Study Curation Guide
This guide is to help data curators learn how to curate a study on their own computer
- To follow this guide the curator should have some familiarity with running commands on the command line. We will be using Docker. No Docker knowledge is required, one will obtain some basic understanding by following the guide.
- Learn how to setup cBioPortal locally here first.
Load an example study
After having followed the steps in the Docker Deployment instructions, you will end up with the study Low-Grade Gliomas (UCSF, Science 2014) loaded locally. Now let's try to import another study:
- Choose another example study from the datahub. Note the name of the folder which is identical to the study id defined in meta_study.txt.
- From the root of the
DATAHUB_STUDIES=my_study_id ./study/init.sh. Change
my_study_idto the study you picked in 1. The study should now be downloaded in
- Import the study by running
docker-compose exec cbioportal metaImport.py -u http://cbioportal:8080 -s study/my_study_id/ -o. Again change
my_study_idto the study you picked in 1. This should import the study.
- Restart the cbioportal instance
docker-compose restart cbioportaland see if the new study shows up on http://localhost:8080
Curate a new study
The cBioPortal team has curated many published studies in formats suitable for import in cBioPortal. These can be found on the datahub and can serve as an example of how our curation processes works. You can find a step by step description of how to curate a new study here.