: Spindle Cell Neoplasm + Medulloblastoma, Desmoplastic nodular morphology, Non-WNT by Immunohistochemistry: Medulloblastoma + Medulloblastoma, classic histology type, non-WNT/non-SHH molecular group: Medulloblastoma + Medulloblastoma, classic morphology, non-WNT by immunohistochemistry: Medulloblastoma + Medulloblastoma, classic type, WHO grade 4: Medulloblastoma + Medulloblastoma, classic variant, WHO Grade 4: Medulloblastoma + Medulloblastoma, favor classical histology (WHO Grade IV): Medulloblastoma + Medulloblastoma, large cell/anaplastic histology , non-WNT/non-SHH group: Medulloblastoma + Metastatic Melanoma: Malignant Melanoma NOS + 'Midline posterior fossa brain, biopsy: Features of Medulloblastoma': Medulloblastoma + Nasopharyngeal carcinoma, undifferentiated type.: Nasopharyngeal Carcinoma + Pilomyxoid astrocytoma, WHO grade II: Pilomyxoid Astrocytoma + Pleuropulmonary blastoma (type 1): Pleuropulmonary Blastoma + Pontine region tumor: Brain Tumor + Positive for brain tumor: Brain Tumor + Possible medulloblastoma: Medulloblastoma + Posterior fossa ependymoma, CNS Who grade 3: Posterior Fossa Ependymoma + "Posterior fossa ependymoma, CNS WHO grade 3": Posterior Fossa Ependymoma + Posterior fossa ependymoma, PFA Molecular subgroup, CNS Who grade 3: Posterior Fossa Ependymoma + Primary brain neoplasm: Brain Neoplasm + Primary low-grade glioma, consistent with pilocytic astrocytoma, WHO grade 1: Glioma + Retiform Sertoli-Leydig cell tumor: Sertoli Leydig Cell Tumor + Rhabdomyosarcoma, favor embryonal type: Rhabdomyosarcoma + Rhabdomyosarcoma, spindle cell type: Rhabdomyosarcoma + SMARCA4-Deficient undifferentiated uterine sarcoma: Sarcoma + Sacrococcygeal mass; Features are most consistent with Chordoma: Chordoma + Schwannoma, CNS Who grade 1: Schwannoma + Schwannoma, CNS WHO grade 1: Schwannoma + Sertoli-Leydig cell tumor with heterologous elements, moderately differentiated: Sertoli Leydig Cell Tumor + Small blue cell tumor, favor medulloblastoma: Medulloblastoma + Soft tissue, left supraclavicular mass; Malignant peripheral nerve sheath tumor, high grade: Malignant Tumor + Solid pseudopapillary neoplasm: Papillary Neoplasm + Spindle cell neoplasm with features of a low-grade fibromyxoid sarcoma: Spindle Cell Neoplasm + Spindle cell/ sclerosing rhabdomyosarcoma, with diffuse anaplasia: Spindle Cell Rhabdomyosarcoma + Spindle cell/sclerosing rhabdomyosarcoma: Spindle Cell Rhabdomyosarcoma + Supraglottis, soft tissue; Small round blue cell tumor, consistent with Rhabdomyosarcoma: Rhabdomyosarcoma + features compatible with malignant rhabdoid tumor: Rhabdoid Tumor, Malignant + supratentorial tumor; Low-grade neuroepithelial tumor (WHO Grade 1): Neuroepithelial Tumor + A diffuse midline glioma, H3 K27-altered CNS WHO grade 4, Diffuse midline glioma, H3 K27-altered CNS WHO grade 4: Diffuse Glioma + Adenocarcinoma with clear cell features: Adenocarcinoma + Alveolar rhabdomyosarcoma, FOXO1-rearranged: Alveolar Rhabdomyosarcoma + Alveolar rhabdomyosarcoma, with FOXO-1 rearrangement by FISH, Alveolar rhabdomyosarcoma, with FOXO1 rearrangement by FISH: Alveolar Rhabdomyosarcoma + Atypical meningioma, WHO grade 2: Meningioma + Atypical teratoid/ rhabdoid tumor: Atypical Teratoid/Rhabdoid Tumor + BCOR-rearranged sarcoma: Sarcoma + Brain, Midline supracellar; Diffuse leptomeningeal glioneuronal tumor: Glioneuronal Tumor + CNS high grade neuroepithelial neoplasm: Neuroepithelial Neoplasm + Central neurocytoma, WHO Grade 2: Neurocytoma + Choroid plexus papilloma (WHO grade 1): Choroid Plexus Papilloma + Compatible with small blue cell tumor; favor primary CNS origin: Small Round Blue Cell Tumor + Craniopharyngioma (WHO Grade I): Craniopharyngioma + Craniopharyngioma, WHO Grade 1: Craniopharyngioma + Diffuse glioma, with focal areas concerning for high grade, at least Grade 3: Diffuse Glioma + Diffuse midline glioma, H3 K27-altered, H3 p.K27M-mutant subgroup, CNS WHO grade 4: Diffuse Glioma + Diffuse midline glioma, H3K27 altered, CNS WHO Grade 4: Diffuse Glioma + Dural Tumor"""" Pediatric-type high grade glioma: Glioma + Dysembryoplastic neuroepithelial tumor (DNT), CNS WHO grade 1: Dysembryoplastic Neuroepithelial Tumor + Embryonal neoplasm, favor medulloblastoma: Embryonal Neoplasm + Embryonal tumor with multilayered rosettes (WHO Grade 4): Embryonal Tumor + Embryonal tumor, with features suggestive of embryonal tumor with multilayered rosettes: Embryonal Tumor + Ependymoma, WHO grade 2: Ependymoma NOS + Ependymoma, favor myxopapillary subtype, WHO grade 2: Ependymoma NOS + Ewing sarcoma with EWSR1 - ETV4 Fusion: Ewing Sarcoma + Extrarenal rhabdoid tumor (malignant rhabdoid tumor): Rhabdoid Tumor, Malignant + Ganglioglioma, CNS WHO Grade 1: Ganglioglioma + "Ganglioglioma, CNS WHO grade 1": Ganglioglioma + Gastrointestinal stromal tumor, mixed type, high grade: Gastrointestinal Stromal Tumor (GIST) + Glial neoplasm (favor astrocytoma family): Glial Neoplasm + Glial neoplasm, favor astrocytoma: Glial Neoplasm + Glial neoplasm, favor supratentorial ependymoma: Glial Neoplasm + Glial neoplasm; most consistent with Pilocytic astrocytoma: Glial Neoplasm + Glial or glioneuronal tumor with BRAF V600E immunoreactivity, favor pleomorphic xanthoastrocytoma, CNS WHO grade 2: Glioneuronal Tumor + Glial/glioneruonal neoplasm, histologically low-grade, Glial/glioneuronal neoplasm, histologically low-grade: Glioneuronal Neoplasm + Glineuronal neoplasm, favor Ganglioglioma: Glioneuronal Neoplasm + Glioma with features suggestive of pilocytic astrocytoma: Glioma + Glioma with piloid features.: Glioma + Glioneuronal lesion with gliosis, inflammation, fibrosis, hemorrhage, and other reactive changes: Glioneuronal Lesion + Glioneuronal neoplasm with low-grade features (NOS): Glioneuronal Neoplasm + Glioneuronal tumor high grade: Glioneuronal Tumor + Hemangioma: Hemangioma + High grade glioma, consistent with glioblastoma: Glioma + High-grade gioma, favored to be """"""""diffuse pediatric-type high-grade glioma, H3 wild type and IDH wild type"""""""" with possible hypermutation (pHGG, H3 wild type in IDH wild type).: Glioma + High-grade glioma with ependymal differentiation: Glioma + Infantile rhabdomyosarcoma, spindle cell type, high grade: Rhabdomyosarcoma + Infiltrative low-grade glioneuronal tumor, favor ganglioglioma: Glioneuronal Tumor + Infiltrative spindle cell proliferation: Glioma + Intermediate grade glioma most consistent with Ependymoma: Glioma + Invasive high-grade differentiated thyroid carcinoma: Thyroid Carcinoma + Low grade glial tumor, hypervascular: Glial Tumor + Low grade glioneuronal neoplasm consistent with ganglioglioma, CNS WHO Grade 1: Glioneuronal Neoplasm + Low-grade astrocytic glioma, favor pilocytic astrocytoma: Glioma + Low-grade compact glioma: Glioma + Low-grade glial neoplasm with BRAF V600E mutation: Low Grade Glial Neoplasm + Low-grade sarcoma: Sarcoma + Malignant neoplasm with features of embryonal tumor with multilayered rosettes, CNS WHO Grade 4: Malignant Neoplasm + Malignant neoplasm with features suggestive of primary intracranial sarcoma, DICER1-mutant: Malignant Neoplasm + Malignant neoplasm with myxoid and rhabdoid features and loss of INI-1 by immunohistochemistry, pending further studies: Malignant Neoplasm + Malignant peripheral nerve sheath tumor, FNCLCC Grade 2: Malignant Tumor + Malignant small blue cell tumor consistent with medulloblastoma: Medulloblastoma + Mass, Sinonasal Tumor; Rhabdomyosarcoma: Rhabdomyosarcoma + Medulloblastoma, """"""""classic"""""""" histopathological subtype (NOS): Medulloblastoma + Medulloblastoma, CNS WHO grade 4: Medulloblastoma + Medulloblastoma, Large cell/anaplastic: Medulloblastoma + 'Medulloblastoma, SHH-activated, p53 wild-type pattern (by IHC). CNS WHO grade: 4': Medulloblastoma + Medulloblastoma, classic histologic variant, WHO grade 4: Medulloblastoma + Medulloblastoma, classic histology, CNS WHO grade 4: Medulloblastoma + Medulloblastoma, classic histology, WNT-driven (WHO Grade 4): Medulloblastoma + Medulloblastoma, classic type, histologically defined, WHO grade 4: Medulloblastoma + Medulloblastoma, classical type, NOS, histologically defines, WHO grade 4: Medulloblastoma + Medulloblastoma, desmoplastic / nodular, CNS WHO 4: Medulloblastoma + Medulloblastoma, large cell anaplastic variant, WHO grade 4.: Medulloblastoma + Medulloblastoma, non-WNT / non-SHH (CNS WHO grade 4): Medulloblastoma + Meningeal Tumor, Meningioma, transitional subtype. CNS WHO Grade 1.: Meningioma + Mesenchymal chondrosarcoma, with HEY-NCOA2 gene fusion: Mesenchymal Chondrosarcoma + Mesenchymal neoplasm, favor meningioma: Mesenchymal Neoplasm + Monophasic Synovial sarcoma: Meningioma + Most consistent with astrocytoma, IDH-1 mutant, WHO grade III: Astrocytoma + Myofibroblastic proliferation most consistent with Desmoplastic fibromatosis: Myofibroma + Myofibroblastic tumor with epithelioid spindle cell morphology: Myofibroma + Myxoid spindle cell neoplasm: Myxoid Neoplasm + Nasal embryonal rhabdomyosarcoma: Embryonal Rhabdomyosarcoma + Papillary carcinoma, Papillary thyroid carcinoma: Papillary Thyroid Carcinoma + Paratesticular embryonal rhabdomyosarcoma: Embryonal Rhabdomyosarcoma + Pilocytic Astrocytoma (WHO grade 1): Pilocytic Astrocytoma + Pilocytic Astrocytoma, WHO GRADE 1: Pilocytic Astrocytoma + Pilocytic astrocytoma with pilomyxoid features WHO grade 1: Pilocytic Astrocytoma + Pilocytic astrocytoma, BRAF p.V600E-mutant (WHO grade 1): Pilocytic Astrocytoma + Pilocytic astrocytoma, WHO Grade 1, in cerebellum: Pilocytic Astrocytoma + Pineal parenchymal tumor of intermediate differentiation (PPTID): Pineal Parenchymal Tumor + Pineal parenchymal tumor of intermediate, differentiation, CNS WHO Grade 2: Pineal Parenchymal Tumor + Poorly differentiated malignant neoplasm consistent with embryonal rhabdomyosarcoma: Embryonal Rhabdomyosarcoma + Posterior Fossa Ependymoma WHO 3: Posterior Fossa Ependymoma + Primary CNS neoplasm: CNS Neoplasm + Primary astrocytic tumor, favor pilocytic astrocytoma: Pilocytic Astrocytoma + Residual Synovial sarcoma: Synovial Sarcoma + Residual low garde glial/glioneuronal tumor, Residual low grade glial/glioneuronal tumor: Glioneuronal Tumor + Rhabdomyosarcoma with spindle cell features, extending to surgical margin resection: Rhabdomyosarcoma + Rhabdomyosarcoma, favor alveolar subtype: Rhabdomyosarcoma + Rhabdomyosrcoma: Rhabdomyosarcoma + Sertoli-Leydig cell tumor, moderately differentiated (intermediate differentiation): Sertoli Leydig Cell Tumor + Skull Base, Nasal Cavity, Right Sphenoid Embryonal rhabdomyosarcoma: Embryonal Rhabdomyosarcoma + Small blue cell tumor favour medulloblastoma: Medulloblastoma + Small round blue cell proliferation compatible with embryonal rhabdomyosarcoma: Embryonal Rhabdomyosarcoma + Small round blue cell tumor suspicious for high-grade glioma/possible medulloblastoma: Medulloblastoma + Spindle cell neoplasm with features of Low-grade fibromyxoid sarcoma: Spindle Cell Neoplasm + Spindled and ovoid cell neoplasm most consistent with solitary fibrous tumor: Spindle Cell Neoplasm + Subependymal giant cell astrocytoma (WHO grade 1), Subependymoma giant cell astrocytoma (WHO grade 1): Subependymal Giant Cell Astrocytoma + Subependymal giant cell astrocytoma, CNS WHO grade 1: Subependymal Giant Cell Astrocytoma + Suspicious for medulloblastoma: Medulloblastoma + Thymoma: Thymoma + Thyroid carcinoma: Thyroid Carcinoma + Well-differentiated neuroendocrine tumor: Neuroendocrine Tumor + Well-differentiated neuroendocrine tumor, G1: Neuroendocrine Tumor + favor pilocytic astrocytoma, cannnot entirely exclude higher grade tumor: Pilocytic Astrocytoma + favor pilomyxoid astrocytoma,: Pilomyxoid Astrocytoma + high-grade astrocytoma: Astrocytoma + low grade glial tumor: Glial Tumor + Embryonal rhabdomyosarcoma, NOS;Alveolar rhabdomyosarcoma: Embryonal Rhabdomyosarcoma + Hepatoblastoma, NOS: Hepatoblastoma + Malignant peripheral nerve sheath tumor, NOS: Malignant Tumor + Neoplasm, uncertain whether benign or malignant;Sarcoma, NOS: Neoplasm + Neuroblastoma, NOS;Schwannoma, NOS: Neuroblastoma + Osteosarcoma, NOS;Chondroblastic osteosarcoma: Osteosarcoma, NOS + Osteosarcoma, NOS;Osteoblastoma, NOS: Osteosarcoma, NOS + Osteosarcoma, NOS;Parosteal osteosarcoma: Osteosarcoma, NOS + Papillary carcinoma, encapsulated of thyroid: Papillary Carcinoma + Renal cell carcinoma, NOS;Medullary carcinoma, NOS: Renal Cell Carcinoma + Sarcoma, NOS;Mesenchymal chondrosarcoma: Mesenchymal Chondrosarcoma + Sarcoma, NOS;Undifferentiated sarcoma: Sarcoma + Undifferentiated sarcoma;Osteosarcoma, NOS: Osteosarcoma, NOS + Undifferentiated sarcoma;Rhabdoid tumor, NOS: Rhabdoid Tumor, Malignant + Yolk sac tumor, NOS: Yolk Sac Tumor + Alveolar soft part sarcoma, Alveolar soft part sarcoma with tumor thrombus: Alveolar Soft Part Sarcoma + Angiomatoid fibrous histiocytoma EWSR1-rearranged: Angiomatoid Fibrous Histiocytoma + Astrocytoma, IDH mutant, WHO grade 3: Astrocytoma + Astrocytoma, IDH-mutant, CNS WHO grade 4 (CDKN2A loss by FISH): Astrocytoma + At least low-grade spindle cell neoplasm: Spindle Cell Sarcoma + Atypical compound melanocytic neoplasm, excised: Neoplasm + Atypical meningioma,WHO grade 2: Meningioma + Atypical spindled and epithelioid neoplasm: Neoplasm + Atypical teratoid-rhabdoid tumor, CNS WHO 4: Atypical Teratoid/Rhabdoid Tumor + Brain tumor consistent with ependymoma: Ependymoma NOS + CIC- rearranged round cell sarcoma, CIC-rearranged round cell sarcoma, Round cell sarcoma: Sarcoma + Circumscribed melanocytic neoplasm, intermediate grade: Neoplasm + Desmoid/fibromatosis, Fibromatosis: Desmoid-type Fibromatosis + Diffuse astrocytoma, MYB-altered, CNS WHO grade 1.: Diffuse Astrocytoma + Diffuse midline glioma, H3K 27-altered, WHO grade 4: Diffuse Glioma + Embryonal Rhabdomyosarcoma, Rhabdomyosarcoma embryonic: Embryonal Rhabdomyosarcoma + Embryonal rhabdomyosarcoma, Rhabdomyosarcoma: Embryonal Rhabdomyosarcoma + Ependymal neoplasm: Neoplasm + Epethelioid inflammatory myofibroblastic sarcoma: Sarcoma + Favor Pilocytic astrocytoma: Pilocytic Astrocytoma + Features consistent with embryonal sarcoma (of liver): Sarcoma + Fibrolamellar variant of hepatocellular carcinoma: Hepatocellular Carcinoma, Fibrolamellar + Ganglioglioma, WHO grade I: Glioma + Glial neoplasm with high grade features: Glial Neoplasm + Glial tumor, representative tissue present. Cannot rule out ependymoma: Glial Neoplasm + Glial vs glioneuronal neoplasm with Rosenthal fibers; low-grade: Glial Neoplasm + Glial/glioneuronal tumor with piloid features: Glial Neoplasm + Glioma with features reminiscent of pilocytic astrocytoma: Glioma + High Grade Glioma, High-Grade Glioma: Glioma + High grade glial/ glioneuronal neoplasm: Glial Neoplasm + High grade papillary thyroid carcinoma, with features of diffuse sclerosing subtype: Papillary Thyroid Carcinoma + High-grade Glioma: Glioma + High-grade glioma with loss of H3K27me3 immunoreactivitiy, suggesting diffuse midline glioma, H3K27-altered: Glioma + High-grade poorly differentiated sarcoma: Sarcoma + High-grade sarcoma with skeletal muscle differentiation involving fibrous connective tissue: Sarcoma + Immature Teratoma with features suspicious for yolk sac tumor: Yolk Sac Tumor + Infiltrating high grade glioma NOS: Glioma + Likely metastatic alveolar rhabdomyosarcoma: Alveolar Rhabdomyosarcoma + Low grade glial/glioneuronal tumor.: Glial Tumor + Low grade glioma with piloid features, histologically consistent with Pilocytic astrocytoma, CNS WHO grade 1: Glioma + Low grade myofibroblastic sarcoma: Sarcoma + Low grade neuroepithelial neoplasm with QKI::NTRK2 gene fusion: Neuroepithelial Tumor + Low grade pediatric tumor consistent with Dysembryoplastic neuroepithelial tumor (DNET): Neuroepithelial Tumor + Low-grade glial versus glioneuronal tumor; favor ganglioglioma, CNS WHO grade 1: Glioneuronal Tumor + Low-grade glioma, favor pilocytic astrocytoma, CNS WHO grade I: Pilocytic Astrocytoma + Low-grade glioma, most consistent with pilocytic astrocytoma: Pilocytic Astrocytoma + Malignant diffuse glioma: Diffuse Glioma + Malignant epithelioid tumor with features suggestive of myoepithelial carcinoma: Epitheloid Neoplasm + Malignant neoplasm consistent with rhabdomyosarcoma, embryonal subtype: Rhabdomyosarcoma + Malignant neuroepithelial tumor, with morphology aligning with/ favoring a high grade glioma/ glioblastoma, CNS WHO Grade 4: Neuroepithelial Tumor + Medulloblastoma with large cell/anaplastic histology, CNS WHO grade 4: Medulloblastoma + Medulloblastoma, Nodular/desmoplastic with anaplastic/large cell features, SHH-activated: Medulloblastoma + Medulloblastoma, WHO grade 4: Medulloblastoma + 'Medulloblastoma, desmoplastic/nodular histologic subtype, with immunoprofile supporting SHH-activated, TP-53 mutant molecular subclass, Medulloblastoma, desmoplastic/nodular histologic subtype, with immunoprofile supporting SHH-activated, TP53-mutant molecular subclass': Medulloblastoma + Mesenchymal neoplasm: Mesenchymal Neoplasm + Metastatic carcinoma, morphologically consistent with known nasopharyngeal carcincoma, undifferentiated., Nasopharyngeal carcinoma, undifferentiated type.: Metastatic Carcinoma + Metastatic poorly differentiated carcinoma most compatible with squamous cell carcinoma (lymphoepithelial type, EBER positive): Metastatic Carcinoma + Moderately cellular glioma, IDH-wildtype by immunohistochemistry: Glioma + Morphologically consistent with high-grade neuroepithelial tumor: Pilocytic Astrocytoma + Multifocal papillary thyroid carcinoma, classic type: Papillary Thyroid Carcinoma + Nasopharyngeal carcinoma: Nasopharyngeal Carcinoma + Neoplasm most consistent with pilocytic astrocytoma: Pilocytic Astrocytoma + Papillary thyroid microcarcinoma, classic variant: Papillary Thyroid Carcinoma + Pediatric type diffuse low-grade appearing glioma: Glioma + Pediatric-type diffuse-type glioma, cannot entirely exclude diffuse midline glioma: Glioma + Pilocytic astrocytoma, CNS WHO grade I: Pilocytic Astrocytoma + Pilocytic astrocytoma, with foci of myxoid tumor, coagulative necrosis, and calcification: Pilocytic Astrocytoma + Polymorphous low-grade neuroepithelial tumor of the young (PLNTY; right temporal lobe of brain): Pilocytic Astrocytoma + Poorly differentiated Sertoli-Leydig cell tumor, Seroli-leydig cell tumor: Sertoli Leydig Cell Tumor + Posterior fossa ependymoma, subgroup A: Ependymoma NOS + Primary central nervous system neoplasm, Differential diagnosis includes dysembryoplastic neuroepithelial tumor and low-grade glioma: Neoplasm + Recurrent/residual low-grade glioma, with morphologic features most consistent with pilocytic astrocytoma, CNS WHO grade 1: Pilocytic Astrocytoma + Residual unifocal submucosal muco-epidermoid carcinoma: Ependymoma NOS + Rhabdomyosarcoma, Rhabdomyosarcoma embryonal: Rhabdomyosarcoma + Rhabdomyosarcoma, embryonal type by morphology: Rhabdomyosarcoma + Rhabdomyosarcoma, spindle cell variant: Rhabdomyosarcoma + Round cell sarcoma, favored to represent Ewing sarcoma: Ewing Sarcoma + Small blue cell tumor (probably embryonic): Small Round Blue Cell Tumor + Spindle cell neoplasm with necrosis: Neoplasm + Supratentorial ependymoma, NOS CNS WHO grade 2: Ependymoma NOS + Thymic carcinoma, lymphoepithelial-like variant: Thymic Carcinoma + Tumour lesion for which malignant or benign nature cannot be determined: Tumor + Well-differentiated neuroendocrine tumor (carcinoid tumor) of the distal appendix: Neuroendocrine Tumor + Acute lymphoblastic leukemia NOS: Acute Lymphoblastic Leukemia + Acute lymphoblastic leukemia precursor cell type: Acute Lymphoblastic Leukemia + Acute myeloid leukemia MLL: Acute Myeloid Leukemia, NOS + Acute megakaryoblastic leukemia: Acute Megakaryoblastic Leukemia + Metastatic papillary thyroid carcinoma: Metastatic Papillary Thyroid Carcinoma + Epitheloid sarcoma: Epitheloid Sarcoma + 4th ventricular brain tumor: 4th Ventricular Brain Tumor + Low-grade glial/glioneuronal tumor: Low-grade Glial/Glioneuronal tumor + Metastatic polyphenotypic malignant neoplasm: Metastatic Polyphenotypic Malignant Neoplasm + Acinar cell carcinoma: Acinar Cell Carcinoma + Diffuse glioma: Diffuse Glioma + embryonal rhabdomyosarcoma: Dysembryoplastic Neuroepithelial Tumor + Astrocytic glioma: Astrocytic Glioma + Glial neoplasm: Glial Neoplasm + Brain tumor: Brain Tumor + Atypical teratoid rhabdoid tumor: Atypical Teratoid/Rhabdoid Tumor + Atypical teratoid-rhabdoid tumor: Atypical Teratoid/Rhabdoid Tumor + Atypical teratoid/rhabdoid tumor: Atypical Teratoid/Rhabdoid Tumor + Diffuse glioma: Diffuse Glioma + Diffuse Low-grade Glioma: Diffuse Glioma + Dysembryoplastic neuroepithelial tumor: Dysembryoplastic Neuroepithelial Tumor + dysembroplastic neuroepithelial tumor: Dysembryoplastic Neuroepithelial Tumor + Pilocytic astrocytoma: Pilocytic Astrocytoma + atypical teratoid rhaboid tumor: Atypical Teratoid/Rhabdoid Tumor + Atypical Teratoid/Rhabdoid tumor: Atypical Teratoid/Rhabdoid Tumor + atypical teratoid rhaboid tumor: Atypical Teratoid/Rhabdoid Tumor + Atypical teratoid rhaboid tumor: Atypical Teratoid/Rhabdoid Tumor + Alveolar rhabdomyosarcoma: Alveolar Rhabdomyosarcoma + Acute myeloid leukemia (megakaryoblastic) with t(1;22)(p13;q13); RBM15-MKL1: Acute Myeloid Leukemia, NOS + Acute myeloid leukemia with biallelic mutation of CEBPA: Acute Myeloid Leukemia, NOS + Acute myeloid leukemia with inv(16)(p13.1q22); CBFB-MYH11: Acute Myeloid Leukemia, NOS + Acute myeloid leukemia with mutated NPM1: Acute Myeloid Leukemia, NOS + Acute myeloid leukemia with t(9;11)(p21.3;q23.3); KMT2A-MLLT3: Acute Myeloid Leukemia, NOS + Acute myeloid leukemia, t(8;21)(q22;q22.1); RUNX1-RUNX1T1: Acute Myeloid Leukemia, NOS + Adamantinomatous craniopharyngioma: Adamantinomatous Craniopharyngioma + Adenocarcinoma combined with other types of carcinoma: Adenocarcinoma + Adenocarcinoma intestinal type: Adenocarcinoma + Adenocarcinoma, moderately differentiated, with extension to serosa: Adenocarcinoma + Adenocarcinoma NOS: Adenocarcinoma + Adrenal cortical tumor, NOS: Adrenal Cortical Tumor + Adrenocortical tumor: Adrenal Cortical Tumor + Alveolar soft part sarcoma with tumor thrombus: Alveolar Soft Part Sarcoma + Anaplastic ependymoma: Anaplastic Ependymoma + Angiocentric glioma: Angiocentric Glioma + Atypical teratoid-rhabdoid tumor, cerebellopontine angle tumor: Atypical Teratoid/Rhabdoid Tumor + Aytpical teratoid/rhabdoid tumor (AT/RT), WHO grade 4, Atypical teratoid/rhabdoid tumor (AT/RT), WHO grade 4: Atypical Teratoid/Rhabdoid Tumor + B-lymphoblastic leukemia, BCR-ABL1-like: B-lymphoblastic leukemia/lymphoma, NOS + B-lymphoblastic leukemia/lymphoma with hyperdiploidy: B-lymphoblastic leukemia/lymphoma, NOS + B-lymphoblastic leukemia/lymphoma with hypodiploidy: B-lymphoblastic leukemia/lymphoma, NOS + B-lymphoblastic leukemia/lymphoma with t(12;21)(p13.2;q22.1); ETV6-RUNX1: B-lymphoblastic leukemia/lymphoma, NOS + B-lymphoblastic leukemia/lymphoma with t(1;19)(q23;p13.3); TCF3-PBX1: B-lymphoblastic leukemia/lymphoma, NOS + B-lymphoblastic leukemia/lymphoma with t(9;22)(q34.1;q11.2): B-lymphoblastic leukemia/lymphoma, NOS + B-lymphoblastic leukemia/lymphoma with t(9;22)(q34.1;q11.2); BCR-ABL1: B-lymphoblastic leukemia/lymphoma, NOS + B-lymphoblastic leukemia/lymphoma with t(v;11q23.3); KMT2A-rearranged: B-lymphoblastic leukemia/lymphoma, NOS + B-lymphoblastic leukemia/lymphoma, BCR-ABL1-like: B-lymphoblastic leukemia/lymphoma, NOS + Brain tumor, Medulloblastoma: Brain Tumor + Brain tumor, low grade glioma: Brain Tumor + Brain tumor, pilocytic astrocytoma: Brain Tumor + CNS Embryonal tumor with rhabdoid features: CNS Embryonal Tumor + CNS embryonal neoplasm looks like ependymoma: CNS Embryonal Tumor + Cellular spindle cell neoplasm: Cellular Neoplasm + Central Nervous system tumor with high grade histological features: Central Nervous System Tumor with High Grade Histological Features + Central nervous system tumor with high grade histological features: Central Nervous System Tumor with High Grade Histological Features + Central neuroblastoma: Central Neuroblastoma + Choroid Plexus Papilloma, Who grade 2 Choroid plexus papilloma Choroid plexus papillary tumor: Choroid Plexus Papilloma + Classic medulloblastoma: Classic Medulloblastoma + DFSP Tumor: Desmoplastic/Nodular Medulloblastoma + Dermatofibrosarcoma protuberans: Desmoplastic/Nodular Medulloblastoma + Desmoid fibromatosis: Desmoplastic/Nodular Medulloblastoma + Desmoid type fibromatosis: Desmoplastic/Nodular Medulloblastoma + Desmoid-Type Fibromatosis: Desmoplastic/Nodular Medulloblastoma + Desmoplastic: Desmoplastic/Nodular Medulloblastoma + Desmoplastic infantile ganglioglioma: Desmoplastic/Nodular Medulloblastoma + Desmoplastic small round cell tumor: Desmoplastic/Nodular Medulloblastoma + Desmoplastic/nodular medulloblastoma: Desmoplastic/Nodular Medulloblastoma + Diffuse Midline Glioma: Diffuse Glioma + Diffuse Midline Glioma, Diffuse midline glioma: Diffuse Glioma + Diffuse midline glioma, Diffuse Midline Glioma: Diffuse Glioma + Diffuse hemispheric glioma: Diffuse Glioma + Diffuse hemispheric high-grade glioma: Diffuse Glioma + Diffuse high-grade glioma: Diffuse Glioma + Diffuse midline glioma: Diffuse Glioma + Diffuse midline glioma H3K27M: Diffuse Glioma + Diffuse paediatric-type high-grade glioma: Diffuse Glioma + Diffuse pediatric-type high-grade glioma: Diffuse Glioma + Diffused astrocytoma: Diffuse Astrocytoma + Ductal carcinoma in situ NOS: Ductal Carcinoma NOS + Dysembroplastic neuroepithelial tumor: Dysembryoplastic Neuroepithelial Tumor + Dysembryoplastic neuropithelial tumor: Dysembryoplastic Neuroepithelial Tumor + Embryonal Rhabdomyosarcoma, Embryonal rhabdomyosarcoma: Embryonal Rhabdomyosarcoma + Embryonal rhabdomyosarcoma, Embryonal Rhabdomyosarcoma: Embryonal Rhabdomyosarcoma + Embryonal rhabdomyosarcoma: Embryonal Rhabdomyosarcoma + Embryonal rhabdomyosarcoma with diffuse anaplasia: Embryonal Rhabdomyosarcoma + Embryonal rhabdomyosarcoma, NOS: Embryonal Rhabdomyosarcoma + Embryonal rhabdomyoscarcoma: Embryonal Rhabdomyosarcoma + Embryonal sarcoma: Embryonal Rhabdomyosarcoma + Embryonal neoplasm: Embryonal Neoplasm + High-grade embryonal neoplasm, favor medulloblastoma: Embryonal Neoplasm + Embryonal undifferentiated sarcoma of the liver: Embryonal sarcoma + Embryonal tumor with epithelial differentiation: Embryonal Tumor + Fourth ventricular mass, embryonal tumor with multilayered rosettes: Embryonal Tumor + Embryonal tumor with multi-layered rosettes (ETMR): Embryonal Tumor + Embryonal tumor with multilayered rosettes: Embryonal Tumor + Embryonal tumor with multilayered rosettes, Embryonal tumor w multilayered rosettes: Embryonal Tumor + Embryonal tumor w multilayered rosettes, Embryonal tumor with multilayered rosettes: Embryonal Tumor + Embryonal undifferentiated sarcoma of the liver: Embryonal Tumor + Primitive Embryonal Tumor, Erythroblastic sarcoma: Embryonal Tumor + Erythroblastic sarcoma, Primitive Embryonal Tumor: Embryonal Tumor + Endodermal cyst or metastatic tumor is epithelial origin: Ependymoma NOS + Ependymoma: Ependymoma NOS + Ependymoma with Anaplasia: Ependymoma NOS + Epetheloid sarcoma: Epitheloid Sarcoma + Extrarenal malignant rhabdoid tumor: Extrarenal Malignant Rhabdoid Tumor + Glial Neoplasm with Pilocytic features: Glial Neoplasm + Glial neoplasm, favor ependymoma: Glial Neoplasm + High grade glial neoplasm: Glial Neoplasm + High- Grade glial neoplasm: Glial Neoplasm + Glial/glioneuronal tumor: Glial Tumor + Glial/glioneuronal neoplasm: Glial-neuronal neoplasm + High-grade glial neoplasm: Glial-neuronal neoplasm + Glioblastoma NOS: Glioblastoma + Gliolblastoma: Glioblastoma + Low-grade glioma: Glioma + Low-grade glioma consistent with pilocytic astrocytoma: Glioma + Low-grade glioma-pilocytic astrocytoma: Glioma + Low-grade piloid glioma: Glioma + low grade glioma consistent with pilocytic astrocytoma: Glioma + Glioma malignant: Glioma + Glioma with morphologic features of ependymoma: Glioma + Glioma with piloid features: Glioma + Glioma, favor high grade: Glioma + High grade glioma: Glioma + High-Grade Glioma: Glioma + High-grade glioma: Glioma + High-grade glioma with MNI-BEND2 fusion: Glioma + Glioneuronal neoplasm, CNS WHO grade 1: Glioneuronal Neoplasm + High grade astrocytoma: High-grade Astrocytoma + High Grade astrocytoma: High-grade Astrocytoma + High grade neoplasm, favor central nervous system embryonal tumor: High-grade Central Nervous System Neoplasm Favor Embryonal + High grade central nervous system neoplasm favor embryonal: High-grade Central Nervous System Neoplasm Favor Embryonal + High grade malignant neoplasm: High-grade Malignant Neoplasm + High grade synovial sarcoma: High-grade Synovial Sarcoma + High-grade angiosarcoma: High-grade Angiosarcoma + High-grade ependymal neoplasm: High-grade Ependymal Neoplasm + High-grade ependymal tumor: High-grade Ependymal Tumor + High-grade tumor, favor choroid plexus carcinoma: High-grade tumor + Low grade glio-neuronal neoplasm: Low Grade Glial Neoplasm + Low grade glial neoplasm, favor pilocytic astrocytoma: Low Grade Glial Neoplasm + Low grade glial or glioneuronal neoplasm: Low Grade Glial Neoplasm + Low grade glial cerebral cortical neoplasm: Low Grade Glial Neoplasm + Low grade glial neoplasm: Low Grade Glial Neoplasm + Low grade glial or glioneuronal tumor: Low Grade Glial Tumor + Low grade glio-neuronal neoplasm: Low Grade Glioneuronal Neoplasm + Low grade spindle cell: Low Grade Spindle Cell Neoplasm + Malignant melanoma: Malignant Melanoma NOS + Malignant rhabdoid: Malignant Rhabdoid Tumor + Medullary carcinoma NOS: Medullary Carcinoma + Medullary carcinoma: Medullary Carcinoma + Medulloblastoma WNT-activated: Medulloblastoma + Medulloblastoma non-WNT/non-SHH: Medulloblastoma + Medulloblastoma with extensive nodularity: Medulloblastoma + Medulloblastoma, Non-WNT, Non-SHH: Medulloblastoma + Medulloblastoma, SHH-activated and TP53-mutant: Medulloblastoma + Medulloblastoma, SHH-activated and TP53-wildtype: Medulloblastoma + Medulloblastoma, non-WNT/ non-SHH: Medulloblastoma + Medulloblastoma; Embryonal neoplasm with focal pleomorphic features: Medulloblastoma + Meningioma anaplastic: Meningioma + Myxopapillary ependymoma: Myxopapillary Ependymoma + Nasopharyngeal carcinoma, nonkeratinizing, undifferentiated subtype: Nasopharyngeal Carcinoma Metastatic + High grade primitive neoplasm: Neoplasm + Neoplasm with glioneuronal history: Neoplasm + Neoplasm, malignant: Neoplasm + High-grade cellular malignant neoplasm: Neoplasm + High-grade malignant neoplasm: Neoplasm + High-grade neoplasm: Neoplasm + High-grade neoplasm with neuroepithelial features: Neoplasm + High-grade neoplasm with primitive/embryonal features: Neoplasm + High-grade neoplasm with sarcoma feature: Neoplasm + Neuroblastoma CNS: Neuroblastoma + Neuroblastoma NOS: Neuroblastoma + Neuroblastoma, NOS: Neuroblastoma + Neuroendocrine: Neuroendocrine Tumor + Neuroendocrine tumor: Neuroendocrine Tumor + High-grade neuroepithelial, neoplasm: Neuroepithelial neoplasm, Glioma + Low-grade neuroepithelial neoplasm: Neuroepithelial neoplasm, Glioma + Neuroepithelial neoplasm, Glioma: Neuroepithelial neoplasm, Glioma + Papillary thyroid carcinoma: Papillary Thyroid Carcinoma + Papillary thyroid carcinoma (metastatic): Papillary Thyroid Carcinoma + Paratesticular rhabdomyosarcoma: Paratesticular Rhabdomyosarcoma + Pilocytic or pilomyxoid astrocytoma: Pilocytic Astrocytoma + Pleomorphic sarcoma: Pleomorphic Sarcoma + High grade pleomorphic sarcoma: Pleomorphic Sarcoma + Rhabdomyosarcoma NOS: Rhabdomyosarcoma + Rhabdomyosarcoma, NOS: Rhabdomyosarcoma + Rhabdomyosarcoma, embryonal: Rhabdomyosarcoma + Rhabdomyosarcoma, embryonal type: Rhabdomyosarcoma + High-grade Sarcoma: Sarcoma + Sarcoma with BCOR genetic alteration: Sarcoma + Sarcoma, NOS: Sarcoma + Sertoli leydig cell tumor: Sertoli Leydig Cell Tumor + Sertoli Leydig Tumor: Sertoli Leydig Cell Tumor + Sertoli-Leydig cell tumor: Sertoli Leydig Cell Tumor + Sertoli-Leydig cell tumor, intermediate differentiation to poorly differentiated: Sertoli Leydig Cell Tumor + Sertoli-leydig cell tumor of the ovary: Sertoli Leydig Cell Tumor + Sertoli-leydig cell tumor, Sertolig-leydig cell tumor: Sertoli Leydig Cell Tumor + Small cell neuroendocrine carcinoma: Small Cell Neuroendocrine Carcinoma + Small round blue cell tumor, consistent INI-1/SMARCB1 mutated sarcoma: Small Round Blue Cell Tumor + Small round blue cell tumor, e-wing sarcoma: Small Round Blue Cell Tumor + Small round blue cell tumor, most consistent with CNS embryonal tumor: Small Round Blue Cell Tumor + Small round blue cell tumor: Small Round Blue Cell Tumor + High-grade Blue Cell Tumor: Small Round Blue Cell Tumor + Small round blue cell tumor, e-wing sarcoma: Small Round Blue Cell Tumor + Malignant small round blue cell tumor: Small Round Blue Cell Tumor + High-grade, small round blue cell sarcoma: Small Round Blue Cell Sarcoma + Small round blue cell tumor, consistent INI-1/SMARCB1 mutated sarcoma: Small Round Blue Cell Sarcoma + Small round blue cell tumor, e-wing sarcoma: Small Round Blue Cell Sarcoma + Small round blue cell tumor, most consistent with CNS embryonal tumor: Small Round Blue Cell Sarcoma + Spindle cell lesion with high mitotic rate: Spindle Cell Lesion + Spindle cell lesion: Spindle Cell Lesion + Spindle Cell Neoplasm: Spindle Cell Neoplasm + Spindle Cell rhabdomyosarcoma: Spindle Cell Rhabdomyosarcoma + Spindle cell sarcoma: Spindle Cell Sarcoma + Supratentorial ependymoma: Supratentorial Choroid Plexus Papilloma + Synovial sarcoma, monophasic-type: Synovial Sarcoma + T-lymphoblastic leukemia/lymphoma: T-lymphoblastic Leukemia + T-lymphoblastic leukemia: T-lymphoblastic Leukemia + T-lymphoblastic lymphoma: T-lymphoblastic Lymphoma + Adrenal cortical carcinoma: Adrenal Cortical Carcinoma + Adrenal cortical tumor: Adrenal Cortical Tumor + Atypical teratoid/rhabdoid: Atypical Teratoid/Rhabdoid Tumor + Atypical teratoid/rhabdoid tumor (AT/RT), WHO grade 4, Aytpical teratoid/rhabdoid tumor (AT/RT), WHO grade 4: Atypical Teratoid/Rhabdoid Tumor + Central neuroblastoma: Central Neuroblastoma + Choroid plexus papillary tumor: Choroid Plexus Papillary Tumor + Choroid plexus papilloma: Choroid Plexus Papillary Tumor + Choroid Plexus Papilloma, Who grade 2: Choroid Plexus Papillary Tumor + Craniopharyngioma adamantinomatous: Craniopharyngioma + Diffuse low-grade glioma: Diffuse Glioma + Embryonal tumor, Embryonal tumor w multilayered rosettes: Embryonal Tumor + Embryonal tumor w multilayered rosettes: Embryonal Tumor + Epitheloid Sarcoma: Epitheloid Sarcoma + High grade astrocytoma: High-grade Astrocytoma + High-grade neuroepithelial tumor consistent with embryonal tumor: Neuroepithelial Tumor + High grade neuroepithelial tumor: Neuroepithelial Tumor + Low grade glioma: Low-grade Glioma + Low-Grade Glioma: Low-grade Glioma + Low-grade neuroepithelial tumor: Neuroepithelial Tumor + Low-grade neuroepithelial tumor favor ganglioglioma: Neuroepithelial Tumor + Low-grade neuroepithelial tumor with FGFR1 pV559M and FGFR1 p.N554K mutations: Neuroepithelial Tumor + Malignant rhabdoid tumor: Malignant Rhabdoid Tumor + Neuroepithelial neoplasm, Glioma: Neuroepithelial Neoplasm + Sertolig-leydig cell tumor, Sertoli-leydig cell tumor: Sertolig Leydig Cell Tumor + High-grade Neuroepithelial tumor: Neuroepithelial Tumor + Sertoli-leydig cell tumor, Sertolig-leydig cell tumor: Sertolig Leydig Cell Tumor + Neuroepithelial tumor: Neuroepithelial Tumor + CIC- rearranged round cell sarcoma: Round Cell Sarcoma + Pleuropulmonary blastoma: Pleuropulmonary Blastoma + Choroid plexus papilloma with focal atypia: Choroid Plexus Papilloma + Germinoma/Seminoma: Germinoma + Unclassified round cell sarcoma: Round Cell Sarcoma + Unclassified sarcoma with epithelioid/round cell morphology: Sarcoma + Low grade glial/glioneuronal tumor: Low-grade glial-glioneuronal tumor + Poorly differentiated malignant epithelioid neoplasm with INI1 loss: Epitheloid neoplasm + Chordoma: Chordoma + Mucoepidermoid carcinoma, low grade: Mucoepidermoid carcinoma + Embryonal Tumor: Embryonal Tumor + Clear cell sarcoma of soft tissue: Clear Cell Sarcoma + High-grade neuroepithelial tumor favor glial: Neuroepithelial Tumor + NTRK3 fusion positive spindle cell neoplasm: Neoplasm + High Grade Glioma: Glioma + Anaplastic embryonal neoplasm: Embryonal Neoplasm + CNS Neuroblastoma, FOXR-2Activated (WHO Grade 4): Neuroblastoma + High-grade Glioma (WHO grade 4) morphologically resembling Glioblastoma: Glioma + Atypical teratoid/Rhaboid tumor: Atypical Teratoid/Rhabdoid Tumor + High grade glioneuronal neoplasm, NOS: Glioneuronal Neoplasm + High-grade Glial Neoplasm: Glial-neuronal neoplasm + Intramucosal adenocarcinoma: Glial-neuronal neoplasm + Alveolar soft part sarcoma metastasis: Alveolar Soft Part Sarcoma + Anaplastic/ large cell medulloblastoma: Medulloblastoma + Adenocarcinoma, NOS: Adenocarcinoma + Neoplasm, NOS: Neoplasm + Chondrosarcoma, NOS: Chondrosarcoma, NOS + Melanoma, NOS: Melanoma + Adenocarcinoma, pancreatobiliary type: Adenocarcinoma + Clear cell adenocarcinoma, NOS: Clear Cell Sarcoma + Soft tissue sarcoma: Sarcoma + Squamous cell carcinoma, NOS: Squamous Cell Carcinoma NOS + Rhabdomyoma, NOS: Rhabdomyoma NOS + Transitional cell carcinoma: Carcinoma NOS + Merkel cell tumor: Merkel Cell Tumor + Carcinoma, NOS: Carcinoma NOS + Control: Control + Acute monoblastic and monocytic leukemia: Acute Monoblastic and Monocytic Leukemia + Acute myeloid leukemia, NOS: Acute Myeloid Leukemia, NOS + Alveolar soft part sarcoma: Alveolar Soft Part Sarcoma + Anaplastic large cell lymphoma, ALK positive: Anaplastic Large Cell Lymphoma, ALK Positive + Anaplastic medulloblastoma: Anaplastic Medulloblastoma + Anaplastic rhabdomyosarcoma: Anaplastic Rhabdomyosarcoma + Angiomatoid fibrous histiocytoma: Angiomatoid Fibrous Histiocytoma + Astrocytic neoplasm: Astrocytic Neoplasm + Atypical cellular proliferation with clear features: Atypical Cellular Proliferation with Clear Features + Atypical central neurocytoma: Atypical Central Neurocytoma + Atypical choroid plexus papilloma: Atypical Choroid Plexus Papilloma + Atypical epithelial neoplasm: Atypical Epithelial Neoplasm + Atypical spindle cell proliferation: Atypical Spindle Cell Proliferation + B lymphoblastic leukemia/lymphoma, NOS: B Lymphoblastic Leukemia/Lymphoma, NOS + Brain mass: Brain Mass + Brain, High grade lesion: Brain, High Grade Lesion + Cellular ependymoma: Cellular Ependymoma + Cellular glial neoplasm: Cellular Glial Neoplasm + Cellular neoplasm: Cellular Neoplasm + Cerebellar mass: Cerebellar Mass + Cerebellar tumor: Cerebellar Tumor + Cerebellopontine angle tumor: Cerebellopontine Angle Tumor + Cervical; INI1-Deficient hematological malignancy: Cervical; INI1-Deficient Hematological Malignancy + Chondroblastic osteosarcoma: Chondroblastic Osteosarcoma + Choroid plexus carcinoma: Choroid Plexus Carcinoma + Choroid plexus neoplasm: Choroid Plexus Neoplasm + Chronic myelogenous leukemia, BCR-ABL positive: Chronic Myelogenous Leukemia, BCR-ABL Positive + Chronic myeloid leukemia, BCR-ABL1-positive: Chronic Myeloid Leukemia, BCR-ABL1-Positive + Clear cell meningioma: Clear Cell Meningioma + Clear cell sarcoma: Clear Cell Sarcoma + CNS primative neuroectodermal tumor (PNET): CNS Primitive Neuroectodermal Tumor (PNET) + Consistent with Oligodendroglioma, IDH mutant: Consistent With Oligodendroglioma, IDH Mutant + Desmoid-type fibromatosis: Desmoid-type Fibromatosis + Desmoplastic nodular medulloblastoma: Desmoplastic Nodular Medulloblastoma + Diffuse astrocytoma: Diffuse Astrocytoma + Ductal carcinoma NOS: Ductal Carcinoma NOS + Embryonal tumor: Embryonal Tumor + Endometrioid adenocarcinoma, NOS: Endometrioid Adenocarcinoma, NOS + Ewing sarcoma: Ewing Sarcoma + Familial adenomatous polyposis: Familial Adenomatous Polyposis + Follicular hyperplasia/metastatic papillary thyroid cancer: Follicular Hyperplasia/Metastatic Papillary Thyroid Cancer + Gastrointestinal Stromal Tumor (GIST): Gastrointestinal stromal tumor (GIST) + Glial tumor: Glial Tumor + Glioneuronal lesion: Glioneuronal Lesion + Glioneuronal neoplasm: Glioneuronal Neoplasm + Glioneuronal tumor: Glioneuronal Tumor + Hepatocellular carcinoma, fibrolamellar: Hepatocellular Carcinoma, Fibrolamellar + High grade neuroepithelial tumor : High Grade Neuroepithelial Tumor + High Grade Angiosarcoma: High-grade Angiosarcoma + High Grade Astrocytoma: High-grade Astrocytoma + High grade Neoplasm: High Grade Neoplasm + High-grade Ependymal Tumor: High Grade Ependymal Tumor + High-grade Diffuse Glioma: High Grade Diffuse Glioma + High-grade diffuse glioma: High Grade Diffuse Glioma + High grade sarcoma : High Grade Sarcoma + High-grade tumor: High Grade Tumor + Histiocytic malignancy: Histiocytic Malignancy + Hodgkin lymphoma, NOS: Hodgkin Lymphoma, NOS + Infant hemispheric glioma: Infant Hemispheric Glioma + Infantile fibrosarcoma: Infantile Fibrosarcoma + Infiltrating duct carcinoma, NOS: Infiltrating Duct Carcinoma, NOS + Infiltrating glioma: Infiltrating Glioma + Infiltrating lobular carcinoma, NOS: Infiltrating Lobular Carcinoma, NOS + Inflammatory myofibroblastic tumor: Inflammatory Myofibroblastic Tumor + Intraductal carcinoma NOS: Intraductal Carcinoma NOS + Intraventricular tumor: Intraventricular Tumor + Juvenile granulosa cell tumor: Juvenile Granulosa Cell Tumor + Juvenile myelomonocytic leukemia: Juvenile Myelomonocytic Leukemia + Large cell medulloblastoma: Large Cell Medulloblastoma + Laryngeal papilloma: Laryngeal Papilloma + Left biopsy chest lesion: Left Biopsy Chest Lesion + Left CP Angle Mass; Schwannoma: Left Cp Angle Mass; Schwannoma + Left thoracic tumor: Left Thoracic Tumor + Lobular adenocarcinoma: Lobular Adenocarcinoma + Lobular and ductal carcinoma: Lobular And Ductal Carcinoma + Lobular carcinoma NOS: Lobular Carcinoma NOS + Low cellularity glioma: Low Cellularity Glioma + Low grade astrocytoma: Low Grade Astrocytoma + Low grade fibromyxoid sarcoma: Low Grade Fibromyxoid Sarcoma + Low grade glial neoplasm: Low Grade Glial Neoplasm + Low grade glial tumor: Low Grade Glial Tumor + Low grade glioma: Low Grade Glioma + Low grade glioneuronal neoplasm: Low Grade Glioneuronal Neoplasm + Low grade glioneuronal tumor: Low Grade Glioneuronal Tumor + Low grade neuroepithelial tumor: Low Grade Neuroepithelial Tumor + Low-grade glial-glioneuronal tumor: Low Grade Glial-Glioneuronal Tumor + Low grade neuroglial tumor: Low Grade Neuroglial Tumor + Low grade primary CNS neoplasm: Low Grade Primary CNS Neoplasm + Low grade spindle cell neoplasm: Low Grade Spindle Cell Neoplasm + Low-grade Glial Neoplasm: Low Grade Glial Neoplasm + Low-grade tumor: Low Grade Tumor + Malignant melanoma NOS: Malignant Melanoma NOS + Malignant neoplasm: Malignant Neoplasm + Mast cell leukaemia: Mast Cell Leukemia + Medullary carcinoma: Medullary Carcinoma + Mesenchymal chondrosarcoma: Mesenchymal Chondrosarcoma + Metastatic alveolar rhabdomyosarcoma: Metastatic Alveolar Rhabdomyosarcoma + Metastatic carcinoma: Metastatic Carcinoma + Metastatic embryonal rhabdomyosarcoma: Metastatic Embryonal Rhabdomyosarcoma + Metastatic rhabdomyosarcoma: Metastatic Rhabdomyosarcoma + Nasopharyngeal carcinoma metastatic: Nasopharyngeal Carcinoma Metastatic + Mixed germ cell tumor: Mixed Germ Cell Tumor + Mixed-phenotype acute leukemia, B/myeloid, not otherwise specified: Mixed-Phenotype Acute Leukemia, B/Myeloid, Not Otherwise Specified + Mixed-phenotype acute leukemia, T/myeloid, not otherwise specified: Mixed-Phenotype Acute Leukemia, T/Myeloid, Not Otherwise Specified + Monophasic synovial sarcoma, intermediate-grade (FNCLCC Grade 2 of 3): Monophasic Synovial Sarcoma, Intermediate-Grade (FNCLCC Grade 2 Of 3) + Mucinous carcinoma: Mucinous Carcinoma + Myelodysplastic syndrome with multilineage dysplasia: Myelodysplastic Syndrome With Multilineage Dysplasia + Myelodysplastic syndrome with single lineage dysplasia: Myelodysplastic Syndrome With Single Lineage Dysplasia + Myxoid Glioneuronal tumor: Myxoid Glioneuronal Tumor + Myxoid liposarcoma: Myxoid Liposarcoma + Myxoid neoplasm: Myxoid Neoplasm + Neuroectodermal tumor: Neuroectodermal Tumor + Neuroepithelial neoplasm: Neuroepithelial Neoplasm + Optic pathway glioma: Optic Pathway Glioma + Ovarian sclerosing stromal tumor: Ovarian Sclerosing Stromal Tumor + Pancreatobiliary-type carcinoma: Pancreatobiliary-Type Carcinoma + Papillary carcinoma: Papillary Carcinoma + Papillary neoplasm, favor choroid plexus tumor: Papillary Neoplasm, Favor Choroid Plexus Tumor + Papillary tumor of the pineal region: Papillary Tumor of The Pineal Region + Piloid glial proliferation: Piloid Glial Proliferation + Pilomyxoid astrocytoma: Pilomyxoid Astrocytoma + Pineal parenchymal tumor: Pineal Parenchymal Tumor + Pituitary tumor: Pituitary Tumor + Pleomorphic xanthoastrocytoma: Pleomorphic Xanthoastrocytoma + Plexifrom fibrohistiocytic tumor: Plexifrom Fibrohistiocytic Tumor + Polymorphous low grade neuroepithelial tumor: Polymorphous Low Grade Neuroepithelial Tumor + Poorly differentiated malignant neoplasm with sarcomatoid features: Poorly Differentiated Malignant Neoplasm with Sarcomatoid Features + Poorly differentiated pulmonary adenocarcinoma: Poorly Differentiated Pulmonary Adenocarcinoma + Poorly differentiated ring cell adenocarcinoma: Poorly Differentiated Ring Cell Adenocarcinoma + Poorly differentiated sarcoma: Poorly Differentiated Sarcoma + Poorly differentiated Sertoli-Leydig cell tumor: Poorly Differentiated Sertoli-Leydig Cell Tumor + Posterior fossa ependymoma: Posterior Fossa Ependymoma + Posterior fossa tumor: Posterior Fossa Tumor + Precursor B-Cell Acute Lymphoblastic Leukemia with hyperdiploidy: Precursor B-Cell Acute Lymphoblastic Leukemia with Hyperdiploidy + Primitive neuroectoderma tumor: Primitive Neuroectoderma Tumor + Primitive sarcoma: Primitive Sarcoma + Psammomatous meningioma: Psammomatous Meningioma + Pure germinoma: Pure Germinoma + PXA vs ganglioglioma: PXA Vs Ganglioglioma + Renal cell adenocarcinoma: Renal Cell Adenocarcinoma + Residual CIC-rearranged sarcoma: Residual CIC-Rearranged Sarcoma + Residual Dermatofibrosarcoma protuberans: Residual Dermatofibrosarcoma Protuberans + Residual high grade astrocytoma with piloid features: Residual High Grade Astrocytoma With Piloid Features + Residual high-grade sarcoma: Residual High-Grade Sarcoma + Residual malignant melanoma: Residual Malignant Melanoma + Residual papillary tumor of pineal region: Residual Papillary Tumor of Pineal Region + Residual pineoblastoma: Residual Pineoblastoma + Residual/Recurrent extraventricular neurocytoma: Residual/Recurrent Extraventricular Neurocytoma + Rhabdoid tumor, malignant: Rhabdoid Tumor, Malignant + Right thigh mass: Right Thigh Mass + Round blue cell tumor: Round Blue Cell Tumor + Round cell sarcoma: Round Cell Sarcoma + Round to spindle cell sarcoma: Round To Spindle Cell Sarcoma + Sclerosing stromal tumor: Sclerosing Stromal Tumor + Serous adenocarcinoma, NOS: Serous Adenocarcinoma, NOS + Serous cystadenocarcinoma NOS: Serous Cystadenocarcinoma NOS + Serous surface papillary carcinoma: Serous Surface Papillary Carcinoma + Signet ring cell carcinoma: Signet Ring Cell Carcinoma + Small Blue Cell tumor: Small Blue Cell Tumor + Small round blue cell tumor: Small Round Blue Cell Tumor + Spinal ependymoma myxopapillary: Spinal Ependymoma Myxopapillary + Spinal tumor: Spinal Tumor + Spindle cell neoplasm: Spindle Cell Neoplasm + Spindle cell rhabdomyosarcoma: Spindle Cell Rhabdomyosarcoma + Squamous cell carcinoma NOS: Squamous Cell Carcinoma NOS + Subependymal giant cell astrocytoma: Subependymal Giant Cell Astrocytoma + Supertentorial ependymoma: Supertentorial Ependymoma + Suprasellar mass: Suprasellar Mass + Supratentorial choroid plexus papilloma: Supratentorial Choroid Plexus Papilloma + Synovial sarcoma: Synovial Sarcoma + T lymphoblastic leukemia/lymphoma: T Lymphoblastic Leukemia/Lymphoma + Thalamic brain tumor: Thalamic Brain Tumor + Therapy related myeloid neoplasm: Therapy Related Myeloid Neoplasm + Undifferential small round blue cell tumor: Undifferential Small Round Blue Cell Tumor + Undifferentiated leukemia: Undifferentiated Leukemia + Undifferentiated malignant neoplasm with rhabdoid morphology and INI1 loss: Undifferentiated Malignant Neoplasm with Rhabdoid Morphology And INI1 Loss + Undifferentiated round cell sarcoma: Undifferentiated Round Cell Sarcoma + Well differentiated embryonal rhabdomyosarcoma: Well Differentiated Embryonal Rhabdomyosarcoma + Well differentiated neuroendocrine tumor: Well Differentiated Neuroendocrine Tumor + Well to moderately differentiated colonic adenocarcinoma: Well To Moderately Differentiated Colonic Adenocarcinoma + Yolk sac tumor: Yolk Sac Tumor + Pilocytic astrocytoma, WHO grade 1: Pilocytic astrocytoma, WHO Grade 1 + Low-grade glioneuronal neoplasm: Low-grade Glioneuronal Neoplasm + CNS Embryonal tumor: CNS Embryonal Tumor + Acute myelomonocytic leukemia: Acute Myelomonocytic Leukemia + Low-grade glial neoplasm: Low-grade Glial Neoplasm + High-grade astrocytoma: High-grade Astrocytoma + Pilocytic astrocytoma (WHO grade 1): Pilocytic astrocytoma (WHO Grade 1) + cervical; INI1-Deficient hematological malignancy: Cervical; INI1-Deficient Hematological Malignancy + Biphasic synovial sarcoma: Biphasic Synovial Sarcoma + Choroid plexus carcinoma, CNS Who grade 3: Choroid plexus carcinoma, CNS WHO grade 3 +platform: + Illumina: ILLUMINA + unknown: Unknown +tumor_grade: + unknown: Unknown +vital_status: + unknown: Unknown +ethnicity: + not hispanic or latino: Not Hispanic or Latino + hispanic or latino: Hispanic or Latino + unknown: Unknown + Unkown: Unknown +last_known_disease_status: + With tumor: With Tumor + unknown tumor status: Unknown Tumor Status +race: + Unkown: Unknown + Not Reported;Unknown: Not Reported + Other: Not Reported +disease_type: + Adenomas and Adenocarcinomas: Adenocarcinoma + Cystic, Mucinous and Serous Neoplasms: Neoplasm + Ductal and Lobular Neoplasm: Neoplasm + Nevi and Melanomas: Melanoma + Transitional Cell Papillomas and Carcinomas: Carcinoma NOS +sample_type: + peripheral blood - Blood Derived Cancer: Blood + Tissue Biospecimen Type: Tissue + Invalid value: null +days_to_last_followup: + Not Reported: null + unknown: null +days_to_last_known_status: + Not Reported: null + unknown: null +days_to_recurrence: + Not Reported: null + unknown: null + Unknown: null +last_known_disease_status: + With Tumor: null +morphology: + "8041-03-01 00:00:00": null + "8045-03-01 00:00:00": null + "8140-03-01 00:00:00": null + "8500-03-01 00:00:00": null + "85003": null + "8520-03-01 00:00:00": null + "8522-03-01 00:00:00": null + "8523-03-01 00:00:00": null + "9500-03-01 00:00:00": null + Adenocarcinoma: null + Adenocarcinoma, Ex-Goblet Cell Carcinoid, with Solid, Signet Ring, and Mucinous Features: null + Adenocarcinoma, with Mucinous Features: null + Adenocarcinoma, with Mucinous and Signet Ring Features: null + Malignant melanoma, NOS: null + Melanoma in situ: null + Metastatic Adenocarcinoma, with Neuroendocrine Features: null + Metastatic melanoma: null + Metastatic/Recurrent Adenocarcinoma: null + Mixed mucinous and signet ring cell: null + Nodular melanoma: null + Recurrent/Residual Adenocarcinoma: null + Superficial spreading melanoma: null + Tonsils: null + unknown: null +de_identification_method_type: + manual: Manual +extra_long_values: + - "Library construction is performed using the Illumina TruSeqÊ DNA Sample Preparation Kit (cat# FC-121-2001, FC-121-2002) using the following methods.Ê Genomic DNA (approximatelyÊ 10 ng to 2 ug) is sheared in a volume of 52.5 ul using a Covaris S2 Focused-ultrasocinicator with the following settings: Intensity 5.0; Duty cycle 10%25; Cycles per Burst 200; Treatment Time 120 seconds.Ê Sheared DNA is converted to blunt-ended fragments with 5'-phosphates and 3'-hydroxyl groups using a combination of enzymes that perform fill-in reactions and exhibit exonuclease activity.Ê Size selection of the blunt-ended DNA (200-450 bp average) is accomplished using bead-based methodologies.Ê An A-base is added to the blunt ends as a means to prepare the fragments for adapter ligation and block concatamer formation during the ligation step.Ê Adapters containing a T-base overhangÊ are ligated to the A-tailed DNA fragments.Ê Ligated fragments are PCR-amplified (2-10 cycles depending on quantity of input template) and the amplified library is purified by bead based methodologies.Ê The concentration of the lamplified ibrary is measured using the Invitrogen Qubit dsDNA HS Assay (Q32851) and an aliquot of the library is resolved on an Agilent 2200 Tape Station using a D1K (cat# 5067-5361 and 5067-5362) or a High Sensitivity D1K (cat# 5067-5363 and 5067-5364) assay to define the size distribution of the sequencing library.Ê Libraries are adjusted to a concentration of approximately 10 nM and quantitative PCR is performed using the KapaBiosystems Kapa Library Quant Kit (cat# KK4824) to calculate the molarity of adapter ligated library molecules.Ê The concentration is further adjusted following qPCR to prepare the library for Illumina sequence analysis." \ No newline at end of file diff --git a/2-Config-Files/cds_config_v1.3/cds_config_example_v1.3.yaml b/2-Config-Files/cds_config_v1.3/cds_config_example_v1.3.yaml new file mode 100644 index 0000000..63b6d22 --- /dev/null +++ b/2-Config-Files/cds_config_v1.3/cds_config_example_v1.3.yaml @@ -0,0 +1,127 @@ +NODE_FILE: ./3-Model-Files/cds-model.yml +DATA_FOLDER: ./0-Raw-Data-Files/cds_raw_data_files_v1.3/ +DATA_BATCH_NAME: cds_data_2024-3-5-March +OUTPUT_FOLDER: ./4-Transformed-Data-Files/cds_transformed_data_files_v1.3/ +RATIO_LIMIT: 0.90 +S3_BUCKET: s3 +S3_RAWDATA_SUBFOLDER: cds_data_2024-3-5-March +MODEL_FILE_PROPS: ./3-Model-Files/cds-model-props.yml +CLEAN_DICT: ./2-Config-Files/cds_config_v1.3/cds_clean_dict_v1.3.yaml +RAW_DATA_DICTIONARY: ./2-Config-Files/cds_config_v1.3/cds_raw_dict_v1.3.yaml +VALIDATION_FILE: ./2-Config-Files/cds_config/UI-database mappings_v3.xlsx +ID_VALIDATION_RESULT_FOLDER: ./5-ID-Validation-Result +#HISTORICAL_PROPERTIES: +# - +# node: study +# property: study_version +# historical_property_file: 2-Config-Files/cds_config_v1.3/historical_study_version.yaml +# - +# node: study +# property: study_data_types +# historical_property_file: 2-Config-Files/cds_config_v1.3/historical_study_data_types.yaml +PARENT_MAPPING_COLUMNS: + - + node: participant + parent_node: study + property: phs_accession + relationship: of_study + - + node: sample + parent_node: participant + property: study_participant_id + relationship: of_participant + - + node: file + parent_node: sample + property: sample_id + relationship: from_sample + - + node: genomic_info + parent_node: file + property: file_id + relationship: of_file + - + node: diagnosis + parent_node: participant + property: study_participant_id + relationship: of_file + - + node: study + parent_node: program + property: program_acronym + relationship: of_program + - + node: file + parent_node: study + property: phs_accession + relationship: of_study + - + node: image + parent_node: file + property: file_id + relationship: of_file + +COMBINE_NODE: + - + node: study + id_column: phs_accession + - + node: program + id_column: program_acronym + - + node: diagnosis + id_column: study_diagnosis_id + +COMBINE_COLUMN: + - + node: sample + column1: sample_id + column2: sample_type + new_column: sample_id + external_node: False + - + node: participant + column1: phs_accession + column2: participant_id + new_column: study_participant_id + external_node: study + - + node: diagnosis + column1: study_participant_id + column2: diagnosis_id + new_column: study_diagnosis_id + external_node: participant + - + node: genomic_info + column1: genomic_info_id + column2: library_id + new_column: genomic_info_id + external_node: False + +SECONDARY_ID_COLUMN: + - + node: diagnosis + node_id: diagnosis_id + secondary_id: participant.participant_id + - + node: genomic_info + node_id: genomic_info_id + secondary_id: file.file_id + - + node: image + node_id: study_link_id + secondary_id: file.file_id + +REMOVE_NODES: + #- diagnosis + - treatment + +NODE_ID_FIELD: + program: program_acronym + file: file_id + sample: sample_id + participant: study_participant_id + study: phs_accession + diagnosis: study_diagnosis_id + genomic_info: genomic_info_id + image: study_link_id \ No newline at end of file diff --git a/2-Config-Files/cds_config_v1.3/cds_config_jenkins_v1.3.yaml.j2 b/2-Config-Files/cds_config_v1.3/cds_config_jenkins_v1.3.yaml.j2 new file mode 100644 index 0000000..63830be --- /dev/null +++ b/2-Config-Files/cds_config_v1.3/cds_config_jenkins_v1.3.yaml.j2 @@ -0,0 +1,127 @@ +NODE_FILE: ./3-Model-Files/cds-model.yml +DATA_FOLDER: ./0-Raw-Data-Files/cds_raw_data_files_v1.3/ +DATA_BATCH_NAME: {{data_batch_name}} +OUTPUT_FOLDER: ./4-Transformed-Data-Files/cds_transformed_data_files_v1.3/ +RATIO_LIMIT: 0.75 +S3_BUCKET: {{s3_bucket}} +S3_RAWDATA_SUBFOLDER: {{s3_rawdata_subfolder}} +MODEL_FILE_PROPS: ./3-Model-Files/cds-model-props.yml +CLEAN_DICT: ./2-Config-Files/cds_config_v1.3/cds_clean_dict_v1.3.yaml +RAW_DATA_DICTIONARY: ./2-Config-Files/cds_config_v1.3/cds_raw_dict_v1.3.yaml +VALIDATION_FILE: ./2-Config-Files/cds_config/UI-database mappings_v3.xlsx +ID_VALIDATION_RESULT_FOLDER: ./5-ID-Validation-Result +HISTORICAL_PROPERTIES: + - + node: study + property: study_version + historical_property_file: 2-Config-Files/cds_config_v1.3/historical_study_version.yaml + - + node: study + property: study_data_types + historical_property_file: 2-Config-Files/cds_config_v1.3/historical_study_data_types.yaml +PARENT_MAPPING_COLUMNS: + - + node: participant + parent_node: study + property: phs_accession + relationship: of_study + - + node: sample + parent_node: participant + property: study_participant_id + relationship: of_participant + - + node: file + parent_node: sample + property: sample_id + relationship: from_sample + - + node: genomic_info + parent_node: file + property: file_id + relationship: of_file + - + node: diagnosis + parent_node: participant + property: study_participant_id + relationship: of_file + - + node: study + parent_node: program + property: program_acronym + relationship: of_program + - + node: file + parent_node: study + property: phs_accession + relationship: of_study + - + node: image + parent_node: file + property: file_id + relationship: of_file + +COMBINE_NODE: + - + node: study + id_column: phs_accession + - + node: program + id_column: program_acronym + - + node: diagnosis + id_column: study_diagnosis_id + +COMBINE_COLUMN: + - + node: sample + column1: sample_id + column2: sample_type + new_column: sample_id + external_node: False + - + node: participant + column1: phs_accession + column2: participant_id + new_column: study_participant_id + external_node: study + - + node: diagnosis + column1: study_participant_id + column2: diagnosis_id + new_column: study_diagnosis_id + external_node: participant + - + node: genomic_info + column1: genomic_info_id + column2: library_id + new_column: genomic_info_id + external_node: False + +SECONDARY_ID_COLUMN: + - + node: diagnosis + node_id: diagnosis_id + secondary_id: participant.participant_id + - + node: genomic_info + node_id: genomic_info_id + secondary_id: file.file_id + - + node: image + node_id: study_link_id + secondary_id: file.file_id + +REMOVE_NODES: + #- diagnosis + - treatment + +NODE_ID_FIELD: + program: program_acronym + file: file_id + sample: sample_id + participant: study_participant_id + study: phs_accession + diagnosis: study_diagnosis_id + genomic_info: genomic_info_id + image: study_link_id \ No newline at end of file diff --git a/2-Config-Files/cds_config_v1.3/cds_raw_dict_v1.3.yaml b/2-Config-Files/cds_config_v1.3/cds_raw_dict_v1.3.yaml new file mode 100644 index 0000000..84dfb86 --- /dev/null +++ b/2-Config-Files/cds_config_v1.3/cds_raw_dict_v1.3.yaml @@ -0,0 +1,141 @@ +file: + experimental_strategy_and_data_subtype: experimental_strategy_and_data_subtypes + file_description: file_description + file_name: file_name + file_size: file_size + file_type: file_type + file_url_in_cds: file_url_in_cds + md5: md5sum + md5sum: md5sum + submission_version: submission_version +study: + FUNDING: funding_agency + acl: acl + adult_or_childhood_study: adult_or_childhood_study + authz: authz + bioproject_accession: bioproject_accession + clinical_trial_arm: clinical_trial_arm + clinical_trial_identifier: clinical_trial_identifier + clinical_trial_repository: clinical_trial_system + clinical_trial_system: clinical_trial_system + co_primary_investigator_email: primary_investigator_email + co_primary_investigator_name: primary_investigator_name + file_types_and_format: file_types_and_format + funding_agency: funding_agency + funding_source_program_name: funding_source_program_name + grant_id: grant_id + number_of_participants: number_of_participants + number_of_samples: number_of_samples + organism_species: organism_species + phs_accession: phs_accession + primary_investigator_email: primary_investigator_email + primary_investigator_name: primary_investigator_name + size_of_data_being_uploaded: size_of_data_being_uploaded + study_access: study_access + study_acronym: study_acronym + study_data_type: study_data_types + study_data_types: study_data_types + study_description: study_description + study_name: study_name + study_version: study_version +participant: + dbGaP_subject_id: dbGaP_subject_id + ethnicity: ethnicity + gender: gender + participant_id: participant_id + race: race +sample: + ADDITIONAL SAMPLE: sample_id + age_at_collection: sample_age_at_collection + biosample_accession: biosample_accession + derived_from_specimen: derived_from_specimen + sample_age_at_collection: sample_age_at_collection + sample_anatomic_site: sample_anatomic_site + sample_id: sample_id + sample_tumor_status: sample_tumor_status + sample_type: sample_type + sample_type_category: sample_type +genomic_info: + avg_read_length: avg_read_length + bases: bases + coverage: coverage + custom_assembly_fasta_file_for_alignment: custom_assembly_fasta_file_for_alignment + design_description: design_description + instrument_model: instrument_model + library_id: library_id + library_layout: library_layout + library_selection: library_selection + library_source: library_source + library_strategy: library_strategy + number_of_reads: number_of_reads + platform: platform + reference_genome_assembly: reference_genome_assembly + sequence_alignment_software: sequence_alignment_software +diagnosis: + age_at_diagnosis: age_at_diagnosis + days_to_last_followup: days_to_last_followup + days_to_last_known_disease_status: days_to_last_known_status + days_to_recurrence: days_to_recurrence + diagnosis_id: diagnosis_id + disease_type: disease_type + last_known_disease_status: last_known_disease_status + morphology: morphology + primary_diagnosis: primary_diagnosis + primary_site: primary_site + progression_or_recurrence: progression_or_recurrence + tumor_grade: tumor_grade + tumor_stage_clinical_m: tumor_stage_clinical_m + tumor_stage_clinical_n: tumor_stage_clinical_n + tumor_stage_clinical_t: tumor_stage_clinical_t + vital_status: vital_status +image: + acquisition_method_type: acquisition_method_type + channel_metadata_filename: channel_metadata_filename + citation_or_DOI: citation_or_DOI + de.identification_method_description: de_identification_method_description + de.identification_method_type: de_identification_method_type + de.identification_software: de_identification_software + embedding_medium: embedding_medium + imaging_assay_type: imaging_assay_type + imaging_equipment_manufacturer: imaging_equipment_manufacturer + imaging_equipment_model: imaging_equipment_model + imaging_modality: image_modality + imaging_protocol: imaging_protocol + imaging_software: imaging_sofware + immersion: immersion + lens_numerical_aperture: lens_numerical_aperture + license: license + longitudinal_temporal_event_offset: longitudinal_temporal_event_offset + longitudinal_temporal_event_type: longitudinal_temporal_event_type + nominal_magnification: nominal_magnification + objective: objective + organ_or_tissue: organ_or_tissue + physical_size_x: physical_size_x + physical_size_y: physical_size_y + physical_size_z: physical_size_z + pyramid: pyramid + size_c: size_c + size_t: size_t + size_x: size_x + size_y: size_y + size_z: size_z + staining_method: staining_method + study_link_ID: study_link_id + tissue_fixative: tissue_fixative + tissue_or_organ_of_origin: organ_or_tissue + tumor_tissue_type: tumor_tissue_type + working_distance: working_distance +treatment: + days_to_treatment: days_to_treatment + therapeutic_agents: therapeutic_agents + treatment_id: treatment_id + treatment_outcome: treatment_outcome + treatment_type: treatment_type +program: + institution: institution + program_acronym: program_acronym + program_description: program_name + program_external_url: program_external_url + program_name: program_name +null: + file_access: file_access diff --git a/2-Config-Files/cds_config_v1.3/cds_raw_dict_v1.3_2024_Mar.yaml b/2-Config-Files/cds_config_v1.3/cds_raw_dict_v1.3_2024_Mar.yaml new file mode 100644 index 0000000..5f8c996 --- /dev/null +++ b/2-Config-Files/cds_config_v1.3/cds_raw_dict_v1.3_2024_Mar.yaml @@ -0,0 +1,125 @@ +diagnosis: + age_at_diagnosis: age_at_diagnosis + days_to_last_followup: days_to_last_followup + days_to_last_known_disease_status: days_to_last_known_status + diagnosis_id: diagnosis_id + disease_type: disease_type + last_known_disease_status: last_known_disease_status + morphology: morphology + primary_diagnosis: primary_diagnosis + primary_site: primary_site + progression_or_recurrence: progression_or_recurrence + tumor_grade: tumor_grade + vital_status: vital_status + tumor_stage_clinical_t: tumor_stage_clinical_t + tumor_stage_clinical_m: tumor_stage_clinical_m + days_to_recurrence: days_to_recurrence +file: + GUID: file_id + guid: file_id + experimental_strategy_and_data_subtype: experimental_strategy_and_data_subtypes + file_id: file_id + file_name: file_name + file_size: file_size + file_type: file_type + file_format: file_type + file_url_in_cds: file_url_in_cds + md5sum: md5sum + md5: md5sum + sample_description: file_description + submission_version: submission_version +image: + channel_metadata_filename: channel_metadata_file_url_in_cds + citation_or_DOI: citation_or_DOI + de.identification_method_type: de_identification_method_type + embedding_medium: embedding_medium + imaging_assay_type: imaging_assay_type + imaging_equipment_manufacturer: imaging_equipment_manufacturer + imaging_equipment_model: imaging_equipment_model + imaging_modality: image_modality + imaging_protocol: imaging_protocol + imaging_software: imaging_sofware + immersion: immersion + lens_numerical_aperture: lens_numerical_aperture + license: license + nominal_magnification: nominal_magnification + objective: objective + organ_or_tissue: organ_or_tissue + physical_size_x: physical_size_x + physical_size_y: physical_size_y + physical_size_z: physical_size_z + pyramid: pyramid + size_c: size_c + size_t: size_t + size_x: size_x + size_y: size_y + size_z: size_z + staining_method: staining_method + study_link_ID: study_link_id + tissue_fixative: tissue_fixative + tumor_tissue_type: tumor_tissue_type + working_distance: working_distance +genomic_info: + avg_read_length: avg_read_length + bases: bases + coverage: coverage + design_description: design_description + instrument_model: instrument_model + library_id: library_id + library_layout: library_layout + library_selection: library_selection + library_source: library_source + library_strategy: library_strategy + number_of_reads: number_of_reads + platform: platform + reference_genome_assembly: reference_genome_assembly + sequence_alignment_software: sequence_alignment_software +participant: + dbGaP_subject_id: dbGaP_subject_id + ethnicity: ethnicity + gender: gender + participant_id: participant_id + race: race +program: + institution: institution + program_acronym: program_acronym + program_description: program_short_description + program_external_url: program_external_url + program_name: program_name +sample: + biosample_accession: biosample_accession + sample_age_at_collection: sample_age_at_collection + sample_anatomic_site: sample_anatomic_site + sample_id: sample_id + sample_tumor_status: sample_tumor_status + sample_type: sample_type + #derived_from_specimen: derived_from_specimen +study: + acl: acl + authz: authz + adult_or_childhood_study: adult_or_childhood_study + bioproject_accession: bioproject_accession + co_primary_investigator_email: co_investigator_email + co_primary_investigator_name: co_investigator_name + file_type: file_types + file_types_and_format: file_types_and_format + funding_agency: funding_agency + funding_source_program_name: funding_source_program_name + grant_id: grant_id + number_of_participants: number_of_participants + number_of_samples: number_of_samples + organism_species: organism_species + phs_accession: phs_accession + primary_investigator_email: primary_investigator_email + primary_investigator_name: primary_investigator_name + study_access: study_access + study_acronym: study_acronym + study_data_types: study_data_types + study_description: study_description + study_name: study_name + study_version: study_version + title_short_description: short_description + external_resources: study_external_url +treatment: + treatment_outcome: treatment_outcome + treatment_type: treatment_type diff --git a/2-Config-Files/cds_config_v1.3/cds_raw_dict_v1.3_example.yaml b/2-Config-Files/cds_config_v1.3/cds_raw_dict_v1.3_example.yaml new file mode 100644 index 0000000..1a3604b --- /dev/null +++ b/2-Config-Files/cds_config_v1.3/cds_raw_dict_v1.3_example.yaml @@ -0,0 +1,129 @@ +diagnosis: + age_at_diagnosis: age_at_diagnosis + days_to_last_followup: days_to_last_followup + days_to_last_known_disease_status: days_to_last_known_status + days_to_recurrence: days_to_recurrence + diagnosis_id: diagnosis_id + disease_type: disease_type + last_known_disease_status: last_known_disease_status + morphology: morphology + primary_diagnosis: primary_diagnosis + primary_site: primary_site + progression_or_recurrence: progression_or_recurrence + tumor_grade: tumor_grade + vital_status: vital_status + tumor_stage_clinical_t: tumor_stage_clinical_t + tumor_stage_clinical_m: tumor_stage_clinical_m + days_to_recurrence: days_to_recurrence +file: + GUID: file_id + guid: file_id + experimental_strategy_and_data_subtype: experimental_strategy_and_data_subtypes + file_id: file_id + file_name: file_name + file_size: file_size + file_type: file_type + file_format: file_type + file_url_in_cds: file_url_in_cds + md5sum: md5sum + md5: md5sum + sum: md5sum + sample_description: file_description + submission_version: submission_version +image: + channel_metadata_filename: channel_metadata_file_url_in_cds + citation_or_DOI: citation_or_DOI + de.identification_method_type: de_identification_method_type + embedding_medium: embedding_medium + imaging_assay_type: imaging_assay_type + imaging_equipment_manufacturer: imaging_equipment_manufacturer + imaging_equipment_model: imaging_equipment_model + imaging_modality: image_modality + imaging_protocol: imaging_protocol + imaging_software: imaging_sofware + immersion: immersion + lens_numerical_aperture: lens_numerical_aperture + license: license + nominal_magnification: nominal_magnification + objective: objective + organ_or_tissue: organ_or_tissue + physical_size_x: physical_size_x + physical_size_y: physical_size_y + physical_size_z: physical_size_z + pyramid: pyramid + size_c: size_c + size_t: size_t + size_x: size_x + size_y: size_y + size_z: size_z + staining_method: staining_method + study_link_ID: study_link_id + tissue_fixative: tissue_fixative + tumor_tissue_type: tumor_tissue_type + working_distance: working_distance +genomic_info: + avg_read_length: avg_read_length + bases: bases + coverage: coverage + design_description: design_description + instrument_model: instrument_model + library_id: library_id + library_layout: library_layout + library_selection: library_selection + library_source: library_source + library_strategy: library_strategy + number_of_reads: number_of_reads + platform: platform + reference_genome_assembly: reference_genome_assembly + sequence_alignment_software: sequence_alignment_software +participant: + dbGaP_subject_id: dbGaP_subject_id + ethnicity: ethnicity + gender: gender + participant_id: participant_id + race: race +program: + institution: institution + program_acronym: program_acronym + program_description: program_short_description + program_external_url: program_external_url + program_name: program_name +sample: + age_at_collection: sample_age_at_collection + biosample_accession: biosample_accession + sample_age_at_collection: sample_age_at_collection + sample_anatomic_site: sample_anatomic_site + sample_id: sample_id + sample_tumor_status: sample_tumor_status + sample_type: sample_type + #derived_from_specimen: derived_from_specimen +study: + acl: acl + authz: authz + adult_or_childhood_study: adult_or_childhood_study + bioproject_accession: bioproject_accession + co_primary_investigator_email: co_investigator_email + co_primary_investigator_name: co_investigator_name + file_type: file_types + file_types_and_format: file_types_and_format + funding_agency: funding_agency + funding_source_program_name: funding_source_program_name + grant_id: grant_id + number_of_participants: number_of_participants + number_of_samples: number_of_samples + organism_species: organism_species + phs_accession: phs_accession + primary_investigator_email: primary_investigator_email + primary_investigator_name: primary_investigator_name + study_access: study_access + study_acronym: study_acronym + study_data_type: study_data_types + study_data_types: study_data_types + study_description: study_description + study_name: study_name + study_version: study_version + title_short_description: short_description + external_resources: study_external_url +treatment: + treatment_outcome: treatment_outcome + treatment_type: treatment_type diff --git a/3-Model-Files/.placeholder b/3-Model-Files/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/3-Model-Files/cds-model-props.yml b/3-Model-Files/cds-model-props.yml new file mode 100644 index 0000000..0ec012b --- /dev/null +++ b/3-Model-Files/cds-model-props.yml @@ -0,0 +1,8026 @@ +PropDefinitions: + #crdc_id + crdc_id: + Desc: The crdc_id is a unique identifier that is generated by Data Hub + Type: string + #image + study_link_id: + Desc: The study_link_id is a unique numerical identifier for each study listed on the collection information sheet. The sole purpose of the study_link_id is to indicate which participant described on worksheet 2 - Participant information belongs to what study/collection described on worksheet 1 - Collection information. + Req: true + Type: string + Key: true + de_identification_method_type: + Desc: General description of the de-identification method + Req: true + Enum: + - Manual + - Semiautomatic + - Automatic + - Not applicable + de_identification_method_description: + Desc: 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. + Type: string + de_identification_software: + Desc: Software that was used to de-identify the images (if used) + Type: string + license: + Desc: Official or legal permission to do or own a specified thing. + Req: true + Enum: + - CC BY 3.0 http://creativecommons.org/licenses/by/3.0/ + - CC BY 4.0 https://creativecommons.org/licenses/by/4.0/ + - CC BY-NC 4.0 https://creativecommons.org/licenses/by-nc/4.0/ + - CC BY-NC 3.0 https://creativecommons.org/licenses/by-nc/3.0/ + - Other + citation_or_DOI: + Desc: Publication and/or digital object identifier of the publication for open access studies + Req: true + Type: string + species: + Desc: Use the NCBI Taxonomy ID to identify species. A label provided by NCBI Taxonomy Database (https://www.ncbi.nlm.nih.gov/taxonomy/), which uniquely identifies group or category, at any level, in a system for classifying plants or animals (including humans) providing ranked categories for the classification of organisms according to their suspected evolutionary relationships. + Req: true + Type: string + image_modality: + Desc: The method in which the images are generated. + Req: true + Enum: + - AR + - BI + - BMD + - EPS + - CR + - CT + - CFM + - DMS + - DG + - DX + - ECG + - EEG + - EMG + - EOG + - ES + - XC + - GM + - HD + - IO + - IVOCT + - IVUS + - KER + - LS + - LEN + - MR + - MG + - NM + - OAM + - OPM + - OP + - OPT + - OPTBSV + - OPTENF + - OPV + - OCT + - OSS + - PX + - PA + - POS + - PT + - RF + - RG + - RESP + - RTIMAGE + - SM + - SRF + - TG + - US + - BDUS + - VA + - XA + imaging_equipment_manufacturer: + Desc: Producer of the imaging equipment that was used to generate the digital image + Req: true + Type: string + imaging_equipment_model: + Desc: The words used to describe the specific model of the instrument used to carry out an imaging experiment. + Type: string + imaging_sofware: + Desc: The name of the software package that was used to capture, generate, and process the image. + Type: string + imaging_protocol: + Desc: A rule which guides how an activity should be performed. 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 image was obtained or generated. + Type: string + organ_or_tissue: + Desc: Site where images are associated + Req: true + Type: string + performed_imaging_study_description: + Desc: The textual representation of the certain or salient aspects, characteristics, or features of the imaging study. [Adapted from www.businessdictionary.com] + Req: true + Type: string + performed_imaging_study_admittingDiagnosisCode: + Desc: The identified disease(s) or illness(es) at the time of the admission during which imaging was performed. + Req: true + Type: string + performed_imaging_study_nonAcquisitionModalitiesInStudyCode: + Desc: A coded value specifying the type of equipment that created the images in this imaging study other than that used to acquire the original data. + Req: true + Type: string + performed_imaging_study_lossyImageCompressionIndicator: + Desc: Specifies whether any images in the study are irreversibly altered during encoding at any time during its life. + Req: true + Type: string + performed_imaging_study_summary: + Desc: A brief statement about the characteristics of this element, which is intended for use by the radiologist, technologist and/or physicist during management of the imaging protocol to understand the characteristics of the element in the protocol. + Req: true + Type: string + performed_imaging_study_primaryAnatomicSiteCode: + Desc: A coded value specifying the anatomic location that is the focus of this imaging process protocol element. + Req: true + Type: string + performed_imaging_study_acquisitionTypeCode: + Desc: A coded value specifying spatial aspects of the mechanism of data collection. + Req: true + Type: string + performed_imaging_study_imageTypeCode: + Desc: A coded value that specifies the most important aspect of the images or their derivation. + Enum: + - DYNAMIC + - STRESS + - RCBV + performed_imaging_study_cardiacSynchronizationTechniqueCode: + Desc: The means used to coordinate the collection or reconstruction of data with the cardiac cycle. + Enum: + - REALTIME + - PROSPECTIVE + - RETROSPECTIVE + - PACED + - NONE + performed_imaging_study_dataCollectionDiameter: + Desc: The diameter of the region over which information is acquired. + Req: true + Type: string + performed_imaging_study_respiratoryMotionTechniqueCode: + Desc: The means to be used to coordinate the collection or reconstruction of data with breathing. + Req: true + Enum: + - BREATH-HOLD + - REALTIME + - GATING + - TRACKING + - RETROSPECTIVE + - CORRECTION + - NONE + performed_imaging_study_bodyPositionCode: + Desc: A coded value specifying the 3-dimensional spatial orientation of a subject during this imaging acquisition protocol element. + Enum: + - Supine + - Trendelenburg + - Standing + performed_imaging_study_typeCode: + Desc: A coded value specifying the kind of algorithm used when reconstructing the image from the data acquired during the acquisition process. + Req: true + Type: string + performed_imaging_study_algorithmCode: + Desc: A coded value specifying the algorithm to use when reconstructing the image from the data acquired during the acquisition process + Req: true + Type: string + performed_imaging_study_reconstructionFieldOfViewHeight: + Desc: The vertical dimension of the rectangular region from which data is used in creating the reconstruction of the image. + Req: true + Type: string + performed_imaging_study_reconstructionFieldOfViewWidth: + Desc: The horizontal dimension of the rectangular region from which data is used in creating the reconstruction of the image. + Req: true + Type: string + performed_imaging_study_reconstructionDiameter: + Desc: The diameter of the region from which data is used in creating the reconstruction of the image. + Req: true + Type: string + performed_imaging_study_sliceThickness: + Desc: The cross plane dimension of the reconstructed image. + Req: true + Type: string + performed_imaging_study_reconstructionInterval: + Desc: The cross plane distance between the centers of adjacent, parallel reconstructed images. + Req: true + Type: string + longitudinal_temporal_event_type: + Desc: The type of event to which Longitudinal Temporal Offset from Event is relative. + Type: number + longitudinal_temporal_event_offset: + Desc: An offset in days from a particular event of significance. May be fractional. In the context of a clinical trial, this is often the days since enrollment, or the baseline imaging Study. + Type: number + CTAquisitionProtocolElement_singleCollimationWidth: + Desc: The width of a single row of acquired data. The units are of linear distince, e.g. mm. + Type: string + CTAquisitionProtocolElement_totalCollimationWidth: + Desc: The width of the total collimation over the area of active x-ray detection. The units are of linear distince, e.g. mm. + Req: true + Type: string + CTAquisitionProtocolElement_gantryDetectorTilt: + Desc: Nominal angle of tilt in degrees of the scanning gantry. The units are of plane angle , e.g. degrees. Zero degrees means the gantry is not tilted, negative degrees are when the top of the gantry is tilted away from where the table enters the gantry. + Req: true + Type: string + CTAquisitionProtocolElement_tableSpeed: + Desc: The distance that the table moves per unit of time during the gathering of data. The units are of linear distance divided by time. + Req: true + Type: string + CTAquisitionProtocolElement_spiralPitchFactor: + Desc: Ratio of the distance that the table moves during a complete revolution of the source around the gantry orbit, to the width of the total collimation over the area of active x-ray detection. The units are of unity. + Req: true + Type: string + CTAquisitionProtocolElement_ctdiVol: + Desc: The average dose over the total volume scanned for the selected CT conditions of operation (calculated according to IEC 60601-2-44, Ed.2.1 (Clause 29.1.103.4)). The units are energy dose, e.g. mGy. + Req: true + Type: string + CTAquisitionProtocolElement_ctdiPhantomTypeCode: + Desc: The type of phantom to use for CTDI measurement according to IEC 60601-2-44 + Req: true + Type: string + CTAquisitionProtocolElement_kVp: + Desc: Peak kilovoltage output of the x-ray generator. The units are of electrical potential. + Req: true + Type: string + CTAquisitionProtocolElement_exposureModulationType_Code: + Desc: The manner in which tube current is varied in order to limit the dose. + Enum: + - NONE + - ANGULAR + - LONGITUDINAL + - ECG-BASED + - ORGAN-BASED + CTImageReconstructionProtocolElement_convolutionKernel: + Desc: A label describing the mathematical operations used to reconstruct images from the acquired data. The values for this attribute are vendor specific and not coded. + Type: string + CTImageReconstructionProtocolElement_convolutionKernelGroupCode: + Desc: A coded value specifying the family of mathematical operations to use to reconstruct images from the acquired data + Type: string + MRImageAcquisitionProtocolElement_echoPulseSequenceCategoryCode: + Desc: A coded value specifying an echo category of pulse sequences. + Enum: + - SPIN + - GRADIENT + - BOTH + MRImageAcquisitionProtocolElement_diffusionBValue: + Desc: The factor by which the acquisition is sensitized to the Brownian motion of water molecules. The units are of time/area, e.g. s/mm2 + Type: string + MRImageAcquisitionProtocolElement_diffusionDirectionalityCode: + Desc: A coded value specifying whether diffusion conditions for the frame are directional, or isotropic with respect to direction + Enum: + - DIRECTIONAL + - BMATRIX + - ISOTROPIC + - NONE + MRImageAcquisitionProtocolElement_magneticFieldStrength: + Desc: "A vector quantity indicating the ability of a magnetic field to exert a force on moving electric charges. [The American Heritage\xAE Science Dictionary]. The units are of magnetic flux density, e.g. tesla." + Type: string + MRImageAcquisitionProtocolElement_resonantNucleusCode: + Desc: A coded value specifying the atomic nucleus that is the target of the acquisition + Enum: + - 1H + - 3HE + - 7LI + - 13C + - 19F + - 23NA + - 31P + - 129XE + MRImageAcquisitionProtocolElement_acquisitionContrastCode: + Desc: A coded value specifying the inherent (as opposed to exogenous) contrast in the acquisition. + Enum: + - DIFFUSION + - FLOW_ENCODED_Flow Encoded contrast + - FLUID_ATTENUATED_Fluid Attenuated T2 weighted contrast + - PERFUSION_Perfusion weighted contrast + - PROTON_DENSITY_Proton Density weighted contrast + - STIR_Short Tau Inversion Recovery + - TAGGING_Superposition of thin saturation bands onto image + - T1_T1 weighted contrast + - T2_T2 weighted contrast + - T2_STAR_T2* weighted contrast + - TOF_Time Of Flight weighted contrast + MRImageAcquisitionProtocolElement_inversionRecoveryIndicator: + Desc: Specifies whether an inversion recovery preparatory sequence is used in the acquisition. + Type: string + MRImageAcquisitionProtocolElement_pulseSequenceName: + Desc: Name of the pulse sequence that is used for the acquisition. This is usually a vendor-specific name. + Type: string + MRImageAcquisitionProtocolElement_multipleSpinEchoIndicator: + Desc: Specifies whether different lines in k-space are collected for a single frame. + Type: string + MRImageAcquisitionProtocolElement_phaseContrastIndicator: + Desc: Specifies whether this is a pulse sequence in which the flowing spins are velocity encoded in phase. + Type: string + MRImageAcquisitionProtocolElement_timeOfFlightContrastIndicator: + Desc: Specifies whether contrast is created by the inflow of blood in the saturated plane. + Type: string + MRImageAcquisitionProtocolElement_arterialSpinLabelingContrastCode: + Desc: A coded value specifying how arterial water is used as a diffusable tracer. + Type: string + MRImageAcquisitionProtocolElement_steadyStatePulseSequenceCode: + Desc: A coded value specifying how residual transverse magnetization is maintained during the acquisition. + Enum: + - FREE PRECESSION + - TRANSVERSE + - TIME REVERSED + - LONGITUDINAL + - NONE + MRImageAcquisitionProtocolElement_echoPlanarPulseSequenceIndicator: + Desc: Specifies whether multiple echos of different phase steps are acquired using rephasing gradients instead of repeated 180-degree pulses. + Type: string + MRImageAcquisitionProtocolElement_saturationRecoveryIndicator: + Desc: Specifies whether a saturation recovery pulse sequence is used + Type: string + MRImageAcquisitionProtocolElement_spectrallySelectedSuppressionCode: + Desc: A coded value specifying the type of substance-specific signal suppression is used. + Enum: + - FAT + - WATER + - FAT AND WATER + - SILICON GEL + - NONE + MRImageReconstructionProtocolElement_complexImageComponentCode: + Desc: A coded value specifying the channel of the quadrature detected data, or the combination derived from those channels, used to reconstruct the image + Enum: + - REAL + - IMAGINARY + - PHASE + - MAGNITUDE + PETImagingAcquisitionProtocolElement_gantryDetectorTilt: + Desc: Nominal angle of tilt in degrees of the scanning gantry. The units are of plane angle , e.g. degrees. Zero degrees means the gantry is not tilted, negative degrees are when the top of the gantry is tilted away from where the table enters the gantry. + Type: string + Radiopharmaceutical_radionuclideCode: + Desc: A coded value that specifies the radioactive isotope in the radiophamaceutical. + Type: string + acquisition_method_type: + Desc: Records the method of acquisition or source for the specimen under consideration + Type: string + tumor_tissue_type: + Desc: Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints) + Type: string + tissue_fixative: + Desc: A compound that preserves tissues and cells for microscopic study. + Req: true + Enum: + - Acetone + - Alcohol + - Formalin + - Glutaraldehyde + - OCT media + - RNAlater + - Saline + - 95% Ethanol + - Dimidoester + - Carbodiimide + - Dimethylacetamide + - Para-benzoquinone + - PAXgene tissue + - TCL lysis buffer + - NP40 lysis buffer + - Methacarn + - Cryo-store + - Carnoy's Fixative + - Polaxamer + - Other + - None + - unknown + embedding_medium: + Desc: A material that infiltrates and supports a specimen and preserves its shape and structure for sectioning and microscopy. + Req: true + Enum: + - Paraffin wax + - Carbowax + - Methacrylate + - Epoxy Resin (Araldite) + - Agar embedding + - Celloidin media + - Gelatin + - Other + - None + - Unknown + staining_method: + Desc: Any of the various methods that use a dye, reagent, or other material for producing coloration in tissues or microorganisms for microscopic examination. + Req: true + Type: string + objective: + Desc: "An\_objective\_is an optical element that gathers light from an object being observed and\_focuses\_the\_light rays\_from it to produce a\_real image\_of the object." + Type: string + nominal_magnification: + Desc: The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units) + Type: string + immersion: + Desc: Immersion medium + Type: string + lens_numerical_aperture: + Desc: The numerical aperture of the lens. Floating point value > 0. + Type: string + working_distance: + Desc: The working distance of the lens, expressed as a floating point number. Floating point > 0. Size needs to be specified in microns (um) + Type: string + imaging_assay_type: + Desc: Type of imaging assay + Req: true + Type: string + pyramid: + Desc: The data file contains an image pyramid + Type: string + physical_size_x: + Desc: Physical size (X-dimension) of a pixel. Floating point value > 0. Size needs to be specified in microns (um) + Type: string + physical_size_y: + Desc: Physical size (Y-dimension) of a pixel. Floating point value > 0. Size needs to be specified in microns (um) + Type: string + physical_size_z: + Desc: Physical size (Z-dimension) of a pixel. Floating point value > 0. Size needs to be specified in microns (um) + Type: string + size_c: + Desc: Number of channels. Integer >= 1 + Type: string + size_t: + Desc: Number of time points. Integer >= 1 + Type: string + size_x: + Desc: 'Size of image: X dimension (in pixels). Integer >= 1' + Type: string + size_y: + Desc: 'Size of image: Y dimension (in pixels). Integer >= 1' + Type: string + size_z: + Desc: 'Size of image: Z dimension (in pixels). Integer >= 1' + Type: string + channel_metadata_filename: + Desc: File name of uploaded companion CSV file containing channel-level metadata details + Req: true + Type: string + channel_metadata_file_url_in_cds: + Desc: '' + Req: true + Type: string + channel_id: + Desc: The unique channel identifier for each channel in this image must match the corresponding field in the OME-TIFF header + Req: true + Type: string + channel_name: + Desc: Channel label for each channel in this image must match the corresponding field in the OME-TIFF header + Req: true + Type: string + cycle_number: + Desc: 'the cycle # in which the co-listed reagent(s) was(were) used' + Type: string + sub_cycle_number: + Desc: 'sub-cycle #' + Type: string + target_name: + Desc: short descriptive name (abbreviation) for this target (antigen) + Type: string + antibody_name: + Desc: short descriptive name for this antibody + Type: string + rrid_identifier: + Desc: Research Resource Identifier + Type: string + fluorophore: + Desc: Fluorescent dye label + Type: string + clone: + Desc: Unique clone identifier + Type: string + lot: + Desc: lot number from vendor + Type: string + vendor: + Desc: Vendor name + Type: string + catalog_number: + Desc: catalog number from vendor + Type: string + excitation_wavelength: + Desc: center/peak of the excitation spectrum (nm) + Type: string + emission_wavelength: + Desc: center/peak of the emission spectrum (nm) + Type: string + excitation_bandwidth: + Desc: nominal width of excitation spectrum (nm) + Type: string + emission_bandwidth: + Desc: nominal width of emission spectrum (nm) + Type: string + metal_isotope_element: + Desc: Element mass number + Type: string + oligo_barcode_upper_strand: + Desc: DNA barcode used for labeling + Type: string + oligo_barcode_lower_strand: + Desc: DNA barcode used for labeling + Type: string + diluation: + Desc: Final dilution ratio used in experiment + Type: string + concentration: + Desc: Final concentration used in experiment + Type: string + passes_qc: + Desc: Identify stains that did not pass QC but are included in the dataset. + Type: string + # file + submission_version: + Desc: Raw data file submission + Type: string + Req: true + file_id: + Desc: File identifier + Type: string + Req: true + Key: true + file_url_in_cds: + Desc: Location of the file on the CDS cloud, using AWS S3 protocol + Type: string + Req: Preferred + file_description: + Desc: Human-readable description of file + Type: string + file_name: + Desc: Name of file + Type: string + Req: true + file_size: + Desc: File size in bytes + Type: integer + Req: false + file_type: + Desc: File type from enumerated list + Enum: + - BAI + - BAM + - BW + - CRAI + - CRAM + - FASTQ + - HTML + - IDAT + - JSON + - MAF + - PDF + - TSV + - TXT + - VCF + - XLSX + Req: true + file_access: + Desc: File access + Enum: + - Open + - Controlled + md5sum: + Desc: MD5 hex digest for this file + Type: + pattern: "^[0-9a-fA-F]{32}$" + Req: true + experimental_strategy_and_data_subtypes: + Desc: | + What is the experimental strategy used for the study (or what + type of data subtypes exist in the study)? + Req: 'Yes' + Enum: + - Amplicon + - Archer Fusion + - Bisulfite-Seq + - Methylation Array + - OTHER + - RNA-Seq + - Targeted Sequencing + - Targeted-Capture + - WGA + - WGS + - WXS + Type: + value_type: list + item_type: string + # participant + ethnicity: + Desc: OMB Ethinicity designator + Enum: + - Hispanic or Latino + - Not Hispanic or Latino + - Unknown + - Not Reported + - Not Allowed to Collect + Req: Preferred + gender: + Desc: Biological gender at birth + Enum: + - Female + - Male + - Unknown + - Unspecified + - Not Reported + Req: true + race: + Desc: OMB Race designator + Enum: + - White + - American Indian or Alaska Native + - Black or African American + - Asian + - Native Hawaiian or Other Pacific Islander + - Unknown + - Not Reported + - Not Allowed to Collect + Req: Preferred + participant_id: + Desc: | + A number or a string that may contain metadata information, for a participant + who has taken part in the investigation or study. + Type: string + Req: true + study_participant_id: + Desc: | + The property study_participant_id is a compound property, combining the property participant_id and the parent property study.phs_accession. + It is the ID property for the node participant. The reason why we are doing that is because is some cases, there are same participant id in different studies repersent different participants. + Type: string + Req: true + Key: true + vital_status: + Desc: Vital status as of last known follow up + Enum: + - Alive + - Dead + - Unknown + - Not Reported + dbGaP_subject_id: + Desc: Identifier for the participant as assigned by dbGaP + Type: string + Req: Preferred + # diagnosis + diagnosis_id: + Desc: Internal identifier + Type: string + study_diagnosis_id: + Desc: | + The property study_diagnosis_id is a compound property, combining the property diagnosis_id and the parent property participant.study_participant_id. + It is the ID property for the node diagnosis. + Type: string + Req: true + Key: true + disease_type: + Desc: Type of disease [?] + Enum: + - Acinar Cell Neoplasm + - Basal Cell Neoplasm + - Blood Vessel Neoplasm + - Bone Neoplasm + - Complex Epithelial Neoplasm + - Epithelial Neoplasm + - Fibroepithelial Neoplasm + - Germ Cell Tumor + - Giant Cell Tumor + - Glioma + - Hodgkin Lymphoma + - Leukemia + - Lipomatous Neoplasm + - Lymphatic Vessel Neoplasm + - Lymphoblastic Lymphoma + - Lymphoid Leukemia + - Lymphoma + - Mast Cell Neoplasm + - Mature B-Cell Non-Hodgkin Lymphoma + - Mature T-Cell and NK-Cell Non-Hodgkin Lymphoma + - Meningioma + - Mesothelial Neoplasm + - Myelodysplastic Syndrome + - Myeloid Leukemia + - Myeloproliferative Neoplasm + - Myomatous Neoplasm + - Neoplasm + - Nerve Sheath Neoplasm + - Neuroepithelial Neoplasm + - Not Applicable + - Not Reported + - Odontogenic Neoplasm + - Plasma Cell Neoplasm + - Skin Appendage Neoplasm + - Squamous Cell Neoplasm + - Thymoma + - Trophoblastic Tumor + - Unknown + - Wolffian Tumor + age_at_diagnosis: + Desc: Participant age at relevant diagnosis + Type: integer + days_to_last_known_status: + Desc: Days to last known status of participant, relative to study index date + Type: integer + days_to_last_followup: + Desc: Days to last participant followup, relative to study index date + Type: integer + days_to_recurrence: + Desc: Days to disease recurrence, relative to study index date + Type: integer + incidence_type: + Desc: For this diagnosis, disease incidence relative to prior status of subject + Enum: + - primary + - progression + - recurrence + - metastasis + - remission + - no_disease + last_known_disease_status: + Desc: Last known disease incidence for this subject and diagnosis + Enum: + - Primary + - Progression + - Recurrence + - Metastasis + - Remission + - No_disease + - Distant met recurrence/progression + - Loco-regional recurrence/progression + - Biochemical evidence of disease without structural correlate + - Tumor free + primary_diagnosis: + Desc: Primary disease diagnosed for this diagnosis and subject + Enum: + # reuse ICD-O-3 value_set + - 4th Ventricular Brain Tumor + - Acinar Cell Carcinoma + - Acute megakaryoblastic leukaemia + - Acute Megakaryoblastic Leukemia + - Acute Monoblastic and Monocytic Leukemia + - Acute monoblastic leukemia + - Acute myeloid leukemia with mutated CEBPA + - Acute myeloid leukemia with t(9;11)(p22;q23); MLLT3-MLL + - Acute myeloid leukemia without maturation + - Acute myeloid leukemia, inv(16)(p13;q22) + - Acute myeloid leukemia, minimal differentiation + - Acute Myeloid Leukemia, NOS + - Acute myeloid leukemia, t(16;16)(p 13;q 11) + - Acute Myelomonocytic Leukemia + - Acute promyelocytic leukaemia, t(15;17)(q22;q11-12) + - Acute Promyelocytic Leukemia + - Adamantinomatous Craniopharyngioma + - Adamantinomatous craniopharyngioma with evidence of prior rupture + - Adamantinomatous craniopharyngioma, WHO grade 1 + - Adenocarcinoma + - Adrenal Cortical Carcinoma + - Adrenal cortical neoplasm + - Adrenal Cortical Tumor + - Alveolar Rhabdomyosarcoma + - Alveolar Soft Part Sarcoma + - Anaplastic Ependymoma + - Anaplastic Ganglioglioma + - Anaplastic Large Cell Lymphoma, ALK Positive + - Anaplastic Medulloblastoma + - Anaplastic Rhabdomyosarcoma + - Angiocentric Glioma + - Angiomatoid Fibrous Histiocytoma + - Astrocytic Glioma + - Astrocytic Neoplasm + - Astrocytic neoplasm with pilocytic/pilomyxoid features + - Astrocytoma + - Astrocytoma IDH-mutant, Atrocytoma IDH-mutant + - Astroglial neoplasm + - Atypical Cellular Proliferation with Clear Features + - Atypical Central Neurocytoma + - Atypical Choroid Plexus Papilloma + - Atypical Epithelial Neoplasm + - Atypical Spindle Cell Proliferation + - Atypical Teratoid/Rhabdoid Tumor + - Atypical Teratoid/Rhabdoid Tumor (AT/RT) + - Atypical teratoid/rhabdoid tumor, CNS WHO GRADE 4 + - Atypical teratoid/rhabdoid tumor; CNS WHO grade 4 + - Aytpical teratoid/rhabdoid tumor (AT/RT), WHO grade 4 + - B lymphoblastic leukemia/lymphoma with hyperdiploidy + - B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL) + - B lymphoblastic leukemia/lymphoma with t(12;21)(p13;q22); TEL-AML1 (ETV6-RUNX1) + - B lymphoblastic leukemia/lymphoma with t(1;19)(q23;p13.3); E2A-PBX1 (TCF3-PBX1) + - B lymphoblastic leukemia/lymphoma with t(9;22)(q34;q11.2); BCR-ABL1 + - B lymphoblastic leukemia/lymphoma with t(v;11q23); MLL rearranged + - B Lymphoblastic Leukemia/Lymphoma, NOS + - B-lymphoblastic leukemia/lymphoma, NOS + - Biphasic Synovial Sarcoma + - Brain Mass + - Brain parenchyma with mild hypercellularity, gliosis and possible cortical dysplasia + - Brain Tumor + - Brain tumor with features most suggestive of ependymoma + - Brain, High Grade Lesion + - Carcinoma NOS + - Carcinosarcoma NOS + - Cellular Ependymoma + - Cellular Glial Neoplasm + - Cellular Neoplasm + - Cellular neoplasm; favor high grade + - Central Nervous System Tumor with High Grade Histological Features + - Central Neuroblastoma + - Central Neurocytoma + - Cerebellar Mass + - Cerebellar Tumor + - "Cerebellar tumor: High-grade, small blue round cell tumor" + - Cerebellopontine Angle Tumor + - Cervical; INI1-Deficient Hematological Malignancy + - Chondroblastic Osteosarcoma + - Chondrosarcoma, NOS + - Chordoma + - Choroid Plexus Carcinoma + - Choroid plexus carcinoma, CNS WHO grade 3 + - Choroid Plexus Neoplasm + - Choroid Plexus Papillary Tumor + - Choroid Plexus Papilloma + - Choroid plexus papilloma, WHO grade 1 + - Chronic Myelogenous Leukemia, BCR-ABL Positive + - Chronic Myeloid Leukemia, BCR-ABL1-Positive + - Classic Ependymoma, Posterior fossa group A by Immunohistochemistry + - Classic Medulloblastoma + - Clear Cell Meningioma + - Clear Cell Sarcoma + - CNS Embryonal Tumor + - CNS primative neuroectodermal tumor (PNET) + - CNS Primitive Neuroectodermal Tumor (PNET) + - Compound melanocytic neoplasm + - Consistent With Oligodendroglioma, IDH Mutant + - Control + - Craniopharyngioma + - Desmoid fibromatosis with CTNNB1 gene mutation + - Desmoid-type Fibromatosis + - Desmoid/fibromatosis + - Desmoplastic Nodular Medulloblastoma + - Desmoplastic/Nodular Medulloblastoma + - Desmoplastic/nodular medulloblastoma, CNS WHO grade 4 + - Diffuse astrocytic glioma with mitotic activity and necrosis + - Diffuse Astrocytoma + - Diffuse Glioma + - Diffuse midline glioma, H3 K27-altered + - Diffuse midline glioma, H3 K27-mutant + - Diffuse midline glioma, H3K27-altered (WHO grade 4) + - Diffuse midline glioma, H3K27M altered, CNS WHO grade 4 + - Diffusely infiltrating high grade glioma + - Ductal Carcinoma NOS + - Dysembryoplastic Neuroepithelial Tumor + - Embryonal Neoplasm + - Embryonal neoplasm most consistent with Medulloblastoma + - Embryonal Rhabdomyosarcoma + - Embryonal rhabdomyosarcoma, botryoid type + - Embryonal rhabdomyosarcoma, minimal focal anaplasia + - Embryonal Tumor + - Endometrioid Adenocarcinoma, NOS + - Endometrioid carcinoma + - Epdendymoma, Ependymoma + - Ependymoma NOS + - Ependymoma, WHO GRADE III + - Ependymoma-like lesion + - Epitheliod sarcoma + - Epitheloid neoplasm + - Epitheloid Sarcoma + - Ewing Sarcoma + - Extrarenal Malignant Rhabdoid Tumor + - Familial Adenomatous Polyposis + - Fatty neoplasm with myxoid features, no definitive high grade features, favor lipoblastoma + - Favor Infiltrating High-Grade Glioma + - Fibromatosis + - Fibromatosis Colli + - Follicular Hyperplasia/Metastatic Papillary Thyroid Cancer + - Fragments of Schwannoma, CNS WHO GRADE 1, with some mild degenerative changes + - Frontal tumor, favor infant-type hemispheric glioma + - Fundic gastrointestinal stromal tumor + - Fusion negative embryonal rhabdomyosarcoma + - Ganglioglioma + - Ganglioneuroblastoma + - Ganglioneuroma + - Gastrointestinal stromal tumor (GIST) + - Gastrointestinal stromal tumor (GIST) epithelioid type, high grade + - Germinoma + - Giant Cell Glioblastoma + - Glial Neoplasm + - Glial neoplasm favor optic glioma + - Glial Tumor + - Glial-neuronal neoplasm + - Glioblastoma + - Glioma + - Glioma, histologically consistent with pilocytic astrocytoma, CNS WHO grade 1 + - Glioma, most consistent with astrocytoma with worrisome features in clinical context + - Glioneuronal Lesion + - Glioneuronal Neoplasm + - Glioneuronal Tumor + - Granulosa cell tumor + - Hemangioblastoma + - Hemangioblastoma, WHO Grade 1 + - Hepatoblastoma + - Hepatocellular Carcinoma, Fibrolamellar + - High grade cellular, malignant neoplasm with necrosis and cellular pleomorphism R/O Medulloblastoma + - High Grade Diffuse Glioma + - High Grade Ependymal Tumor + - High Grade Glioma with H3 K27M and BRAF V600E mutations + - High grade glioma, NOS, WHO CNS histologic grade 4 + - High Grade Neoplasm + - High Grade Neuroepithelial Tumor + - High grade neuroepithelial tumor with glial and neuronal differentiation and focal embryonal morphology. + - High grade neuroepithelial tumor, favor medulloblastoma + - High Grade Sarcoma + - High grade spindle cell sarcoma + - High Grade Tumor + - High grade tumor consistent with embryonal tumor + - High-grade Angiosarcoma + - High-grade astrocytic neoplasm + - High-grade Astrocytoma + - High-grade blue cell tumor + - High-grade Central Nervous System Neoplasm Favor Embryonal + - High-grade CNS embryonal tissue + - High-grade CNS Neoplasm + - High-grade Ependymal Neoplasm + - High-grade Ependymal Tumor + - High-grade glioma with DICER1 and other mutations + - High-grade glioma, favor ependymoma, WHO GRADE III + - High-grade infiltrating glioma + - High-grade Malignant Neoplasm + - High-grade malignant neoplasm with mesenchymal phenotype + - High-grade malignant neoplasm, small round blue cell category. + - High-grade neoplasm, favor embryonal tumor + - High-grade neoplasm, favor high-grade glioma + - High-grade neuroepithelial neoplasm + - High-grade neuroepithelial tumor + - High-grade neuroepithelial tumor, consistent with supratentorial ependymoma + - High-grade pleomorphic sarcoma + - High-grade primary CNS neoplasia + - High-grade primitive appearing neoplasm + - High-grade rhabdomyosarcoma with pleomorphic features + - High-grade sarcoma with myogenic differentiation + - High-grade serous carcinoma + - High-grade spindle cell sarcoma compatible with high grade malignant peripheral nerve sheath tumor + - High-grade Synovial Sarcoma + - High-grade tumor + - High-grade undifferentiated sarcoma + - High-grade, primitive neuroepithelial neoplasm + - Histiocytic Malignancy + - Histologically low-grade glioneuronal tumor + - Histologically low-grade neuroepithelial tumor + - Hodgkin Lymphoma, NOS + - Infant Hemispheric Glioma + - Infant-type hemispheric glioma + - Infantile Fibrosarcoma + - Infiltrating duct and lobular carcinoma + - Infiltrating duct and mucinous carcinoma + - Infiltrating duct carcinoma NOS + - Infiltrating Duct Carcinoma, NOS + - Infiltrating Glioma + - Infiltrating high grade neoplasm, favor infiltrating high grade glioma + - Infiltrating Lobular Carcinoma, NOS + - Infiltrating Neoplasm + - Infiltrating neuroepithelial neoplasm + - Inflammatory Myofibroblastic Tumor + - INI-Deficient High-grade Malignant Neoplasm + - Intracerebral schwannoma + - Intraductal Carcinoma NOS + - Intraductal papillary carcinoma + - Intradural tumor with marked atypia c/w malignant lesion, Marked atypia c/w malignant lesion, Marked atypia consistent with malignant lesion + - Intraventricular Tumor + - Invasive lobular carcinoma + - Juvenile Granulosa Cell Tumor + - Juvenile Myelomonocytic Leukemia + - Large Cell Medulloblastoma + - Large cell/anaplastic Medulloblastoma + - Laryngeal Papilloma + - Left Biopsy Chest Lesion + - Left Cp Angle Mass; Schwannoma + - Left Temporal Tumor + - Left Thoracic Tumor + - Lobular Adenocarcinoma + - Lobular And Ductal Carcinoma + - Lobular Carcinoma NOS + - Low Cellularity Glioma + - Low Grade Astrocytoma + - Low Grade Fibromyxoid Sarcoma + - Low Grade Glial Neoplasm + - Low Grade Glial Tumor + - Low Grade Glial-Glioneuronal Tumor + - Low Grade Glioma + - Low grade glioma which morphologically aligns best with pilocytic astrocytoma, CNS WHO Grade 1 + - Low grade glioma, cannot rule out additional neuronal component + - Low grade glioma, morphologically aligning best with pilocytic astrocytoma + - Low Grade Glioneuronal Neoplasm + - Low Grade Glioneuronal Tumor + - Low grade mixed glial-neuronal tumor, morphology is consistent with/ aligns with/ favors ganglioglioma + - Low Grade Neuroepithelial Tumor + - Low grade neuroepithelial tumor (preliminary path report) + - Low grade neuroepithelial tumor consistent with polymorphous low grade neuro-epithelial tumor of the young + - Low Grade Neuroglial Tumor + - Low Grade Primary CNS Neoplasm + - Low Grade Spindle Cell Neoplasm + - Low Grade Tumor + - Low-cellularity glioma + - Low-grade astrocytoma + - Low-grade circumscribed glial/glioneuronal tumor + - Low-grade fibromyxoid sarcoma + - Low-grade Glial Neoplasm + - Low-grade glial neoplasm, favor pilomyxoid/pilocytic actrocytoma + - Low-grade glial neoplasm, with features most consistent with a pilocytic astrocytoma. + - Low-grade glial-glioneuronal tumor + - Low-grade glial/glioneuronal neoplasm + - Low-grade Glial/Glioneuronal tumor + - Low-grade glial/glioneuronal tumor with adjacent cortical dysplastic changes. + - Low-grade Glioma + - Low-grade glioma, favored to represent a pilocytic astrocytoma + - Low-grade Glioneuronal Neoplasm + - Low-grade glioneuronal tumor + - Low-grade glioneuronal tumor, favor Dysembryoplastic neuroepithelial tumor + - Low-grade spindle cell neoplasm + - Low-grade tumor + - Lymphoma, NOS + - Malignant embryonal tumor, favor medulloblastoma + - Malignant epithelioid neoplasm, Malignant epithelioid neoplasm with EWSR1::KLF5 fusion + - Malignant glioma + - Malignant Melanoma NOS + - Malignant melanoma, spitzoid type + - Malignant myoepithelial of pediatric type + - Malignant Neoplasm + - Malignant neoplasm most consistent with embryonal tumor + - Malignant neoplasm of prostate + - Malignant neuroepithelial tumor + - Malignant Pecoma + - Malignant peripheral nerve sheath tumor + - Malignant primary brain tumor + - Malignant Rhabdoid Tumor + - Malignant small blue cell neoplasm, consistent with rhabdomyosarcoma + - Malignant small round blue cell neoplasm, favor rhabdomyosarcoma + - Malignant small round blue cell tumor, most consistent with desmoplastic small round cell tumor + - Malignant Tumor + - Mast Cell Leukemia + - Medullary Carcinoma + - Medulloblastoma + - Medulloblastoma (CNS WHO grade 4) + - Medulloblastoma, anaplastic histology, WHO grade 4 + - Medulloblastoma, anaplastic/large cell histology, Non-WNT NON-SHH (By IHC), WHO grade 4 + - Medulloblastoma, classic + - Medulloblastoma, classic histologic type, non-WNT/non-SHH molecular group, CNS WHO grade 4 + - Medulloblastoma, classical histology + - Medulloblastoma, CNS WHO Grade 4 + - Medulloblastoma, desmoplastic/nodular histology, SHH-activated (WHO grade 4) + - Medulloblastoma, favored + - Medulloblastoma, non-WNT, non-SHH + - Medulloblastoma, SHH-activated and TP53-wild type + - Medulloblastoma, SHH-activated and TP53-wildtype, Medulloblastoma with extensive nodularity (MBEN) + - Medulloblastoma, WHO Grade 4 + - Medulloblastoma, WHO Grade IV + - Melanoma + - Meningioma + - Merkel Cell Tumor + - Mesenchymal Chondrosarcoma + - Mesenchymal Neoplasm + - Metastatic Alveolar Rhabdomyosarcoma + - Metastatic Carcinoma + - Metastatic Embryonal Rhabdomyosarcoma + - Metastatic embryonal rhabdomyosarcoma in three nodules + - Metastatic nasopharyngeal carcinoma, nonkeratinizing squamous cell carcinoma subtype + - Metastatic Papillary Thyroid Carcinoma + - Metastatic Polyphenotypic Malignant Neoplasm + - Metastatic Rhabdomyosarcoma + - Mixed Germ Cell Tumor + - Mixed germ cell w/ matrue teratoma + - Mixed malignant germ cell tumor with components of embryonal carcinoma, choriocarcinoma, and mature teratoma + - Mixed malignant germ cell tumor with yolk sac tumor + - Mixed-Phenotype Acute Leukemia, B/Myeloid, Not Otherwise Specified + - Mixed-Phenotype Acute Leukemia, T/Myeloid, Not Otherwise Specified + - Monophasic Synovial Sarcoma, Intermediate-Grade (FNCLCC Grade 2 Of 3) + - Most consistent with atypical teratoid/rhabdoid tumor, most consistent with atypical teratoid/rhabdoid tumor + - Mucinous Carcinoma + - Mucoepidermoid carcinoma + - Myelodysplastic Syndrome With Multilineage Dysplasia + - Myelodysplastic Syndrome With Single Lineage Dysplasia + - Myeloid leukemia associated with Down Syndrome + - Myofibroblastic proliferation suggestive of inflammatory myofibroblastic tumor + - Myofibroma + - Myxoid Glioneuronal Tumor + - Myxoid Liposarcoma + - Myxoid Neoplasm + - Myxopapillary Ependymoma + - Myxopapillary ependymoma, CNS WHO grade 2 + - Nasopharyngeal Carcinoma Metastatic + - Nasopharyngeal carcinoma, non-keratinizing squamous cell carcinoma type + - Neoplasm + - Nephroblastoma (Wilms Tumor) + - Neuroblastoma + - Neurocytoma + - Neuroectodermal Tumor + - Neuroectodermal tumor, NTRK1 altered, with low-grade morphologic features + - Neuroendocrine Tumor + - Neuroepithelial Neoplasm + - Neuroepithelial neoplasm, Glioma + - Neuroepithelial Tumor + - Neurofibromatosis; Moderately cellular neoplasm + - Non-WNT/non-SHH medulloblastoma + - Not Reported + - Optic Pathway Glioma + - Osteosarcoma, NOS + - Ovarian Sclerosing Stromal Tumor + - Pancreatobiliary-Type Carcinoma + - Papillary Carcinoma + - Papillary carcinoma of thyroid + - Papillary Neoplasm, Favor Choroid Plexus Tumor + - Papillary Thyroid Carcinoma + - Papillary thyroid carcinoma, classic + - Papillary Tumor of The Pineal Region + - Paraganglioma + - Paratesticular Rhabdomyosarcoma + - Paratesticular rhabdomyosarcoma, favor embryonal + - Paratesticular Spindle Cell/Sclerosing Rhabdomyosarcoma + - Pediatric neuroepithelial tumor with ROS1 fusion + - Pediatric type diffuse low grad astrocytoma, consistent with methylation array finding suggestive of MYB/MYBL1-altered (CNS WHO grade 1) + - PFA Ependymoma + - Pheochromocytoma + - Pilocytic Astrocytoma + - Pilocytic astrocytoma (WHO Grade 1) + - Pilocytic astrocytoma, CNS WHO grade 1 + - Pilocytic astrocytoma, CNS WHO GRADE 1, Pilocytic astrocytoma, CNS WHO grade 1 + - Pilocytic Astrocytoma, CNS WHO Grade I + - Pilocytic astrocytoma, KIAA1549::BRAF fusion-positive (WHO grade 1) + - Pilocytic astrocytoma, WHO Grade 1 + - Pilocytic astrocytoma, WHO grade I + - Piloid Glial Proliferation + - Pilomyxoid Astrocytoma + - Pineal Parenchymal Tumor + - Pineoblastoma + - Pineoblastoma, WHO grade 4 + - Pituitary Adenoma + - Pituitary Tumor + - Pleomorphic Sarcoma + - Pleomorphic Xanthoastrocytoma + - Pleuropulmonary Blastoma + - Plexifrom Fibrohistiocytic Tumor + - Polymorphous Low Grade Neuroepithelial Tumor + - Poorly Differentiated Malignant Neoplasm with Sarcomatoid Features + - Poorly Differentiated Pulmonary Adenocarcinoma + - Poorly Differentiated Ring Cell Adenocarcinoma + - Poorly Differentiated Sarcoma + - Poorly Differentiated Sertoli-Leydig Cell Tumor + - Positive for lesional tissue, favor low-grade glioma, additional studies pending. + - Possible Synovial Sarcoma + - Posterior Fossa Ependymoma + - Posterior fossa ependymoma, group A + - Posterior fossa ependymoma, group A (CNS group grade III) + - Posterior fossa ependymoma, group B + - Posterior fossa ependymoma, WHO grade 2, with retained H3 K27 tri-methylation + - Posterior fossa group A (PFA) Ependymoma (WHO GRADE 3) + - Posterior fossa group A ependymoma + - Posterior Fossa Tumor + - Posterior Fossa, Forth Ventricular Tumor, Posterior Fossa, Fourth Ventricular Tumor + - Precursor B-Cell Acute Lymphoblastic Leukemia with Hyperdiploidy + - Primary central nervous system neoplasm consistent with high grade glioma + - Primary mediastinal (thymic) large B-cell lymphoma + - Primitive malignant neoplasm with mesenchymal features + - Primitive Neuroectoderma Tumor + - Primitive Sarcoma + - Primitive/embryonal tumor with high-grade features; compatible with medulloblastoma + - Psammomatous Meningioma + - Pure Germinoma + - PXA Vs Ganglioglioma + - Renal Cell Adenocarcinoma + - Renal cell carcinoma, NOS + - Renal medullary carcinoma + - Residual CIC-Rearranged Sarcoma + - Residual Dermatofibrosarcoma Protuberans + - Residual High Grade Astrocytoma With Piloid Features + - Residual High-Grade Sarcoma + - Residual Malignant Melanoma + - Residual Papillary Tumor of Pineal Region + - Residual Pineoblastoma + - Residual/Recurrent Extraventricular Neurocytoma + - Retinoblastoma + - Retinoblastoma, moderately differentiated + - Rhabdoid Tumor, Malignant + - Rhabdomyoma NOS + - Rhabdomyosarcoma + - Rhabdomyosarcoma strongly suspected + - Rhabdomyosarcoma, favor embryonal subtype pending molecular studies + - Right Thigh Mass + - Round Blue Cell Tumor + - Round Cell Sarcoma + - Round To Spindle Cell Sarcoma + - Sarcoma + - Schwannoma + - Sclerosing Stromal Tumor + - Seroli-leydig cell tumor + - Serous Adenocarcinoma, NOS + - Serous Cystadenocarcinoma NOS + - Serous Surface Papillary Carcinoma + - Sertoli Leydig Cell Tumor + - Sertoli-Leydig cell tumor, moderately differentiated + - Sertoli-Leydig cell tumor, poorly differentiated + - Sertolig Leydig Cell Tumor + - Signet Ring Cell Carcinoma + - Small Blue Cell Tumor + - Small Cell Neuroendocrine Carcinoma + - Small Round Blue Cell Sarcoma + - Small Round Blue Cell Tumor + - Small round blue cell tumor consistent with rhabdomyosarcoma + - "Small round blue cell tumor: rhabdomyosarcoma" + - SMARCB1-deficient undifferentiated round cell sarcoma + - Spinal Ependymoma Myxopapillary + - Spinal Tumor + - Spindle Cell Lesion + - Spindle Cell Neoplasm + - Spindle Cell Rhabdomyosarcoma + - Spindle Cell Sarcoma + - Squamous Cell Carcinoma NOS + - Subependymal Giant Cell Astrocytoma + - Supertentorial Ependymoma + - Suprasellar Mass + - Supratentorial Choroid Plexus Papilloma + - Supratentorial Ependymoma + - Supratentorial ependymoma, WHO Grade 2 + - Synovial Sarcoma + - T Lymphoblastic Leukemia/Lymphoma + - T-lymphoblastic Leukemia + - T-lymphoblastic Lymphoma + - Testicular mass + - Thalamic Brain Tumor + - Therapy Related Myeloid Neoplasm + - Therapy-related myeloid neoplasms + - Unclassified pleomorphic sarcoma + - Undifferential Small Round Blue Cell Tumor + - Undifferentiated leukaemia + - Undifferentiated Leukemia + - Undifferentiated Malignant Neoplasm with Rhabdoid Morphology And INI1 Loss + - Undifferentiated Round Cell Sarcoma + - Undifferentiated sarcoma + - Undifferentiated small round cell sarcoma + - Undifferentiated, high-grade neoplasm/sarcoma + - Unknown + - Well Differentiated Embryonal Rhabdomyosarcoma + - Well Differentiated Neuroendocrine Tumor + - Well To Moderately Differentiated Colonic Adenocarcinoma + - Yolk Sac Tumor + Req: true + primary_site: + Desc: Anatomical site of disease in primary diagnosis for this diagnosis + Enum: + # reuse GDC anatomical site list + - Adrenal Gland + - Base of the Tongue + - Bladder + - Brain + - Breast + - Cervix Uteri + - Colon + - Corpus Uteri + - Esophagus + - Floor of Mouth + - Gallbladder + - Gingiva + - Hypopharynx + - Kidney + - Larynx + - Limb Skeletal System + - Lip + - Lung/Bronchus + - Lymph Node + - Meninges + - Nasopharynx + - Not Reported + - Oropharynx + - Other and Ill Defined Digestive Organs ICD-O-3 + - Other and Ill-Defined Sites ICD-O-3 + - Other and Ill-Defined Sites in Lip, Oral Cavity and Pharynx ICD-O-3 + - Other and Ill-Defined Sites within Respiratory System and Intrathoracic Organs ICD-O-3 + - Other and Unspecified Female Genital Organs ICD-O-3 + - Other and Unspecified Major Salivary Glands ICD-O-3 + - Other and Unspecified Male Genital Organs ICD-O-3 + - Other and Unspecified Parts of Biliary Tract ICD-O-3 + - Other and Unspecified Parts of Mouth ICD-O-3 + - Other and Unspecified Parts of Tongue ICD-O-3 + - Other and Unspecified Urinary Organs ICD-O-3 + - Other Endocrine Glands and Related Structures ICD-O-3 + - Ovary + - Palate + - Pancreas + - Paranasal Sinus + - Parotid Gland + - Penis + - Peritoneum and Retroperitoneum + - Placenta + - Prostate Gland + - Pyriform Sinus + - Rectosigmoid Region + - Rectum + - Renal Pelvis + - Skin + - Small Intestine + - Stomach + - Testis + - Thymus Gland + - Thyroid Gland + - Tonsil + - Trachea + - Unknown + - Ureter + - Uterus + - Vagina + - Vulva + morphology: + Desc: ICD-O-3 Morphology term associated with this diagnosis + Enum: + # ICD-O-3 M + - 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 + - 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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 + tumor_grade: + Desc: Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness. + Enum: + - G1 + - G2 + - G3 + - G4 + - GX + - GB + - High Grade + - Intermediate Grade + - Low Grade + - Unknown + - Not Reported + tumor_stage_clinical_t: + Desc: Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment. + Enum: + - 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 + - TX + - Ta + - Tis + - Tis (DCIS) + - Tis (LCIS) + - Tis (Paget's) + - Unknown + - Not Reported + tumor_stage_clinical_n: + Desc: Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment. + Enum: + - 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 + tumor_stage_clinical_m: + Desc: Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment. + Enum: + - M0 + - M1 + - M1a + - M1b + - M1c + - MX + - cM0 (i+) + - Unknown + - Not Reported + progression_or_recurrence: + Desc: Yes/No/Unknown indicator to identify whether a patient has had a new tumor event after initial treatment. + Enum: + - 'Yes' + - 'No' + - Unknown + - Not Reported + - Not Allowed To Collect + # study + study_version: + Desc: The version of the phs accession + Type: string + Req: true + bioproject_accession: + Desc: NCBI BioProject accession ID + Type: + pattern: "^PRJNA[0-9]+$" + Req: 'Preferred' + study_data_types: + Desc: Types of scientific data in the study + Enum: + - Genomic + - Proteomic + - Imaging + Req: 'Yes' + data_access_level: + Desc: Is data open, controlled, or mixed? + Enum: + - open + - controlled + - mixed + Req: 'Preferred' + index_date: + Desc: Index date (Day 0) to which all dates are relative, for this study + Enum: + - date_of_diagnosis + - date_of_enrollment + - date_of_collection + - date_of_birth + phs_accession: + Desc: PHS accession number (a.k.a dbGaP accession) + Req: true + Key: true + Type: + pattern: "^phs[0-9]+([.]v[0-9]+)*$" + study_acronym: + Desc: Short acronym or other study desginator + Type: string + study_description: + Desc: Human-readable study description + Type: string + Req: Preferred + study_access: + Desc: Study access + Enum: + - Open + - Controlled + Req: true + short_description: + Desc: | + Short description that will identify the dataset on public pages + A clear and concise formula for the title would be like: + {methodology} of {organism}: {sample info} + Type: string + Req: Preferred + study_external_url: + Desc: Website or other url relevant to study + Type: url + Req: Preferred + study_name: + Desc: Official name of study + Type: string + Req: 'Yes' + primary_investigator_name: + Desc: Name of principal investigator + Type: string + Req: Preferred + acl: + Desc: open or restricted access to data + Type: string + primary_investigator_email: + Desc: Email of principal investigator + Type: string + Req: Preferred + co_investigator_name: + Desc: Name of co-principal investigator + Type: string + co_investigator_email: + Desc: Email of co-principal investigator + Type: string + cds_primary_bucket: + Desc: The primary bucket for depositing data + Type: string + Req: Preferred + cds_secondary_bucket: + Desc: Secondary bucket for depositing data (non-sequence files) + Type: string + cds_tertiary_bucket: + Desc: Secondary bucket for depositing data (non-sequence files) + Type: string + authz: + Desc: multifactor authorization + Type: string + # sample + biosample_accession: + Desc: NCBI BioSample accession ID (SAMN) for this sample + Type: + pattern: "^SAMN[0-9]+$" + Req: Preferred + sample_age_at_collection: + Desc: Number of days to collection, relative to index date + Type: integer + sample_anatomic_site: + Desc: Anatomic site from which sample was collected + Enum: + # use GDC anatomic site list + - Bone marrow + - post mortem blood + - post mortem liver + - Frontal Lobe + - Peripheral blood + - Lung + - tumor + - post mortem liver tumor + - Left Bone marrow + - Right Bone marrow + - Left thigh + - Lung/pleura + - R. femur/rib/verebra + - Femur + - Paraspinal mass + - Abdominal mass + - Kidney + - Brain stem + - Cerebrum + - Cerebellum + - R. Buttock + - Shoulder + - L. Kidney + - R. Kidney + - Ventricular mass + - Bilateral + - Retroperitoneal mass + - Adrenal mass + - R. Breast metastasis + - Paracaval Lymph Node metastasis + - Transverse Colon + - Lymph Node met + - Orbit + - Lung met + - Liver + - 4th ventricle + - L. Occipital mass + - Posterior mediastil mass (mediastinum) + - R. Proximal Ulna + - R. Sylvian Fissure + - Lung metastasis + - Liver metastasis + - R. Parietal Lobe + - Tibia + - Humerus + - Lung mass + - R. Distal Femur + - R. Humerus + - L. Femur + - Distal femur + - L. Distal Femur + - Os frontalis + - L. Proximal Tibia + - Arm + - Perineum + - Bone Marrow metastasis + - Paratesticular + - Cervical node + - R. Neck mass + - Pleural effusion met + - not reported + - Abdomen + - Abdominal Wall + - Acetabulum + - Adenoid + - Adipose + - Adrenal + - Alveolar Ridge + - Amniotic Fluid + - Ampulla Of Vater + - Anal Sphincter + - Ankle + - Anorectum + - Antecubital Fossa + - Antrum + - Anus + - Aorta + - Aortic Body + - Appendix + - Aqueous Fluid + - Artery + - Ascending Colon + - Ascending Colon Hepatic Flexure + - Auditory Canal + - Autonomic Nervous System + - Axilla + - Back + - Bile Duct + - Bladder + - Blood + - Blood Vessel + - Bone + - Bone Marrow + - Bowel + - Brain + - Brain Stem + - Breast + - Broad Ligament + - Bronchiole + - Bronchus + - Brow + - Buccal Cavity + - Buccal Mucosa + - Buttock + - Calf + - Capillary + - Cardia + - Carina + - Carotid Artery + - Carotid Body + - Cartilage + - Cecum + - Cell-Line + - Central Nervous System + - Cerebral Cortex + - Cerebrospinal Fluid + - Cervical Spine + - Cervix + - Chest + - Chest Wall + - Chin + - Clavicle + - Clitoris + - Colon + - Colon - Mucosa Only + - Common Duct + - Conjunctiva + - Connective Tissue + - Dermal + - Descending Colon + - Diaphragm + - Duodenum + - Ear + - Ear Canal + - Ear, Pinna (External) + - Effusion + - Elbow + - Endocrine Gland + - Epididymis + - Epidural Space + - Esophageal; Distal + - Esophageal; Mid + - Esophageal; Proximal + - Esophagogastric Junction + - Esophagus + - Esophagus - Mucosa Only + - Eye + - Fallopian Tube + - Femoral Artery + - Femoral Vein + - Fibroblasts + - Fibula + - Finger + - Floor Of Mouth + - Fluid + - Foot + - Forearm + - Forehead + - Foreskin + - Frontal Cortex + - Fundus Of Stomach + - Gallbladder + - Ganglia + - Gastroesophageal Junction + - Gastrointestinal Tract + - Glottis + - Groin + - Gum + - Hand + - Hard Palate + - Head - Face Or Neck, Nos + - Head & Neck + - Heart + - Hepatic + - Hepatic Duct + - Hepatic Flexure + - Hepatic Vein + - Hip + - Hippocampus + - Hypopharynx + - Ileum + - Ilium + - Index Finger + - Ischium + - Islet Cells + - Jaw + - Jejunum + - Joint + - Knee + - Lacrimal Gland + - Large Bowel + - Laryngopharynx + - Larynx + - Leg + - Leptomeninges + - Ligament + - Lip + - Lumbar Spine + - Lymph Node + - Lymph Node(s) Axilla + - Lymph Node(s) Cervical + - Lymph Node(s) Distant + - Lymph Node(s) Epitrochlear + - Lymph Node(s) Femoral + - Lymph Node(s) Hilar + - Lymph Node(s) Iliac-Common + - Lymph Node(s) Iliac-External + - Lymph Node(s) Inguinal + - Lymph Node(s) Internal Mammary + - Lymph Node(s) Mammary + - Lymph Node(s) Mesenteric + - Lymph Node(s) Occipital + - Lymph Node(s) Paraaortic + - Lymph Node(s) Parotid + - Lymph Node(s) Pelvic + - Lymph Node(s) Popliteal + - Lymph Node(s) Regional + - Lymph Node(s) Retroperitoneal + - Lymph Node(s) Scalene + - Lymph Node(s) Splenic + - Lymph Node(s) Subclavicular + - Lymph Node(s) Submandibular + - Lymph Node(s) Supraclavicular + - Lymph Nodes(s) Mediastinal + - Mandible + - Maxilla + - Mediastinal Soft Tissue + - Mediastinum + - Mesentery + - Mesothelium + - Middle Finger + - Mitochondria + - Muscle + - Nails + - Nasal Cavity + - Nasal Soft Tissue + - Nasopharynx + - Neck + - Nerve + - Nerve(s) Cranial + - Not Allowed To Collect + - Occipital Cortex + - Ocular Orbits + - Omentum + - Oral Cavity + - Oral Cavity - Mucosa Only + - Oropharynx + - Other + - Ovary + - Palate + - Pancreas + - Paranasal Sinuses + - Paraspinal Ganglion + - Parathyroid + - Parotid Gland + - Patella + - Pelvis + - Penis + - Pericardium + - Periorbital Soft Tissue + - Peritoneal Cavity + - Peritoneum + - Pharynx + - Pineal + - Pineal Gland + - Pituitary Gland + - Placenta + - Pleura + - Popliteal Fossa + - Prostate + - Pylorus + - Rectosigmoid Junction + - Rectum + - Retina + - Retro-Orbital Region + - Retroperitoneum + - Rib + - Ring Finger + - Round Ligament + - Sacrum + - Salivary Gland + - Scalp + - Scapula + - Sciatic Nerve + - Scrotum + - Seminal Vesicle + - Sigmoid Colon + - Sinus + - Sinus(es), Maxillary + - Skeletal Muscle + - Skin + - Skull + - Small Bowel + - Small Bowel - Mucosa Only + - Small Finger + - Soft Tissue + - Spinal Column + - Spinal Cord + - Spleen + - Splenic Flexure + - Sternum + - Stomach + - Stomach - Mucosa Only + - Subcutaneous Tissue + - Subglottis + - Sublingual Gland + - Submandibular Gland + - Supraglottis + - Synovium + - Temporal Cortex + - Tendon + - Testis + - Thigh + - Thoracic Spine + - Thorax + - Throat + - Thumb + - Thymus + - Thyroid + - Tongue + - Tonsil + - Tonsil (Pharyngeal) + - Trachea / Major Bronchi + - Trunk + - Umbilical Cord + - Ureter + - Urethra + - Urinary Tract + - Uterus + - Uvula + - Vagina + - Vas Deferens + - Vein + - Venous + - Vertebra + - Vulva + - White Blood Cells + - Wrist + - Unknown + - Not Reported + sample_id: + Desc: Sample identifier as submitted by requestor + Type: string + Req: 'Yes' + Key: true + sample_tumor_status: + Desc: Tumor or normal status + Enum: + - Tumor + - Normal + - Abnormal + - Peritumoral + - Unknown + Req: 'Yes' + sample_type: + Desc: Tissue type of this sample + Enum: + # use GDC list of tissue types + - Ascites + - Blood + - Blood Derived Normal + - Bone Marrow + - Buccal Mucosa + - Buffy Coat + - Cell Line Derived Xenograft Tissue + - DNA + - Fluids + - Metastatic + - Mouthwash + - Normal + - Not specified in data + - Pleural Fluid + - Primary Tumor + - Primary Xenograft Tissue + - RNA + - Saliva + - Skin + - Solid Tissue Normal + - Tissue + - Tumor + - Tumor Adjacent Normal + - Unknown + - Unspecified + - Xenograft Tissue + - Additional - New Primary + - Additional Metastatic + - Benign Neoplasms + - 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 + - Bone Marrow Normal + - Buccal Cell Normal + - Cell Lines + - Control Analyte + - 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 + - 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 + - Recurrent Blood Derived Cancer - Bone Marrow + - Recurrent Blood Derived Cancer - Peripheral Blood + - Recurrent Tumor + - Repli-G (Qiagen) DNA + - Repli-G X (Qiagen) DNA + - Slides + - Total RNA + - Tumor Adjacent Normal - Post Neo-adjuvant Therapy + - Not Reported + Req: 'Yes' + derived_from_specimen: + Desc: Identier of the parent specimen of this sample + Type: string + # treatment + treatment_id: + Desc: Internal identifier + Type: string + Key: true + days_to_treatment: + Desc: Days to start of treatment, relative to index date + Type: integer + treatment_outcome: + Desc: Text term that describes the patient's final outcome after the treatment was administered + Enum: + # use GDC outcome list? + - Complete Response + - Mixed Response + - No Measurable Disease + - No Response + - Not Reported + - Partial Response + - Persistent Disease + - Progressive Disease + - Stable Disease + - Treatment Ongoing + - Treatment Stopped Due to Toxicity + - Unknown + - Very Good Partial Response + treatment_type: + Desc: Text term that describes the kind of treatment administered + Enum: + # use CMB list? + - Ablation, Cryo + - Ablation, Ethanol Injection + - Ablation, Microwave + - Ablation, NOS + - Ablation, Radiofrequency + - Ablation, Radiosurgical + - Ancillary Treatment + - Antiseizure Treatment + - Bisphosphonate Therapy + - Blinded Study, Treatment Unknown + - Brachytherapy, High Dose + - Brachytherapy, Low Dose + - Brachytherapy, NOS + - Chemoembolization + - Chemoprotectant + - Chemotherapy + - Concurrent Chemoradiation + - Cryoablation + - Embolization + - Ethanol Injection Ablation + - External Beam Radiation + - Hormone Therapy + - I-131 Radiation Therapy + - Immunotherapy (Including Vaccines) + - Internal Radiation + - Isolated Limb Perfusion (ILP) + - Organ Transplantation + - Other + - Pharmaceutical Therapy, NOS + - Pleurodesis + - Pleurodesis, Talc + - Pleurodesis, NOS + - Radiation Therapy, NOS + - Radiation, 2D Conventional + - Radiation, 3D Conformal + - Radiation, Combination + - Radiation, Cyberknife + - Radiation, External Beam + - Radiation, Hypofractionated + - Radiation, Implants + - Radiation, Intensity-Modulated Radiotherapy + - Radiation, Internal + - Radiation, Mixed Photon Beam + - Radiation, Photon Beam + - Radiation, Proton Beam + - Radiation, Radioisotope + - Radiation, Stereotactic/Gamma Knife/SRS + - Radiation, Systemic + - Radioactive Iodine Therapy + - Radioembolization + - Radiosensitizing Agent + - Stem Cell Transplantation, Allogeneic + - Stem Cell Transplantation, Autologous + - Stem Cell Transplantation, Double Autologous + - Stem Cell Transplantation, Haploidentical + - Stem Cell Transplantation, Non-Myeloablative + - Stem Cell Transplantation, NOS + - Stem Cell Transplantation, Syngenic + - Stem Cell Treatment + - Stereotactic Radiosurgery + - Steroid Therapy + - Surgery + - Targeted Molecular Therapy + - Unknown + - Not Reported + therapeutic_agents: + Desc: Text identification of the individual agent(s) used as part of a treatment regimen. + Enum: + - 10-Deacetyltaxol + - 11C Topotecan + - 11D10 AluGel Anti-Idiotype Monoclonal Antibody + - 12-Allyldeoxoartemisinin + - 13-Deoxydoxorubicin + - 14C BMS-275183 + - 17beta-Hydroxysteroid Dehydrogenase Type 5 Inhibitor ASP9521 + - 2-Deoxy-D-glucose + - 2-Ethylhydrazide + - 2-Fluoroadenine + - 2-Fluorofucose-containing SGN-2FF + - 2-Hydroxyestradiol + - 2-Hydroxyestrone + - 2-Hydroxyflutamide Depot + - 2-Hydroxyoleic Acid + - 2-Methoxyestradiol + - 2-Methoxyestradiol Nanocrystal Colloidal Dispersion + - 2-Methoxyestrone + - 2-O, 3-O Desulfated Heparin + - 2,6-Diaminopurine + - 2,6-Dimethoxyquinone + - 2'-F-ara-deoxyuridine + - 3'-C-ethynylcytidine + - 3'-dA Phosphoramidate NUC-7738 + - 4-Nitroestrone 3-Methyl Ether + - 4-Thio-2-deoxycytidine + - 4'-Iodo-4'-Deoxydoxorubicin + - 5-Aza-4'-thio-2'-deoxycytidine + - 5-Fluoro-2-Deoxycytidine + - 6-Phosphofructo-2-kinase/fructose-2,6-bisphosphatases Isoform 3 Inhibitor ACT-PFK-158 + - 7-Cyanoquinocarcinol + - 7-Ethyl-10-Hydroxycamptothecin + - 7-Hydroxystaurosporine + - 8-Azaguanine + - 9-Ethyl 6-Mercaptopurine + - 9H-Purine-6Thio-98D + - A2A Receptor Antagonist EOS100850 + - Abagovomab + - Abarelix + - Abemaciclib + - Abemaciclib Mesylate + - Abexinostat + - Abexinostat Tosylate + - Abiraterone + - Abiraterone Acetate + - Abituzumab + - Acai Berry Juice + - Acalabrutinib + - Acalisib + - Aceglatone + - Acetylcysteine + - Acitretin + - Acivicin + - Aclacinomycin B + - Aclarubicin + - Acodazole + - Acodazole Hydrochloride + - Acolbifene Hydrochloride + - Acridine + - Acridine Carboxamide + - Acronine + - Actinium Ac 225 Lintuzumab + - Actinium Ac 225-FPI-1434 + - Actinium Ac-225 Anti-PSMA Monoclonal Antibody J591 + - Actinomycin C2 + - Actinomycin C3 + - Actinomycin F1 + - Activin Type 2B Receptor Fc Fusion Protein STM 434 + - Acyclic Nucleoside Phosphonate Prodrug ABI-1968 + - Ad-RTS-hIL-12 + - Adagloxad Simolenin + - Adavosertib + - Adecatumumab + - Adenosine A2A Receptor Antagonist AZD4635 + - Adenosine A2A Receptor Antagonist CS3005 + - Adenosine A2A Receptor Antagonist NIR178 + - Adenosine A2A Receptor Antagonist/Phosphodiesterase 10A PBF-999 + - Adenosine A2A/A2B Receptor Antagonist AB928 + - Adenosine A2B Receptor Antagonist PBF-1129 + - Adenovector-transduced AP1903-inducible MyD88/CD40-expressing Autologous PSMA-specific Prostate Cancer Vaccine BPX-201 + - Adenoviral Brachyury Vaccine ETBX-051 + - Adenoviral Cancer Vaccine PF-06936308 + - Adenoviral MUC1 Vaccine ETBX-061 + - Adenoviral PSA Vaccine ETBX-071 + - Adenoviral Transduced hIL-12-expressing Autologous Dendritic Cells INXN-3001 Plus Activator Ligand INXN-1001 + - Adenoviral Tumor-specific Neoantigen Priming Vaccine GAd-209-FSP + - Adenoviral Tumor-specific Neoantigen Priming Vaccine GRT-C901 + - Adenovirus 5/F35-Human Guanylyl Cyclase C-PADRE + - Adenovirus Serotype 26-expressing HPV16 Vaccine JNJ-63682918 + - Adenovirus Serotype 26-expressing HPV18 Vaccine JNJ-63682931 + - Adenovirus-expressing TLR5/TLR5 Agonist Nanoformulation M-VM3 + - Adenovirus-mediated Human Interleukin-12 INXN-2001 Plus Activator Ligand INXN-1001 + - Aderbasib + - ADH-1 + - AE37 Peptide/GM-CSF Vaccine + - AEE788 + - Aerosol Gemcitabine + - Aerosolized Aldesleukin + - Aerosolized Liposomal Rubitecan + - Afatinib + - Afatinib Dimaleate + - Afimoxifene + - Afuresertib + - Agatolimod Sodium + - Agerafenib + - Aglatimagene Besadenovec + - Agonistic Anti-CD40 Monoclonal Antibody ADC-1013 + - Agonistic Anti-OX40 Monoclonal Antibody INCAGN01949 + - Agonistic Anti-OX40 Monoclonal Antibody MEDI6469 + - AKR1C3-activated Prodrug OBI-3424 + - AKT 1/2 Inhibitor BAY1125976 + - AKT Inhibitor ARQ 092 + - Akt Inhibitor LY2780301 + - Akt Inhibitor MK2206 + - Akt Inhibitor SR13668 + - Akt/ERK Inhibitor ONC201 + - Alacizumab Pegol + - Alanosine + - Albumin-binding Cisplatin Prodrug BTP-114 + - Aldesleukin + - Aldoxorubicin + - Alectinib + - Alefacept + - Alemtuzumab + - Alestramustine + - Alflutinib Mesylate + - Algenpantucel-L + - Alisertib + - Alitretinoin + - ALK Inhibitor + - ALK Inhibitor ASP3026 + - ALK Inhibitor PLB 1003 + - ALK Inhibitor RO5424802 + - ALK Inhibitor TAE684 + - ALK Inhibitor WX-0593 + - ALK-2 Inhibitor TP-0184 + - ALK-FAK Inhibitor CEP-37440 + - ALK/c-Met Inhibitor TQ-B3139 + - ALK/FAK/Pyk2 Inhibitor CT-707 + - ALK/ROS1/Met Inhibitor TQ-B3101 + - ALK/TRK Inhibitor TSR-011 + - Alkotinib + - Allodepleted T Cell Immunotherapeutic ATIR101 + - Allogeneic Anti-BCMA CAR-transduced T-cells ALLO-715 + - Allogeneic Anti-BCMA-CAR T-cells PBCAR269A + - Allogeneic Anti-BCMA/CS1 Bispecific CAR-T Cells + - Allogeneic Anti-CD19 CAR T-cells ALLO-501A + - Allogeneic Anti-CD19 Universal CAR-T Cells CTA101 + - Allogeneic Anti-CD19-CAR T-cells PBCAR0191 + - Allogeneic Anti-CD20 CAR T-cells LUCAR-20S + - Allogeneic Anti-CD20-CAR T-cells PBCAR20A + - Allogeneic CD22-specific Universal CAR-expressing T-lymphocytes UCART22 + - Allogeneic CD3- CD19- CD57+ NKG2C+ NK Cells FATE-NK100 + - Allogeneic CD56-positive CD3-negative Natural Killer Cells CYNK-001 + - Allogeneic CD8+ Leukemia-associated Antigens Specific T Cells NEXI-001 + - Allogeneic Cellular Vaccine 1650-G + - Allogeneic CRISPR-Cas9 Engineered Anti-BCMA T Cells CTX120 + - Allogeneic CRISPR-Cas9 Engineered Anti-CD70 CAR-T Cells CTX130 + - Allogeneic CS1-specific Universal CAR-expressing T-lymphocytes UCARTCS1A + - Allogeneic GM-CSF-secreting Breast Cancer Vaccine SV-BR-1-GM + - Allogeneic GM-CSF-secreting Lethally Irradiated Prostate Cancer Vaccine + - Allogeneic GM-CSF-secreting Lethally Irradiated Whole Melanoma Cell Vaccine + - Allogeneic GM-CSF-secreting Tumor Vaccine PANC 10.05 pcDNA-1/GM-Neo + - Allogeneic GM-CSF-secreting Tumor Vaccine PANC 6.03 pcDNA-1/GM-Neo + - Allogeneic IL13-Zetakine/HyTK-Expressing-Glucocorticoid Resistant Cytotoxic T Lymphocytes GRm13Z40-2 + - Allogeneic Irradiated Melanoma Cell Vaccine CSF470 + - Allogeneic Large Multivalent Immunogen Melanoma Vaccine LP2307 + - Allogeneic Melanoma Vaccine AGI-101H + - Allogeneic Natural Killer Cell Line MG4101 + - Allogeneic Natural Killer Cell Line NK-92 + - Allogeneic Plasmacytoid Dendritic Cells Expressing Lung Tumor Antigens PDC*lung01 + - Allogeneic Renal Cell Carcinoma Vaccine MGN1601 + - Allogeneic Third-party Suicide Gene-transduced Anti-HLA-DPB1*0401 CD4+ T-cells CTL 19 + - Allosteric ErbB Inhibitor BDTX-189 + - Allovectin-7 + - Almurtide + - Alobresib + - Alofanib + - Alpelisib + - Alpha Galactosylceramide + - Alpha V Beta 1 Inhibitor ATN-161 + - Alpha V Beta 8 Antagonist PF-06940434 + - alpha-Folate Receptor-targeting Thymidylate Synthase Inhibitor ONX-0801 + - Alpha-Gal AGI-134 + - Alpha-lactalbumin-derived Synthetic Peptide-lipid Complex Alpha1H + - Alpha-Thioguanine Deoxyriboside + - Alpha-tocopheryloxyacetic Acid + - Alsevalimab + - Altiratinib + - Altretamine + - Alvespimycin + - Alvespimycin Hydrochloride + - Alvocidib + - Alvocidib Hydrochloride + - Alvocidib Prodrug TP-1287 + - Amatuximab + - Ambamustine + - Ambazone + - Amblyomin-X + - Amcasertib + - Ametantrone + - Amifostine + - Amino Acid Injection + - Aminocamptothecin + - Aminocamptothecin Colloidal Dispersion + - Aminoflavone Prodrug AFP464 + - Aminopterin + - Aminopterin Sodium + - Amivantamab + - Amolimogene Bepiplasmid + - Amonafide L-Malate + - Amrubicin + - Amrubicin Hydrochloride + - Amsacrine + - Amsacrine Lactate + - Amsilarotene + - Amustaline + - Amustaline Dihydrochloride + - Amuvatinib + - Amuvatinib Hydrochloride + - Anakinra + - Anastrozole + - Anaxirone + - Ancitabine + - Ancitabine Hydrochloride + - Andecaliximab + - Androgen Antagonist APC-100 + - Androgen Receptor Antagonist BAY 1161116 + - Androgen Receptor Antagonist SHR3680 + - Androgen Receptor Antagonist TAS3681 + - Androgen Receptor Antagonist TRC253 + - Androgen Receptor Antisense Oligonucleotide AZD5312 + - Androgen Receptor Antisense Oligonucleotide EZN-4176 + - Androgen Receptor Degrader ARV-110 + - Androgen Receptor Degrader CC-94676 + - Androgen Receptor Downregulator AZD3514 + - Androgen Receptor Inhibitor EPI-7386 + - Androgen Receptor Ligand-binding Domain-encoding Plasmid DNA Vaccine MVI-118 + - Androgen Receptor/Glucocorticoid Receptor Antagonist CB-03-10 + - Andrographolide + - Androstane Steroid HE3235 + - Anetumab Ravtansine + - Ang2/VEGF-Binding Peptides-Antibody Fusion Protein CVX-241 + - Angiogenesis Inhibitor GT-111 + - Angiogenesis Inhibitor JI-101 + - Angiogenesis/Heparanase Inhibitor PG545 + - Angiopoietin-2-specific Fusion Protein PF-04856884 + - Anhydrous Enol-oxaloacetate + - Anhydrovinblastine + - Aniline Mustard + - Anlotinib Hydrochloride + - Annamycin + - Annamycin Liposomal + - Annonaceous Acetogenins + - Ansamitomicin P-3 + - Anthramycin + - Anthrapyrazole + - Anti c-KIT Antibody-drug Conjugate LOP628 + - Anti-5T4 Antibody-drug Conjugate ASN004 + - Anti-5T4 Antibody-Drug Conjugate PF-06263507 + - Anti-5T4 Antibody-drug Conjugate SYD1875 + - Anti-A33 Monoclonal Antibody KRN330 + - Anti-A5B1 Integrin Monoclonal Antibody PF-04605412 + - Anti-ACTR/4-1BB/CD3zeta-Viral Vector-transduced Autologous T-Lymphocytes ACTR087 + - Anti-AG7 Antibody Drug Conjugate AbGn-107 + - Anti-AGS-16 Monoclonal Antibody AGS-16M18 + - Anti-AGS-5 Antibody-Drug Conjugate ASG-5ME + - Anti-AGS-8 Monoclonal Antibody AGS-8M4 + - Anti-alpha BCMA/Anti-alpha CD3 T-cell Engaging Bispecific Antibody TNB-383B + - Anti-alpha5beta1 Integrin Antibody MINT1526A + - Anti-ANG2 Monoclonal Antibody MEDI-3617 + - Anti-angiopoietin Monoclonal Antibody AMG 780 + - Anti-APRIL Monoclonal Antibody BION-1301 + - Anti-AXL Fusion Protein AVB-S6-500 + - Anti-AXL/PBD Antibody-drug Conjugate ADCT-601 + - Anti-B7-H3 Antibody DS-5573a + - Anti-B7-H3/DXd Antibody-drug Conjugate DS-7300a + - Anti-B7-H4 Monoclonal Antibody FPA150 + - Anti-B7H3 Antibody-drug Conjugate MGC018 + - Anti-BCMA Antibody SEA-BCMA + - Anti-BCMA Antibody-drug Conjugate AMG 224 + - Anti-BCMA Antibody-drug Conjugate CC-99712 + - Anti-BCMA Antibody-drug Conjugate GSK2857916 + - Anti-BCMA SparX Protein Plus BCMA-directed Anti-TAAG ARC T-cells CART-ddBCMA + - Anti-BCMA/Anti-CD3 Bispecific Antibody REGN5459 + - Anti-BCMA/CD3 BiTE Antibody AMG 420 + - Anti-BCMA/CD3 BiTE Antibody AMG 701 + - Anti-BCMA/CD3 BiTE Antibody REGN5458 + - Anti-BCMA/PBD ADC MEDI2228 + - Anti-BTLA Monoclonal Antibody TAB004 + - Anti-BTN3A Agonistic Monoclonal Antibody ICT01 + - Anti-c-fms Monoclonal Antibody AMG 820 + - Anti-c-KIT Monoclonal Antibody CDX 0158 + - Anti-c-Met Antibody-drug Conjugate HTI-1066 + - Anti-c-Met Antibody-drug Conjugate TR1801 + - Anti-c-Met Monoclonal Antibody ABT-700 + - Anti-c-Met Monoclonal Antibody ARGX-111 + - Anti-c-Met Monoclonal Antibody HLX55 + - Anti-c-MET Monoclonal Antibody LY2875358 + - Anti-C-met Monoclonal Antibody SAIT301 + - Anti-C4.4a Antibody-Drug Conjugate BAY1129980 + - Anti-C5aR Monoclonal Antibody IPH5401 + - Anti-CA19-9 Monoclonal Antibody 5B1 + - Anti-CA6-DM4 Immunoconjugate SAR566658 + - Anti-CCR7 Antibody-drug Conjugate JBH492 + - Anti-CD117 Monoclonal Antibody JSP191 + - Anti-CD122 Humanized Monoclonal Antibody Mik-Beta-1 + - Anti-CD123 ADC IMGN632 + - Anti-CD123 Monoclonal Antibody CSL360 + - Anti-CD123 Monoclonal Antibody KHK2823 + - Anti-CD123 x Anti-CD3 Bispecific Antibody XmAb1404 + - Anti-CD123-Pyrrolobenzodiazepine Dimer Antibody Drug Conjugate SGN-CD123A + - Anti-CD123/CD3 Bispecific Antibody APVO436 + - Anti-CD123/CD3 Bispecific Antibody JNJ-63709178 + - Anti-CD123/CD3 BiTE Antibody SAR440234 + - Anti-CD137 Agonistic Monoclonal Antibody ADG106 + - Anti-CD137 Agonistic Monoclonal Antibody AGEN2373 + - Anti-CD137 Agonistic Monoclonal Antibody ATOR-1017 + - Anti-CD137 Agonistic Monoclonal Antibody CTX-471 + - Anti-CD137 Agonistic Monoclonal Antibody LVGN6051 + - Anti-CD157 Monoclonal Antibody MEN1112 + - Anti-CD166 Probody-drug Conjugate CX-2009 + - Anti-CD19 Antibody-drug Conjugate SGN-CD19B + - Anti-CD19 Antibody-T-cell Receptor-expressing T-cells ET019003 + - Anti-CD19 iCAR NK Cells + - Anti-CD19 Monoclonal Antibody DI-B4 + - Anti-CD19 Monoclonal Antibody MDX-1342 + - Anti-CD19 Monoclonal Antibody MEDI-551 + - Anti-CD19 Monoclonal Antibody XmAb5574 + - Anti-CD19-DM4 Immunoconjugate SAR3419 + - Anti-CD19/Anti-CD22 Bispecific Immunotoxin DT2219ARL + - Anti-CD19/CD22 CAR NK Cells + - Anti-CD19/CD3 BiTE Antibody AMG 562 + - Anti-CD19/CD3 Tetravalent Antibody AFM11 + - Anti-CD20 Monoclonal Antibody B001 + - Anti-CD20 Monoclonal Antibody BAT4306F + - Anti-CD20 Monoclonal Antibody MIL62 + - Anti-CD20 Monoclonal Antibody PRO131921 + - Anti-CD20 Monoclonal Antibody SCT400 + - Anti-CD20 Monoclonal Antibody TL011 + - Anti-CD20 Monoclonal Antibody-Interferon-alpha Fusion Protein IGN002 + - Anti-CD20-engineered Toxin Body MT-3724 + - Anti-CD20/Anti-CD3 Bispecific IgM Antibody IGM2323 + - Anti-CD20/CD3 Monoclonal Antibody REGN1979 + - Anti-CD20/CD3 Monoclonal Antibody XmAb13676 + - Anti-CD205 Antibody-drug Conjugate OBT076 + - Anti-CD22 ADC TRPH-222 + - Anti-CD22 Monoclonal Antibody-MMAE Conjugate DCDT2980S + - Anti-CD228/MMAE Antibody-drug Conjugate SGN-CD228A + - Anti-CD25 Monoclonal Antibody RO7296682 + - Anti-CD25-PBD Antibody-drug Conjugate ADCT-301 + - Anti-CD26 Monoclonal Antibody YS110 + - Anti-CD27 Agonistic Monoclonal Antibody MK-5890 + - Anti-CD27L Antibody-Drug Conjugate AMG 172 + - Anti-CD3 Immunotoxin A-dmDT390-bisFv(UCHT1) + - Anti-CD3/Anti-5T4 Bispecific Antibody GEN1044 + - Anti-CD3/Anti-BCMA Bispecific Monoclonal Antibody JNJ-64007957 + - Anti-CD3/Anti-BCMA Bispecific Monoclonal Antibody PF-06863135 + - Anti-CD3/Anti-CD20 Trifunctional Bispecific Monoclonal Antibody FBTA05 + - Anti-CD3/Anti-GPRC5D Bispecific Monoclonal Antibody JNJ-64407564 + - Anti-CD3/Anti-GUCY2C Bispecific Antibody PF-07062119 + - Anti-CD3/CD20 Bispecific Antibody GEN3013 + - Anti-CD3/CD38 Bispecific Monoclonal Antibody AMG 424 + - Anti-CD3/CD7-Ricin Toxin A Immunotoxin + - Anti-CD30 Monoclonal Antibody MDX-1401 + - Anti-CD30 Monoclonal Antibody XmAb2513 + - Anti-CD30/CD16A Monoclonal Antibody AFM13 + - Anti-CD30/DM1 Antibody-drug Conjugate F0002 + - Anti-CD32B Monoclonal Antibody BI-1206 + - Anti-CD33 Antibody-drug Conjugate IMGN779 + - Anti-CD33 Antigen/CD3 Receptor Bispecific Monoclonal Antibody AMV564 + - Anti-CD33 Monoclonal Antibody BI 836858 + - Anti-CD33 Monoclonal Antibody-DM4 Conjugate AVE9633 + - Anti-CD33/CD3 Bispecific Antibody GEM 333 + - Anti-CD33/CD3 Bispecific Antibody JNJ-67571244 + - Anti-CD33/CD3 BiTE Antibody AMG 330 + - Anti-CD33/CD3 BiTE Antibody AMG 673 + - Anti-CD352 Antibody-drug Conjugate SGN-CD352A + - Anti-CD37 Antibody-Drug Conjugate IMGN529 + - Anti-CD37 Bispecific Monoclonal Antibody GEN3009 + - Anti-CD37 MMAE Antibody-drug Conjugate AGS67E + - Anti-CD37 Monoclonal Antibody BI 836826 + - Anti-CD38 Antibody-drug Conjugate STI-6129 + - Anti-CD38 Monoclonal Antibody MOR03087 + - Anti-CD38 Monoclonal Antibody SAR442085 + - Anti-CD38 Monoclonal Antibody TAK-079 + - Anti-CD38-targeted IgG4-attenuated IFNa TAK-573 + - Anti-CD38/CD28xCD3 Tri-specific Monoclonal Antibody SAR442257 + - Anti-CD38/CD3 Bispecific Monoclonal Antibody GBR 1342 + - Anti-CD39 Monoclonal Antibody SRF617 + - Anti-CD39 Monoclonal Antibody TTX-030 + - Anti-CD40 Agonist Monoclonal Antibody ABBV-927 + - Anti-CD40 Agonist Monoclonal Antibody CDX-1140 + - Anti-CD40 Monoclonal Antibody Chi Lob 7/4 + - Anti-CD40 Monoclonal Antibody SEA-CD40 + - Anti-CD40/Anti-4-1BB Bispecific Agonist Monoclonal Antibody GEN1042 + - Anti-CD40/Anti-TAA Bispecific Monoclonal Antibody ABBV-428 + - Anti-CD40L Fc-Fusion Protein BMS-986004 + - Anti-CD44 Monoclonal Antibody RO5429083 + - Anti-CD45 Monoclonal Antibody AHN-12 + - Anti-CD46 Antibody-drug Conjugate FOR46 + - Anti-CD47 ADC SGN-CD47M + - Anti-CD47 Monoclonal Antibody AO-176 + - Anti-CD47 Monoclonal Antibody CC-90002 + - Anti-CD47 Monoclonal Antibody Hu5F9-G4 + - Anti-CD47 Monoclonal Antibody IBI188 + - Anti-CD47 Monoclonal Antibody IMC-002 + - Anti-CD47 Monoclonal Antibody SHR-1603 + - Anti-CD47 Monoclonal Antibody SRF231 + - Anti-CD47 Monoclonal Antibody TJC4 + - Anti-CD47/CD19 Bispecific Monoclonal Antibody TG-1801 + - Anti-CD48/MMAE Antibody-drug Conjugate SGN-CD48A + - Anti-CD52 Monoclonal Antibody ALLO-647 + - Anti-CD70 Antibody-Drug Conjugate MDX-1203 + - Anti-CD70 Antibody-drug Conjugate SGN-CD70A + - Anti-CD70 CAR-expressing T Lymphocytes + - Anti-CD70 Monoclonal Antibody MDX-1411 + - Anti-CD71/vcMMAE Probody-drug Conjugate CX-2029 + - Anti-CD73 Monoclonal Antibody BMS-986179 + - Anti-CD73 Monoclonal Antibody CPI-006 + - Anti-CD73 Monoclonal Antibody NZV930 + - Anti-CD73 Monoclonal Antibody TJ4309 + - Anti-CD74 Antibody-drug Conjugate STRO-001 + - Anti-CD98 Monoclonal Antibody IGN523 + - Anti-CDH6 Antibody-drug Conjugate HKT288 + - Anti-CEA BiTE Monoclonal Antibody AMG211 + - Anti-CEA/Anti-DTPA-In (F6-734) Bispecific Antibody + - Anti-CEA/Anti-HSG Bispecific Monoclonal Antibody TF2 + - Anti-CEACAM1 Monoclonal Antibody CM-24 + - Anti-CEACAM5 Antibody-Drug Conjugate SAR408701 + - Anti-CEACAM6 AFAIKL2 Antibody Fragment/Jack Bean Urease Immunoconjugate L-DOS47 + - Anti-CEACAM6 Antibody BAY1834942 + - Anti-claudin18.2 Monoclonal Antibody AB011 + - Anti-Claudin18.2 Monoclonal Antibody TST001 + - Anti-CLDN6 Monoclonal Antibody ASP1650 + - Anti-CLEC12A/CD3 Bispecific Antibody MCLA117 + - Anti-CLEVER-1 Monoclonal Antibody FP-1305 + - Anti-CSF1 Monoclonal Antibody PD-0360324 + - Anti-CSF1R Monoclonal Antibody IMC-CS4 + - Anti-CSF1R Monoclonal Antibody SNDX-6352 + - Anti-CTGF Monoclonal Antibody FG-3019 + - Anti-CTLA-4 Monoclonal Antibody ADG116 + - Anti-CTLA-4 Monoclonal Antibody ADU-1604 + - Anti-CTLA-4 Monoclonal Antibody AGEN1181 + - Anti-CTLA-4 Monoclonal Antibody BCD-145 + - Anti-CTLA-4 Monoclonal Antibody HBM4003 + - Anti-CTLA-4 Monoclonal Antibody MK-1308 + - Anti-CTLA-4 Monoclonal Antibody ONC-392 + - Anti-CTLA-4 Monoclonal Antibody REGN4659 + - Anti-CTLA-4 Probody BMS-986288 + - Anti-CTLA-4/Anti-PD-1 Monoclonal Antibody Combination BCD-217 + - Anti-CTLA-4/LAG-3 Bispecific Antibody XmAb22841 + - Anti-CTLA-4/OX40 Bispecific Antibody ATOR-1015 + - Anti-CTLA4 Antibody Fc Fusion Protein KN044 + - Anti-CTLA4 Monoclonal Antibody BMS-986218 + - Anti-CXCR4 Monoclonal Antibody PF-06747143 + - Anti-Denatured Collagen Monoclonal Antibody TRC093 + - Anti-DKK-1 Monoclonal Antibody LY2812176 + - Anti-DKK1 Monoclonal Antibody BHQ880 + - Anti-DLL3/CD3 BiTE Antibody AMG 757 + - Anti-DLL4 Monoclonal Antibody MEDI0639 + - Anti-DLL4/VEGF Bispecific Monoclonal Antibody OMP-305B83 + - Anti-DR5 Agonist Monoclonal Antibody TRA-8 + - Anti-DR5 Agonistic Antibody DS-8273a + - Anti-DR5 Agonistic Monoclonal Antibody INBRX-109 + - Anti-EGFR Monoclonal Antibody CPGJ 602 + - Anti-EGFR Monoclonal Antibody EMD 55900 + - Anti-EGFR Monoclonal Antibody GC1118 + - Anti-EGFR Monoclonal Antibody GT-MAB 5.2-GEX + - Anti-EGFR Monoclonal Antibody HLX-07 + - Anti-EGFR Monoclonal Antibody Mixture MM-151 + - Anti-EGFR Monoclonal Antibody RO5083945 + - Anti-EGFR Monoclonal Antibody SCT200 + - Anti-EGFR Monoclonal Antibody SYN004 + - Anti-EGFR TAP Antibody-drug Conjugate IMGN289 + - Anti-EGFR/c-Met Bispecific Antibody EMB-01 + - Anti-EGFR/c-Met Bispecific Antibody JNJ-61186372 + - Anti-EGFR/CD16A Bispecific Antibody AFM24 + - Anti-EGFR/DM1 Antibody-drug Conjugate AVID100 + - Anti-EGFR/HER2/HER3 Monoclonal Antibody Mixture Sym013 + - Anti-EGFR/PBD Antibody-drug Conjugate ABBV-321 + - Anti-EGFRvIII Antibody Drug Conjugate AMG 595 + - Anti-EGFRvIII Immunotoxin MR1-1 + - Anti-EGFRvIII/CD3 BiTE Antibody AMG 596 + - Anti-EGP-2 Immunotoxin MOC31-PE + - Anti-ENPP3 Antibody-Drug Conjugate AGS-16C3F + - Anti-ENPP3/MMAF Antibody-Drug Conjugate AGS-16M8F + - Anti-Ep-CAM Monoclonal Antibody ING-1 + - Anti-EphA2 Antibody-directed Liposomal Docetaxel Prodrug MM-310 + - Anti-EphA2 Monoclonal Antibody DS-8895a + - Anti-EphA2 Monoclonal Antibody-MMAF Immunoconjugate MEDI-547 + - Anti-ErbB2/Anti-ErbB3 Bispecific Monoclonal Antibody MM-111 + - Anti-ErbB3 Antibody ISU104 + - Anti-ErbB3 Monoclonal Antibody AV-203 + - Anti-ErbB3 Monoclonal Antibody CDX-3379 + - Anti-ErbB3 Monoclonal Antibody REGN1400 + - Anti-ErbB3/Anti-IGF-1R Bispecific Monoclonal Antibody MM-141 + - Anti-ETBR/MMAE Antibody-Drug Conjugate DEDN6526A + - Anti-FAP/Interleukin-2 Fusion Protein RO6874281 + - Anti-FCRH5/CD3 BiTE Antibody BFCR4350A + - Anti-FGFR2 Antibody BAY1179470 + - Anti-FGFR3 Antibody-drug Conjugate LY3076226 + - Anti-FGFR4 Monoclonal Antibody U3-1784 + - Anti-FLT3 Antibody-drug Conjugate AGS62P1 + - Anti-FLT3 Monoclonal Antibody 4G8-SDIEM + - Anti-FLT3 Monoclonal Antibody IMC-EB10 + - Anti-FLT3/CD3 BiTE Antibody AMG 427 + - Anti-Folate Receptor-alpha Antibody Drug Conjugate STRO-002 + - Anti-FRA/Eribulin Antibody-drug Conjugate MORAb-202 + - Anti-fucosyl-GM1 Monoclonal Antibody BMS-986012 + - Anti-Ganglioside GM2 Monoclonal Antibody BIW-8962 + - Anti-GARP Monoclonal Antibody ABBV-151 + - Anti-GCC Antibody-Drug Conjugate MLN0264 + - Anti-GCC Antibody-Drug Conjugate TAK-164 + - Anti-GD2 hu3F8/Anti-CD3 huOKT3 Bispecific Antibody + - Anti-GD2 Monoclonal Antibody hu14.18K322A + - Anti-GD2 Monoclonal Antibody MORAb-028 + - Anti-GD3 Antibody-drug Conjugate PF-06688992 + - Anti-GITR Agonistic Monoclonal Antibody ASP1951 + - Anti-GITR Agonistic Monoclonal Antibody BMS-986156 + - Anti-GITR Agonistic Monoclonal Antibody INCAGN01876 + - Anti-GITR Monoclonal Antibody GWN 323 + - Anti-GITR Monoclonal Antibody MK-4166 + - Anti-Globo H Monoclonal Antibody OBI-888 + - Anti-Globo H/MMAE Antibody-drug Conjugate OBI 999 + - Anti-Glypican 3/CD3 Bispecific Antibody ERY974 + - Anti-GnRH Vaccine PEP223 + - Anti-gpA33/CD3 Monoclonal Antibody MGD007 + - Anti-GPR20/DXd Antibody-drug Conjugate DS-6157a + - Anti-gremlin-1 Monoclonal Antibody UCB6114 + - Anti-GRP78 Monoclonal Antibody PAT-SM6 + - Anti-HA Epitope Monoclonal Antibody MEDI8852 + - Anti-HB-EGF Monoclonal Antibody KHK2866 + - Anti-HBEGF Monoclonal Antibody U3-1565 + - Anti-hepcidin Monoclonal Antibody LY2787106 + - Anti-HER-2 Bispecific Antibody KN026 + - Anti-HER2 ADC DS-8201a + - Anti-HER2 Antibody Conjugated Natural Killer Cells ACE1702 + - Anti-HER2 Antibody-drug Conjugate A166 + - Anti-HER2 Antibody-drug Conjugate ARX788 + - Anti-HER2 Antibody-drug Conjugate BAT8001 + - Anti-HER2 Antibody-drug Conjugate DP303c + - Anti-HER2 Antibody-drug Conjugate MEDI4276 + - Anti-HER2 Antibody-drug Conjugate RC48 + - Anti-HER2 Bi-specific Monoclonal Antibody ZW25 + - Anti-HER2 Bispecific Antibody-drug Conjugate ZW49 + - Anti-HER2 Immune Stimulator-antibody Conjugate NJH395 + - Anti-HER2 Monoclonal Antibody B002 + - Anti-HER2 Monoclonal Antibody CT-P6 + - Anti-HER2 Monoclonal Antibody HLX22 + - Anti-HER2 Monoclonal Antibody/Anti-CD137Anticalin Bispecific Fusion Protein PRS-343 + - Anti-HER2-DM1 ADC B003 + - Anti-HER2-DM1 Antibody-drug Conjugate GQ1001 + - Anti-HER2-vc0101 ADC PF-06804103 + - Anti-HER2/Anti-CD3 Bispecific Monoclonal Antibody BTRC 4017A + - Anti-HER2/Anti-CD3 Bispecific Monoclonal Antibody GBR 1302 + - Anti-HER2/Anti-HER3 Bispecific Monoclonal Antibody MCLA-128 + - Anti-HER2/Auristatin Payload Antibody-drug Conjugate XMT-1522 + - Anti-HER2/MMAE Antibody-drug Conjugate MRG002 + - Anti-HER2/PBD-MA Antibody-drug Conjugate DHES0815A + - Anti-HER3 Antibody-drug Conjugate U3 1402 + - Anti-HER3 Monoclonal Antibody GSK2849330 + - Anti-HGF Monoclonal Antibody TAK-701 + - Anti-HIF-1alpha LNA Antisense Oligonucleotide EZN-2968 + - Anti-HIV-1 Lentiviral Vector-expressing sh5/C46 Cal-1 + - Anti-HLA-DR Monoclonal Antibody IMMU-114 + - Anti-HLA-G Antibody TTX-080 + - Anti-human GITR Monoclonal Antibody AMG 228 + - Anti-human GITR Monoclonal Antibody TRX518 + - Anti-ICAM-1 Monoclonal Antibody BI-505 + - Anti-ICOS Agonist Antibody GSK3359609 + - Anti-ICOS Agonist Monoclonal Antibody BMS-986226 + - Anti-ICOS Monoclonal Antibody KY1044 + - Anti-ICOS Monoclonal Antibody MEDI-570 + - Anti-IGF-1R Monoclonal Antibody AVE1642 + - Anti-IGF-1R Recombinant Monoclonal Antibody BIIB022 + - Anti-IL-1 alpha Monoclonal Antibody MABp1 + - Anti-IL-13 Humanized Monoclonal Antibody TNX-650 + - Anti-IL-15 Monoclonal Antibody AMG 714 + - Anti-IL-8 Monoclonal Antibody BMS-986253 + - Anti-IL-8 Monoclonal Antibody HuMax-IL8 + - Anti-ILDR2 Monoclonal Antibody BAY 1905254 + - Anti-ILT4 Monoclonal Antibody MK-4830 + - Anti-integrin Beta-6/MMAE Antibody-drug Conjugate SGN-B6A + - Anti-Integrin Monoclonal Antibody-DM4 Immunoconjugate IMGN388 + - Anti-IRF4 Antisense Oligonucleotide ION251 + - Anti-KIR Monoclonal Antibody IPH 2101 + - Anti-KSP/Anti-VEGF siRNAs ALN-VSP02 + - Anti-LAG-3 Monoclonal Antibody IBI-110 + - Anti-LAG-3 Monoclonal Antibody INCAGN02385 + - Anti-LAG-3 Monoclonal Antibody LAG525 + - Anti-LAG-3 Monoclonal Antibody REGN3767 + - Anti-LAG-3/PD-L1 Bispecific Antibody FS118 + - Anti-LAG3 Monoclonal Antibody BI 754111 + - Anti-LAG3 Monoclonal Antibody MK-4280 + - Anti-LAG3 Monoclonal Antibody TSR-033 + - Anti-LAMP1 Antibody-drug Conjugate SAR428926 + - Anti-latent TGF-beta 1 Monoclonal Antibody SRK-181 + - Anti-Lewis B/Lewis Y Monoclonal Antibody GNX102 + - Anti-LGR5 Monoclonal Antibody BNC101 + - Anti-LIF Monoclonal Antibody MSC-1 + - Anti-LILRB4 Monoclonal Antibody IO-202 + - Anti-LIV-1 Monoclonal Antibody-MMAE Conjugate SGN-LIV1A + - Anti-Ly6E Antibody-Drug Conjugate RG 7841 + - Anti-MAGE-A4 T-cell Receptor/Anti-CD3 scFv Fusion Protein IMC-C103C + - Anti-Melanin Monoclonal Antibody PTI-6D2 + - Anti-mesothelin Antibody-drug Conjugate BMS-986148 + - Anti-mesothelin-Pseudomonas Exotoxin 24 Cytolytic Fusion Protein LMB-100 + - Anti-mesothelin/MMAE Antibody-Drug Conjugate DMOT4039A + - Anti-mesothelin/MMAE Antibody-drug Conjugate RC88 + - Anti-Met Monoclonal Antibody Mixture Sym015 + - Anti-Met/EGFR Monoclonal Antibody LY3164530 + - Anti-MMP-9 Monoclonal Antibody GS-5745 + - Anti-MUC1 Monoclonal Antibody BTH1704 + - Anti-MUC16/CD3 Bispecific Antibody REGN4018 + - Anti-MUC16/CD3 BiTE Antibody REGN4018 + - Anti-MUC16/MMAE Antibody-Drug Conjugate DMUC4064A + - Anti-MUC17/CD3 BiTE Antibody AMG 199 + - Anti-Myeloma Monoclonal Antibody-DM4 Immunoconjugate BT-062 + - Anti-myostatin Monoclonal Antibody LY2495655 + - Anti-NaPi2b Antibody-drug Conjugate XMT-1592 + - Anti-NaPi2b Monoclonal Antibody XMT-1535 + - Anti-nectin-4 Monoclonal Antibody-Drug Conjugate AGS-22M6E + - Anti-Neuropilin-1 Monoclonal Antibody MNRP1685A + - Anti-nf-P2X7 Antibody Ointment BIL-010t + - Anti-NRP1 Antibody ASP1948 + - Anti-Nucleolin Aptamer AS1411 + - Anti-NY-ESO-1 Immunotherapeutic GSK-2241658A + - Anti-NY-ESO1/LAGE-1A TCR/scFv Anti-CD3 IMCnyeso + - Anti-OFA Immunotherapeutic BB-MPI-03 + - Anti-OX40 Agonist Monoclonal Antibody ABBV-368 + - Anti-OX40 Agonist Monoclonal Antibody BGB-A445 + - Anti-OX40 Agonist Monoclonal Antibody PF-04518600 + - Anti-OX40 Antibody BMS 986178 + - Anti-OX40 Hexavalent Agonist Antibody INBRX-106 + - Anti-OX40 Monoclonal Antibody GSK3174998 + - Anti-OX40 Monoclonal Antibody IBI101 + - Anti-PD-1 Antibody-interleukin-21 Mutein Fusion Protein AMG 256 + - Anti-PD-1 Checkpoint Inhibitor PF-06801591 + - Anti-PD-1 Fusion Protein AMP-224 + - Anti-PD-1 Monoclonal Antibody 609A + - Anti-PD-1 Monoclonal Antibody AK105 + - Anti-PD-1 Monoclonal Antibody AMG 404 + - Anti-PD-1 Monoclonal Antibody BAT1306 + - Anti-PD-1 Monoclonal Antibody BCD-100 + - Anti-PD-1 Monoclonal Antibody BI 754091 + - Anti-PD-1 Monoclonal Antibody CS1003 + - Anti-PD-1 Monoclonal Antibody F520 + - Anti-PD-1 Monoclonal Antibody GLS-010 + - Anti-PD-1 Monoclonal Antibody HLX10 + - Anti-PD-1 Monoclonal Antibody HX008 + - Anti-PD-1 Monoclonal Antibody JTX-4014 + - Anti-PD-1 Monoclonal Antibody LZM009 + - Anti-PD-1 Monoclonal Antibody MEDI0680 + - Anti-PD-1 Monoclonal Antibody MGA012 + - Anti-PD-1 Monoclonal Antibody SCT-I10A + - Anti-PD-1 Monoclonal Antibody Sym021 + - Anti-PD-1 Monoclonal Antibody TSR-042 + - Anti-PD-1/Anti-CTLA4 DART Protein MGD019 + - Anti-PD-1/Anti-HER2 Bispecific Antibody IBI315 + - Anti-PD-1/Anti-LAG-3 Bispecific Antibody RO7247669 + - Anti-PD-1/Anti-LAG-3 DART Protein MGD013 + - Anti-PD-1/Anti-PD-L1 Bispecific Antibody IBI318 + - Anti-PD-1/Anti-PD-L1 Bispecific Antibody LY3434172 + - Anti-PD-1/CD47 Infusion Protein HX009 + - Anti-PD-1/CTLA-4 Bispecific Antibody AK104 + - Anti-PD-1/CTLA-4 Bispecific Antibody MEDI5752 + - Anti-PD-1/TIM-3 Bispecific Antibody RO7121661 + - Anti-PD-1/VEGF Bispecific Antibody AK112 + - Anti-PD-L1 Monoclonal Antibody A167 + - Anti-PD-L1 Monoclonal Antibody BCD-135 + - Anti-PD-L1 Monoclonal Antibody BGB-A333 + - Anti-PD-L1 Monoclonal Antibody CBT-502 + - Anti-PD-L1 Monoclonal Antibody CK-301 + - Anti-PD-L1 Monoclonal Antibody CS1001 + - Anti-PD-L1 Monoclonal Antibody FAZ053 + - Anti-PD-L1 Monoclonal Antibody GR1405 + - Anti-PD-L1 Monoclonal Antibody HLX20 + - Anti-PD-L1 Monoclonal Antibody IMC-001 + - Anti-PD-L1 Monoclonal Antibody LY3300054 + - Anti-PD-L1 Monoclonal Antibody MDX-1105 + - Anti-PD-L1 Monoclonal Antibody MSB2311 + - Anti-PD-L1 Monoclonal Antibody RC98 + - Anti-PD-L1 Monoclonal Antibody SHR-1316 + - Anti-PD-L1 Monoclonal Antibody TG-1501 + - Anti-PD-L1 Monoclonal Antibody ZKAB001 + - Anti-PD-L1/4-1BB Bispecific Antibody INBRX-105 + - Anti-PD-L1/Anti-4-1BB Bispecific Monoclonal Antibody GEN1046 + - Anti-PD-L1/CD137 Bispecific Antibody MCLA-145 + - Anti-PD-L1/IL-15 Fusion Protein KD033 + - Anti-PD-L1/TIM-3 Bispecific Antibody LY3415244 + - Anti-PD1 Monoclonal Antibody AGEN2034 + - Anti-PD1/CTLA4 Bispecific Antibody XmAb20717 + - Anti-PGF Monoclonal Antibody RO5323441 + - Anti-PKN3 siRNA Atu027 + - Anti-PLGF Monoclonal Antibody TB-403 + - Anti-PR1/HLA-A2 Monoclonal Antibody Hu8F4 + - Anti-PRAME Immunotherapeutic GSK2302032A + - Anti-PRAME T-cell Receptor/Anti-CD3 scFv Fusion Protein IMC-F106C + - Anti-PRL-3 Monoclonal Antibody PRL3-zumab + - Anti-prolactin Receptor Antibody LFA102 + - Anti-PSCA Monoclonal Antibody AGS-1C4D4 + - Anti-PSMA Monoclonal Antibody MDX1201-A488 + - Anti-PSMA Monoclonal Antibody MLN591-DM1 Immunoconjugate MLN2704 + - Anti-PSMA Monoclonal Antibody-MMAE Conjugate + - Anti-PSMA/CD28 Bispecific Antibody REGN5678 + - Anti-PSMA/CD3 Bispecific Antibody CCW702 + - Anti-PSMA/CD3 Bispecific Antibody JNJ-63898081 + - Anti-PSMA/CD3 Monoclonal Antibody MOR209/ES414 + - Anti-PSMA/PBD ADC MEDI3726 + - Anti-PTK7/Auristatin-0101 Antibody-drug Conjugate PF-06647020 + - Anti-PVRIG Monoclonal Antibody COM701 + - Anti-RANKL Monoclonal Antibody GB-223 + - Anti-RANKL Monoclonal Antibody JMT103 + - Anti-Ribonucleoprotein Antibody ATRC-101 + - Anti-ROR1 ADC VLS-101 + - Anti-ROR1/PNU-159682 Derivative Antibody-drug Conjugate NBE-002 + - Anti-S15 Monoclonal Antibody NC318 + - Anti-sCLU Monoclonal Antibody AB-16B5 + - Anti-SIRPa Monoclonal Antibody CC-95251 + - Anti-SLITRK6 Monoclonal Antibody-MMAE Conjugate AGS15E + - Anti-TAG-72 Monoclonal Antibody scFV CC-49/218 + - Anti-TF Monoclonal Antibody ALT-836 + - Anti-TGF-beta Monoclonal Antibody NIS793 + - Anti-TGF-beta Monoclonal Antibody SAR-439459 + - Anti-TGF-beta RII Monoclonal Antibody IMC-TR1 + - Anti-TIGIT Monoclonal Antibody AB154 + - Anti-TIGIT Monoclonal Antibody BGB-A1217 + - Anti-TIGIT Monoclonal Antibody BMS-986207 + - Anti-TIGIT Monoclonal Antibody COM902 + - Anti-TIGIT Monoclonal Antibody OMP-313M32 + - Anti-TIGIT Monoclonal Antibody SGN-TGT + - Anti-TIM-3 Antibody BMS-986258 + - Anti-TIM-3 Monoclonal Antibody BGB-A425 + - Anti-TIM-3 Monoclonal Antibody INCAGN02390 + - Anti-TIM-3 Monoclonal Antibody MBG453 + - Anti-TIM-3 Monoclonal Antibody Sym023 + - Anti-TIM-3 Monoclonal Antibody TSR-022 + - Anti-TIM3 Monoclonal Antibody LY3321367 + - Anti-TIM3 Monoclonal Antibody SHR-1702 + - Anti-Tissue Factor Monoclonal Antibody MORAb-066 + - Anti-TRAILR2/CDH17 Tetravalent Bispecific Antibody BI 905711 + - Anti-TROP2 Antibody-drug Conjugate BAT8003 + - Anti-TROP2 Antibody-drug Conjugate SKB264 + - Anti-TROP2/DXd Antibody-drug Conjugate DS-1062a + - Anti-TWEAK Monoclonal Antibody RG7212 + - Anti-VEGF Anticalin PRS-050-PEG40 + - Anti-VEGF Monoclonal Antibody hPV19 + - Anti-VEGF/ANG2 Nanobody BI 836880 + - Anti-VEGF/TGF-beta 1 Fusion Protein HB-002T + - Anti-VEGFC Monoclonal Antibody VGX-100 + - Anti-VEGFR2 Monoclonal Antibody HLX06 + - Anti-VEGFR2 Monoclonal Antibody MSB0254 + - Anti-VEGFR3 Monoclonal Antibody IMC-3C5 + - Anti-VISTA Monoclonal Antibody JNJ 61610588 + - Antiangiogenic Drug Combination TL-118 + - Antibody-drug Conjugate ABBV-011 + - Antibody-drug Conjugate ABBV-085 + - Antibody-drug Conjugate ABBV-155 + - Antibody-drug Conjugate ABBV-176 + - Antibody-drug Conjugate ABBV-838 + - Antibody-drug Conjugate ADC XMT-1536 + - Antibody-drug Conjugate Anti-TIM-1-vcMMAE CDX-014 + - Antibody-Drug Conjugate DFRF4539A + - Antibody-drug Conjugate MEDI7247 + - Antibody-drug Conjugate PF-06647263 + - Antibody-drug Conjugate PF-06664178 + - Antibody-drug Conjugate SC-002 + - Antibody-drug Conjugate SC-003 + - Antibody-drug Conjugate SC-004 + - Antibody-drug Conjugate SC-005 + - Antibody-drug Conjugate SC-006 + - Antibody-drug Conjugate SC-007 + - Antibody-like CD95 Receptor/Fc-fusion Protein CAN-008 + - Antigen-presenting Cells-expressing HPV16 E6/E7 SQZ-PBMC-HPV + - Antimetabolite FF-10502 + - Antineoplastic Agent Combination SM-88 + - Antineoplastic Vaccine + - Antineoplastic Vaccine GV-1301 + - Antineoplaston A10 + - Antineoplaston AS2-1 + - Antisense Oligonucleotide GTI-2040 + - Antisense Oligonucleotide QR-313 + - Antitumor B Key Active Component-alpha + - Antrodia cinnamomea Supplement + - Antroquinonol Capsule + - Apalutamide + - Apatorsen + - Apaziquone + - APC8015F + - APE1/Ref-1 Redox Inhibitor APX3330 + - Aphidicoline Glycinate + - Apilimod Dimesylate Capsule + - Apitolisib + - Apolizumab + - Apomab + - Apomine + - Apoptosis Inducer BZL101 + - Apoptosis Inducer GCS-100 + - Apoptosis Inducer MPC-2130 + - Apricoxib + - Aprinocarsen + - Aprutumab + - Aprutumab Ixadotin + - AR Antagonist BMS-641988 + - Arabinoxylan Compound MGN3 + - Aranose + - ARC Fusion Protein SL-279252 + - Archexin + - Arcitumomab + - Arfolitixorin + - Arginase Inhibitor INCB001158 + - Arginine Butyrate + - Arnebia Indigo Jade Pearl Topical Cream + - Arsenic Trioxide + - Arsenic Trioxide Capsule Formulation ORH 2014 + - Artemether Sublingual Spray + - Artemisinin Dimer + - Artesunate + - Arugula Seed Powder + - Aryl Hydrocarbon Receptor Antagonist BAY2416964 + - Aryl Hydrocarbon Receptor Inhibitor IK-175 + - Asaley + - Asciminib + - Ascrinvacumab + - Ashwagandha Root Powder Extract + - ASP4132 + - Aspacytarabine + - Asparaginase + - Asparaginase Erwinia chrysanthemi + - Astatine At 211 Anti-CD38 Monoclonal Antibody OKT10-B10 + - Astatine At 211 Anti-CD45 Monoclonal Antibody BC8-B10 + - Astuprotimut-R + - Asulacrine + - Asulacrine Isethionate + - Asunercept + - At 211 Monoclonal Antibody 81C6 + - Atamestane + - Atezolizumab + - Atiprimod + - Atiprimod Dihydrochloride + - Atiprimod Dimaleate + - ATM Inhibitor M 3541 + - ATM Kinase Inhibitor AZD0156 + - ATM Kinase Inhibitor AZD1390 + - Atorvastatin Calcium + - Atorvastatin Sodium + - ATR Inhibitor RP-3500 + - ATR Kinase Inhibitor BAY1895344 + - ATR Kinase Inhibitor M1774 + - ATR Kinase Inhibitor M6620 + - ATR Kinase Inhibitor VX-803 + - Atrasentan Hydrochloride + - Attenuated Listeria monocytogenes CRS-100 + - Attenuated Live Listeria Encoding HPV 16 E7 Vaccine ADXS11-001 + - Attenuated Measles Virus Encoding SCD Transgene TMV-018 + - Atuveciclib + - Audencel + - Auranofin + - Aurora A Kinase Inhibitor LY3295668 + - Aurora A Kinase Inhibitor LY3295668 Erbumine + - Aurora A Kinase Inhibitor MK5108 + - Aurora A Kinase Inhibitor TAS-119 + - Aurora A Kinase/Tyrosine Kinase Inhibitor ENMD-2076 + - Aurora B Serine/Threonine Kinase Inhibitor TAK-901 + - Aurora B/C Kinase Inhibitor GSK1070916A + - Aurora kinase A/B inhibitor TT-00420 + - Aurora Kinase Inhibitor AMG 900 + - Aurora Kinase Inhibitor BI 811283 + - Aurora Kinase Inhibitor MLN8054 + - Aurora Kinase Inhibitor PF-03814735 + - Aurora Kinase Inhibitor SNS-314 + - Aurora Kinase Inhibitor TTP607 + - Aurora Kinase/VEGFR2 Inhibitor CYC116 + - Autologous ACTR-CD16-CD28-expressing T-lymphocytes ACTR707 + - Autologous AFP Specific T Cell Receptor Transduced T Cells C-TCR055 + - Autologous Anti-BCMA CAR T-cells PHE885 + - Autologous Anti-BCMA CAR-transduced T-cells KITE-585 + - Autologous Anti-BCMA CD8+ CAR T-cells Descartes-11 + - Autologous Anti-BCMA-CAR Expressing Stem Memory T-cells P-BCMA-101 + - Autologous Anti-BCMA-CAR-4-1BB-CD3zeta-expressing CD4+/CD8+ T-lymphocytes JCARH125 + - Autologous Anti-BCMA-CAR-4-1BB-CD3zeta-expressing Memory T-lymphocytes bb21217 + - Autologous Anti-BCMA-CAR-4-1BB-CD3zeta-expressing T-cells C-CAR088 + - Autologous Anti-BCMA-CAR-4-1BB-CD3zeta-expressing T-cells CT053 + - Autologous Anti-BCMA-CAR-expressing CD4+/CD8+ T-lymphocytes FCARH143 + - Autologous Anti-CD123 CAR-T Cells + - Autologous Anti-CD19 CAR T-cells 19(T2)28z1xx + - Autologous Anti-CD19 CAR T-cells IM19 + - Autologous Anti-CD19 CAR TCR-zeta/4-1BB-transduced T-lymphocytes huCART19 + - Autologous Anti-CD19 CAR-4-1BB-CD3zeta-expressing T-cells CNCT19 + - Autologous Anti-CD19 CAR-CD28 T-cells ET019002 + - Autologous Anti-CD19 CAR-CD3zeta-4-1BB-expressing T-cells PZ01 + - Autologous Anti-CD19 CAR-expressing T-lymphocytes CLIC-1901 + - Autologous Anti-CD19 Chimeric Antigen Receptor T-cells AUTO1 + - Autologous Anti-CD19 Chimeric Antigen Receptor T-cells SJCAR19 + - Autologous Anti-CD19 T-cell Receptor T cells ET190L1 + - Autologous Anti-CD19 TAC-T cells TAC01-CD19 + - Autologous Anti-CD19/CD20 Bispecific Nanobody-based CAR-T cells + - Autologous Anti-CD19/CD22 CAR T-cells AUTO3 + - Autologous Anti-CD19CAR-4-1BB-CD3zeta-EGFRt-expressing CD4+/CD8+ Central Memory T-lymphocytes JCAR014 + - Autologous Anti-CD19CAR-HER2t/CD22CAR-EGFRt-expressing T-cells + - Autologous Anti-CD20 CAR Transduced CD4/CD8 Enriched T-cells MB-CART20.1 + - Autologous Anti-CD22 CAR-4-1BB-TCRz-transduced T-lymphocytes CART22-65s + - Autologous Anti-EGFR CAR-transduced CXCR 5-modified T-lymphocytes + - Autologous Anti-FLT3 CAR T Cells AMG 553 + - Autologous Anti-HLA-A*02/AFP TCRm-expressing T-cells ET140202 + - Autologous Anti-HLA-A*0201/AFP CAR T-cells ET1402L1 + - Autologous Anti-ICAM-1-CAR-CD28-4-1BB-CD3zeta-expressing T-cells AIC100 + - Autologous Anti-kappa Light Chain CAR-CD28-expressing T-lymphocytes + - Autologous Anti-NY-ESO-1/LAGE-1 TCR-transduced c259 T Lymphocytes GSK3377794 + - Autologous Anti-PD-1 Antibody-activated Tumor-infiltrating Lymphocytes + - Autologous Anti-PSMA CAR-T Cells P-PSMA-101 + - Autologous AXL-targeted CAR T-cells CCT301-38 + - Autologous B-cell/Monocyte-presenting HER2/neu Antigen Vaccine BVAC-B + - Autologous BCMA-targeted CAR T Cells CC-98633 + - Autologous BCMA-targeted CAR T Cells LCAR-B4822M + - Autologous Bi-epitope BCMA-targeted CAR T-cells JNJ-68284528 + - Autologous Bispecific BCMA/CD19-targeted CAR-T Cells GC012F + - Autologous Bispecific CD19/CD22-targeted CAR-T Cells GC022 + - Autologous Bone Marrow-derived CD34/CXCR4-positive Stem Cells AMR-001 + - Autologous CAR-mbIL15-Safety Switch T-cells PRGN-3005 + - Autologous CAR-mbIL15-Safety Switch T-cells PRGN-3006 + - Autologous CD123-4SCAR-expressing T-cells 4SCAR123 + - Autologous CD19 CAR-expressing CD4+/CD8+ T-cells MB-CART19.1 + - Autologous CD19-targeted CAR T Cells CC-97540 + - Autologous CD19-targeted CAR T Cells JWCAR029 + - Autologous CD19-targeted CAR-T Cells GC007F + - Autologous CD19/PD-1 Bispecific CAR-T Cells + - Autologous CD20-4SCAR-expressing T-cells 4SCAR20 + - Autologous CD22-4SCAR-expressing T-cells 4SCAR22 + - Autologous CD38-4SCAR-expressing T-cells 4SCAR38 + - Autologous Clonal Neoantigen T Cells ATL001 + - Autologous CRISPR-edited Anti-CD19 CAR T Cells XYF19 + - Autologous Deep IL-15 Primed T-cells TRQ15-01 + - Autologous Dendritic Cell Vaccine ACT2001 + - Autologous Dendritic Cell-based Immunotherapeutic AV0113 + - Autologous FRa-4SCAR-expressing T-cells 4SCAR-FRa + - Autologous Genetically-modified MAGE-A4 C1032 CD8alpha T Cells + - Autologous Genetically-modified MAGE-A4 C1032 T Cells + - Autologous Heat-Shock Protein 70 Peptide Vaccine AG-858 + - Autologous HPV16 E7-specific HLA-A*02:01-restricted TCR Gene Engineered Lymphocytes KITE-439 + - Autologous LMP1/LMP2/EBNA1-specific HLA-A02:01/24:02/11:01-restricted TCR-expressing T-lymphocytes YT-E001 + - Autologous MAGE-A3/A6-specific TCR Gene-engineered Lymphocytes KITE-718 + - Autologous MCPyV-specific HLA-A02-restricted TCR-transduced CD4+ and CD8+ T-cells FH-MCVA2TCR + - Autologous Mesenchymal Stem Cells Apceth_101 + - Autologous Mesothelin-specific Human mRNA CAR-transfected PBMCs MCY-M11 + - Autologous Monocyte-derived Lysate-pulsed Dendritic Cell Vaccine PV-001-DC + - Autologous Multi-lineage Potential Cells + - Autologous Nectin-4/FAP-targeted CAR-T Cells + - Autologous NKG2D CAR T-cells CYAD-02 + - Autologous NKG2D CAR-CD3zeta-DAP10-expressing T-Lymphocytes CYAD-01 + - Autologous Pancreatic Adenocarcinoma Lysate and mRNA-loaded Dendritic Cell Vaccine + - Autologous Peripheral Blood Lymphocytes from Ibrutinib-treated Chronic Lymphocytic Leukemia Patients IOV-2001 + - Autologous Prostate Cancer Antigen-expressing Dendritic Cell Vaccine BPX-101 + - Autologous Prostate Stem Cell Antigen-specific CAR T Cells BPX-601 + - Autologous Rapamycin-resistant Th1/Tc1 Cells RAPA-201 + - Autologous ROR2-targeted CAR T-cells CCT301-59 + - Autologous TAAs-loaded Autologous Dendritic Cells AV-GBM-1 + - Autologous TCR-engineered T-cells IMA201 + - Autologous TCR-engineered T-cells IMA202 + - Autologous TCR-engineered T-cells IMA203 + - Autologous TCRm-expressing T-cells ET140203 + - Autologous Tetravalent Dendritic Cell Vaccine MIDRIX4-LUNG + - Autologous Tumor Infiltrating Lymphocytes LN-144 + - Autologous Tumor Infiltrating Lymphocytes LN-145 + - Autologous Tumor Infiltrating Lymphocytes LN-145-S1 + - Autologous Tumor Infiltrating Lymphocytes MDA-TIL + - Autologous Universal CAR-expressing T-lymphocytes UniCAR02-T + - Avadomide + - Avadomide Hydrochloride + - Avapritinib + - Avdoralimab + - Avelumab + - Aviscumine + - Avitinib Maleate + - Axalimogene Filolisbac + - Axatilimab + - Axicabtagene Ciloleucel + - Axitinib + - AXL Inhibitor DS-1205c + - AXL Inhibitor SLC-391 + - AXL Receptor Tyrosine Kinase/cMET Inhibitor BPI-9016M + - AXL/ FLT3/VEGFR2 Inhibitor KC1036 + - Axl/Mer Inhibitor INCB081776 + - Axl/Mer Inhibitor PF-07265807 + - Azacitidine + - Azapicyl + - Azaribine + - Azaserine + - Azathioprine + - Azimexon + - Azintuxizumab Vedotin + - Aziridinylbenzoquinone RH1 + - Azotomycin + - Azurin:50-77 Cell Penetrating Peptide p28 + - B-Raf/VEGFR-2 Inhibitor RAF265 + - Babaodan Capsule + - Bacillus Calmette-Guerin Substrain Connaught Live Antigen + - Bactobolin + - Bafetinib + - Balixafortide + - Balstilimab + - Baltaleucel-T + - Banoxantrone + - Barasertib + - Bardoxolone + - Bardoxolone Methyl + - Baricitinib + - Batabulin + - Batabulin Sodium + - Batimastat + - Bavituximab + - Bazedoxifene + - Bazlitoran + - BC-819 Plasmid/Polyethylenimine Complex + - BCG Solution + - BCG Tokyo-172 Strain Solution + - BCG Vaccine + - Bcl-2 Inhibitor APG 2575 + - Bcl-2 Inhibitor BCL201 + - Bcl-2 Inhibitor BGB-11417 + - Bcl-2 Inhibitor LP-108 + - Bcl-2 Inhibitor S65487 + - Bcl-Xs Adenovirus Vaccine + - BCMA x CD3 T-cell Engaging Antibody CC-93269 + - BCMA-CD19 Compound CAR T Cells + - BCMA/CD3e Tri-specific T-cell Activating Construct HPN217 + - Bcr-Abl Kinase Inhibitor K0706 + - Bcr-Abl Kinase Inhibitor PF-114 + - BCR-ABL/KIT/AKT/ERK Inhibitor HQP1351 + - Beauvericin + - Becatecarin + - Belagenpumatucel-L + - Belantamab Mafodotin + - Belapectin + - Belimumab + - Belinostat + - Belotecan Hydrochloride + - Belvarafenib + - Belzutifan + - Bemarituzumab + - Bemcentinib + - Bempegaldesleukin + - Benaxibine + - Bendamustine + - Bendamustine Hydrochloride + - Bendamustine-containing Nanoparticle-based Formulation RXDX-107 + - Benzaldehyde Dimethane Sulfonate + - Benzoylphenylurea + - Berberine Chloride + - Bermekimab + - Bersanlimab + - Berubicin Hydrochloride + - Berzosertib + - BET Bromodomain Inhibitor ZEN-3694 + - BET Inhibitor ABBV-744 + - BET Inhibitor BAY1238097 + - BET inhibitor BI 894999 + - BET Inhibitor BMS-986158 + - BET Inhibitor CC-90010 + - BET Inhibitor CPI-0610 + - BET Inhibitor FT-1101 + - BET Inhibitor GS-5829 + - BET Inhibitor GSK2820151 + - BET Inhibitor INCB054329 + - BET Inhibitor INCB057643 + - BET Inhibitor RO6870810 + - BET-bromodomain Inhibitor ODM-207 + - Beta Alethine + - Beta-Carotene + - Beta-elemene + - Beta-Glucan + - Beta-Glucan MM-10-001 + - Beta-lapachone Prodrug ARQ 761 + - Beta-Thioguanine Deoxyriboside + - Betaglucin Gel + - Betulinic Acid + - Bevacizumab + - Bexarotene + - Bexmarilimab + - BF-200 Gel Formulation + - BH3 Mimetic ABT-737 + - Bi-functional Alkylating Agent VAL-083 + - Bicalutamide + - Bimiralisib + - Binetrakin + - Binimetinib + - Bintrafusp Alfa + - Birabresib + - Birinapant + - Bis(choline)tetrathiomolybdate + - Bisantrene + - Bisantrene Hydrochloride + - Bisnafide + - Bisnafide Dimesylate + - Bispecific Antibody 2B1 + - Bispecific Antibody AGEN1223 + - Bispecific Antibody AMG 509 + - Bispecific Antibody GS-1423 + - Bispecific Antibody MDX-H210 + - Bispecific Antibody MDX447 + - Bisthianostat + - BiTE Antibody AMG 910 + - Bivalent BRD4 Inhibitor AZD5153 + - Bizalimogene Ralaplasmid + - Bizelesin + - BL22 Immunotoxin + - Black Cohosh + - Black Raspberry Nectar + - Bleomycin + - Bleomycin A2 + - Bleomycin B2 + - Bleomycin Sulfate + - Blinatumomab + - Blueberry Powder Supplement + - BMI1 Inhibitor PTC596 + - BMS-184476 + - BMS-188797 + - BMS-214662 + - BMS-275183 + - Boanmycin Hydrochloride + - Bomedemstat + - Boronophenylalanine-Fructose Complex + - Bortezomib + - Bosutinib + - Bosutinib Monohydrate + - Botanical Agent BEL-X-HG + - Botanical Agent LEAC-102 + - Bovine Cartilage + - Bozitinib + - BP-Cx1-Platinum Complex BP-C1 + - BR96-Doxorubicin Immunoconjugate + - Brachyury-expressing Yeast Vaccine GI-6301 + - BRAF Inhibitor + - BRAF Inhibitor ARQ 736 + - BRAF Inhibitor BGB-3245 + - BRAF Inhibitor PLX8394 + - BRAF(V600E) Kinase Inhibitor ABM-1310 + - BRAF(V600E) Kinase Inhibitor RO5212054 + - BRAF/EGFR Inhibitor BGB-283 + - BRAFV600/PI3K Inhibitor ASN003 + - BRD4 Inhibitor PLX2853 + - BRD4 Inhibitor PLX51107 + - Breflate + - Brentuximab + - Brentuximab Vedotin + - Brequinar + - Brequinar Sodium + - Briciclib Sodium + - Brigatinib + - Brilanestrant + - Brimonidine Tartrate Nanoemulsion OCU-300 + - Brivanib + - Brivanib Alaninate + - Brivudine + - Brivudine Phosphoramidate + - Broad-Spectrum Human Papillomavirus Vaccine V505 + - Broccoli Sprout/Broccoli Seed Extract Supplement + - Bromacrylide + - Bromebric Acid + - Bromocriptine Mesylate + - Brontictuzumab + - Brostacillin Hydrochloride + - Brostallicin + - Broxuridine + - Bruceanol A + - Bruceanol B + - Bruceanol C + - Bruceanol D + - Bruceanol E + - Bruceanol F + - Bruceanol G + - Bruceanol H + - Bruceantin + - Bryostatin 1 + - BTK Inhibitor ARQ 531 + - BTK Inhibitor CT-1530 + - BTK Inhibitor DTRMWXHS-12 + - BTK Inhibitor HZ-A-018 + - BTK Inhibitor ICP-022 + - BTK Inhibitor LOXO-305 + - BTK Inhibitor M7583 + - BTK inhibitor TG-1701 + - Budigalimab + - Budotitane + - Bufalin + - Buparlisib + - Burixafor + - Burixafor Hydrobromide + - Burosumab + - Buserelin + - Bushen Culuan Decoction + - Bushen-Jianpi Decoction + - Busulfan + - Buthionine Sulfoximine + - BXQ-350 Nanovesicle Formulation + - c-Kit Inhibitor PLX9486 + - c-Met Inhibitor ABN401 + - c-Met Inhibitor AL2846 + - c-Met Inhibitor AMG 208 + - c-Met Inhibitor AMG 337 + - c-Met Inhibitor GST-HG161 + - c-Met Inhibitor HS-10241 + - c-Met Inhibitor JNJ-38877605 + - c-Met Inhibitor MK2461 + - c-Met Inhibitor MK8033 + - c-Met Inhibitor MSC2156119J + - C-myb Antisense Oligonucleotide G4460 + - c-raf Antisense Oligonucleotide ISIS 5132 + - C-VISA BikDD:Liposome + - C/EBP Beta Antagonist ST101 + - CAB-ROR2-ADC BA3021 + - Cabazitaxel + - Cabiralizumab + - Cabozantinib + - Cabozantinib S-malate + - Cactinomycin + - Caffeic Acid Phenethyl Ester + - CAIX Inhibitor DTP348 + - CAIX Inhibitor SLC-0111 + - Calaspargase Pegol-mknl + - Calcitriol + - Calcium Release-activated Channel Inhibitor CM4620 + - Calcium Release-activated Channels Inhibitor RP4010 + - Calcium Saccharate + - Calculus bovis/Moschus/Olibanum/Myrrha Capsule + - Calicheamicin Gamma 1I + - Camidanlumab Tesirine + - Camptothecin + - Camptothecin Analogue TLC388 + - Camptothecin Glycoconjugate BAY 38-3441 + - Camptothecin Sodium + - Camptothecin-20(S)-O-Propionate Hydrate + - Camrelizumab + - Camsirubicin + - Cancell + - Cancer Peptide Vaccine S-588410 + - Canerpaturev + - Canertinib Dihydrochloride + - Canfosfamide + - Canfosfamide Hydrochloride + - Cannabidiol + - Cantrixil + - Cantuzumab Ravtansine + - Capecitabine + - Capecitabine Rapidly Disintegrating Tablet + - Capivasertib + - Capmatinib + - Captopril + - CAR T-Cells AMG 119 + - Caracemide + - Carbendazim + - Carbetimer + - Carbogen + - Carbon C 14-pamiparib + - Carboplatin + - Carboquone + - Carboxyamidotriazole + - Carboxyamidotriazole Orotate + - Carboxyphenyl Retinamide + - Carfilzomib + - Caricotamide/Tretazicar + - Carlumab + - Carmofur + - Carmustine + - Carmustine Implant + - Carmustine in Ethanol + - Carmustine Sustained-Release Implant Wafer + - Carotuximab + - Carubicin + - Carubicin Hydrochloride + - Carzelesin + - Carzinophilin + - Cathelicidin LL-37 + - Cationic Liposome-Encapsulated Paclitaxel + - Cationic Peptide Cream Cypep-1 + - Catumaxomab + - CBP/beta-catenin Antagonist PRI-724 + - CBP/beta-catenin Modulator E7386 + - CCR2 Antagonist CCX872-B + - CCR2 Antagonist PF-04136309 + - CCR2/CCR5 Antagonist BMS-813160 + - CCR4 Inhibitor FLX475 + - CD11b Agonist GB1275 + - CD123-CD33 Compound CAR T Cells + - CD123-specific Targeting Module TM123 + - CD20-CD19 Compound CAR T Cells + - CD28/ICOS Antagonist ALPN-101 + - CD4-specific Telomerase Peptide Vaccine UCPVax + - CD40 Agonist Monoclonal Antibody CP-870,893 + - CD40 Agonistic Monoclonal Antibody APX005M + - CD44 Targeted Agent SPL-108 + - CD44v6-specific CAR T-cells + - CD47 Antagonist ALX148 + - CD73 Inhibitor AB680 + - CD73 Inhibitor LY3475070 + - CD80-Fc Fusion Protein ALPN-202 + - CD80-Fc Fusion Protein FPT155 + - CDC7 Inhibitor TAK-931 + - CDC7 Kinase Inhibitor BMS-863233 + - CDC7 Kinase Inhibitor LY3143921 Hydrate + - CDC7 Kinase Inhibitor NMS-1116354 + - CDK Inhibitor AT7519 + - CDK Inhibitor R547 + - CDK Inhibitor SNS-032 + - CDK/JAK2/FLT3 Inhibitor TG02 Citrate + - CDK1 Inhibitor BEY1107 + - CDK1/2/4 Inhibitor AG-024322 + - CDK2 Inhibitor PF-07104091 + - CDK2/4/6/FLT3 Inhibitor FN-1501 + - CDK2/5/9 Inhibitor CYC065 + - CDK4 Inhibitor P1446A-05 + - CDK4/6 Inhibitor + - CDK4/6 Inhibitor BPI-16350 + - CDK4/6 Inhibitor CS3002 + - CDK4/6 Inhibitor FCN-437 + - CDK4/6 Inhibitor G1T38 + - CDK4/6 Inhibitor HS-10342 + - CDK4/6 Inhibitor SHR6390 + - CDK4/6 Inhibitor TQB3616 + - CDK7 Inhibitor CT7001 + - CDK7 Inhibitor SY-1365 + - CDK7 Inhibitor SY-5609 + - CDK8/19 Inhibitor SEL 120 + - CDK9 Inhibitor AZD4573 + - CEA-MUC-1-TRICOM Vaccine CV301 + - CEA-targeting Agent RG6123 + - CEBPA-targeting saRNA MTL-CEBPA Liposome + - Cedazuridine + - Cedazuridine/Azacitidine Combination Agent ASTX030 + - Cedazuridine/Decitabine Combination Agent ASTX727 + - Cedefingol + - Cediranib + - Cediranib Maleate + - Celecoxib + - Cell Cycle Checkpoint/DNA Repair Antagonist IC83 + - Cemadotin + - Cemadotin Hydrochloride + - Cemiplimab + - Cenersen + - Cenisertib + - CENP-E Inhibitor GSK-923295 + - Ceralasertib + - Ceramide Nanoliposome + - Cerdulatinib + - Cereblon E3 Ubiquitin Ligase Modulating Agent CC-92480 + - Cereblon E3 Ubiquitin Ligase Modulating Agent CC-99282 + - Cereblon Modulator CC-90009 + - Cergutuzumab Amunaleukin + - Ceritinib + - Cesalin + - cEt KRAS Antisense Oligonucleotide AZD4785 + - Cetrelimab + - Cetuximab + - Cetuximab Sarotalocan + - Cetuximab-IR700 Conjugate RM-1929 + - Cetuximab-loaded Ethylcellulose Polymeric Nanoparticles Decorated with Octreotide (SY) + - Cevipabulin + - Cevipabulin Fumarate + - Cevipabulin Succinate + - Cevostamab + - cFMS Tyrosine Kinase Inhibitor ARRY-382 + - Chaparrin + - Chaparrinone + - Checkpoint Kinase Inhibitor AZD7762 + - Checkpoint Kinase Inhibitor XL844 + - Chemotherapy + - Chiauranib + - Chimeric Monoclonal Antibody 81C6 + - ChiNing Decoction + - Chk1 Inhibitor CCT245737 + - Chk1 Inhibitor GDC-0425 + - Chk1 Inhibitor GDC-0575 + - CHK1 Inhibitor MK-8776 + - CHK1 Inhibitor PF-477736 + - Chlorambucil + - Chlorodihydropyrimidine + - Chloroquine + - Chloroquinoxaline Sulfonamide + - Chlorotoxin + - Chlorotoxin (EQ)-CD28-CD3zeta-CD19t-expressing CAR T-lymphocytes + - Chlorozotocin + - Choline Kinase Alpha Inhibitor TCD-717 + - CHP-NY-ESO-1 Peptide Vaccine IMF-001 + - Chromomycin A3 + - Chrysanthemum morifolium/Ganoderma lucidum/Glycyrrhiza glabra/Isatis indigotica/Panax pseudoginseng/Rabdosia rubescens/Scutellaria baicalensis/Serona repens Supplement + - Cibisatamab + - Ciclopirox Prodrug CPX-POM + - Cidan Herbal Capsule + - Ciforadenant + - Cilengitide + - Ciltacabtagene Autoleucel + - Cimetidine + - Cinacalcet Hydrochloride + - Cinobufagin + - Cinobufotalin + - Cinrebafusp Alfa + - Cintirorgon + - Cintredekin Besudotox + - Cirmtuzumab + - cis-Urocanic Acid + - Cisplatin + - Cisplatin Liposomal + - Cisplatin-E Therapeutic Implant + - Cisplatin/Vinblastine/Cell Penetration Enhancer Formulation INT230-6 + - Citarinostat + - Citatuzumab Bogatox + - Cixutumumab + - CK1alpha/CDK7/CDK9 Inhibitor BTX-A51 + - CK2-targeting Synthetic Peptide CIGB-300 + - CL 246738 + - Cladribine + - Clanfenur + - Clarithromycin + - Class 1/4 Histone Deacetylase Inhibitor OKI-179 + - Clinical Trial + - Clinical Trial Agent + - Clioquinol + - Clivatuzumab + - Clodronate Disodium + - Clodronic Acid + - Clofarabine + - Clomesone + - Clomiphene + - Clomiphene Citrate + - Clostridium Novyi-NT Spores + - Cobimetinib + - Cobolimab + - Cobomarsen + - Codrituzumab + - Coenzyme Q10 + - Cofetuzumab Pelidotin + - Colchicine-Site Binding Agent ABT-751 + - Cold Contaminant-free Iobenguane I-131 + - Colloidal Gold-Bound Tumor Necrosis Factor + - Colorectal Cancer Peptide Vaccine PolyPEPI1018 + - Colorectal Tumor-Associated Peptides Vaccine IMA910 + - Coltuximab Ravtansine + - Combretastatin + - Combretastatin A-1 + - Combretastatin A1 Diphosphate + - Commensal Bacterial Strain Formulation VE800 + - Compound Kushen Injection + - Conatumumab + - Conbercept + - Concentrated Lingzhi Mushroom Extract + - Conditionally Active Biologic Anti-AXL Antibody-drug Conjugate BA3011 + - Copanlisib + - Copanlisib Hydrochloride + - Copper Cu 64-ATSM + - Copper Cu 67 Tyr3-octreotate + - Copper Gluconate + - Cord Blood Derived CAR T-Cells + - Cord Blood-derived Expanded Natural Killer Cells PNK-007 + - Cordycepin + - Cordycepin Triphosphate + - Coriolus Versicolor Extract + - Corticorelin Acetate + - Cortisone Acetate + - Cosibelimab + - Cositecan + - Coxsackievirus A21 + - Coxsackievirus V937 + - CpG Oligodeoxynucleotide GNKG168 + - Crenolanib + - Crenolanib Besylate + - Crizotinib + - Crolibulin + - Cryptophycin + - Cryptophycin 52 + - Crystalline Genistein Formulation AXP107-11 + - CSF-1R Inhibitor BLZ945 + - CSF1R Inhibitor ABSK021 + - CSF1R Inhibitor DCC-3014 + - CSF1R Inhibitor PLX73086 + - CT2584 HMS + - CTLA-4-directed Probody BMS-986249 + - Curcumin + - Curcumin/Doxorubicin-encapsulating Nanoparticle IMX-110 + - Cusatuzumab + - Custirsen Sodium + - CXC Chemokine Receptor 2 Antagonist AZD5069 + - CXCR1/2 Inhibitor SX-682 + - CXCR2 Antagonist QBM076 + - CXCR4 Antagonist BL-8040 + - CXCR4 Antagonist USL311 + - CXCR4 Inhibitor Q-122 + - CXCR4 Peptide Antagonist LY2510924 + - CXCR4/E-selectin Antagonist GMI-1359 + - Cyclin-dependent Kinase 8/19 Inhibitor BCD 115 + - Cyclin-dependent Kinase Inhibitor PF-06873600 + - Cyclodextrin-Based Polymer-Camptothecin CRLX101 + - Cyclodisone + - Cycloleucine + - Cyclopentenyl Cytosine + - Cyclophosphamide + - Cyclophosphamide Anhydrous + - Cyclosporine + - CYL-02 Plasmid DNA + - CYP11A1 inhibitor ODM-208 + - CYP11A1 Inhibitor ODM-209 + - CYP17 Inhibitor CFG920 + - CYP17 Lyase Inhibitor ASN001 + - CYP17/Androgen Receptor Inhibitor ODM 204 + - CYP17/CYP11B2 Inhibitor LAE001 + - Cyproterone + - Cyproterone Acetate + - Cytarabine + - Cytarabine Monophosphate Prodrug MB07133 + - Cytarabine-asparagine Prodrug BST-236 + - Cytidine Analog RX-3117 + - Cytochlor + - Cytokine-based Biologic Agent IRX-2 + - D-methionine Formulation MRX-1024 + - DAB389 Epidermal Growth Factor + - Dabrafenib + - Dabrafenib Mesylate + - Dacarbazine + - Dacetuzumab + - DACH Polymer Platinate AP5346 + - DACH-Platin Micelle NC-4016 + - Daclizumab + - Dacomitinib + - Dacplatinum + - Dactinomycin + - Dactolisib + - Dactolisib Tosylate + - Dalantercept + - Dalotuzumab + - Daniquidone + - Danusertib + - Danvatirsen + - Daporinad + - Daratumumab + - Daratumumab and Hyaluronidase-fihj + - Daratumumab/rHuPH20 + - Darinaparsin + - Darleukin + - Darolutamide + - Daromun + - Dasatinib + - Daunorubicin + - Daunorubicin Citrate + - Daunorubicin Hydrochloride + - DEC-205/NY-ESO-1 Fusion Protein CDX-1401 + - Decitabine + - Decitabine and Cedazuridine + - Defactinib + - Defactinib Hydrochloride + - Deferoxamine + - Deferoxamine Mesylate + - Degarelix + - Degarelix Acetate + - Delanzomib + - Delolimogene Mupadenorepvec + - Demcizumab + - Demecolcine + - Demplatin Pegraglumer + - Dendrimer-conjugated Bcl-2/Bcl-XL Inhibitor AZD0466 + - Dendritic Cell Vaccine + - Dendritic Cell-Autologous Lung Tumor Vaccine + - Dendritic Cell-targeting Lentiviral Vector ID-LV305 + - Denenicokin + - Dengue Virus Adjuvant PV-001-DV + - Denibulin + - Denibulin Hydrochloride + - Denileukin Diftitox + - Denintuzumab Mafodotin + - Denosumab + - Deoxycytidine Analogue TAS-109 + - Deoxycytidine Analogue TAS-109 Hydrochloride + - Depatuxizumab + - Depatuxizumab Mafodotin + - Derazantinib + - Deslorelin + - Deslorelin Acetate + - Detirelix + - Detorubicin + - Deuteporfin + - Deuterated Enzalutamide + - Devimistat + - Dexamethason + - Dexamethasone + - Dexamethasone Phosphate + - Dexamethasone Sodium Phosphate + - Dexanabinol + - Dexrazoxane + - Dexrazoxane Hydrochloride + - Dezaguanine + - Dezaguanine Mesylate + - Dezapelisib + - DHA-Paclitaxel + - DHEA Mustard + - DI-Leu16-IL2 Immunocytokine + - Dianhydrogalactitol + - Diarylsulfonylurea Compound ILX-295501 + - Diazepinomicin + - Diaziquone + - Diazooxonorleucine + - Dibrospidium Chloride + - Dichloroallyl Lawsone + - Dicycloplatin + - Didox + - Dienogest + - Diethylnorspermine + - Digitoxin + - Digoxin + - Dihydro-5-Azacytidine + - Dihydrolenperone + - Dihydroorotate Dehydrogenase Inhibitor AG-636 + - Dihydroorotate Dehydrogenase Inhibitor BAY2402234 + - Diindolylmethane + - Dilpacimab + - Dimethylmyleran + - Dinaciclib + - Dinutuximab + - Dioscorea nipponica Makino Extract DNE3 + - Diphencyprone + - Diphtheria Toxin Fragment-Interleukin-2 Fusion Protein E7777 + - Ditiocarb + - DKK1-Neutralizing Monoclonal Antibody DKN-01 + - DM-CHOC-PEN + - DM4-Conjugated Anti-Cripto Monoclonal Antibody BIIB015 + - DNA Interference Oligonucleotide PNT2258 + - DNA Minor Groove Binding Agent SG2000 + - DNA Plasmid Encoding Interleukin-12 INO-9012 + - DNA Plasmid-encoding Interleukin-12 INO-9012/PSA/PSMA DNA Plasmids INO-5150 Formulation INO-5151 + - DNA Plasmid-encoding Interleukin-12/HPV DNA Plasmids Therapeutic Vaccine MEDI0457 + - DNA Vaccine VB10.16 + - DNA-dependent Protein Kinase Inhibitor VX-984 + - DNA-PK inhibitor AZD7648 + - DNA-PK/PI3K-delta Inhibitor BR101801 + - DNA-PK/TOR Kinase Inhibitor CC-115 + - DNMT1 Inhibitor NTX-301 + - DNMT1 Mixed-Backbone Antisense Oligonucleotide MG 98 + - Docetaxel + - Docetaxel Anhydrous + - Docetaxel Emulsion ANX-514 + - Docetaxel Formulation CKD-810 + - Docetaxel Lipid Microspheres + - Docetaxel Nanoparticle CPC634 + - Docetaxel Polymeric Micelles + - Docetaxel-loaded Nanopharmaceutical CRLX301 + - Docetaxel-PNP + - Docetaxel/Ritonavir + - Dociparstat sodium + - Dolastatin 10 + - Dolastatin 15 + - Domatinostat + - Donafenib + - Dopamine-Somatostatin Chimeric Molecule BIM-23A760 + - Dostarlimab + - Double-armed TMZ-CD40L/4-1BBL Oncolytic Ad5/35 Adenovirus LOAd703 + - Dovitinib + - Dovitinib Lactate + - Doxazosin + - Doxercalciferol + - Doxifluridine + - Doxorubicin + - Doxorubicin Hydrochloride + - Doxorubicin Prodrug L-377,202 + - Doxorubicin Prodrug/Prodrug-activating Biomaterial SQ3370 + - Doxorubicin-Eluting Beads + - Doxorubicin-HPMA Conjugate + - Doxorubicin-loaded EGFR-targeting Nanocells + - Doxorubicin-Magnetic Targeted Carrier Complex + - DPT/BCG/Measles/Serratia/Pneumococcus Vaccine + - DPT/Typhoid/Staphylococcus aureus/Paratyphoid A/Paratyphoid B Vaccine + - DPX-E7 HPV Vaccine + - DR5 HexaBody Agonist GEN1029 + - DR5-targeting Tetrameric Nanobody Agonist TAS266 + - Dromostanolone Propionate + - Drozitumab + - DTRMWXHS-12/Everolimus/Pomalidomide Combination Agent DTRM-555 + - Dual IGF-1R/InsR Inhibitor BMS-754807 + - Dual Variable Domain Immunoglobulin ABT-165 + - Dual-affinity B7-H3/CD3-targeted Protein MGD009 + - Dubermatinib + - Duborimycin + - Dulanermin + - Duligotuzumab + - Dupilumab + - Durvalumab + - Dusigitumab + - dUTPase/DPD Inhibitor TAS-114 + - Duvelisib + - Duvortuxizumab + - Dynemicin + - Dynemicin A + - E2F1 Pathway Activator ARQ 171 + - EBNA-1 inhibitor VK-2019 + - Echinomycin + - Ecromeximab + - Edatrexate + - Edelfosine + - Edicotinib + - Edodekin alfa + - Edotecarin + - Edrecolomab + - EED Inhibitor MAK683 + - Efatutazone + - Efatutazone Dihydrochloride + - Efizonerimod + - Eflornithine + - Eflornithine Hydrochloride + - Eftilagimod Alpha + - Eftozanermin Alfa + - Eg5 Kinesin-Related Motor Protein Inhibitor 4SC-205 + - Eg5 Kinesin-Related Motor Protein Inhibitor ARQ 621 + - EGb761 + - EGFR Antagonist Hemay022 + - EGFR Antisense DNA BB-401 + - EGFR Inhibitor AZD3759 + - EGFR Inhibitor BIBX 1382 + - EGFR Inhibitor DBPR112 + - EGFR Inhibitor PD-168393 + - EGFR Inhibitor TY-9591 + - EGFR Mutant-selective Inhibitor TQB3804 + - EGFR Mutant-specific Inhibitor BPI-7711 + - EGFR Mutant-specific Inhibitor CK-101 + - EGFR Mutant-specific Inhibitor D-0316 + - EGFR Mutant-specific Inhibitor ZN-e4 + - EGFR T790M Antagonist BPI-15086 + - EGFR T790M Inhibitor HS-10296 + - EGFR/EGFRvIII Inhibitor WSD0922-FU + - EGFR/FLT3/Abl Inhibitor SKLB1028 + - EGFR/HER1/HER2 Inhibitor PKI166 + - EGFR/HER2 Inhibitor AP32788 + - EGFR/HER2 Inhibitor AV-412 + - EGFR/HER2 Inhibitor DZD9008 + - EGFR/HER2 Kinase Inhibitor TAK-285 + - EGFR/TGFb Fusion Monoclonal Antibody BCA101 + - EGFR/VEGFR/RET Inhibitor HA121-28 + - Eicosapentaenoic Acid + - eIF4E Antisense Oligonucleotide ISIS 183750 + - Elacestrant + - Elacytarabine + - Elagolix + - Elbasvir/Grazoprevir + - Elesclomol + - Elesclomol Sodium + - Elgemtumab + - Elinafide + - Elisidepsin + - Elliptinium + - Elliptinium Acetate + - Elmustine + - Elotuzumab + - Elpamotide + - Elsamitrucin + - Eltanexor + - Emactuzumab + - Emapalumab + - Emepepimut-S + - Emibetuzumab + - Emitefur + - Emofolin Sodium + - Empesertib + - Enadenotucirev + - Enadenotucirev-expressing Anti-CD40 Agonistic Monoclonal Antibody NG-350A + - Enadenotucirev-expressing FAP/CD3 Bispecific FAP-TAc NG-641 + - Enasidenib + - Enasidenib Mesylate + - Enavatuzumab + - Encapsulated Rapamycin + - Encelimab + - Enclomiphene + - Enclomiphene Citrate + - Encorafenib + - Endothelin B Receptor Blocker ENB 003 + - Endothelin Receptor Type A Antagonist YM598 + - Enfortumab Vedotin + - Engineered Human Umbilical Vein Endothelial Cells AB-205 + - Engineered Red Blood Cells Co-expressing 4-1BBL and IL-15TP RTX-240 + - Engineered Toxin Body Targeting CD38 TAK-169 + - Engineered Toxin Body Targeting HER2 MT-5111 + - Eniluracil/5-FU Combination Tablet + - Enloplatin + - Enoblituzumab + - Enobosarm + - Enoticumab + - Enpromate + - Ensartinib + - Ensituximab + - Enteric-Coated TRPM8 Agonist D-3263 Hydrochloride + - Enterococcus gallinarum Strain MRx0518 + - Entinostat + - Entolimod + - Entospletinib + - Entrectinib + - Envafolimab + - Enzalutamide + - Enzastaurin + - Enzastaurin Hydrochloride + - EP2/EP4 Antagonist TPST-1495 + - EP4 Antagonist INV-1120 + - EP4 Antagonist ONO-4578 + - Epacadostat + - Epcoritamab + - EphA2-targeting Bicycle Toxin Conjugate BT5528 + - Epipodophyllotoxin Analog GL331 + - Epipropidine + - Epirubicin + - Epirubicin Hydrochloride + - Epitinib Succinate + - Epitiostanol + - Epothilone Analog UTD1 + - Epothilone KOS-1584 + - Epratuzumab + - Epratuzumab-cys-tesirine + - ER alpha Proteolysis-targeting Chimera Protein Degrader ARV-471 + - ERa36 Modulator Icaritin + - Erastin Analogue PRLX 93936 + - Erbulozole + - Erdafitinib + - Eribulin + - Eribulin Mesylate + - ERK 1/2 Inhibitor ASTX029 + - ERK Inhibitor CC-90003 + - ERK Inhibitor GDC-0994 + - ERK Inhibitor LTT462 + - ERK Inhibitor MK-8353 + - ERK1/2 Inhibitor ASN007 + - ERK1/2 Inhibitor HH2710 + - ERK1/2 Inhibitor JSI-1187 + - ERK1/2 Inhibitor KO-947 + - ERK1/2 Inhibitor LY3214996 + - Erlotinib + - Erlotinib Hydrochloride + - Ertumaxomab + - Erythrocyte-encapsulated L-asparaginase Suspension + - Esorubicin + - Esorubicin Hydrochloride + - Esperamicin A1 + - Essiac + - Esterified Estrogens + - Estradiol Valerate + - Estramustine + - Estramustine Phosphate Sodium + - Estrogen Receptor Agonist GTx-758 + - Estrogens, Conjugated + - Etalocib + - Etanercept + - Etanidazole + - Etaracizumab + - Etarotene + - Ethaselen + - Ethinyl Estradiol + - Ethyleneimine + - Ethylnitrosourea + - Etidronate-Cytarabine Conjugate MBC-11 + - Etigilimab + - Etirinotecan Pegol + - Etoglucid + - Etoposide + - Etoposide Phosphate + - Etoposide Toniribate + - Etoprine + - Etoricoxib + - Ets-family Transcription Factor Inhibitor TK216 + - Everolimus + - Everolimus Tablets for Oral Suspension + - Evofosfamide + - Ex Vivo-expanded Autologous T Cells IMA101 + - Exatecan Mesylate + - Exatecan Mesylate Anhydrous + - Exemestane + - Exicorilant + - Exisulind + - Extended Release Flucytosine + - Extended Release Metformin Hydrochloride + - Extended-release Onapristone + - Ezabenlimab + - EZH1/2 Inhibitor DS-3201 + - EZH1/2 Inhibitor HH2853 + - EZH2 inhibitor CPI-0209 + - EZH2 Inhibitor CPI-1205 + - EZH2 Inhibitor PF-06821497 + - EZH2 Inhibitor SHR2554 + - F16-IL2 Fusion Protein + - FACT Complex-targeting Curaxin CBL0137 + - Factor VII-targeting Immunoconjugate Protein ICON-1 + - Factor VIIa Inhibitor PCI-27483 + - Fadraciclib + - Fadrozole Hydrochloride + - FAK Inhibitor GSK2256098 + - FAK Inhibitor PF-00562271 + - FAK Inhibitor VS-4718 + - FAK/ALK/ROS1 Inhibitor APG-2449 + - Falimarev + - Famitinib + - FAP/4-1BB-targeting DARPin MP0310 + - FAP/4-1BB-targeting Fusion Protein RO7122290 + - Farletuzumab + - Farnesyltransferase/Geranylgeranyltransferase Inhibitor L-778,123 + - Fas Ligand-treated Allogeneic Mobilized Peripheral Blood Cells + - Fas Receptor Agonist APO010 + - Fascin Inhibitor NP-G2-044 + - FASN Inhibitor TVB-2640 + - Favezelimab + - Fazarabine + - Fc-engineered Anti-CD40 Agonist Antibody 2141-V11 + - Febuxostat + - Fedratinib + - Fedratinib Hydrochloride + - Feladilimab + - Felzartamab + - Fenebrutinib + - Fenretinide + - Fenretinide Lipid Matrix + - Fenretinide Phospholipid Suspension ST-001 + - FGF Receptor Antagonist HGS1036 + - FGF/FGFR Pathway Inhibitor E7090 + - FGFR Inhibitor ASP5878 + - FGFR Inhibitor AZD4547 + - FGFR Inhibitor CPL304110 + - FGFR Inhibitor Debio 1347 + - FGFR Inhibitor TAS-120 + - FGFR/CSF-1R Inhibitor 3D185 + - FGFR/VEGFR/PDGFR/FLT3/SRC Inhibitor XL999 + - FGFR1/2/3 Inhibitor HMPL-453 + - FGFR2 Inhibitor RLY-4008 + - FGFR4 Antagonist INCB062079 + - FGFR4 Inhibitor BLU 9931 + - FGFR4 Inhibitor FGF401 + - FGFR4 Inhibitor H3B-6527 + - FGFR4 Inhibitor ICP-105 + - Fianlimab + - Fibromun + - Ficlatuzumab + - Figitumumab + - Filanesib + - Filgotinib + - Filgrastim + - Fimaporfin A + - Fimepinostat + - Firtecan Pegol + - Fisogatinib + - Flanvotumab + - Flotetuzumab + - Floxuridine + - FLT3 Inhibitor FF-10101 Succinate + - FLT3 Inhibitor HM43239 + - FLT3 Inhibitor SKI-G-801 + - Flt3 Ligand/Anti-CTLA-4 Antibody/IL-12 Engineered Oncolytic Vaccinia Virus RIVAL-01 + - FLT3 Tyrosine Kinase Inhibitor TTT-3002 + - FLT3/ABL/Aurora Kinase Inhibitor KW-2449 + - FLT3/CDK4/6 Inhibitor FLX925 + - FLT3/FGFR Dual Kinase Inhibitor MAX-40279 + - FLT3/KIT Kinase Inhibitor AKN-028 + - FLT3/KIT/CSF1R Inhibitor NMS-03592088 + - Flt3/MerTK Inhibitor MRX-2843 + - Fludarabine + - Fludarabine Phosphate + - Flumatinib + - Flumatinib Mesylate + - Fluorine F 18 Ara-G + - Fluorodopan + - Fluorouracil + - Fluorouracil Implant + - Fluorouracil-E Therapeutic Implant + - Fluoxymesterone + - Flutamide + - Fluvastatin + - Fluvastatin Sodium + - Fluzoparib + - FMS Inhibitor JNJ-40346527 + - Fms/Trk Tyrosine Kinase Inhibitor PLX7486 Tosylate + - Folate Receptor Targeted Epothilone BMS753493 + - Folate Receptor-Targeted Tubulysin Conjugate EC1456 + - Folate Receptor-Targeted Vinca Alkaloid EC0489 + - Folate Receptor-Targeted Vinca Alkaloid/Mitomycin C EC0225 + - Folate-FITC + - Folic Acid + - Folitixorin + - Foretinib + - Foritinib Succinate + - Formestane + - Forodesine Hydrochloride + - Fosaprepitant + - Fosbretabulin + - Fosbretabulin Disodium + - Fosbretabulin Tromethamine + - Fosgemcitabine Palabenamide + - Fosifloxuridine Nafalbenamide + - Foslinanib + - Foslinanib Disodium + - Fosquidone + - Fostriecin + - Fotemustine + - Fotretamine + - FPV Vaccine CV301 + - FPV-Brachyury-TRICOM Vaccine + - Fresolimumab + - Fruquintinib + - Fulvestrant + - Fumagillin-Derived Polymer Conjugate XMT-1107 + - Fursultiamine + - Futibatinib + - Futuximab + - Futuximab/Modotuximab Mixture + - G Protein-coupled Estrogen Receptor Agonist LNS8801 + - G-Quadruplex Stabilizer BMVC + - Galamustine + - Galarubicin + - Galectin Inhibitor GR-MD-02 + - Galectin-1 Inhibitor OTX008 + - Galeterone + - Galiximab + - Gallium-based Bone Resorption Inhibitor AP-002 + - Galocitabine + - Galunisertib + - Gamboge Resin Extract TSB-9-W1 + - Gamma-delta Tocotrienol + - Gamma-Secretase Inhibitor LY3039478 + - Gamma-Secretase Inhibitor RO4929097 + - Gandotinib + - Ganetespib + - Ganglioside GD2 + - Ganglioside GM2 + - Ganitumab + - Ganoderma lucidum Spores Powder Capsule + - Garlic + - Gastrin Immunotoxin + - Gastrin/cholecystokinin Type B Receptor Inhibitor Z-360 + - Gataparsen Sodium + - Gatipotuzumab + - GBM Antigens and Alloantigens Immunotherapeutic Vaccine + - Gedatolisib + - Gefitinib + - Geldanamycin + - Gelonin + - Gemcitabine + - Gemcitabine Elaidate + - Gemcitabine Hydrochloride + - Gemcitabine Hydrochloride Emulsion + - Gemcitabine Prodrug LY2334737 + - Gemcitabine-Phosphoramidate Hydrochloride NUC-1031 + - Gemcitabine-Releasing Intravesical System + - Gemtuzumab Ozogamicin + - Genetically Modified Interleukin-12 Transgene-encoding Bifidobacterium longum + - Genistein + - Gentuximab + - Geranylgeranyltransferase I Inhibitor + - GI-4000 Vaccine + - Giloralimab + - Gilteritinib + - Gilteritinib Fumarate + - Gimatecan + - Gimeracil + - Ginsenoside Rg3 Capsule + - Giredestrant + - Girentuximab + - Girodazole + - GITR Agonist MEDI1873 + - Givinostat + - Glasdegib + - Glasdegib Maleate + - Glaucarubolone + - Glecaprevir/Pibrentasvir + - Glembatumumab Vedotin + - Glesatinib + - Glioblastoma Cancer Vaccine ERC1671 + - Glioblastoma Multiforme Multipeptide Vaccine IMA950 + - Glioma Lysate Vaccine GBM6-AD + - Glioma-associated Peptide-loaded Dendritic Cell Vaccine SL-701 + - Globo H-DT Vaccine OBI-833 + - Glofitamab + - Glucarpidase + - Glucocorticoid Receptor Antagonist ORIC-101 + - Glufosfamide + - Glumetinib + - Glutaminase Inhibitor CB-839 + - Glutaminase Inhibitor CB-839 Hydrochloride + - Glutaminase Inhibitor IPN60090 + - Glutamine Antagonist DRP-104 + - Glutathione Pegylated Liposomal Doxorubicin Hydrochloride Formulation 2B3-101 + - Glyco-engineered Anti-CD20 Monoclonal Antibody CHO H01 + - Glycooptimized Trastuzumab-GEX + - GM-CSF-encoding Oncolytic Adenovirus CGTG-102 + - Gold Sodium Thiomalate + - Golnerminogene Pradenovec + - Golotimod + - Golvatinib + - Gonadotropin-releasing Hormone Analog + - Goserelin + - Goserelin Acetate + - Goserelin Acetate Extended-release Microspheres LY01005 + - Gossypol + - Gossypol Acetic Acid + - Grapiprant + - Green Tea Extract-based Antioxidant Supplement + - GS/pan-Notch Inhibitor AL101 + - GS/pan-Notch Inhibitor BMS-986115 + - GSK-3 Inhibitor 9-ING-41 + - GSK-3 Inhibitor LY2090314 + - Guadecitabine + - Guanabenz Acetate + - Guselkumab + - Gusperimus Trihydrochloride + - Gutolactone + - H-ras Antisense Oligodeoxynucleotide ISIS 2503 + - H1299 Tumor Cell Lysate Vaccine + - HAAH Lambda phage Vaccine SNS-301 + - Hafnium Oxide-containing Nanoparticles NBTXR3 + - Halichondrin Analogue E7130 + - Halichondrin B + - Halofuginone + - Halofuginone Hydrobromide + - HCV DNA Vaccine INO-8000 + - HDAC Class I/IIb Inhibitor HG146 + - HDAC Inhibitor AR-42 + - HDAC inhibitor CG200745 + - HDAC Inhibitor CHR-2845 + - HDAC Inhibitor CKD-581 + - HDAC Inhibitor CXD101 + - HDAC Inhibitor MPT0E028 + - HDAC Inhibitor OBP-801 + - HDAC/EGFR/HER2 Inhibitor CUDC-101 + - HDAC6 Inhibitor KA2507 + - HDAC8 Inhibitor NBM-BMX + - HDM2 Inhibitor HDM201 + - HDM2 Inhibitor MK-8242 + - Hedgehog Inhibitor IPI-609 + - Hematoporphyrin Derivative + - Hemiasterlin Analog E7974 + - Henatinib Maleate + - Heparan Sulfate Glycosaminoglycan Mimetic M402 + - Heparin Derivative SST0001 + - HER-2-positive B-cell Peptide Antigen P467-DT-CRM197/Montanide Vaccine IMU-131 + - HER2 ECD+TM Virus-like Replicon Particles Vaccine AVX901 + - HER2 Inhibitor CP-724,714 + - HER2 Inhibitor DZD1516 + - HER2 Inhibitor TAS0728 + - HER2 Tri-specific Natural Killer Cell Engager DF1001 + - HER2-directed TLR8 Agonist SBT6050 + - HER2-targeted DARPin MP0274 + - HER2-targeted Liposomal Doxorubicin Hydrochloride MM-302 + - HER2-targeting Antibody Fc Fragment FS102 + - Herba Scutellaria Barbata + - Herbimycin + - Heterodimeric Interleukin-15 + - Hexamethylene Bisacetamide + - Hexaminolevulinate + - Hexylresorcinol + - HIF-1alpha Inhibitor PX-478 + - HIF-2alpha Inhibitor PT2385 + - HIF-2alpha Inhibitor PT2977 + - HIF2a RNAi ARO-HIF2 + - Histone-Lysine N-Methyltransferase EZH2 Inhibitor GSK2816126 + - Histrelin Acetate + - HLA-A*0201 Restricted TERT(572Y)/TERT(572) Peptides Vaccine Vx-001 + - HLA-A*2402-Restricted Multipeptide Vaccine S-488410 + - HLA-A2-restricted Melanoma-specific Peptides Vaccine GRN-1201 + - HM2/MMAE Antibody-Drug Conjugate ALT-P7 + - Hodgkin's Antigens-GM-CSF-Expressing Cell Vaccine + - Holmium Ho 166 Poly(L-Lactic Acid) Microspheres + - Hormone Therapy + - HPPH + - HPV 16 E6/E7-encoding Arenavirus Vaccine HB-202 + - HPV 16 E7 Antigen-expressing Lactobacillis casei Vaccine BLS-ILB-E710c + - HPV DNA Plasmids Therapeutic Vaccine VGX-3100 + - HPV E6/E7 DNA Vaccine GX-188E + - HPV E6/E7-encoding Arenavirus Vaccine HB-201 + - HPV Types 16/18 E6/E7-Adenoviral Transduced Autologous Lymphocytes/alpha-Galactosylceramide Vaccine BVAC-C + - HPV-16 E6 Peptides Vaccine/Candida albicans Extract + - HPV-6-targeting Immunotherapeutic Vaccine INO-3106 + - HPV16 E7-specific HLA-A*02:01-restricted IgG1-Fc Fusion Protein CUE-101 + - HPV16 L2/E6/E7 Fusion Protein Vaccine TA-CIN + - HPV6/11-targeted DNA Plasmid Vaccine INO-3107 + - Hsp90 Antagonist KW-2478 + - Hsp90 Inhibitor AB-010 + - Hsp90 Inhibitor BIIB021 + - Hsp90 Inhibitor BIIB028 + - Hsp90 Inhibitor Debio 0932 + - Hsp90 Inhibitor DS-2248 + - Hsp90 Inhibitor HSP990 + - Hsp90 Inhibitor MPC-3100 + - Hsp90 Inhibitor PU-H71 + - Hsp90 Inhibitor SNX-5422 Mesylate + - Hsp90 Inhibitor SNX-5542 Mesylate + - Hsp90 Inhibitor TQB3474 + - Hsp90 Inhibitor XL888 + - Hsp90-targeted Photosensitizer HS-201 + - HSP90-targeted SN-38 Conjugate PEN-866 + - HSP90alpha/beta Inhibitor TAS-116 + - hTERT Multipeptide/Montanide ISA-51 VG/Imiquimod Vaccine GX 301 + - hTERT Vaccine V934/V935 + - hTERT-encoding DNA Vaccine INVAC-1 + - Hu14.18-IL2 Fusion Protein EMD 273063 + - HuaChanSu + - Huaier Extract Granule + - Huang Lian + - huBC1-huIL12 Fusion Protein AS1409 + - Human Combinatorial Antibody Library-based Monoclonal Antibody VAY736 + - Human MHC Non-Restricted Cytotoxic T-Cell Line TALL-104 + - Human MOAB LICO 28a32 + - Human Monoclonal Antibody 216 + - Human Monoclonal Antibody B11-hCG Beta Fusion Protein CDX-1307 + - Human Papillomavirus 16 E7 Peptide/Padre 965.10 + - Hyaluronidase-zzxf/Pertuzumab/Trastuzumab + - Hycanthone + - Hydralazine Hydrochloride + - Hydrocortisone Sodium Succinate + - Hydroxychloroquine + - Hydroxyprogesterone Caproate + - Hydroxytyrosol + - Hydroxyurea + - Hypericin + - Hypoxia-activated Prodrug TH-4000 + - I 131 Antiferritin Immunoglobulin + - I 131 Monoclonal Antibody A33 + - I 131 Monoclonal Antibody CC49 + - I 131 Monoclonal Antibody F19 + - I 131 Monoclonal Antibody Lym-1 + - Iadademstat + - Ianalumab + - IAP Inhibitor APG-1387 + - IAP Inhibitor AT-406 + - IAP Inhibitor HGS1029 + - Ibandronate Sodium + - Iberdomide + - Iboctadekin + - Ibritumomab Tiuxetan + - Ibrutinib + - Icotinib Hydrochloride + - Icrucumab + - ICT-121 Dendritic Cell Vaccine + - Idarubicin + - Idarubicin Hydrochloride + - Idarubicin-Eluting Beads + - Idasanutlin + - Idecabtagene Vicleucel + - Idelalisib + - Idetrexed + - IDH1 Mutant Inhibitor LY3410738 + - IDH1(R132) Inhibitor IDH305 + - IDH1R132H-Specific Peptide Vaccine PEPIDH1M + - Idiotype-Pulsed Autologous Dendritic Cell Vaccine APC8020 + - IDO Peptide Vaccine IO102 + - IDO-1 Inhibitor LY3381916 + - IDO/TDO Inhibitor HTI-1090 + - IDO/TDO Inhibitor LY-01013 + - IDO1 Inhibitor KHK2455 + - IDO1 Inhibitor MK-7162 + - IDO1 Inhibitor PF-06840003 + - IDO1/TDO2 Inhibitor DN1406131 + - IDO1/TDO2 Inhibitor M4112 + - Idronoxil + - Idronoxil Suppository NOX66 + - Ieramilimab + - Ifabotuzumab + - Ifetroban + - Ifosfamide + - IGF-1R Inhibitor + - IGF-1R Inhibitor PL225B + - IGF-1R/IR Inhibitor KW-2450 + - IGF-methotrexate Conjugate + - IL-10 Immunomodulator MK-1966 + - IL-12-expressing HSV-1 NSC 733972 + - IL-12-expressing Mesenchymal Stem Cell Vaccine GX-051 + - IL-12sc, IL-15sushi, IFNa and GM-CSF mRNA-based Immunotherapeutic Agent SAR441000 + - IL-2 Recombinant Fusion Protein ALT-801 + - IL-2/9/15 Gamma Chain Receptor Inhibitor BNZ-1 + - IL4-Pseudomonas Exotoxin Fusion Protein MDNA55 + - Ilginatinib + - Ilixadencel + - Iloprost + - Ilorasertib + - Imalumab + - Imaradenant + - Imatinib + - Imatinib Mesylate + - Imetelstat + - Imetelstat Sodium + - Imexon + - Imgatuzumab + - Imidazole Mustard + - Imidazole-Pyrazole + - Imifoplatin + - Imipramine Blue + - Imiquimod + - Immediate-release Onapristone + - Immediate-release Tablet Afuresertib + - Immune Checkpoint Inhibitor ASP8374 + - Immunoconjugate RO5479599 + - Immunocytokine NHS-IL12 + - Immunocytokine NHS-IL2-LT + - Immunomodulator LAM-003 + - Immunomodulator OHR/AVR118 + - Immunomodulatory Agent CC-11006 + - Immunomodulatory Oligonucleotide HYB2055 + - Immunotherapeutic Combination Product CMB305 + - Immunotherapeutic GSK1572932A + - Immunotherapy Regimen MKC-1106-MT + - Immunotoxin CMD-193 + - IMT-1012 Immunotherapeutic Vaccine + - Inactivated Oncolytic Virus Particle GEN0101 + - Inalimarev + - Incyclinide + - Indatuximab Ravtansine + - Indibulin + - Indicine-N-Oxide + - Indisulam + - Individualized MVA-based Vaccine TG4050 + - Indocyanine Green-labeled Polymeric Micelles ONM-100 + - Indole-3-Carbinol + - Indomethacin + - Indoximod + - Indoximod Prodrug NLG802 + - Indusatumab Vedotin + - Inebilizumab + - Inecalcitol + - Infigratinib + - Infigratinib Mesylate + - Infliximab + - Ingenol Mebutate + - Ingenol Mebutate Gel + - Iniparib + - iNKT Cell Agonist ABX196 + - Innate Immunostimulator rBBX-01 + - INO-1001 + - Inodiftagene Vixteplasmid + - iNOS Dimerization Inhibitor ASP9853 + - Inosine 5'-monophosphate Dehydrogenase Inhibitor FF-10501-01 + - Inosine Monophosphate Dehydrogenase Inhibitor AVN944 + - Inositol + - Inotuzumab Ozogamicin + - Inproquone + - Integrin alpha-2 Inhibitor E7820 + - Integrin Receptor Antagonist GLPG0187 + - Interferon + - Interferon Alfa-2B + - Interferon Alfa-N1 + - Interferon Alfa-N3 + - Interferon Alfacon-1 + - Interferon Beta-1A + - Interferon Gamma-1b + - Interferon-gamma-expressing Adenovirus Vaccine ASN-002 + - Interleukin Therapy + - Interleukin-12-Fc Fusion Protein DF6002 + - Interleukin-15 Agonist Fusion Protein SHR1501 + - Interleukin-15 Fusion Protein BJ-001 + - Interleukin-15/Interleukin-15 Receptor Alpha Complex-Fc Fusion Protein XmAb24306 + - Interleukin-15/Interleukin-15 Receptor Alpha Sushi+ Domain Fusion Protein SO-C101 + - Interleukin-2 Liposome + - Intermediate-affinity Interleukin-2 Receptor Agonist ALKS 4230 + - Intetumumab + - Intiquinatine + - Intoplicine + - Inulin + - Iobenguane I-131 + - Iodine I 124 Monoclonal Antibody A33 + - Iodine I 124 Monoclonal Antibody M5A + - Iodine I 125-Anti-EGFR-425 Monoclonal Antibody + - Iodine I 131 Anti-Fibronectin Antibody Fragment L19-SIP + - Iodine I 131 Apamistamab + - Iodine I 131 Derlotuximab Biotin + - Iodine I 131 Ethiodized Oil + - Iodine I 131 IPA + - Iodine I 131 MIP-1095 + - Iodine I 131 Monoclonal Antibody 81C6 + - Iodine I 131 Monoclonal Antibody BC8 + - Iodine I 131 Monoclonal Antibody CC49-deltaCH2 + - Iodine I 131 Monoclonal Antibody F16SIP + - Iodine I 131 Monoclonal Antibody G-250 + - Iodine I 131 Monoclonal Antibody muJ591 + - Iodine I 131 Omburtamab + - Iodine I 131 Rituximab + - Iodine I 131 Tenatumomab + - Iodine I 131 TM-601 + - Iodine I 131 Tositumomab + - Iodine I-131 + - Ioflubenzamide I-131 + - Ionomycin + - Ipafricept + - Ipatasertib + - Ipilimumab + - Ipomeanol + - Iproplatin + - iPSC-derived CD16-expressing Natural Killer Cells FT516 + - iPSC-derived CD16/IL-15RF-expressing Anti-CD19 CAR-NK Cells FT596 + - iPSC-derived Natural Killer Cells FT500 + - IRAK4 Inhibitor CA-4948 + - Iratumumab + - Iridium Ir 192 + - Irinotecan + - Irinotecan Hydrochloride + - Irinotecan Sucrosofate + - Irinotecan-Eluting Beads + - Irinotecan/P-glycoprotein Inhibitor HM30181AK Combination Tablet + - Irofulven + - Iroplact + - Irosustat + - Irradiated Allogeneic Human Lung Cancer Cells Expressing OX40L-Ig Vaccine HS-130 + - Isatuximab + - Iso-fludelone + - Isobrucein B + - Isocoumarin NM-3 + - Isotretinoin + - Ispinesib + - Ispinesib Mesylate + - ISS 1018 CpG Oligodeoxynucleotide + - Istiratumab + - Itacitinib + - Itacitinib Adipate + - ITK Inhibitor CPI-818 + - Itraconazole + - Itraconazole Dispersion In Polymer Matrix + - Ivaltinostat + - Ivosidenib + - Ivuxolimab + - Ixabepilone + - Ixazomib + - Ixazomib Citrate + - JAK Inhibitor + - JAK Inhibitor INCB047986 + - JAK1 Inhibitor AZD4205 + - JAK1 Inhibitor INCB052793 + - JAK2 Inhibitor AZD1480 + - JAK2 Inhibitor BMS-911543 + - JAK2 Inhibitor XL019 + - JAK2/Src Inhibitor NS-018 + - Jin Fu Kang + - JNK Inhibitor CC-401 + - Kanglaite + - Kanitinib + - Ketoconazole + - Ketotrexate + - KRAS G12C Inhibitor GDC-6036 + - KRAS G12C Inhibitor LY3499446 + - KRAS G12C Inhibitor MRTX849 + - KRAS Mutant-targeting AMG 510 + - KRAS-MAPK Signaling Pathway Inhibitor JAB-3312 + - KRASG12C Inhibitor JNJ-74699157 + - KRN5500 + - KSP Inhibitor AZD4877 + - KSP Inhibitor SB-743921 + - Kunecatechins Ointment + - L-Gossypol + - L-methylfolate + - Labetuzumab Govitecan + - Lactoferrin-derived Lytic Peptide LTX-315 + - Lacutamab + - Ladiratuzumab Vedotin + - Ladirubicin + - Laetrile + - LAIR-2 Fusion Protein NC410 + - Landogrozumab + - Laniquidar + - Lanreotide Acetate + - Lapachone + - Lapatinib + - Lapatinib Ditosylate + - Laprituximab Emtansine + - Lapuleucel-T + - Laromustine + - Larotaxel + - Larotinib Mesylate + - Larotrectinib + - Larotrectinib Sulfate + - Lavendustin A + - Lazertinib + - Lead Pb 212 TCMC-trastuzumab + - Lefitolimod + - Leflunomide + - Lenalidomide + - Lenalidomide Analog KPG-121 + - Lentinan + - Lenvatinib + - Lenvatinib Mesylate + - Lenzilumab + - Lerociclib + - Lestaurtinib + - Letetresgene Autoleucel + - Letolizumab + - Letrozole + - Leucovorin + - Leucovorin Calcium + - Leuprolide + - Leuprolide Acetate + - Leuprolide Mesylate Injectable Suspension + - Leurubicin + - Levetiracetam + - Levoleucovorin Calcium + - Levothyroxine + - Levothyroxine Sodium + - Lexatumumab + - Lexibulin + - Liarozole + - Liarozole Fumarate + - Liarozole Hydrochloride + - Licartin + - Licorice + - Lifastuzumab Vedotin + - Lifileucel + - Lifirafenib + - Light-activated AU-011 + - Light-Emitting Oncolytic Vaccinia Virus GL-ONC1 + - Lilotomab + - Limonene, (+)- + - Limonene, (+/-)- + - Linifanib + - Linoleyl Carbonate-Paclitaxel + - Linperlisib + - Linrodostat + - Linsitinib + - Lintuzumab + - Liothyronine I-131 + - Liothyronine Sodium + - Lipid Encapsulated Anti-PLK1 siRNA TKM-PLK1 + - Lipid Nanoparticle Encapsulated mRNAs Encoding Human IL-12A/IL-12B MEDI-1191 + - Lipid Nanoparticle Encapsulated OX40L mRNA-2416 + - Lipid Nanoparticle Encapsulating Glutathione S-transferase P siRNA NBF-006 + - Lipid Nanoparticle Encapsulating mRNAs Encoding Human OX40L/IL-23/IL-36gamma mRNA-2752 + - Liposomal Bcl-2 Antisense Oligonucleotide BP1002 + - Liposomal c-raf Antisense Oligonucleotide + - Liposomal Curcumin + - Liposomal Cytarabine + - Liposomal Daunorubicin Citrate + - Liposomal Docetaxel + - Liposomal Eribulin Mesylate + - Liposomal HPV-16 E6/E7 Multipeptide Vaccine PDS0101 + - Liposomal Irinotecan + - Liposomal Mitoxantrone Hydrochloride + - Liposomal MUC1/PET-lipid A Vaccine ONT-10 + - Liposomal NDDP + - Liposomal Rhenium Re 186 + - Liposomal SN-38 + - Liposomal Topotecan FF-10850 + - Liposomal Vinorelbine + - Liposomal Vinorelbine Tartrate + - Liposome + - Liposome-encapsulated Daunorubicin-Cytarabine + - Liposome-Encapsulated Doxorubicin Citrate + - Liposome-encapsulated miR-34 Mimic MRX34 + - Liposome-encapsulated OSI-7904 + - Liposome-encapsulated RB94 Plasmid DNA Gene Therapy Agent SGT-94 + - Liposome-encapsulated TAAs mRNA Vaccine W_ova1 + - Lirilumab + - Lisavanbulin + - Lisocabtagene Maraleucel + - Listeria monocytogenes-LLO-PSA Vaccine ADXS31-142 + - Litronesib + - Live-attenuated Double-deleted Listeria monocytogenes Bacteria JNJ-64041809 + - Live-Attenuated Listeria Encoding Human Mesothelin Vaccine CRS-207 + - Live-attenuated Listeria monocytogenes-encoding EGFRvIII-NY-ESO-1 Vaccine ADU-623 + - Liver X Receptor beta Agonist RGX-104 + - Lm-tLLO-neoantigens Vaccine ADXS-NEO + - LMB-1 Immunotoxin + - LMB-2 Immunotoxin + - LMB-7 Immunotoxin + - LMB-9 Immunotoxin + - LmddA-LLO-chHER2 Fusion Protein-secreting Live-attenuated Listeria Cancer Vaccine ADXS31-164 + - LMP-2:340-349 Peptide Vaccine + - LMP-2:419-427 Peptide Vaccine + - LMP2-specific T Cell Receptor-transduced Autologous T-lymphocytes + - LMP7 Inhibitor M3258 + - Lobaplatin + - Lodapolimab + - Lometrexol + - Lometrexol Sodium + - Lomustine + - Lonafarnib + - Loncastuximab Tesirine + - Long Peptide Vaccine 7 + - Long-acting Release Pasireotide + - Lontucirev + - Lorlatinib + - Lorukafusp alfa + - Lorvotuzumab Mertansine + - Losatuxizumab Vedotin + - Losoxantrone + - Losoxantrone Hydrochloride + - Lovastatin + - LOXL2 Inhibitor PAT-1251 + - LRP5 Antagonist BI 905681 + - LRP5/6 Antagonist BI 905677 + - LSD1 Inhibitor CC-90011 + - LSD1 Inhibitor GSK2879552 + - LSD1 Inhibitor IMG-7289 + - LSD1 Inhibitor RO7051790 + - LSD1 Inhibitor SYHA1807 + - Lucanthone + - Lucatumumab + - Lucitanib + - Luminespib + - Luminespib Mesylate + - Lumretuzumab + - Lung-targeted Immunomodulator QBKPN + - Lupartumab Amadotin + - Lurbinectedin + - Lurtotecan + - Lurtotecan Liposome + - Lutetium Lu 177 Anti-CA19-9 Monoclonal Antibody 5B1 + - Lutetium Lu 177 DOTA-biotin + - Lutetium Lu 177 DOTA-N3-CTT1403 + - Lutetium Lu 177 DOTA-Tetulomab + - Lutetium Lu 177 Dotatate + - Lutetium Lu 177 Lilotomab-satetraxetan + - Lutetium Lu 177 Monoclonal Antibody CC49 + - Lutetium Lu 177 Monoclonal Antibody J591 + - Lutetium Lu 177 PP-F11N + - Lutetium Lu 177 Satoreotide Tetraxetan + - Lutetium Lu 177-DOTA-EB-TATE + - Lutetium Lu 177-DTPA-omburtamab + - Lutetium Lu 177-Edotreotide + - Lutetium Lu 177-NeoB + - Lutetium Lu 177-PSMA-617 + - Lutetium Lu-177 Capromab + - Lutetium Lu-177 Girentuximab + - Lutetium Lu-177 PSMA-R2 + - Lutetium Lu-177 Rituximab + - LV.IL-2/B7.1-Transduced AML Blast Vaccine RFUSIN2-AML1 + - Lyophilized Black Raspberry Lozenge + - Lyophilized Black Raspberry Saliva Substitute + - Lysine-specific Demethylase 1 Inhibitor INCB059872 + - Lyso-Thermosensitive Liposome Doxorubicin + - Maackia amurensis Seed Lectin + - Macimorelin + - Macitentan + - Macrocycle-bridged STING Agonist E7766 + - Maekmoondong-tang + - Mafosfamide + - MAGE-10.A2 + - MAGE-A1-specific T Cell Receptor-transduced Autologous T-cells + - MAGE-A3 Multipeptide Vaccine GL-0817 + - MAGE-A3 Peptide Vaccine + - MAGE-A3-specific Immunotherapeutic GSK 2132231A + - MAGE-A4-specific TCR Gene-transduced Autologous T Lymphocytes TBI-1201 + - Magnesium Valproate + - Magrolimab + - MALT1 Inhibitor JNJ-67856633 + - Manelimab + - Mannosulfan + - Mannosylerythritol Lipid + - Mapatumumab + - Maraba Oncolytic Virus Expressing Mutant HPV E6/E7 + - Marcellomycin + - MARCKS Protein Inhibitor BIO-11006 + - Margetuximab + - Marimastat + - Marizomib + - Masitinib Mesylate + - Masoprocol + - MAT2A Inhibitor AG-270 + - Matrix Metalloproteinase Inhibitor MMI270 + - Matuzumab + - Mavelertinib + - Mavorixafor + - Maytansine + - MCL-1 Inhibitor ABBV-467 + - MCL-1 Inhibitor AMG 176 + - MCL-1 inhibitor AMG 397 + - Mcl-1 Inhibitor AZD5991 + - Mcl-1 Inhibitor MIK665 + - MDM2 Antagonist ASTX295 + - MDM2 Antagonist RO5045337 + - MDM2 Antagonist RO6839921 + - MDM2 Inhibitor AMG-232 + - MDM2 Inhibitor AMGMDS3 + - MDM2 Inhibitor BI 907828 + - MDM2 Inhibitor KRT-232 + - MDM2/MDMX Inhibitor ALRN-6924 + - MDR Modulator CBT-1 + - Mechlorethamine + - Mechlorethamine Hydrochloride + - Mechlorethamine Hydrochloride Gel + - Medorubicin + - Medroxyprogesterone + - Medroxyprogesterone Acetate + - Megestrol Acetate + - MEK 1/2 Inhibitor AS703988/MSC2015103B + - MEK 1/2 Inhibitor FCN-159 + - MEK Inhibitor AZD8330 + - MEK Inhibitor CI-1040 + - MEK inhibitor CS3006 + - MEK Inhibitor GDC-0623 + - MEK Inhibitor HL-085 + - MEK Inhibitor PD0325901 + - MEK Inhibitor RO4987655 + - MEK Inhibitor SHR 7390 + - MEK Inhibitor TAK-733 + - MEK Inhibitor WX-554 + - MEK-1/MEKK-1 Inhibitor E6201 + - MEK/Aurora Kinase Inhibitor BI 847325 + - Melanoma Monoclonal Antibody hIgG2A + - Melanoma TRP2 CTL Epitope Vaccine SCIB1 + - Melapuldencel-T + - MELK Inhibitor OTS167 + - Melphalan + - Melphalan Flufenamide + - Melphalan Hydrochloride + - Melphalan Hydrochloride/Sulfobutyl Ether Beta-Cyclodextrin Complex + - Membrane-Disrupting Peptide EP-100 + - Menatetrenone + - Menin-MLL Interaction Inhibitor SNDX-5613 + - Menogaril + - Merbarone + - Mercaptopurine + - Mercaptopurine Anhydrous + - Mercaptopurine Oral Suspension + - Merestinib + - Mesna + - Mesothelin/CD3e Tri-specific T-cell Activating Construct HPN536 + - MET Kinase Inhibitor OMO-1 + - MET Tyrosine Kinase Inhibitor BMS-777607 + - MET Tyrosine Kinase Inhibitor EMD 1204831 + - MET Tyrosine Kinase Inhibitor PF-04217903 + - MET Tyrosine Kinase Inhibitor SAR125844 + - MET Tyrosine Kinase Inhibitor SGX523 + - MET x MET Bispecific Antibody REGN5093 + - Metamelfalan + - MetAP2 Inhibitor APL-1202 + - MetAP2 Inhibitor SDX-7320 + - Metarrestin + - Metatinib Tromethamine + - Metformin + - Metformin Hydrochloride + - Methanol Extraction Residue of BCG + - Methazolamide + - Methionine Aminopeptidase 2 Inhibitor M8891 + - Methionine Aminopeptidase 2 Inhibitor PPI-2458 + - Methotrexate + - Methotrexate Sodium + - Methotrexate-E Therapeutic Implant + - Methotrexate-Encapsulating Autologous Tumor-Derived Microparticles + - Methoxsalen + - Methoxyamine + - Methoxyamine Hydrochloride + - Methyl-5-Aminolevulinate Hydrochloride Cream + - Methylcantharidimide + - Methylmercaptopurine Riboside + - Methylprednisolone + - Methylprednisolone Acetate + - Methylprednisolone Sodium Succinate + - Methylselenocysteine + - Methyltestosterone + - Metoprine + - Mevociclib + - Mezagitamab + - Mibefradil + - Mibefradil Dihydrochloride + - Micellar Nanoparticle-encapsulated Epirubicin + - Micro Needle Array-Doxorubicin + - Microbiome GEN-001 + - Microbiome-derived Peptide Vaccine EO2401 + - Microparticle-encapsulated CYP1B1-encoding DNA Vaccine ZYC300 + - Microtubule Inhibitor SCB01A + - Midostaurin + - Mifamurtide + - Mifepristone + - Milademetan Tosylate + - Milataxel + - Milatuzumab + - Milatuzumab-Doxorubicin Antibody-Drug Conjugate IMMU-110 + - Milciclib Maleate + - Milk Thistle + - Miltefosine + - Minretumomab + - Mipsagargin + - Miptenalimab + - Mirabegron + - Miransertib + - Mirdametinib + - Mirvetuximab Soravtansine + - Mirzotamab Clezutoclax + - Misonidazole + - Mistletoe Extract + - Mitazalimab + - Mitindomide + - Mitobronitol + - Mitochondrial Oxidative Phosphorylation Inhibitor ATR-101 + - Mitoclomine + - Mitoflaxone + - Mitoguazone + - Mitoguazone Dihydrochloride + - Mitolactol + - Mitomycin + - Mitomycin A + - Mitomycin B + - Mitomycin C Analog KW-2149 + - Mitosis Inhibitor T 1101 Tosylate + - Mitotane + - Mitotenamine + - Mitoxantrone + - Mitoxantrone Hydrochloride + - Mitozolomide + - Mivavotinib + - Mivebresib + - Mivobulin + - Mivobulin Isethionate + - Mixed Bacteria Vaccine + - MK0731 + - MKC-1 + - MKNK1 Inhibitor BAY 1143269 + - MMP Inhibitor S-3304 + - MNK1/2 Inhibitor ETC-1907206 + - Mobocertinib + - Mocetinostat + - Modakafusp Alfa + - Modified Vaccinia Ankara-vectored HPV16/18 Vaccine JNJ-65195208 + - Modified Vitamin D Binding Protein Macrophage Activator EF-022 + - Modotuximab + - MOF Compound RiMO-301 + - Mofarotene + - Mogamulizumab + - Molibresib + - Molibresib Besylate + - Momelotinib + - Monalizumab + - Monocarboxylate Transporter 1 Inhibitor AZD3965 + - Monoclonal Antibody 105AD7 Anti-idiotype Vaccine + - Monoclonal Antibody 11D10 + - Monoclonal Antibody 11D10 Anti-Idiotype Vaccine + - Monoclonal Antibody 14G2A + - Monoclonal Antibody 1F5 + - Monoclonal Antibody 3622W94 + - Monoclonal Antibody 3F8 + - Monoclonal Antibody 3H1 Anti-Idiotype Vaccine + - Monoclonal Antibody 4B5 Anti-Idiotype Vaccine + - Monoclonal Antibody 7C11 + - Monoclonal Antibody 81C6 + - Monoclonal Antibody A1G4 Anti-Idiotype Vaccine + - Monoclonal Antibody A27.15 + - Monoclonal Antibody A33 + - Monoclonal Antibody AbGn-7 + - Monoclonal Antibody AK002 + - Monoclonal Antibody ASP1948 + - Monoclonal Antibody CAL + - Monoclonal Antibody CC49-delta CH2 + - Monoclonal Antibody CEP-37250/KHK2804 + - Monoclonal Antibody D6.12 + - Monoclonal Antibody E2.3 + - Monoclonal Antibody F19 + - Monoclonal Antibody GD2 Anti-Idiotype Vaccine + - Monoclonal Antibody HeFi-1 + - Monoclonal Antibody Hu3S193 + - Monoclonal Antibody HuAFP31 + - Monoclonal Antibody HuHMFG1 + - Monoclonal Antibody huJ591 + - Monoclonal Antibody HuPAM4 + - Monoclonal Antibody IMMU-14 + - Monoclonal Antibody L6 + - Monoclonal Antibody Lym-1 + - Monoclonal Antibody m170 + - Monoclonal Antibody Me1-14 F(ab')2 + - Monoclonal Antibody muJ591 + - Monoclonal Antibody MX35 F(ab')2 + - Monoclonal Antibody NEO-201 + - Monoclonal Antibody R24 + - Monoclonal Antibody RAV12 + - Monoclonal Antibody SGN-14 + - Monoclonal Antibody TRK-950 + - Monoclonal Microbial EDP1503 + - Monoclonal T-cell Receptor Anti-CD3 scFv Fusion Protein IMCgp100 + - Monomethyl Auristatin E + - Morinda Citrifolia Fruit Extract + - Morpholinodoxorubicin + - Mosedipimod + - Mosunetuzumab + - Motesanib + - Motesanib Diphosphate + - Motexafin Gadolinium + - Motexafin Lutetium + - Motixafortide + - Motolimod + - MOv-gamma Chimeric Receptor Gene + - Moxetumomab Pasudotox + - Mps1 Inhibitor BAY 1217389 + - Mps1 Inhibitor BOS172722 + - mRNA-based Personalized Cancer Vaccine mRNA-4157 + - mRNA-based Personalized Cancer Vaccine NCI-4650 + - mRNA-based TriMix Melanoma Vaccine ECI-006 + - mRNA-based Tumor-specific Neoantigen Boosting Vaccine GRT-R902 + - mRNA-derived KRAS-targeted Vaccine V941 + - mRNA-derived Lung Cancer Vaccine BI 1361849 + - mRNA-Derived Prostate Cancer Vaccine CV9103 + - mRNA-derived Prostate Cancer Vaccine CV9104 + - MTF-1 Inhibitor APTO-253 HCl + - mTOR Inhibitor GDC-0349 + - mTOR Kinase Inhibitor AZD8055 + - mTOR Kinase Inhibitor CC-223 + - mTOR Kinase Inhibitor OSI-027 + - mTOR Kinase Inhibitor PP242 + - mTOR1/2 Kinase Inhibitor ME-344 + - mTORC 1/2 Inhibitor LXI-15029 + - mTORC1/2 Kinase Inhibitor BI 860585 + - mTORC1/mTORC2/DHFR Inhibitor ABTL0812 + - MUC-1/WT1 Peptide-primed Autologous Dendritic Cells + - MUC1-targeted Peptide GO-203-2C + - Mucoadhesive Paclitaxel Formulation + - Multi-AGC Kinase Inhibitor AT13148 + - Multi-epitope Anti-folate Receptor Peptide Vaccine TPIV 200 + - Multi-epitope HER2 Peptide Vaccine H2NVAC + - Multi-epitope HER2 Peptide Vaccine TPIV100 + - Multi-glioblastoma-peptide-targeting Autologous Dendritic Cell Vaccine ICT-107 + - Multi-kinase Inhibitor TPX-0022 + - Multi-kinase Inhibitor XL092 + - Multi-mode Kinase Inhibitor EOC317 + - Multi-neo-epitope Vaccine OSE 2101 + - Multifunctional/Multitargeted Anticancer Agent OMN54 + - Multikinase Inhibitor 4SC-203 + - Multikinase Inhibitor AEE788 + - Multikinase Inhibitor AT9283 + - Multikinase Inhibitor SAR103168 + - Multipeptide Vaccine S-588210 + - Multitargeted Tyrosine Kinase Inhibitor JNJ-26483327 + - Muparfostat + - Mureletecan + - Murizatoclax + - Muscadine Grape Extract + - Mutant IDH1 Inhibitor DS-1001 + - Mutant p53 Activator COTI-2 + - Mutant-selective EGFR Inhibitor PF-06459988 + - MVA Tumor-specific Neoantigen Boosting Vaccine MVA-209-FSP + - MVA-BN Smallpox Vaccine + - MVA-FCU1 TG4023 + - MVX-1-loaded Macrocapsule/autologous Tumor Cell Vaccine MVX-ONCO-1 + - MYC-targeting siRNA DCR-MYC + - Mycobacterium tuberculosis Arabinomannan Z-100 + - Mycobacterium w + - Mycophenolic Acid + - N-(5-tert-butyl-3-isoxazolyl)-N-(4-(4-pyridinyl)oxyphenyl) Urea + - N-dihydrogalactochitosan + - N-Methylformamide + - N,N-Dibenzyl Daunomycin + - NA17-A Antigen + - NA17.A2 Peptide Vaccine + - Nab-paclitaxel + - Nab-paclitaxel/Rituximab-coated Nanoparticle AR160 + - Nadofaragene Firadenovec + - Nagrestipen + - Namirotene + - Namodenoson + - NAMPT Inhibitor OT-82 + - Nanafrocin + - Nanatinostat + - Nanocell-encapsulated miR-16-based microRNA Mimic + - Nanoparticle Albumin-Bound Docetaxel + - Nanoparticle Albumin-Bound Rapamycin + - Nanoparticle Albumin-bound Thiocolchicine Dimer nab-5404 + - Nanoparticle Paclitaxel Ointment SOR007 + - Nanoparticle-based Paclitaxel Suspension + - Nanoparticle-encapsulated Doxorubicin Hydrochloride + - Nanoscale Coordination Polymer Nanoparticles CPI-100 + - Nanosomal Docetaxel Lipid Suspension + - Napabucasin + - Naphthalimide Analogue UNBS5162 + - Naptumomab Estafenatox + - Naquotinib + - Naratuximab Emtansine + - Narnatumab + - Natalizumab + - Natural IFN-alpha OPC-18 + - Natural Killer Cells ZRx101 + - Navarixin + - Navicixizumab + - Navitoclax + - Navoximod + - Navy Bean Powder + - Naxitamab + - Nazartinib + - ncmtRNA Oligonucleotide Andes-1537 + - Necitumumab + - Nedaplatin + - NEDD8 Activating Enzyme E1 Inhibitor TAS4464 + - Nedisertib + - Nelarabine + - Nelipepimut-S + - Nelipepimut-S Plus GM-CSF Vaccine + - Nemorubicin + - Nemorubicin Hydrochloride + - Neoantigen Vaccine GEN-009 + - Neoantigen-based Glioblastoma Vaccine + - Neoantigen-based Melanoma-Poly-ICLC Vaccine + - Neoantigen-based Renal Cell Carcinoma-Poly-ICLC Vaccine + - Neoantigen-based Therapeutic Cancer Vaccine GRT-C903 + - Neoantigen-based Therapeutic Cancer Vaccine GRT-R904 + - Neoantigen-HSP70 Peptide Cancer Vaccine AGEN2017 + - Neratinib + - Neratinib Maleate + - Nesvacumab + - NG-nitro-L-arginine + - Niacinamide + - Niclosamide + - Nicotinamide Riboside + - Nidanilimab + - Nifurtimox + - Nilotinib + - Nilotinib Hydrochloride Anhydrous + - Nilotinib Hydrochloride Monohydrate + - Nilutamide + - Nimesulide-Hyaluronic Acid Conjugate CA102N + - Nimodipine + - Nimotuzumab + - Nimustine + - Nimustine Hydrochloride + - Ningetinib Tosylate + - Nintedanib + - Niraparib + - Niraparib Tosylate Monohydrate + - Nirogacestat + - Nitric Oxide-Releasing Acetylsalicylic Acid Derivative + - Nitrogen Mustard Prodrug PR-104 + - Nitroglycerin Transdermal Patch + - Nivolumab + - NLRP3 Agonist BMS-986299 + - Nocodazole + - Nogalamycin + - Nogapendekin Alfa + - Nolatrexed Dihydrochloride + - Non-Small Cell Lung Cancer mRNA-Derived Vaccine CV9201 + - Norgestrel + - North American Ginseng Extract AFX-2 + - Nortopixantrone + - Noscapine + - Noscapine Hydrochloride + - Not Otherwise Specified + - Notch Signaling Inhibitor PF-06650808 + - Notch Signaling Pathway Inhibitor MK0752 + - NTRK/ROS1 Inhibitor DS-6051b + - Nucleolin Antagonist IPP-204106N + - Nucleoside Analog DFP-10917 + - Nucleotide Analog Prodrug NUC-3373 + - Nucleotide Analogue GS 9219 + - Numidargistat + - Nurulimab + - Nutlin-3a + - Nutraceutical TBL-12 + - NY-ESO-1 Plasmid DNA Cancer Vaccine pPJV7611 + - NY-ESO-1-specific TCR Gene-transduced T Lymphocytes TBI-1301 + - NY-ESO-1/GLA-SE Vaccine ID-G305 + - NY-ESO-B + - O-Chloroacetylcarbamoylfumagillol + - O6-Benzylguanine + - Obatoclax Mesylate + - Obinutuzumab + - Oblimersen Sodium + - Ocaratuzumab + - Ocrelizumab + - Octreotide + - Octreotide Acetate + - Octreotide Pamoate + - Odronextamab + - Ofatumumab + - Ofranergene Obadenovec + - Oglufanide Disodium + - Olaparib + - Olaptesed Pegol + - Olaratumab + - Oleandrin + - Oleclumab + - Oligo-fucoidan + - Oligonucleotide SPC2996 + - Olinvacimab + - Olivomycin + - Olmutinib + - Oltipraz + - Olutasidenib + - Olvimulogene Nanivacirepvec + - Omacetaxine Mepesuccinate + - Ombrabulin + - Omipalisib + - Onalespib + - Onalespib Lactate + - Onartuzumab + - Onatasertib + - Oncolytic Adenovirus Ad5-DNX-2401 + - Oncolytic Adenovirus ORCA-010 + - Oncolytic Herpes Simplex Virus-1 ONCR-177 + - Oncolytic HSV-1 C134 + - Oncolytic HSV-1 Expressing IL-12 and Anti-PD-1 Antibody T3011 + - Oncolytic HSV-1 G207 + - Oncolytic HSV-1 NV1020 + - Oncolytic HSV-1 rQNestin34.5v.2 + - Oncolytic HSV-1 rRp450 + - Oncolytic HSV1716 + - Oncolytic Measles Virus Encoding Helicobacter pylori Neutrophil-activating Protein + - Oncolytic Newcastle Disease Virus MEDI5395 + - Oncolytic Newcastle Disease Virus MTH-68H + - Oncolytic Newcastle Disease Virus Strain PV701 + - Oncolytic Virus ASP9801 + - Oncolytic Virus RP1 + - Ondansetron Hydrochloride + - Ontorpacept + - Ontuxizumab + - Onvansertib + - Onvatilimab + - Opaganib + - OPCs/Green Tea/Spirullina/Curcumin/Antrodia Camphorate/Fermented Soymilk Extract Capsule + - Opioid Growth Factor + - Opolimogene Capmilisbac + - Oportuzumab Monatox + - Oprozomib + - Opucolimab + - Oral Aminolevulinic Acid Hydrochloride + - Oral Azacitidine + - Oral Cancer Vaccine V3-OVA + - Oral Docetaxel + - Oral Fludarabine Phosphate + - Oral Hsp90 Inhibitor IPI-493 + - Oral Ixabepilone + - Oral Microencapsulated Diindolylmethane + - Oral Milataxel + - Oral Myoma Vaccine V3-myoma + - Oral Pancreatic Cancer Vaccine V3-P + - Oral Picoplatin + - Oral Sodium Phenylbutyrate + - Oral Topotecan Hydrochloride + - Orantinib + - Oraxol + - Oregovomab + - Orelabrutinib + - Ormaplatin + - Ortataxel + - Orteronel + - Orvacabtagene Autoleucel + - Osilodrostat + - Osimertinib + - Other + - Otlertuzumab + - Ovapuldencel-T + - Ovarian Cancer Stem Cell/hTERT/Survivin mRNAs-loaded Autologous Dendritic Cell Vaccine DC-006 + - Ovine Submaxillary Mucin + - OX40L-expressing Oncolytic Adenovirus DNX-2440 + - Oxaliplatin + - Oxaliplatin Eluting Beads + - Oxaliplatin-Encapsulated Transferrin-Conjugated N-glutaryl Phosphatidylethanolamine Liposome + - Oxcarbazepine + - Oxeclosporin + - Oxidative Phosphorylation Inhibitor IACS-010759 + - Oxidative Phosphorylation Inhibitor IM156 + - Oxidopamine + - OxPhos Inhibitor VLX600 + - Ozarelix + - P-cadherin Antagonist PF-03732010 + - P-cadherin Inhibitor PCA062 + - P-cadherin-targeting Agent PF-06671008 + - P-p68 Inhibitor RX-5902 + - P-TEFb Inhibitor BAY1143572 + - p300/CBP Bromodomain Inhibitor CCS1477 + - p38 MAPK Inhibitor LY3007113 + - p53 Peptide Vaccine MPS-128 + - p53-HDM2 Interaction Inhibitor MI-773 + - p53-HDM2 Protein-protein Interaction Inhibitor APG-115 + - p53/HDM2 Interaction Inhibitor CGM097 + - p70S6K Inhibitor LY2584702 + - p70S6K/Akt Inhibitor MSC2363318A + - p97 Inhibitor CB-5083 + - p97 Inhibitor CB-5339 + - p97 Inhibitor CB-5339 Tosylate + - Paclitaxel + - Paclitaxel Ceribate + - Paclitaxel Injection Concentrate for Nanodispersion + - Paclitaxel Liposome + - Paclitaxel Poliglumex + - Paclitaxel Polymeric Micelle Formulation NANT-008 + - Paclitaxel PPE Microspheres + - Paclitaxel Trevatide + - Paclitaxel Vitamin E-Based Emulsion + - Paclitaxel-Loaded Polymeric Micelle + - Pacmilimab + - Pacritinib + - Padeliporfin + - Padoporfin + - PAK4 Inhibitor PF-03758309 + - PAK4/NAMPT Inhibitor KPT-9274 + - Palbociclib + - Palbociclib Isethionate + - Palifosfamide + - Palifosfamide Tromethamine + - Palladium Pd-103 + - Palonosetron Hydrochloride + - Pamidronate Disodium + - Pamidronic Acid + - Pamiparib + - Pamrevlumab + - pan FGFR Inhibitor PRN1371 + - Pan HER/VEGFR2 Receptor Tyrosine Kinase Inhibitor BMS-690514 + - Pan-AKT Inhibitor ARQ751 + - Pan-AKT Kinase Inhibitor GSK690693 + - Pan-FGFR Inhibitor LY2874455 + - Pan-FLT3/Pan-BTK Multi-kinase Inhibitor CG-806 + - pan-HER Kinase Inhibitor AC480 + - Pan-IDH Mutant Inhibitor AG-881 + - Pan-KRAS Inhibitor BI 1701963 + - Pan-Mutant-IDH1 Inhibitor Bay-1436032 + - Pan-mutation-selective EGFR Inhibitor CLN-081 + - pan-PI3K Inhibitor CLR457 + - pan-PI3K/mTOR Inhibitor SF1126 + - Pan-PIM Inhibitor INCB053914 + - pan-PIM Kinase Inhibitor AZD1208 + - pan-PIM Kinase Inhibitor NVP-LGB-321 + - pan-RAF Inhibitor LXH254 + - Pan-RAF Inhibitor LY3009120 + - pan-RAF Kinase Inhibitor CCT3833 + - pan-RAF Kinase Inhibitor TAK-580 + - Pan-RAR Agonist/AP-1 Inhibitor LGD 1550 + - Pan-TRK Inhibitor NOV1601 + - Pan-TRK Inhibitor ONO-7579 + - Pan-VEGFR/TIE2 Tyrosine Kinase Inhibitor CEP-11981 + - Pancratistatin + - Panitumumab + - Panobinostat + - Panobinostat Nanoparticle Formulation MTX110 + - Panulisib + - Paricalcitol + - PARP 1/2 Inhibitor IMP4297 + - PARP 1/2 Inhibitor NOV1401 + - PARP Inhibitor AZD2461 + - PARP Inhibitor CEP-9722 + - PARP Inhibitor E7016 + - PARP Inhibitor NMS-03305293 + - PARP-1/2 Inhibitor ABT-767 + - PARP/Tankyrase Inhibitor 2X-121 + - PARP7 Inhibitor RBN-2397 + - Parsaclisib + - Parsaclisib Hydrochloride + - Parsatuzumab + - Partially Engineered T-regulatory Cell Donor Graft TRGFT-201 + - Parvovirus H-1 + - Pasireotide + - Pasotuxizumab + - Patidegib + - Patidegib Topical Gel + - Patritumab + - Patritumab Deruxtecan + - Patupilone + - Paxalisib + - Pazopanib + - Pazopanib Hydrochloride + - pbi-shRNA STMN1 Lipoplex + - PBN Derivative OKN-007 + - PCNU + - PD-1 Directed Probody CX-188 + - PD-1 Inhibitor + - PD-L1 Inhibitor GS-4224 + - PD-L1 Inhibitor INCB086550 + - PD-L1/4-1BB/HSA Trispecific Fusion Protein NM21-1480 + - PD-L1/PD-L2/VISTA Antagonist CA-170 + - PDK1 Inhibitor AR-12 + - pDNA-encoding Emm55 Autologous Cancer Cell Vaccine IFx-Hu2.0 + - PE/HPV16 E7/KDEL Fusion Protein/GPI-0100 TVGV-1 + - PEG-interleukin-2 + - PEG-PEI-cholesterol Lipopolymer-encased IL-12 DNA Plasmid Vector GEN-1 + - PEG-Proline-Interferon Alfa-2b + - Pegargiminase + - Pegaspargase + - Pegdinetanib + - Pegfilgrastim + - Pegilodecakin + - Peginterferon Alfa-2a + - Peginterferon Alfa-2b + - Pegvisomant + - Pegvorhyaluronidase Alfa + - Pegylated Deoxycytidine Analogue DFP-14927 + - Pegylated Interferon Alfa + - Pegylated Liposomal Belotecan + - Pegylated Liposomal Doxorubicin Hydrochloride + - Pegylated Liposomal Irinotecan + - Pegylated Liposomal Mitomycin C Lipid-based Prodrug + - Pegylated Liposomal Mitoxantrone Hydrochloride + - Pegylated Liposomal Nanoparticle-based Docetaxel Prodrug MNK-010 + - Pegylated Paclitaxel + - Pegylated Recombinant Human Arginase I BCT-100 + - Pegylated Recombinant Human Hyaluronidase PH20 + - Pegylated Recombinant Interleukin-2 THOR-707 + - Pegylated Recombinant L-asparaginase Erwinia chrysanthemi + - Pegylated SN-38 Conjugate PLX038 + - Pegzilarginase + - Pelabresib + - Pelareorep + - Peldesine + - Pelitinib + - Pelitrexol + - Pembrolizumab + - Pemetrexed + - Pemetrexed Disodium + - Pemigatinib + - Pemlimogene Merolisbac + - Penberol + - Penclomedine + - Penicillamine + - Pentamethylmelamine + - Pentamustine + - Pentostatin + - Pentoxifylline + - PEOX-based Polymer Encapsulated Paclitaxel FID-007 + - PEP-3-KLH Conjugate Vaccine + - Pepinemab + - Peplomycin + - Peplomycin Sulfate + - Peposertib + - Peptichemio + - Peptide 946 Melanoma Vaccine + - Peptide 946-Tetanus Peptide Conjugate Melanoma Vaccine + - Peretinoin + - Perflenapent Emulsion + - Perfosfamide + - Perifosine + - Perillyl Alcohol + - Personalized ALL-specific Multi-HLA-binding Peptide Vaccine + - Personalized and Adjusted Neoantigen Peptide Vaccine PANDA-VAC + - Personalized Cancer Vaccine RO7198457 + - Personalized Neoantigen DNA Vaccine GNOS-PV01 + - Personalized Neoantigen DNA Vaccine GNOS-PVO2 + - Personalized Neoantigen Peptide Vaccine iNeo-Vac-P01 + - Personalized Neoepitope Yeast Vaccine YE-NEO-001 + - Personalized Peptide Cancer Vaccine NEO-PV-01 + - Pertuzumab + - Pevonedistat + - Pexastimogene Devacirepvec + - Pexidartinib + - Pexmetinib + - PGG Beta-Glucan + - PGLA/PEG Copolymer-Based Paclitaxel + - PH20 Hyaluronidase-expressing Adenovirus VCN-01 + - Phaleria macrocarpa Extract DLBS-1425 + - Pharmacological Ascorbate + - Phellodendron amurense Bark Extract + - Phenesterin + - Phenethyl Isothiocyanate + - Phenethyl Isothiocyanate-containing Watercress Juice + - Phenyl Acetate + - Phenytoin Sodium + - Phosphaplatin PT-112 + - Phosphatidylcholine-Bound Silybin + - Phospholipid Ether-drug Conjugate CLR 131 + - Phosphoramide Mustard + - Phosphorodiamidate Morpholino Oligomer AVI-4126 + - Phosphorus P-32 + - Photodynamic Compound TLD-1433 + - Photosensitizer LUZ 11 + - Phytochlorin Sodium-Polyvinylpyrrolidone Complex + - PI3K Alpha/Beta Inhibitor BAY1082439 + - PI3K Alpha/mTOR Inhibitor PWT33597 Mesylate + - PI3K Inhibitor ACP-319 + - PI3K Inhibitor BGT226 + - PI3K Inhibitor GDC-0084 + - PI3K Inhibitor GDC0077 + - PI3K Inhibitor GSK1059615 + - PI3K Inhibitor WX-037 + - PI3K Inhibitor ZSTK474 + - PI3K p110beta/delta Inhibitor KA2237 + - PI3K-alpha Inhibitor MEN1611 + - PI3K-beta Inhibitor GSK2636771 + - PI3K-beta Inhibitor SAR260301 + - PI3K-delta Inhibitor AMG 319 + - PI3K-delta Inhibitor HMPL 689 + - PI3K-delta Inhibitor INCB050465 + - PI3K-delta Inhibitor PWT143 + - PI3K-delta Inhibitor SHC014748M + - PI3K-delta Inhibitor YY-20394 + - PI3K-gamma Inhibitor IPI-549 + - PI3K/BET Inhibitor LY294002 + - PI3K/mTOR Kinase Inhibitor DS-7423 + - PI3K/mTOR Kinase Inhibitor PF-04691502 + - PI3K/mTOR Kinase Inhibitor VS-5584 + - PI3K/mTOR Kinase Inhibitor WXFL10030390 + - PI3K/mTOR/ALK-1/DNA-PK Inhibitor P7170 + - PI3K/mTORC1/mTORC2 Inhibitor DCBCI0901 + - PI3Ka/mTOR Inhibitor PKI-179 + - PI3Kalpha Inhibitor AZD8835 + - PI3Kbeta Inhibitor AZD8186 + - PI3Kdelta Inhibitor GS-9901 + - Pibenzimol + - Pibrozelesin + - Pibrozelesin Hydrobromide + - Picibanil + - Picoplatin + - Picrasinoside H + - Picropodophyllin + - Pictilisib + - Pictilisib Bismesylate + - Pidilizumab + - Pilaralisib + - PIM Kinase Inhibitor LGH447 + - PIM Kinase Inhibitor SGI-1776 + - PIM Kinase Inhibitor TP-3654 + - PIM/FLT3 Kinase Inhibitor SEL24 + - Pimasertib + - Pimitespib + - Pimurutamab + - Pinatuzumab Vedotin + - Pingyangmycin + - Pinometostat + - Pioglitazone + - Pioglitazone Hydrochloride + - Pipendoxifene + - Piperazinedione + - Piperine Extract (Standardized) + - Pipobroman + - Piposulfan + - Pirarubicin + - Pirarubicin Hydrochloride + - Pirfenidone + - Piritrexim + - Piritrexim Isethionate + - Pirotinib + - Piroxantrone + - Piroxantrone Hydrochloride + - Pixantrone + - Pixantrone Dimaleate + - Pixatimod + - PKA Regulatory Subunit RIalpha Mixed-Backbone Antisense Oligonucleotide GEM 231 + - PKC-alpha Antisense Oligodeoxynucleotide ISIS 3521 + - PKC-beta Inhibitor MS-553 + - Placebo + - Pladienolide Derivative E7107 + - Plamotamab + - Plasmid DNA Vaccine pING-hHER3FL + - Platinum + - Platinum Acetylacetonate-Titanium Dioxide Nanoparticles + - Platinum Compound + - Plevitrexed + - Plicamycin + - Plinabulin + - Plitidepsin + - Plk1 Inhibitor BI 2536 + - PLK1 Inhibitor CYC140 + - PLK1 Inhibitor TAK-960 + - Plocabulin + - Plozalizumab + - pNGVL4a-CRT-E6E7L2 DNA Vaccine + - pNGVL4a-Sig/E7(detox)/HSP70 DNA and HPV16 L2/E6/E7 Fusion Protein TA-CIN Vaccine PVX-2 + - Pol I Inhibitor CX5461 + - Polatuzumab Vedotin + - Polidocanol + - Poliglusam + - Polo-like Kinase 1 Inhibitor GSK461364 + - Polo-like Kinase 1 Inhibitor MK1496 + - Polo-like Kinase 1 Inhibitor NMS-1286937 + - Polo-like Kinase 4 Inhibitor CFI-400945 Fumarate + - Poly-alendronate Dextran-Guanidine Conjugate + - Poly-gamma Glutamic Acid + - Polyamine Analog SL11093 + - Polyamine Analogue PG11047 + - Polyamine Analogue SBP-101 + - Polyamine Transport Inhibitor AMXT-1501 Dicaprate + - Polyandrol + - Polyethylene Glycol Recombinant Endostatin + - Polyethyleneglycol-7-ethyl-10-hydroxycamptothecin DFP-13318 + - Polymer-conjugated IL-15 Receptor Agonist NKTR-255 + - Polymer-encapsulated Luteolin Nanoparticle + - Polymeric Camptothecin Prodrug XMT-1001 + - Polypodium leucotomos Extract + - Polysaccharide-K + - Polysialic Acid + - Polyunsaturated Fatty Acid + - Polyvalent Melanoma Vaccine + - Pomalidomide + - Pomegranate Juice + - Pomegranate Liquid Extract + - Ponatinib + - Ponatinib Hydrochloride + - Porcupine Inhibitor CGX1321 + - Porcupine Inhibitor ETC-1922159 + - Porcupine Inhibitor RXC004 + - Porcupine Inhibitor WNT974 + - Porcupine Inhibitor XNW7201 + - Porfimer Sodium + - Porfiromycin + - Poziotinib + - PPAR Alpha Antagonist TPST-1120 + - PR1 Leukemia Peptide Vaccine + - Pracinostat + - Pralatrexate + - Pralsetinib + - Praluzatamab Ravtansine + - PRAME-targeting T-cell Receptor/Inducible Caspase 9 BPX-701 + - Pravastatin Sodium + - Prednimustine + - Prednisolone + - Prednisolone Acetate + - Prednisolone Sodium Phosphate + - Prednisone + - Prexasertib + - Prexigebersen + - PRIMA-1 Analog APR-246 + - Prime Cancer Vaccine MVA-BN-CV301 + - Prinomastat + - PRMT1 Inhibitor GSK3368715 + - PRMT5 Inhibitor JNJ-64619178 + - PRMT5 Inhibitor PRT811 + - Proapoptotic Sulindac Analog CP-461 + - Procarbazine + - Procarbazine Hydrochloride + - Procaspase Activating Compound-1 VO-100 + - Progestational IUD + - Prohibitin-Targeting Peptide 1 + - Prolgolimab + - Prostaglandin E2 EP4 Receptor Inhibitor AN0025 + - Prostaglandin E2 EP4 Receptor Inhibitor E7046 + - Prostate Cancer Vaccine ONY-P1 + - Prostate Health Cocktail Dietary Supplement + - Prostatic Acid Phosphatase-Sargramostim Fusion Protein PA2024 + - Protease-activated Anti-PD-L1 Antibody Prodrug CX-072 + - Protein Arginine Methyltransferase 5 Inhibitor GSK3326595 + - Protein Arginine Methyltransferase 5 Inhibitor PF-06939999 + - Protein Arginine Methyltransferase 5 Inhibitor PRT543 + - Protein Kinase C Inhibitor IDE196 + - Protein Phosphatase 2A Inhibitor LB-100 + - Protein Stabilized Liposomal Docetaxel Nanoparticles + - Protein Tyrosine Kinase 2 Inhibitor IN10018 + - Proxalutamide + - PSA/IL-2/GM-CSF Vaccine + - PSA/PSMA DNA Plasmid INO-5150 + - Pseudoisocytidine + - PSMA-targeted Docetaxel Nanoparticles BIND-014 + - PSMA-targeted Tubulysin B-containing Conjugate EC1169 + - PSMA/CD3 Tri-specific T-cell Activating Construct HPN424 + - PTEF-b/CDK9 Inhibitor BAY1251152 + - Pterostilbene + - Pumitepa + - Puquitinib + - Puquitinib Mesylate + - Puromycin + - Puromycin Hydrochloride + - PV-10 + - PVA Microporous Hydrospheres/Doxorubicin Hydrochloride + - Pyrazinamide + - Pyrazoloacridine + - Pyridyl Cyanoguanidine CHS 828 + - Pyrotinib + - Pyrotinib Dimaleate + - Pyroxamide + - Pyruvate Kinase Inhibitor TLN-232 + - Pyruvate Kinase M2 Isoform Activator TP-1454 + - Qilisheng Immunoregulatory Oral Solution + - Quadrivalent Human Papillomavirus (types 6, 11, 16, 18) Recombinant Vaccine + - Quarfloxin + - Quinacrine Hydrochloride + - Quinine + - Quisinostat + - Quizartinib + - R-(-)-Gossypol Acetic Acid + - Rabusertib + - Racemetyrosine/Methoxsalen/Phenytoin/Sirolimus SM-88 + - Racotumomab + - RAD51 Inhibitor CYT-0851 + - Radgocitabine + - Radgocitabine Hydrochloride + - Radioactive Iodine + - Radiolabeled CC49 + - Radium Ra 223 Dichloride + - Radium Ra 224-labeled Calcium Carbonate Microparticles + - Radix Angelicae Sinensis/Radix Astragali Herbal Supplement + - Radotinib Hydrochloride + - Raf Kinase Inhibitor HM95573 + - RAF Kinase Inhibitor L-779450 + - RAF Kinase Inhibitor XL281 + - Ragifilimab + - Ralaniten Acetate + - Ralimetinib Mesylate + - Raloxifene + - Raloxifene Hydrochloride + - Raltitrexed + - Ramucirumab + - Ranibizumab + - Ranimustine + - Ranolazine + - Ranpirnase + - RARalpha Agonist IRX5183 + - Ras Inhibitor + - Ras Peptide ASP + - Ras Peptide CYS + - Ras Peptide VAL + - Razoxane + - Realgar-Indigo naturalis Formulation + - Rebastinib Tosylate + - Rebeccamycin + - Rebimastat + - Receptor Tyrosine Kinase Inhibitor R1530 + - Recombinant Adenovirus-p53 SCH-58500 + - Recombinant Anti-WT1 Immunotherapeutic GSK2302024A + - Recombinant Bacterial Minicells VAX014 + - Recombinant Bispecific Single-Chain Antibody rM28 + - Recombinant CD40-Ligand + - Recombinant Erwinia asparaginase JZP-458 + - Recombinant Erythropoietin + - Recombinant Fas Ligand + - Recombinant Fractalkine + - Recombinant Granulocyte-Macrophage Colony-Stimulating Factor + - Recombinant Human 6Ckine + - Recombinant Human Adenovirus Type 5 H101 + - Recombinant Human Angiotensin Converting Enzyme 2 APN01 + - Recombinant Human Apolipoprotein(a) Kringle V MG1102 + - Recombinant Human EGF-rP64K/Montanide ISA 51 Vaccine + - Recombinant Human Endostatin + - Recombinant Human Hsp110-gp100 Chaperone Complex Vaccine + - Recombinant Human Papillomavirus 11-valent Vaccine + - Recombinant Human Papillomavirus Bivalent Vaccine + - Recombinant Human Papillomavirus Nonavalent Vaccine + - Recombinant Human Plasminogen Kringle 5 Domain ABT 828 + - Recombinant Human TRAIL-Trimer Fusion Protein SCB-313 + - Recombinant Humanized Anti-HER-2 Bispecific Monoclonal Antibody MBS301 + - Recombinant Interferon + - Recombinant Interferon Alfa + - Recombinant Interferon Alfa-1b + - Recombinant Interferon Alfa-2a + - Recombinant Interferon Alfa-2b + - Recombinant Interferon Alpha 2b-like Protein + - Recombinant Interferon Beta + - Recombinant Interferon Gamma + - Recombinant Interleukin-12 + - Recombinant Interleukin-13 + - Recombinant Interleukin-18 + - Recombinant Interleukin-2 + - Recombinant Interleukin-6 + - Recombinant KSA Glycoprotein CO17-1A + - Recombinant Leukocyte Interleukin + - Recombinant Leukoregulin + - Recombinant Luteinizing Hormone + - Recombinant Macrophage Colony-Stimulating Factor + - Recombinant MAGE-3.1 Antigen + - Recombinant MIP1-alpha Variant ECI301 + - Recombinant Modified Vaccinia Ankara-5T4 Vaccine + - Recombinant Oncolytic Poliovirus PVS-RIPO + - Recombinant Platelet Factor 4 + - Recombinant PRAME Protein Plus AS15 Adjuvant GSK2302025A + - Recombinant Saccharomyces Cerevisia-CEA(610D)-Expressing Vaccine GI-6207 + - Recombinant Super-compound Interferon + - Recombinant Thyroglobulin + - Recombinant Thyrotropin Alfa + - Recombinant Transforming Growth Factor-Beta + - Recombinant Transforming Growth Factor-Beta-2 + - Recombinant Tumor Necrosis Factor-Alpha + - Recombinant Tyrosinase-Related Protein-2 + - Recombinant Vesicular Stomatitis Virus-expressing Human Interferon Beta and Sodium-Iodide Symporter + - Redaporfin + - Refametinib + - Regorafenib + - Relacorilant + - Relatlimab + - Relugolix + - Remetinostat + - Renal Cell Carcinoma Peptides Vaccine IMA901 + - Reparixin + - Repotrectinib + - Resiquimod + - Resiquimod Topical Gel + - Resistant Starch + - Resminostat + - Resveratrol + - Resveratrol Formulation SRT501 + - RET Inhibitor DS-5010 + - RET Mutation/Fusion Inhibitor BLU-667 + - RET/SRC Inhibitor TPX-0046 + - Retaspimycin + - Retaspimycin Hydrochloride + - Retelliptine + - Retifanlimab + - Retinoic Acid Agent Ro 16-9100 + - Retinoid 9cUAB30 + - Retinol + - Retinyl Acetate + - Retinyl Palmitate + - Retrovector Encoding Mutant Anti-Cyclin G1 + - Revdofilimab + - Rexinoid NRX 194204 + - Rezivertinib + - RFT5-dgA Immunotoxin IMTOX25 + - Rhenium Re 188 BMEDA-labeled Liposomes + - Rhenium Re-186 Hydroxyethylidene Diphosphonate + - Rhenium Re-188 Ethiodized Oil + - Rhenium Re-188 Etidronate + - Rhizoxin + - RhoC Peptide Vaccine RV001V + - Ribociclib + - Ribociclib/Letrozole + - Ribonuclease QBI-139 + - Ribosome-Inactivating Protein CY503 + - Ribozyme RPI.4610 + - Rice Bran + - Ricolinostat + - Ridaforolimus + - Rigosertib + - Rigosertib Sodium + - Rilimogene Galvacirepvec + - Rilimogene Galvacirepvec/Rilimogene Glafolivec + - Rilimogene Glafolivec + - Rilotumumab + - Rindopepimut + - Ripertamab + - RIPK1 Inhibitor GSK3145095 + - Ripretinib + - Risperidone Formulation in Rumenic Acid + - Ritrosulfan + - Rituximab + - Rituximab and Hyaluronidase Human + - Rituximab Conjugate CON-4619 + - Riviciclib + - Rivoceranib + - Rivoceranib Mesylate + - RNR Inhibitor COH29 + - Robatumumab + - Roblitinib + - ROBO1-targeted BiCAR-NKT Cells + - Rocakinogene Sifuplasmid + - Rocapuldencel-T + - Rociletinib + - Rodorubicin + - Roducitabine + - Rofecoxib + - Roflumilast + - Rogaratinib + - Rogletimide + - Rolinsatamab Talirine + - Romidepsin + - Roneparstat + - Roniciclib + - Ropeginterferon Alfa-2B + - Ropidoxuridine + - Ropocamptide + - Roquinimex + - RORgamma Agonist LYC-55716 + - Rosabulin + - Rose Bengal Solution PV-10 + - Rosiglitazone Maleate + - Rosmantuzumab + - Rosopatamab + - Rosuvastatin + - Rovalpituzumab Tesirine + - RSK1-4 Inhibitor PMD-026 + - Rubitecan + - Rucaparib + - Rucaparib Camsylate + - Rucaparib Phosphate + - Ruthenium Ru-106 + - Ruthenium-based Small Molecule Therapeutic BOLD-100 + - Ruthenium-based Transferrin Targeting Agent NKP-1339 + - Ruxolitinib + - Ruxolitinib Phosphate + - Ruxotemitide + - S-Adenosylmethionine + - S-equol + - S1P Receptor Agonist KRP203 + - Sabarubicin + - Sabatolimab + - Sacituzumab Govitecan + - Sacubitril/Valsartan + - Safingol + - Sagopilone + - Salirasib + - Salmonella VNP20009 + - Sam68 Modulator CWP232291 + - Samalizumab + - Samarium Sm 153-DOTMP + - Samotolisib + - Samrotamab Vedotin + - Samuraciclib + - Sapacitabine + - Sapanisertib + - Sapitinib + - Saracatinib + - Saracatinib Difumarate + - SarCNU + - Sardomozide + - Sargramostim + - Sasanlimab + - Satraplatin + - Savolitinib + - SBIL-2 + - Scopoletin + - SDF-1 Receptor Antagonist PTX-9908 + - Seclidemstat + - Sedoxantrone Trihydrochloride + - Selatinib Ditosilate + - Selective Androgen Receptor Modulator RAD140 + - Selective Cytokine Inhibitory Drug CC-1088 + - Selective Estrogen Receptor Degrader AZD9496 + - Selective Estrogen Receptor Degrader AZD9833 + - Selective Estrogen Receptor Degrader LSZ102 + - Selective Estrogen Receptor Degrader LX-039 + - Selective Estrogen Receptor Degrader LY3484356 + - Selective Estrogen Receptor Degrader SRN-927 + - Selective Estrogen Receptor Modulator CC-8490 + - Selective Estrogen Receptor Modulator TAS-108 + - Selective Glucocorticoid Receptor Antagonist CORT125281 + - Selective Human Estrogen-receptor Alpha Partial Agonist TTC-352 + - Seliciclib + - Selicrelumab + - Selinexor + - Selitrectinib + - Selonsertib + - Selpercatinib + - Selumetinib + - Selumetinib Sulfate + - Semaxanib + - Semuloparin + - Semustine + - Seneca Valley Virus-001 + - Seocalcitol + - Sepantronium Bromide + - Serabelisib + - Serclutamab Talirine + - SERD D-0502 + - SERD G1T48 + - SERD GDC-9545 + - SERD SAR439859 + - SERD SHR9549 + - SERD ZN-c5 + - Serdemetan + - Sergiolide + - Seribantumab + - Serine/Threonine Kinase Inhibitor CBP501 + - Serine/Threonine Kinase Inhibitor XL418 + - Serplulimab + - Sevacizumab + - Seviteronel + - Shared Anti-Idiotype-AB-S006 + - Shared Anti-Idiotype-AB-S024A + - Shark Cartilage + - Shark Cartilage Extract AE-941 + - Shenqi Fuzheng Injection SQ001 + - Sho-Saiko-To + - Short Chain Fatty Acid HQK-1004 + - SHP-1 Agonist SC-43 + - SHP2 Inhibitor JAB-3068 + - SHP2 Inhibitor RLY-1971 + - SHP2 Inhibitor RMC-4630 + - SHP2 Inhibitor TNO155 + - Shu Yu Wan Formula + - Sialyl Tn Antigen + - Sialyl Tn-KLH Vaccine + - Sibrotuzumab + - siG12D LODER + - Silatecan AR-67 + - Silibinin + - Silicon Phthalocyanine 4 + - Silmitasertib Sodium + - Siltuximab + - Simalikalactone D + - Simeprevir + - Simlukafusp Alfa + - Simmitinib + - Simotaxel + - Simtuzumab + - Simurosertib + - Sintilimab + - Siplizumab + - Sipuleucel-T + - Siremadlin + - siRNA-transfected Peripheral Blood Mononuclear Cells APN401 + - Sirolimus + - SIRPa-4-1BBL Fusion Protein DSP107 + - SIRPa-Fc Fusion Protein TTI-621 + - SIRPa-Fc-CD40L Fusion Protein SL-172154 + - SIRPa-IgG4-Fc Fusion Protein TTI-622 + - Sitimagene Ceradenovec + - Sitravatinib + - Sivifene + - Sizofiran + - SLC6A8 Inhibitor RGX-202 + - SLCT Inhibitor GNS561 + - SMAC Mimetic BI 891065 + - Smac Mimetic GDC-0152 + - Smac Mimetic GDC-0917 + - Smac Mimetic LCL161 + - SMO Protein Inhibitor ZSP1602 + - Smoothened Antagonist BMS-833923 + - Smoothened Antagonist LDE225 Topical + - Smoothened Antagonist LEQ506 + - Smoothened Antagonist TAK-441 + - SN-38-Loaded Polymeric Micelles NK012 + - SNS01-T Nanoparticles + - Sobuzoxane + - Sodium Borocaptate + - Sodium Butyrate + - Sodium Dichloroacetate + - Sodium Iodide I-131 + - Sodium Metaarsenite + - Sodium Phenylbutyrate + - Sodium Salicylate + - Sodium Selenite + - Sodium Stibogluconate + - Sodium-Potassium Adenosine Triphosphatase Inhibitor RX108 + - Sofituzumab Vedotin + - Solitomab + - Sonepcizumab + - Sonidegib + - Sonolisib + - Sorafenib + - Sorafenib Tosylate + - Sorghum bicolor Supplement + - Sotigalimab + - Sotorasib + - Sotrastaurin + - Sotrastaurin Acetate + - Soy Isoflavones + - Soy Protein Isolate + - Spanlecortemlocel + - Sparfosate Sodium + - Sparfosic Acid + - Spartalizumab + - Spebrutinib + - Spherical Nucleic Acid Nanoparticle NU-0129 + - Spirogermanium + - Spiromustine + - Spiroplatin + - Splicing Inhibitor H3B-8800 + - Spongistatin + - Squalamine Lactate + - SR-BP1/HSI Inhibitor SR31747A + - SR-T100 Gel + - Src Kinase Inhibitor AP 23846 + - Src Kinase Inhibitor KX2-391 + - Src Kinase Inhibitor KX2-391 Ointment + - Src Kinase Inhibitor M475271 + - Src/Abl Kinase Inhibitor AZD0424 + - Src/tubulin Inhibitor KX02 + - SRPK1/ABCG2 Inhibitor SCO-101 + - ssRNA-based Immunomodulator CV8102 + - SSTR2-targeting Protein/DM1 Conjugate PEN-221 + - St. John's Wort + - Stallimycin + - Staphylococcal Enterotoxin A + - Staphylococcal Enterotoxin B + - STAT Inhibitor OPB-111077 + - STAT3 Inhibitor DSP-0337 + - STAT3 Inhibitor OPB-31121 + - STAT3 Inhibitor OPB-51602 + - STAT3 Inhibitor TTI-101 + - STAT3 Inhibitor WP1066 + - Staurosporine + - STING Agonist BMS-986301 + - STING Agonist GSK3745417 + - STING Agonist IMSA101 + - STING Agonist MK-1454 + - STING Agonist SB 11285 + - STING Agonist TAK-676 + - STING-activating Cyclic Dinucleotide Agonist MIW815 + - STING-expressing E. coli SYNB1891 + - Streptonigrin + - Streptozocin + - Strontium Chloride Sr-89 + - Submicron Particle Paclitaxel Sterile Suspension + - Sugemalimab + - Sulfatinib + - Sulforaphane + - Sulindac + - Sulofenur + - Sumoylation Inhibitor TAK-981 + - Sunitinib + - Sunitinib Malate + - Super Enhancer Inhibitor GZ17-6.02 + - Superagonist Interleukin-15:Interleukin-15 Receptor alphaSu/Fc Fusion Complex ALT-803 + - Superoxide Dismutase Mimetic GC4711 + - Suramin + - Suramin Sodium + - Survivin Antigen + - Survivin Antigen Vaccine DPX-Survivac + - Survivin mRNA Antagonist EZN-3042 + - Survivin-expressing CVD908ssb-TXSVN Vaccine + - Sustained-release Lipid Inhaled Cisplatin + - Sustained-release Mitomycin C Hydrogel Formulation UGN-101 + - Sustained-release Mitomycin C Hydrogel Formulation UGN-102 + - Syk Inhibitor HMPL-523 + - Synchrotope TA2M Plasmid DNA Vaccine + - Synchrovax SEM Plasmid DNA Vaccine + - Synthetic Alkaloid PM00104 + - Synthetic Glioblastoma Mutated Tumor-specific Peptides Vaccine Therapy APVAC2 + - Synthetic Glioblastoma Tumor-associated Peptides Vaccine Therapy APVAC1 + - Synthetic hTERT DNA Vaccine INO-1400 + - Synthetic hTERT DNA Vaccine INO-1401 + - Synthetic Hypericin + - Synthetic Long E6 Peptide-Toll-like Receptor Ligand Conjugate Vaccine ISA201 + - Synthetic Long E6/E7 Peptides Vaccine HPV-01 + - Synthetic Long HPV16 E6/E7 Peptides Vaccine ISA101b + - Synthetic Plumbagin PCUR-101 + - T900607 + - Tabalumab + - Tabelecleucel + - Tacedinaline + - Tafasitamab + - Tagraxofusp-erzs + - Talabostat + - Talabostat Mesylate + - Talacotuzumab + - Talactoferrin Alfa + - Taladegib + - Talampanel + - Talaporfin Sodium + - Talazoparib + - Taletrectinib + - Talimogene Laherparepvec + - Tallimustine + - Talmapimod + - Talotrexin + - Talotrexin Ammonium + - Taltobulin + - TAM/c-Met Inhibitor RXDX-106 + - Tamibarotene + - Taminadenant + - Tamoxifen + - Tamoxifen Citrate + - Tamrintamab Pamozirine + - Tandutinib + - Tanespimycin + - Tanibirumab + - Tankyrase Inhibitor STP1002 + - Tanomastat + - Tapotoclax + - Tarenflurbil + - Tarextumab + - Tariquidar + - Tasadenoturev + - Taselisib + - Tasidotin + - Tasisulam + - Tasisulam Sodium + - Tasquinimod + - Taurolidine + - Tauromustine + - Taurultam + - Taurultam Analogue GP-2250 + - Tavokinogene Telseplasmid + - Tavolimab + - Taxane Analogue TPI 287 + - Taxane Compound + - Taxol Analogue SID 530 + - Tazarotene + - Tazemetostat + - Tebentafusp + - Teclistamab + - Tecogalan Sodium + - Tefinostat + - Tegafur + - Tegafur-gimeracil-oteracil Potassium + - Tegafur-Gimeracil-Oteracil Potassium-Leucovorin Calcium Oral Formulation + - Tegafur-Uracil + - Tegavivint + - Teglarinad + - Teglarinad Chloride + - Telaglenastat + - Telaglenastat Hydrochloride + - Telapristone + - Telapristone Acetate + - Telatinib Mesylate + - Telisotuzumab + - Telisotuzumab Vedotin + - Telomerase Inhibitor FJ5002 + - Telomerase-specific Type 5 Adenovirus OBP-301 + - Teloxantrone + - Teloxantrone Hydrochloride + - Telratolimod + - Temarotene + - Temoporfin + - Temozolomide + - Temsirolimus + - Tenalisib + - Tenifatecan + - Teniposide + - Tepoditamab + - Tepotinib + - Teprotumumab + - Terameprocol + - Terfluranol + - Tergenpumatucel-L + - Teroxirone + - Tertomotide + - Tesetaxel + - Tesevatinib + - Tesidolumab + - Testolactone + - Testosterone Enanthate + - Tetanus Toxoid Vaccine + - Tetradecanoylphorbol Acetate + - Tetrahydrouridine + - Tetraphenyl Chlorin Disulfonate + - Tetrathiomolybdate + - Tezacitabine + - Tezacitabine Anhydrous + - TGF-beta Receptor 1 Inhibitor PF-06952229 + - TGF-beta Receptor 1 Kinase Inhibitor SH3051 + - TGF-beta Receptor 1 Kinase Inhibitor YL-13027 + - TGFa-PE38 Immunotoxin + - TGFbeta Inhibitor LY3200882 + - TGFbeta Receptor Ectodomain-IgG Fc Fusion Protein AVID200 + - Thalicarpine + - Thalidomide + - Theliatinib + - Theramide + - Therapeutic Angiotensin-(1-7) + - Therapeutic Breast/Ovarian/Prostate Peptide Cancer Vaccine DPX-0907 + - Therapeutic Cancer Vaccine ATP128 + - Therapeutic Estradiol + - Therapeutic Hydrocortisone + - Therapeutic Liver Cancer Peptide Vaccine IMA970A + - Thiarabine + - Thiodiglycol + - Thioguanine + - Thioguanine Anhydrous + - Thioinosine + - Thioredoxin-1 Inhibitor PX-12 + - Thiotepa + - Thioureidobutyronitrile + - THL-P + - Thorium Th 227 Anetumab + - Thorium Th 227 Anetumab Corixetan + - Thorium Th 227 Anti-HER2 Monoclonal Antibody BAY2701439 + - Thorium Th 227 Anti-PSMA Monoclonal Antibody BAY 2315497 + - Threonine Tyrosine Kinase Inhibitor CFI-402257 + - Thymidylate Synthase Inhibitor CX1106 + - Thymidylate Synthase Inhibitor DFP-11207 + - Thymopentin + - Thyroid Extract + - Tiazofurin + - Tidutamab + - Tigapotide + - Tigatuzumab + - TIGIT Inhibitor M6223 + - TIGIT-targeting Agent MK-7684 + - Tilarginine + - Tilogotamab + - Tilsotolimod Sodium + - Timonacic + - Tin Ethyl Etiopurpurin + - Tinostamustine + - Tinzaparin Sodium + - Tiomolibdate Choline + - Tiomolibdate Diammonium + - Tipapkinogene Sovacivec + - Tipifarnib + - Tipiracil + - Tipiracil Hydrochloride + - Tirabrutinib + - Tiragolumab + - Tirapazamine + - Tirbanibulin + - Tisagenlecleucel + - Tislelizumab + - Tisotumab Vedotin + - Tivantinib + - Tivozanib + - TLC ELL-12 + - TLR Agonist BDB001 + - TLR Agonist BSG-001 + - TLR Agonist CADI-05 + - TLR-Directed Cationic Lipid-DNA Complex JVRS-100 + - TLR7 Agonist 852A + - TLR7 agonist BNT411 + - TLR7 Agonist LHC165 + - TLR7/8/9 Antagonist IMO-8400 + - TLR8 Agonist DN1508052 + - TLR9 Agonist AST-008 + - TM4SF1-CAR/EpCAM-CAR-expressing Autologous T Cells + - Tocilizumab + - Tocladesine + - Tocotrienol + - Tocotrienol-rich Fraction + - Tolebrutinib + - Toll-like Receptor 7 Agonist DSP-0509 + - Tolnidamine + - Tomaralimab + - Tomato-Soy Juice + - Tomivosertib + - Topical Betulinic Acid + - Topical Celecoxib + - Topical Fluorouracil + - Topical Gemcitabine Hydrochloride + - Topical Potassium Dobesilate + - Topical Trichloroacetic Acid + - Topixantrone + - Topoisomerase I Inhibitor Genz-644282 + - Topoisomerase I Inhibitor LMP400 + - Topoisomerase I Inhibitor LMP776 + - Topoisomerase I/II Inhibitor NEV-801 + - Topoisomerase-1 Inhibitor LMP744 + - Topoisomerase-II Inhibitor Racemic XK469 + - Topoisomerase-II-beta Inhibitor Racemic XK469 + - Topotecan + - Topotecan Hydrochloride + - Topotecan Hydrochloride Liposomes + - Topotecan Sustained-release Episcleral Plaque + - Topsalysin + - TORC1/2 Kinase Inhibitor DS-3078a + - Toremifene + - Toremifene Citrate + - Toripalimab + - Tosedostat + - Tositumomab + - Total Androgen Blockade + - Tovetumab + - Tozasertib Lactate + - TP40 Immunotoxin + - Trabectedin + - Trabedersen + - TRAIL Receptor Agonist ABBV-621 + - Trametinib + - Trametinib Dimethyl Sulfoxide + - Trans Sodium Crocetinate + - Transdermal 17beta-Estradiol Gel BHR-200 + - Transdermal 4-Hydroxytestosterone + - Transferrin Receptor-Targeted Anti-RRM2 siRNA CALAA-01 + - Transferrin Receptor-Targeted Liposomal p53 cDNA + - Transferrin-CRM107 + - Tranylcypromine Sulfate + - Trapoxin + - Trastuzumab + - Trastuzumab Conjugate BI-CON-02 + - Trastuzumab Deruxtecan + - Trastuzumab Duocarmazine + - Trastuzumab Emtansine + - Trastuzumab Monomethyl Auristatin F + - Trastuzumab-TLR 7/8 Agonist BDC-1001 + - Trastuzumab/Hyaluronidase-oysk + - Trastuzumab/Tesirine Antibody-drug Conjugate ADCT-502 + - Trebananib + - Tremelimumab + - Treosulfan + - Tretazicar + - Tretinoin + - Tretinoin Liposome + - Triamcinolone Acetonide + - Triamcinolone Hexacetonide + - Triapine + - Triazene Derivative CB10-277 + - Triazene Derivative TriN2755 + - Triazinate + - Triaziquone + - Tributyrin + - Triciribine Phosphate + - Trientine Hydrochloride + - Triethylenemelamine + - Trifluridine + - Trifluridine and Tipiracil Hydrochloride + - Trigriluzole + - Trilaciclib + - Trimelamol + - Trimeric GITRL-Fc OMP-336B11 + - Trimethylcolchicinic Acid + - Trimetrexate + - Trimetrexate Glucuronate + - Trioxifene + - Triplatin Tetranitrate + - Triptolide Analog + - Triptorelin + - Triptorelin Pamoate + - Tris-acryl Gelatin Microspheres + - Tritylcysteine + - TRK Inhibitor AZD6918 + - TRK Inhibitor TQB3558 + - TrkA Inhibitor VMD-928 + - Trodusquemine + - Trofosfamide + - Troglitazone + - Tropomyosin Receptor Kinase Inhibitor AZD7451 + - Troriluzole + - Troxacitabine + - Troxacitabine Nucleotide Prodrug MIV-818 + - TRPM8 Agonist D-3263 + - TRPV6 Calcium Channel Inhibitor SOR-C13 + - TSP-1 Mimetic ABT-510 + - TSP-1 Mimetic Fusion Protein CVX-045 + - Tubercidin + - Tubulin Binding Agent TTI-237 + - Tubulin Inhibitor ALB 109564 Dihydrochloride + - Tubulin Inhibitor ALB-109564 + - Tubulin Polymerization Inhibitor AEZS 112 + - Tubulin Polymerization Inhibitor CKD-516 + - Tubulin Polymerization Inhibitor VERU-111 + - Tubulin-Binding Agent SSR97225 + - Tucatinib + - Tucidinostat + - Tucotuzumab Celmoleukin + - Tyroserleutide + - Tyrosinase Peptide + - Tyrosinase-KLH + - Tyrosinase:146-156 Peptide + - Tyrosine Kinase Inhibitor + - Tyrosine Kinase Inhibitor OSI-930 + - Tyrosine Kinase Inhibitor SU5402 + - Tyrosine Kinase Inhibitor TL-895 + - Tyrosine Kinase Inhibitor XL228 + - UAE Inhibitor TAK-243 + - Ubenimex + - Ubidecarenone Nanodispersion BPM31510n + - Ublituximab + - Ulinastatin + - Ulixertinib + - Ulocuplumab + - Umbralisib + - Uncaria tomentosa Extract + - Upamostat + - Upifitamab + - Uproleselan + - Uprosertib + - Urabrelimab + - Uracil Ointment + - Urelumab + - Uroacitides + - Urokinase-Derived Peptide A6 + - Ursolic Acid + - USP14/UCHL5 Inhibitor VLX1570 + - Utomilumab + - Uzansertib + - V930 Vaccine + - Vaccine-Sensitized Draining Lymph Node Cells + - Vaccinium myrtillus/Macleaya cordata/Echinacea angustifolia Extract Granules + - Vactosertib + - Vadacabtagene Leraleucel + - Vadastuximab Talirine + - Vadimezan + - Valecobulin + - Valemetostat + - Valproic Acid + - Valrubicin + - Valspodar + - Vandetanib + - Vandetanib-eluting Radiopaque Bead BTG-002814 + - Vandortuzumab Vedotin + - Vantictumab + - Vanucizumab + - Vapreotide + - Varlilumab + - Varlitinib + - Varlitinib Tosylate + - Vascular Disrupting Agent BNC105 + - Vascular Disrupting Agent BNC105P + - Vascular Disrupting Agent ZD6126 + - Vatalanib + - Vatalanib Succinate + - Vecabrutinib + - Vector-peptide Conjugated Paclitaxel + - Vedolizumab + - VEGF Inhibitor PTC299 + - VEGF/HGF-targeting DARPin MP0250 + - VEGFR Inhibitor KRN951 + - VEGFR-2 DNA Vaccine VXM01 + - VEGFR/FGFR Inhibitor ODM-203 + - VEGFR/PDGFR Tyrosine Kinase Inhibitor TAK-593 + - VEGFR2 Tyrosine Kinase Inhibitor PF-00337210 + - VEGFR2/PDGFR/c-Kit/Flt-3 Inhibitor SU014813 + - Veliparib + - Veltuzumab + - Vemurafenib + - Venetoclax + - Verapamil + - Verpasep Caltespen + - Verubulin + - Verubulin Hydrochloride + - Vesencumab + - Vesigenurtucel-L + - VGEF Mixed-Backbone Antisense Oligonucleotide GEM 220 + - VGEFR/c-kit/PDGFR Tyrosine Kinase Inhibitor XL820 + - Viagenpumatucel-L + - Vibecotamab + - Vibostolimab + - Vilaprisan + - Vinblastine + - Vinblastine Sulfate + - Vincristine + - Vincristine Liposomal + - Vincristine Sulfate + - Vincristine Sulfate Liposome + - Vindesine + - Vinepidine + - Vinflunine + - Vinflunine Ditartrate + - Vinfosiltine + - Vinorelbine + - Vinorelbine Tartrate + - Vinorelbine Tartrate Emulsion + - Vinorelbine Tartrate Oral + - Vintafolide + - Vinzolidine + - Vinzolidine Sulfate + - Virulizin + - Vismodegib + - Vistusertib + - Vitamin D3 Analogue ILX23-7553 + - Vitamin E Compound + - Vitespen + - VLP-encapsulated TLR9 Agonist CMP-001 + - Vocimagene Amiretrorepvec + - Vofatamab + - Volasertib + - Volociximab + - Vonlerolizumab + - Vopratelimab + - Vorasidenib + - Vorinostat + - Vorolanib + - Vorsetzumab Mafodotin + - Vosaroxin + - Vosilasarm + - Voxtalisib + - Vulinacimab + - Warfarin Sodium + - Wee1 Inhibitor ZN-c3 + - Wee1 Kinase Inhibitor Debio 0123 + - White Carrot + - Wnt Signaling Inhibitor SM04755 + - Wnt Signaling Pathway Inhibitor SM08502 + - Wnt-5a Mimic Hexapeptide Foxy-5 + - Wobe-Mugos E + - WT1 Peptide Vaccine OCV-501 + - WT1 Peptide Vaccine WT2725 + - WT1 Protein-derived Peptide Vaccine DSP-7888 + - WT1-A10/AS01B Immunotherapeutic GSK2130579A + - WT1/PSMA/hTERT-encoding Plasmid DNA INO-5401 + - Xanthohumol + - XBP1-US/XBP1-SP/CD138/CS1 Multipeptide Vaccine PVX-410 + - Xeloda + - Xentuzumab + - Xevinapant + - Xiaoai Jiedu Decoction + - XIAP Antisense Oligonucleotide AEG35156 + - XIAP/cIAP1 Antagonist ASTX660 + - Xiliertinib + - Xisomab 3G3 + - XPO1 Inhibitor SL-801 + - Y 90 Monoclonal Antibody CC49 + - Y 90 Monoclonal Antibody HMFG1 + - Y 90 Monoclonal Antibody Lym-1 + - Y 90 Monoclonal Antibody m170 + - Y 90 Monoclonal Antibody M195 + - Yang Yin Fu Zheng + - Yangzheng Xiaoji Extract + - Yiqi-yangyin-jiedu Herbal Decoction + - Yttrium Y 90 Anti-CD19 Monoclonal Antibody BU12 + - Yttrium Y 90 Anti-CD45 Monoclonal Antibody AHN-12 + - Yttrium Y 90 Anti-CD45 Monoclonal Antibody BC8 + - Yttrium Y 90 Anti-CDH3 Monoclonal Antibody FF-21101 + - Yttrium Y 90 Anti-CEA Monoclonal Antibody cT84.66 + - Yttrium Y 90 Basiliximab + - Yttrium Y 90 Colloid + - Yttrium Y 90 Daclizumab + - Yttrium Y 90 DOTA Anti-CEA Monoclonal Antibody M5A + - Yttrium Y 90 Glass Microspheres + - Yttrium Y 90 Monoclonal Antibody B3 + - Yttrium Y 90 Monoclonal Antibody BrE-3 + - Yttrium Y 90 Monoclonal Antibody Hu3S193 + - Yttrium Y 90 Monoclonal Antibody MN-14 + - Yttrium Y 90 Resin Microspheres + - Yttrium Y 90 Tabituximab Barzuxetan + - Yttrium Y 90-DOTA-Biotin + - Yttrium Y 90-DOTA-di-HSG Peptide IMP-288 + - Yttrium Y 90-Edotreotide + - Yttrium Y 90-labeled Anti-FZD10 Monoclonal Antibody OTSA101 + - Yttrium Y-90 Clivatuzumab Tetraxetan + - Yttrium Y-90 Epratuzumab Tetraxetan + - Yttrium Y-90 Ibritumomab Tiuxetan + - Yttrium Y-90 Tacatuzumab Tetraxetan + - Yttrium-90 Polycarbonate Brachytherapy Plaque + - Z-Endoxifen Hydrochloride + - Zalcitabine + - Zalifrelimab + - Zalutumumab + - Zandelisib + - Zanidatamab + - Zanolimumab + - Zanubrutinib + - Zebularine + - Zelavespib + - Zibotentan + - Zinc Finger Nuclease ZFN-603 + - Zinc Finger Nuclease ZFN-758 + - Zinostatin + - Zinostatin Stimalamer + - Zirconium Zr 89 Panitumumab + - Ziv-Aflibercept + - Zolbetuximab + - Zoledronic Acid + - Zoptarelin Doxorubicin + - Zorifertinib + - Zorubicin + - Zorubicin Hydrochloride + - Zotatifin + - Zotiraciclib Citrate + - Zuclomiphene Citrate + - Unknown + - Not Reported + #genomic_info + genomic_info_id: + Desc: Genomic info identifier, the ID property for the ndoe genomic_info. + Type: string + Req: true + Key: true + reference_genome_assembly: + Desc: Accession or name of genome reference or assembly used for alignment + Enum: + - GRCh37 + - GRCh37-lite + - GRCh38 + Req: Preferred + avg_read_length: + Desc: Average sequence read length + Type: number + Req: Preferred + coverage: + Desc: Average depth of coverage on reference used + Type: number + Req: Preferred + bases: + Desc: Total number of unique bases read + Type: integer + Req: Preferred + number_of_reads: + Desc: Total number of reads performed + Type: integer + Req: Preferred + design_description: + Desc: Human-readable description of methods used to create sequencing library + Type: string + Req: Preferred + platform: + Desc: Instrument platform or manufacturer + Req: Preferred + Enum: + - LS454 + - ILLUMINA + - HELICOS + - ABI_SOLID + - COMPLETE_GENOMICS + - PACBIO_SMRT + - ION_TORRENT + - CAPILLARY + - OXFORD_NANOPORE + - BGISEQ + - Illumina HiSeq 2500 + - Illumina HiSeq X Ten + - Illumina Next Seq 500 + - Illumina Next Seq 550 + - Illumina NextSeq + - Illumina NovaSeq 6000 + - NovaSeqS4 + instrument_model: + Desc: Instrument model + Req: Preferred + Enum: + - 454 GS + - 454 GS 20 + - 454 GS FLX + - 454 GS FLX+ + - 454 GS FLX Titanium + - 454 GS Junior + - HiSeq X Five + - HiSeq X Ten + - Illumina Genome Analyzer + - Illumina Genome Analyzer II + - Illumina Genome Analyzer IIx + - Illumina HiScanSQ + - Illumina HiSeq + - Illumina HiSeq 1000 + - Illumina HiSeq 1500 + - Illumina HiSeq 2000 + - Illumina HiSeq 2500 + - Illumina HiSeq 3000 + - Illumina HiSeq 4000 + - Illumina iSeq 100 + - Illumina NovaSeq 6000 + - llumina NovaSeq + - Illumina MiniSeq + - Illumina MiSeq + - Illumina NextSeq + - NextSeq 500 + - NextSeq 550 + - Helicos HeliScope + - AB 5500 Genetic Analyzer + - AB 5500xl Genetic Analyzer + - AB 5500x-Wl Genetic Analyzer + - AB SOLiD 3 Plus System + - AB SOLiD 4 System + - AB SOLiD 4hq System + - AB SOLiD PI System + - AB SOLiD System + - AB SOLiD System 2.0 + - AB SOLiD System 3.0 + - Complete Genomics + - PacBio RS + - PacBio RS II + - PacBio Sequel + - PacBio Sequel II + - Ion Torrent PGM + - Ion Torrent Proton + - Ion Torrent S5 XL + - Ion Torrent S5 + - 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 + - GridION + - MinION + - PromethION + - BGISEQ-500 + - DNBSEQ-G400 + - DNBSEQ-T7 + - DNBSEQ-G50 + - MGISEQ-2000RS + library_id: + Desc: Library identifier as submitted by requestor + Type: string + library_layout: + Desc: Library layout as submitted by requestor + Req: Preferred + Enum: + - Paired-end + - Single-end + - Single-indexed + library_source: + Desc: Source material used to create library + Req: Preferred + Enum: + - Genomic + - Transcriptomic + - Metagenomic + - Metatranscriptomic + - Synthetic + - Viral RNA + - Genomic Single Cell + - Single Nucleus + - Transcriptomic Single Cell + - Other + - Bulk Whole Cell + - Single Cell + library_selection: + Desc: Library selection method + Req: Preferred + Enum: + - Hybrid Selection + - other + - PCR + - Poly-T Enrichment + - PolyA + - Random + - 5-methylcytidine antibody + - CAGE + - cDNA + - cDNA_oligo_dT + - cDNA_randomPriming + - CF-H + - CF-M + - CF-S + - CF-T + - ChIP + - DNAse + - HMPR + - Inverse rRNA + - MBD2 protein methyl-CpG binding domain + - MDA + - MF + - MNase + - MSLL + - Oligo-dT + - Padlock probes capture method + - Race + - Random PCR + - Reduced Representation + - repeat fractionation + - Restriction Digest + - RT-PCR + - size fractionation + - unspecified + library_strategy: + Desc: Nucleic acid capture or processing strategy for this library + Req: Preferred + Enum: + - AMPLICON + - ATAC-seq + - Bisulfite-Seq + - ChIA-PET + - ChIP-Seq + - CLONE + - CLONEEND + - CTS + - DNase-Hypersensitivity + - 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 + - SELEX + - ssRNA-seq + - Synthetic-Long-Read + - Targeted-Capture + - Tethered Chromatin Conformation Capture + - Tn-Seq + - WCS + - WGA + - WGS + - WXS + sequence_alignment_software: + Desc: Name of software program used to align nucleotide sequence data + Type: string + Req: Preferred + custom_assembly_fasta_file_for_alignment: + Desc: File name of any custom assembly fasta file used during alignment + Type: string + Req: Preferred + + # cds requestor + cds_requestor: + Desc: Identifies the user requesting storage in CDS + Type: string + data_types: + Desc: Data types for storage + Type: + value_type: list + item_type: string + file_types: + Desc: File types for storage + Type: + value_type: list + item_type: string + funding_agency: + Desc: Funding agency of the requestor study + Type: string + Req: 'Preferred' + funding_source_program_name: + Desc: The funding source organization/sponsor + Type: string + Req: 'Preferred' + grant_id: + Desc: Grant or contract identifier + Type: string + Req: 'Preferred' + clinical_trial_system: + Desc: | + Organization that provides clinical trial identifier (if study + is a clinical trial) + Type: string + clinical_trial_identifier: + Desc: | + Study identifier in the given clinical trial system + Type: string + clinical_trial_arm: + Desc: Arm of clinical trial, if appropriate + Type: string + organism_species: + Desc: Species binomial of study participants + Type: string + Req: Preferred + adult_or_childhood_study: + Desc: Study participants are adult, pediatric, or other + Req: Preferred + Enum: + - Adult + - Pediatric + specimen_id: + Desc: Identifier for specimen (parent of sample) as provided by requestor + Type: string + Key: true + number_of_participants: + Desc: How many participants in the study + Type: number + Req: 'Yes' + number_of_samples: + Desc: How many total samples in the study + Type: number + Req: 'Yes' + file_types_and_format: + Desc: | + Specific kinds of files in the dataset that will be uploaded to CDS + Type: + value_type: list + item_type: string + Req: 'Yes' + size_of_data_being_uploaded: + Desc: Size of the data being uploaded to CDS + Type: + value_type: number + units: [ 'GB', 'TB', 'PB' ] + Req: Preferred + + # program props + program_acronym: + Desc: The name of the program under which related studies will be grouped, expressed in the form of the acronym by which it will identified within the UI.
This property is used as the key via which study records can be associated with the appropriate program during data loading, and to identify the correct records during data updates. + Src: Internally-curated + Type: string + Req: 'Yes' + Key: true + program_external_url: + Desc: The external url to which users should be directed in order to learn more about the program. + Src: Internally-curated + Type: string + Req: Preferred + program_full_description: + Desc: A more detailed, multiple sentence description of the program. + Src: Internally-curated + Type: string + Req: Preferred + program_name: + Desc: The name of the program under which related studies will be grouped, in full text and unabbreviated form, exactly as it will be displayed within the UI. + Src: Internally-curated + Type: string + Req: 'Yes' + program_short_description: + Desc: An abbreviated, single sentence description of the program. + Src: Internally-curated + Type: string + Req: Preferred + program_sort_order: + Desc: An arbitrarily-assigned value used to dictate the order in which programs are displayed within the application's UI. + Src: Internally-curated + Type: integer + Req: 'No' + institution: + Desc: TBD + Type: String + Req: Preferred \ No newline at end of file diff --git a/3-Model-Files/cds-model.yml b/3-Model-Files/cds-model.yml new file mode 100644 index 0000000..c21fa0c --- /dev/null +++ b/3-Model-Files/cds-model.yml @@ -0,0 +1,345 @@ +Handle: CDS +Version: v2.1.0 +Nodes: + program: + Desc: "Program in the Cancer Data Service refer to a broad framework of goals under which related projects or other research activities are grouped. Example - Clinical Proteomic Tumor Analysis Consortium (CPTAC)" + Tags: + Category: study + Assignment: core + Class: primary + Template: 'Yes' + Props: + - program_name + - program_acronym + - program_short_description + - program_full_description + - program_external_url + - program_sort_order + - institution + - crdc_id + + study: + Desc: "The narrative title used as a textual label for a research data collection. Example – University of Texas PDX Development and Trial Center Grant" + Tags: + Category: study + Assignment: core + Class: primary + Template: 'Yes' + Props: + - study_name + - study_acronym + - study_description + - short_description + - study_external_url + - primary_investigator_name + - primary_investigator_email + - co_investigator_name + - co_investigator_email + - phs_accession + - bioproject_accession + - index_date # what are relative dates relative to? dx date, collection date, etc. + - cds_requestor + - funding_agency + - funding_source_program_name + - grant_id + - clinical_trial_system + - clinical_trial_identifier + - clinical_trial_arm + - organism_species + - adult_or_childhood_study # adult, pediatric + - data_types # list from enumerated values + - file_types # list from enumerated values + - data_access_level + - cds_primary_bucket + - cds_secondary_bucket + - cds_tertiary_bucket + - number_of_participants + - number_of_samples + - study_data_types + - file_types_and_format + - size_of_data_being_uploaded + - acl + - study_access + - authz + - study_version + - crdc_id + + participant: + Desc: "Individual who takes part in the study" + Tags: + Category: study + Assignment: core + Class: primary + Template: 'Yes' + Props: + - study_participant_id + - participant_id + - race + - gender + - ethnicity + # - vital_status + - dbGaP_subject_id + - crdc_id + + diagnosis: # may have multiple dxs for multiple timepoints? + Desc: "Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O)." + Tags: + Category: case + Assignment: core + Class: primary + Template: 'Yes' + Props: + - study_diagnosis_id + - diagnosis_id + - disease_type + - vital_status + - primary_diagnosis + - primary_site + - age_at_diagnosis + - tumor_grade + - tumor_stage_clinical_m + - tumor_stage_clinical_n + - tumor_stage_clinical_t + - morphology + - incidence_type # primary, metastatic, recurrence, progression + - progression_or_recurrence + - days_to_recurrence + - days_to_last_followup + - last_known_disease_status + - days_to_last_known_status + - crdc_id + + treatment: + Desc: "An action or administration of therapeutic agents to produce an effect that is intended to alter the course of a pathologic process." + Tags: + Category: case + Assignment: core + Class: secondary + Template: 'No' + Props: + - treatment_id + - treatment_type + - treatment_outcome + - days_to_treatment + - therapeutic_agents + - crdc_id + + sample: # aka subspecimen (CMB) + Desc: "An action or administration of therapeutic agents to produce an effect that is intended to alter the course of a pathologic process." + Tags: + Category: case + Assignment: core + Class: primary + Template: 'Yes' + Props: + - sample_id + - sample_type + - sample_tumor_status # tumor or normal + - sample_anatomic_site + - sample_age_at_collection + - derived_from_specimen + - biosample_accession + - crdc_id + + file: + Desc: "A set of related records kept together provided by a submitter." + Tags: + Category: data_file + Assignment: core + Class: primary + Template: 'Yes' + Props: + - file_id + - file_name + - file_type + - file_description + - file_size + - md5sum + - file_url_in_cds + - experimental_strategy_and_data_subtypes + - submission_version + - crdc_id + #- file_access + + genomic_info: + Desc: "In CDS genomic info refers to the sequencing methodsm techniques and equipment." + Tags: + Category: data_file + Assignment: core + Class: primary + Template: 'Yes' + Props: + - genomic_info_id + - library_id + - bases + - number_of_reads + - avg_read_length + - coverage + - reference_genome_assembly + - custom_assembly_fasta_file_for_alignment + - design_description + - library_strategy + - library_layout + - library_source + - library_selection + - platform + - instrument_model + - sequence_alignment_software + - crdc_id + + image: + Tags: + Category: data_file + Assignment: core + Class: primary + Template: 'Yes' + Desc: "The imaging data from DICOM and non-DICOM standards into CDS." + Props: + - study_link_id + - de_identification_method_type + - de_identification_method_description + - de_identification_software + - license + - citation_or_DOI + - species + - image_modality + - imaging_equipment_manufacturer + - imaging_equipment_model + - imaging_sofware + - imaging_protocol + - organ_or_tissue + - performed_imaging_study_description + - performed_imaging_study_admittingDiagnosisCode + - performed_imaging_study_nonAcquisitionModalitiesInStudyCode + - performed_imaging_study_lossyImageCompressionIndicator + - performed_imaging_study_summary + - performed_imaging_study_primaryAnatomicSiteCode + - performed_imaging_study_acquisitionTypeCode + - performed_imaging_study_imageTypeCode + - performed_imaging_study_cardiacSynchronizationTechniqueCode + - performed_imaging_study_dataCollectionDiameter + - performed_imaging_study_respiratoryMotionTechniqueCode + - performed_imaging_study_bodyPositionCode + - performed_imaging_study_typeCode + - performed_imaging_study_algorithmCode + - performed_imaging_study_reconstructionFieldOfViewHeight + - performed_imaging_study_reconstructionFieldOfViewWidth + - performed_imaging_study_reconstructionDiameter + - performed_imaging_study_sliceThickness + - performed_imaging_study_reconstructionInterval + - longitudinal_temporal_event_type + - longitudinal_temporal_event_offset + - CTAquisitionProtocolElement_singleCollimationWidth + - CTAquisitionProtocolElement_totalCollimationWidth + - CTAquisitionProtocolElement_gantryDetectorTilt + - CTAquisitionProtocolElement_tableSpeed + - CTAquisitionProtocolElement_spiralPitchFactor + - CTAquisitionProtocolElement_ctdiVol + - CTAquisitionProtocolElement_ctdiPhantomTypeCode + - CTAquisitionProtocolElement_kVp + - CTAquisitionProtocolElement_exposureModulationType_Code + - CTImageReconstructionProtocolElement_convolutionKernel + - CTImageReconstructionProtocolElement_convolutionKernelGroupCode + - MRImageAcquisitionProtocolElement_echoPulseSequenceCategoryCode + - MRImageAcquisitionProtocolElement_diffusionBValue + - MRImageAcquisitionProtocolElement_diffusionDirectionalityCode + - MRImageAcquisitionProtocolElement_magneticFieldStrength + - MRImageAcquisitionProtocolElement_resonantNucleusCode + - MRImageAcquisitionProtocolElement_acquisitionContrastCode + - MRImageAcquisitionProtocolElement_inversionRecoveryIndicator + - MRImageAcquisitionProtocolElement_pulseSequenceName + - MRImageAcquisitionProtocolElement_multipleSpinEchoIndicator + - MRImageAcquisitionProtocolElement_phaseContrastIndicator + - MRImageAcquisitionProtocolElement_timeOfFlightContrastIndicator + - MRImageAcquisitionProtocolElement_arterialSpinLabelingContrastCode + - MRImageAcquisitionProtocolElement_steadyStatePulseSequenceCode + - MRImageAcquisitionProtocolElement_echoPlanarPulseSequenceIndicator + - MRImageAcquisitionProtocolElement_saturationRecoveryIndicator + - MRImageAcquisitionProtocolElement_spectrallySelectedSuppressionCode + - MRImageReconstructionProtocolElement_complexImageComponentCode + - PETImagingAcquisitionProtocolElement_gantryDetectorTilt + - Radiopharmaceutical_radionuclideCode + - acquisition_method_type + - tumor_tissue_type + - tissue_fixative + - embedding_medium + - staining_method + - objective + - nominal_magnification + - immersion + - lens_numerical_aperture + - working_distance + - imaging_assay_type + - pyramid + - physical_size_x + - physical_size_y + - physical_size_z + - size_c + - size_t + - size_x + - size_y + - size_z + - channel_metadata_filename + - channel_metadata_file_url_in_cds + - channel_id + - channel_name + - cycle_number + - sub_cycle_number + - target_name + - antibody_name + - rrid_identifier + - fluorophore + - clone + - lot + - vendor + - catalog_number + - excitation_wavelength + - emission_wavelength + - excitation_bandwidth + - emission_bandwidth + - metal_isotope_element + - oligo_barcode_upper_strand + - oligo_barcode_lower_strand + - diluation + - concentration + - passes_qc + - crdc_id + +Relationships: + of_program: + Props: null + Mul: many_to_one + Ends: + - Src: study + Dst: program + of_study: + Props: null + Mul: many_to_one + Ends: + - Src: participant + Dst: study + - Src: file + Dst: study + of_participant: + Props: null + Mul: many_to_one + Ends: + - Src: diagnosis + Dst: participant + - Src: sample + Dst: participant + from_sample: + Props: null + Mul: many_to_many + Ends: + - Src: file + Dst: sample + of_file: + Props: null + Mul: many_to_one + Ends: + - Src: genomic_info + Dst: file + - Src: image + Dst: file + Mul: one_to_one \ No newline at end of file diff --git a/4-Transformed-Data-Files/.placeholder b/4-Transformed-Data-Files/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/4-Transformed-Data-Files/cds_transformed_data_files_v1.2/.placeholder b/4-Transformed-Data-Files/cds_transformed_data_files_v1.2/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/4-Transformed-Data-Files/cds_transformed_data_files_v1.3/.placeholder b/4-Transformed-Data-Files/cds_transformed_data_files_v1.3/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/5-ID-Validation-Result/.placeholder b/5-ID-Validation-Result/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/README.md b/README.md index 386274c..c002c16 100644 --- a/README.md +++ b/README.md @@ -1 +1,18 @@ -# data-transformation \ No newline at end of file +# cds-etl transformation script +Code to transform CDS data.
+To run the python script for transforming CDS data, the user should first place the raw CDS data file in the s3 bucket
+```python3 cds-transformation.py cds_config_example.yaml```
+To run the python script for transforming CDS data with the data format v1.2, the user should first place all the raw CDS data files in ./0-Raw-Data-Files/cds_raw_data_files_v1.2 folder than use the command to extrat raw data dictionary
+```python3 1-Transformation-Scripts/cds-transformation_v1.2.py --config_file 2-Config-Files/cds_config_v1.2/cds_config_example_v1.2.yaml --extract_raw_data_dictionary```
+After extracting the raw data dictionary, the user can use the command to transform raw data.
+```python3 1-Transformation-Scripts/cds-transformation_v1.2.py --config_file 2-Config-Files/cds_config_v1.2/cds_config_example_v1.2.yaml```
+If the user want to upload the transformed data to the s3 folder, the user can use the command below.
+```python3 1-Transformation-Scripts/cds-transformation_v1.2.py --config_file 2-Config-Files/cds_config_v1.2/cds_config_example_v1.2.yaml --upload_s3```
+To run the python script for transforming CDS data with the data format v1.3, the user should first place all the raw CDS data files in ./0-Raw-Data-Files/cds_raw_data_files_v1.3 folder than use the command
+```python3 1-Transformation-Scripts/cds-transformation_v1.3.py --config_file 2-Config-Files/cds_config_v1.3/cds_config_example_v1.3.yaml --extract_raw_data_dictionary```
+After extracting the raw data dictionary, the user can use the command to transform raw data.
+```python3 1-Transformation-Scripts/cds-transformation_v1.3.py --config_file 2-Config-Files/cds_config_v1.3/cds_config_example_v1.3.yaml```
+If the user want to download data from s3, the user can use the command to transform raw data.
+```python3 1-Transformation-Scripts/cds-transformation_v1.3.py --config_file 2-Config-Files/cds_config_v1.3/cds_config_example_v1.3.yaml --download_s3```
+If the user want to upload the transformed data to the s3 folder, the user can use the command below.
+```python3 1-Transformation-Scripts/cds-transformation_v1.3.py --config_file 2-Config-Files/cds_config_v1.3/cds_config_example_v1.3.yaml --upload_s3```
diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..4f77031 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,6 @@ +pyyaml +pandas +numpy +openpyxl +boto3 +openai \ No newline at end of file