How and where can I find clinical data dictionary of all known clinical attributes?

[aghil hooshmand]

Hi All,

We have some clinical features for liquid biopsy (sample/patient). As mentioned in cbioportal document in custome clinical data part, for better normalization with other data in cbioportal, Its better to use and compare with clinical data dictionary at first (name and type of each feature). The link that mentioned there is https://oncotree.mskcc.org/cdd/swagger-ui.html#/ that dosent work. As far as I know the correct mskcc api is here : https://oncotree.mskcc.org/#/home , but you can just see some api for cancer type not any thing about clinical feature. As far as I searched in cbioportal git hub, I found https://github.com/cBioPortal/clinical-data-dictionary , but I couldnt run this one. Dose any one know how can I do it and where can I find clinical data dictionary for cbioportal? I'd be greatfull If help me.

[Sowmiyaa Kumar]

Hi Aghil, 

Thank you for reaching out! Can you please check this link? 

If you have any more questions, please remember to Reply All to this thread so that we can keep the rest of the community in the loop. 

Kind regards, 

Sowmiyaa

On Tue, Apr 2, 2024 at 2:51 PM aghil hooshmand <aghil.h...@gmail.com> wrote:

Hi All,

We have some clinical features for liquid biopsy (sample/patient). As mentioned in cbioportal document in custome clinical data part, for better normalization with other data in cbioportal, Its better to use and compare with clinical data dictionary at first (name and type of each feature). The link that mentioned there is https://oncotree.mskcc.org/cdd/swagger-ui.html#/ that dosent work. As far as I know the correct mskcc api is here : https://oncotree.mskcc.org/#/home , but you can just see some api for cancer type not any thing about clinical feature. As far as I searched in cbioportal git hub, I found https://github.com/cBioPortal/clinical-data-dictionary , but I couldnt run this one. Dose any one know how can I do it and where can I find clinical data dictionary for cbioportal? I'd be greatfull If help me.

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Sowmiyaa Senthil Kumar

Data Engineer

E sowmiyaa@thehyve.nl

T +31 68 27 10264

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