TCGA GDC / ICGC alike Data Portal
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4 months ago
ResearchR ▴ 110

Dear all,

we produce a LOT of sequencing and imaging data in our department and since data organization becomes more and more difficult, I would like to set up a department internal data portal similar to the GDC/ ICGC portal with its convenient data structure (disease, study, data type etc...), selection and export functionality. Since GDC and ICGC are quite alike in function (as far as I can tell) and look, I thought they might be of the same origin. Since we use both of these data sources quite extensively and mix it with our data, such a solution seemed to be just perfect. Of course, I could be completely mistaken here, but I was wondering if an open source solution for such a portal exists. It should not be, in any way, made be accessible publicly nor is it meant for production. I search the WWW already for such solutions, but I was not too satisfied with my findings. If you have any good ideas or suggestions...they are very welcome and much appreciated.

Have a good start in 2022 and try to stay healthy! Cheers

P.S.: Examples of my rather unsuccessful search: https://ckan.org/, https://getdkan.org/, https://www.truedat.io/

data ICGC TCGA GDC portal • 447 views
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cBioPortal is a good option to lay out data by studies. There are 3rd party companies you can hire (like Hive) that can help you set it up.

If you don't care about displaying molecular data (oncogrid, etc), GEN3 is another option https://ctds.uchicago.edu/datacommons that has been used for support many data commons of various sizes

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4 months ago
GenoMax 115k

GDC/ICGC are large projects supported by many people. I am not sure if it would be a simple exercise to install a local instance. ICGC source code appears to be public so you can decide for yourself.

While not quite the same you may want to look at cBioPortal (LINK). Their code is public but may or may not work for your use case.

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I checked the ICGC source code, it is indeed not straight forward to install. The cBioPortal seems interesting, just going through their back-end architecture. Thanks for pointing it out!

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