obo-community-health

This repository contains code for downloading the OBO Foundry and assessing the completeness, correctness, and goodness of each ontology's metadata. The assessment is highly opinionated, but fills in several huge gaps in the current OBO Foundry pipeline for assessing the completeness and utility of metadata given by submitters as well as keeping track and pointing out obviously abandoned efforts.

Pages

Ontology View

The ontology view gives insight into which OBO Foundry ontologies are actively being updated and have appropriate metadata.

Contact View

The contacts view gives insight into who is responsible for each OBO Foundry ontology, how easy they are to get in contact with, and whether they are actually actively participating in GitHub (e.g., this shows there are several people who have completely shirked responsibility).

Why Does this Exist?

I wanted quantitative metrics to propose ontologies to be marked as abandoned on the OBO Foundry. Suggesting to mark ontologies as abandoned has a huge risk of hurting people's feelings, so I hope that having quantitative metrics demonstrating the following on many ontologies could help the process:

1. lack of engagement of users
2. lack of engagement maintainers
3. lack of conformance to required metadata based on OBO standards
4. lack of obviously useful metadata (for which the OBO community is slow to impose requirements)

Secondarily, this demonstrates how simple (less than 300 or so lines) a script that performs checks for OBO metadata standards (such as requiring a homepage) could be written.

Build

Check the OBO Foundry repositories to see what's going on. To run this, you'll need either the GITHUB_TOKEN environment variable set up with a github token, or any other valid way to specify the token key in the github namespace via pystow. Installation and running is handled with tox. Run with the following lines in your shell:

shell $ pip install tox $ tox

For a non-standard build using a bleeding edge build of the OBO Foundry config, use:

shell python build_contacts.py --path ~/dev/OBOFoundry.github.io/_config.yml python build.py --path ~/dev/OBOFoundry.github.io/_config.yml --force

Charts

This repository implements a highly opinionated scoring system. Here's a summary of the distribution of scores across the OBO Foundry

How divided is responsibility across all ontologies?

Embed

The Bioregistry provides a wrapper around the Shields.io badge generation service to make beautiful badges showing off the community health of your ontology, like :

You can embed the score of your resource using the following HTML using your prefix (e.g., go) in place of <YOUR PREFIX HERE>:

```html