In the sample list, click on add sample and select External files (CSV or XLSX)
Download our XLSX or CSV template
Open the XLSX file with Excel or the CSV file with LibreOffice
Encode the file
Good to know
One row by sample
No case sensitivity, you can use lowercase and uppercase.
Do not delete nor edit the headers of the columns.
If you have already created the patient case (readable ID), the run template (name) or the oncologist (email) on the OncoKDM platform, they will be reused without creating a new one.
If a field is not required, you do not have to encode anything.
Encoding help
run_template__name (*)
readable_id (*), same as the patient id
patient_sex (* only if related to a new patient) must be M or F.
patient_country* must be written in English or ISO code
patient__birthdate* be of the format « YYYY-MM-DD ».
oncologist_firstname
oncologist_lastname
oncologist_email (* only if related to a new patient)
cancer_name (*) must be chosen from the different cancer types of the oncotree standard. Please note that the cancer_primary_site_name and the cancer_name must have the same relationship that on the oncotree standard.
cancer_primary_site_name (*) must be chosen from the different cancer types of the oncotree standard. Please note that the cancer_primary_site_name and the cancer_name must have the same relationship that on the oncotree standard.
external_id (*), is the sample id
files_names (*): VCF, BAM, or FastQ file name. If you have several files to integrate into the files_names column, you must separate them with a pipe (“|”). Example: sample1.fastq|sample2.fastq
METASTASES: yes; no; unknown
METASTASES_LOCATION: free text (mandatory if the previous answer is yes)
PREVIOUS_MEDICATION: yes; no; unknown
PREVIOUS_MEDICATION_DESCRIPTION: free text (mandatory if the previous answer is yes)
COMORBIDITIES: yes; no; unknown
COMORBIDITIES_WHICH: free text (mandatory if the previous answer is yes)
CONCOMITANT_MEDICATION: yes; no; unknown
MACRO_DISSECTION: yes; no; unknown
TUMOR_CELL_PERCENTAGE number (float number with 2 decimals, e.g. 46,7%)
LABORATORY_ORIGIN
SAMPLE_ORIGIN: free text
COLLECTION_DATE be of the format « YYYY-MM-DD ».
(*): Mandatory fields
Examples of encoded files
If you need any further information, please email us at: oncokdm_team@oncodna.com