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:
- lack of engagement of users
- lack of engagement maintainers
- lack of conformance to required metadata based on OBO standards
- 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:
$ pip install tox
$ tox
For a non-standard build using a bleeding edge build of the OBO Foundry config, use:
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>:
<object data="https://bioregistry.io/health/<YOUR PREFIX HERE>"></object>
More simply, it can be embedded as an image, but this doesn't auto-generate a link:
<img src="https://bioregistry.io/health/<YOUR PREFIX HERE>"/>