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How to deploy a custom OBO dashboard

Contributed by @XinsongDu, edited by @matentzn

  1. Clone https://github.com/OBOFoundry/obo-nor.github.io and copy all its contents to a new GitHub repo under your account. Ensure that the .gitignore from the obo-nor.github.io repo is also copied to your new repo (it is frequently skipped or hidden from the user in Finder or when using the cp command) and push to everything to GitHub.
  2. Pull the Ontology Development Kit from Docker Hub (can take a while):
docker pull obolibrary/odkfull
  1. Modify the dashboard-config.yml file, in particular the ontologies section:
    1. Important: Add your ontology ID to the ID 'id' field
    2. Add the path to your ontology to the mirror_from field.
  2. Get the "base uri namespace" of the ontology using the following steps: a. Open the ontology in Protégé b. Select a class and press "command + u" (MacOS), the stem of the path would be the base URI namespace (e.g., in EDAM ontology, the base uri namespace is http://edamontology.org/, for Uberon it would be http://purl.obolibrary.org/obo/UBERON_)
  3. Add the base uri namespace to 'base_ns' field of your ontology in the dashboard-config.yml
  4. (As of October 2021 make sure there are multiple ontologies in the dashboard-config.yml, otherwise errors would be reported while running the code. There are currently some bugs in the dashboard code that require at least 2 or 3 ontologies in the list).
  5. In the Makefile uncomment the # before pip install networkx==2.6.2 to ensure the correct network x version is installed.
  6. Run sh run-dash.sh (make sure dashboard folder is empty before running, e.g. rm -rf dashboard/*).
  7. When run successfully, push all changes to GitHub.
  8. Go to GitHub repo you just created, and go to Settings, then Pages, and select your main/master branch as "source", and your root directory. You will see a website URL highlighted in green, where your OBO dashboard is deployed.