INCATools / INCATools/ontology-access-kit

Create a generic Jupyter notebook parameterizable by ontology selector

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documentation
Dominant language
Python
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Description

Create a generic notebook that demonstrates all core functionality

- CLI and Python side by side
- show timings for each command

Create a workflow that will execute this using papermill for core backends

- sqlite
- ubergraph
- obo/pronto
- rdf

This will serve multiple purposes

- integration tests (should be run outside github actions, these may involve large sqlite files, network connections, ...)
- documentation of which methods are implemented where

This will give us something like the robot docs system (e.g http://robot.obolibrary.org/reason), in which documentation is tested over.

Contributor guide

Open the contributing guide

Research direction

Start by locating the project's notebook and workflow conventions, then review how the CLI and Python interfaces expose core functionality. Build a generic parameterizable notebook and a papermill workflow covering sqlite, ubergraph, obo/pronto, and rdf backends. Done means the notebook shows side-by-side commands and timings, and the workflow documents and tests backend method coverage outside GitHub Actions.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, python, sqlite
Domain
database, documentation, testing
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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