Clinical data

Those files are potentially common to all modalities

Patient-level clinical data

• Objective of the file: for clinical info, demographics, staging, survival

• Requirements:

• Named clinical_data_table

• In parquet format

• patient_id as primary key

• Contains the mandatory columns in the table below

• File columns & description:

Name	Type	Mandatory	Description
patient_id	str	TRUE	Patient identifier. There can be mutliple bk_sample_id for one patient_id.
indication	str	FALSE

Example of clinical columns currently used by K columns:

'alcohol_intake',
 'smoking_status',
 'pfs_years',
 'pfs_event',
 'cancer_stage',
 'beta_2_microglobulin_level',
 'cd10_ihc_positive',
 'largest_diameter_of_the_primary_tumor',
 'ldh_level',
 'menopause_status',
 'metastatic_status',
 'treatment_path',
 'has_received_chemotherapy',
 'chemotherapy_best_response',
 'chemotherapy_treatment_line',
 'chemotherapy_treatment_setting',

Sample level metadata: sample_metadata_table

• Objective of the file: Contains sample-to-patient mapping, tissue type

• Example format: sample_metadata_table.parquet

• Requirements:

• Named sample_metadata_table

• In parquet format

• sample_id as primary key

• Contains the mandatory columns in the table below

• File columns & description:

Name	Type	Mandatory	Description
sample_id	str	TRUE	Sample identifier
patient_id	str	TRUE	Patient identifier. Maps to the linked clinical data file. There can be mutliple bk_sample_id for one patient_id.
sample_tissue	str	FALSE	Example values: 'Testis', 'Colon', 'Kidney'
histo_sample_type	str	FALSE	Example values: 'recurrent tumor', 'primary tumor', 'tumor'
sample_label	str	FALSE	Example values: 'Category_1', 'Category_2', 'Category_3', 'Category_4', 'Category_5'

Mutation metadata

• Objective of the file: Contains variant classification for genes per patient

• Example format: mutation_table.parquet

• Requirements:

• Named mutation_table

• In parquet format

• patient_id ; gene_nameas primary keys

• Contains the mandatory columns in the table below

• File columns & description:

Name	Type	Mandatory	Description
patient_id	str	TRUE	Patient identifier. Maps to the linked clinical data file. There can be mutliple bk_sample_id for one patient_id.
gene_name	str	TRUE	Patient identifier. Maps to the linked clinical data file. There can be mutliple bk_sample_id for one patient_id.
is_mutated	bool	TRUE
HGVSp_Short	str	?	the HGVS coding sequence name mapped as categories
HGVSc	str	?	the HGVS protein sequence name mapped as categories
Variant_Classification	str	?