Groups keyboard shortcuts have been updated
Dismiss
See shortcuts

Clinical Track Ordering

15 views
Skip to first unread message

Aaron Atkinson

unread,
Sep 26, 2024, 5:44:43 PM9/26/24
to cBioPortal for Cancer Genomics Discussion Group
Hello!

Per the cBioPortal documents (https://docs.cbioportal.org/file-formats/#event-types) event types are ordered as follows:
Specimen
Surgery
Status
Diagnostics
Diagnostic
Imaging
Lab_test
Treatment
First custom event
etc.

Currently the diagnoses are last however. Any help is appreciated. Thanks, Aaron. 

The meta file is:
cancer_study_identifier: REDACTED
data_filename: DIAGNOSIS.txt
datatype: TIMELINE
genetic_alteration_type: CLINICAL

The header and first row for the DIAGNOSIS.txt are:
PATIENT_ID START_DATE STOP_DATE EVENT_TYPE ICD-O SITE CODE ICD-O SITE ICD-O HISTO CODE ICD-O HISTOLOGY GENERAL STAGE T N M STAGE STAGED FROM STAGE SEER SYSTEM TUMOR SIZE # REG NODES EXAMINED # POS REG NODES METS AT DX? METS AT DX DESC (IF KNOWN) HEIGHT AT DX (CM) DAYS FROM DX TO HEIGHT WEIGHT AT DX (KG) DAYS FROM DX TO WEIGHT BMI AT DX RECUR TYPE
EXAMPLE_ID 20352 Diagnosis C50.4 Breast, upper-outer quadrant 8520/3 Lobular carcinoma, NOS (C50._) Stage II 2 0 X 2A Path 35 2 0 N 170 6 72.7 6 25.1557

Aaron L

unread,
Sep 26, 2024, 6:27:35 PM9/26/24
to Aaron Atkinson, cBioPortal for Cancer Genomics Discussion Group
Hi Aaron (from a fellow Aaron)

Can you send me the response for this request on your portal (with host and parameters for your study and patient obviously).




--
You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cbioportal+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/46b967e2-1f6b-48c5-9749-e61fb891dac3n%40googlegroups.com.
Reply all
Reply to author
Forward
0 new messages