ontology-ui-overlay-data

Overview

This repository contains ontology-related data that is not currently held in upstream ontologies (buty maybe should be) needed for some GO UIs. Specifically, some edge glyphs, colors, and labels. These are kept in a YAML file

This is meant to starting to dig ourselves out from some very very old decisions made for AmiGO that ended up getting adopted by early software for Noctua. E.g. https://github.com/geneontology/noctua/issues/804 and https://github.com/geneontology/noctua/issues/801.

Workflow

Requires NPM OTPs.

git clone https://github.com/geneontology/ontology-ui-overlay-data
cd ~/local/src/git/ontology-ui-overlay-data
docker run -v `pwd`:'/work' -w /work -i -t ubuntu:jammy /bin/bash
apt-get update && apt-get -u install npm nodejs
npm login
[make modifications]
npm publish

The "make modifications" here is currently what we'd like to automate in the future, preferably from upstream ontology data. The most direct thing we have at the moment is functionally:

cp ../amigo/javascript/npm/amigo2-instance-data/generation-templates/context.js.tmpl ./lib/ontology-ui-overlay-data.js

That copied file is made by injecting the output for yaml2json from the ../amigo/conf/context.yaml file (see the topmatter for the latter file).

Troubleshooting

TBD: how to sync or not sync from AmiGO amigo2-instance-data. Let's just see if this works first...