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https://github.com/cthoyt/obo-community-health

🫀 Check the OBO Foundry repositories to see what's going on
https://github.com/cthoyt/obo-community-health

obofoundry

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🫀 Check the OBO Foundry repositories to see what's going on

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# 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](https://cthoyt.github.io/obo-community-health/) gives

insight into which OBO Foundry ontologies are actively being updated and have

appropriate metadata.



### Contact View



The [contacts view](https://cthoyt.github.io/obo-community-health/contacts)

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`](https://github.com/cthoyt/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



![Scores](docs/score_histogram.png)



How divided is responsibility across all ontologies?



![Responsibilities](docs/responsibility_histogram.png)



## Embed



The [Bioregistry](https://bioregistry.io) provides a wrapper around the

[Shields.io](https://shields.io/) badge generation service to make beautiful

badges showing off the community health of your ontology, like [![GO OBO Community Health Score](https://bioregistry.io/health/go)](https://cthoyt.github.io/obo-community-health):



You can embed the score of your resource using the following HTML using

your prefix (e.g., `go`) in place of ``:



```html



```



More simply, it can be embedded as an image, but this doesn't auto-generate a

link:



```html



```