cBioPortal - ICD10 Codes

7 views
Skip to first unread message

Joseph, Greg

unread,
Nov 17, 2022, 11:07:56 AM11/17/22
to cbiop...@googlegroups.com

Hello,

 

We are currently working toward importing ICD10 code data into our study. Is there an existing method for the portal to handle and properly parse ICD10 codes? Our data has multiple codes per record, so we would want to have the portal handle the codes in a “one to many” relationship and not as a long string.

 

Thanks,

Greg

 

Gregory Joseph, MS

Research Informatics Analyst

Winship DATA Shared Resource

Winship Cancer Institute at Emory University

1814 Clairmont Road

Decatur, GA 30033

 

Robert Sheridan

unread,
Nov 17, 2022, 12:45:30 PM11/17/22
to cBioPortal for Cancer Genomics Discussion Group
Hi Greg .. I am not sure I fully understand what you would like the cbioportal website to do when you say "parse" ICD10 codes. I think there would be no problem in adding a clinical attribute for your samples which contained a list of ICD10 codes with whatever list format you choose. These lists could be retrieved as clinical data through the API or viewed through the website UI. However, they would simply be strings attached to identified samples in your sample clinical data.

The file format for data_clinical_sample.txt describe the clinical values which determine a study's associated cancer type descriptions : (https://docs.cbioportal.org/file-formats/#columns-with-specific-functionality) through fields CANCER_TYPE and CANCER_TYPE_DETAILED. And the meta_study.txt file has a field for declaring the cancer type code to be used when placing the study in the categorized sample list on the home page. In the public cbioportal, these codes correspond to the codes available at https://oncotree.info/#/home .. for example ( https://oncotree.info/#/home?search_term=(LUAD) ) has code 'luad'

It would be possible to create your own set of codes to represent cancer types and construct a database which holds those codes in the type_of_cancer table, but that would take some work. Also, the codes from that table must form a strict tree structure with parent-child links between all nodes. But I do not think the cBioPortal code base supports the use of multiple cancer type codes for a sample or for a study. We do have a special code "mixed" which we use for studies which combine samples of various cancer types. https://oncotree.info/#/home?search_term=(MIXED)

And lastly, we created a tool to convert oncotree codes to/from ICD0 codes (as well as other ontologies). You can see the details here:
https://oncotree.info/#/home?tab=mapping under the section Ontology to Ontology Mapping Tool

I hope this information is helpful.

--Rob

Robert Sheridan

unread,
Nov 17, 2022, 12:52:18 PM11/17/22
to cBioPortal for Cancer Genomics Discussion Group

Sorry .. 2 quick corrections:

This:
"The file format for data_clinical_sample.txt describe the clinical values which determine a study's associated cancer type descriptions"
should have been:
"The file format for data_clinical_sample.txt describe the clinical values which determine a sample's associated cancer type descriptions"

and This:
"when placing the study in the categorized sample list on the home page"
should have been:
"when placing the study in the categorized study list on the home page"

--Rob
Reply all
Reply to author
Forward
0 new messages