cmonnom
commented
4 years ago To link a list of patient/sample ids from KCE to Cbioportal, there are multiple options (the highlighted one is the currently preferred one). On Cbioportal v3 (not installed anywhere on campus as far as I know. I've tried to install it on the cbioportal server (biohpc) but couldn't so far):
- the url can handle filter parameters directly to the view we want. Eg. https://www.cbioportal.org/study/clinicalData?id=msk_impact_2017#filterJson={"sampleIdentifiers":[{"sampleId":"P-0000004-T01-IM3","studyId":"msk_impact_2017"}]} The problem is that it won't scale and we could hit a limit for the number of characters that a web browser can handle for large cohorts.
On Cbioportal2 (the version used on the cbioportal server and the campus wide cbioportal (Melody's team):
- we can create virtual studies and create a link to them (think like sharing a Google photo album). The issue is that there's no way to do it programmatically. Someone has to use the cbioportal UI to build and save and share the virtual study. This also requires installing the API modules (which involves a lot more work, mongoDB and other packages)
- 2-step process:
- when the user clicks on the Cbioportal link in KCE, we put the list of patient/sample ids in the clipboard and open cbioportal at the appropriate page (for instance, for a cohort covering multiple studies, we can open cbioportal to a list of all the samples in those studies, either at the Summary or the Clinical Data page. Eg. http://198.215.54.74:8080/cbioportal2/study?id=pancancer_utsw%2Cstudy_es_0&tab=summary
- then the user pastes the list of patient/sample ids to the "Custom Selection" filter to only see the sample in his/her cohort.
Here is quick demo: https://codepen.io/cmonnom/pen/mdJwYzx
Description: KCE patient Id(s) to cbioportal. Basically build a cohort in kce and see the data for the selected patient ids in cbioportal. See if there's an API to do that already (plan A). Build a cohort on the fly and import it (plan B). plan C?
API to load data into cbioportal?