Can you help us create an imaging-focused vignette?

[kirbyju]

I recently saw https://cda.readthedocs.io/en/latest/documentation/cdapython/vignettes/ and was wondering if we could collaborate on something that is focused on creating a patient-centric query approach that would let our users select cohorts using all available clinical data from other nodes for subjects who exist in TCIA/IDC. I believe the most useful/authoritative clinical data live in GDC for our TCGA patients, PDC for our CPTAC patients and CTDC for our Biobank patients.

We have also been having some exploratory conversations with Todd Pihl about harmonizing clinical data from the very large National Lung Screening Trial that we host (over 26k subjects) which would a LOT of clinical data to CRDC if it were part of CDA. I am also not really sure what the status is for IDC and CDA indexing all of the other clinical data that live in TCIA in the form of spreadsheets that submitters provide to us. It'd be great to clarify that and make sure you're receiving everything we are making available to you.

Best,
Justin

[cda-bot]

Hey there, I would love to work on these! What we get from data submitters is a subset of what is submitted to the original data repository, so I honestly don't know whether we get everything you submit. We don't have any special systems set up with the DCs, we just pull our data from their public release APIs, It would be really great to have a way to tell if we are getting everything that is relevant. And I am always interested in building systems that improve search by clinical and patient data. I think the best way to get started would probably be to set up a meeting and chat about what each of us have and figure out next steps. To keep it simple, I think we can start with just me from our side, and then I can bring in my engineering folks for more specifics. My calendar is generally open all day on Wednesdays, all day on Thursdays except 2-3pm est, and all day Fridays after 11am est. Mondays and Tuesdays have openings, but they're very hit or miss. Would tomorrow (Thursday) at 11am work for you? If not, feel free to suggest another time. You can email me directly at amanda.charbonneau@gdit.com

…

-amanda

On Mon, Mar 31, 2025 at 4:08 PM Justin Kirby ***@***.***> wrote: I recently saw https://cda.readthedocs.io/en/latest/documentation/cdapython/vignettes/ and was wondering if we could collaborate on something that is focused on creating a patient-centric query approach that would let our users select cohorts using all available clinical data from other nodes for subjects who exist in TCIA/IDC. I believe the most useful/authoritative clinical data live in GDC for our TCGA patients, PDC for our CPTAC patients and CTDC for our Biobank patients. We have also been having some exploratory conversations with Todd Pihl about harmonizing clinical data from the very large National Lung Screening Trial <https://www.cancerimagingarchive.net/collection/nlst/> that we host (over 26k subjects) which would a LOT of clinical data to CRDC if it were part of CDA. I am also not really sure what the status is for IDC and CDA indexing all of the other clinical data that live in TCIA in the form of spreadsheets that submitters provide to us. It'd be great to clarify that and make sure you're receiving everything we are making available to you. Best, Justin — Reply to this email directly, view it on GitHub <#93>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A2TPWO3GPMFKIR4G63NNHO32XGOFHAVCNFSM6AAAAAB2FEUFNKVHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZYGE2TCMJTHA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[kirbyju]

Awesome, I'll email you to set the meeting.