Refactor documentation system

[cmungall]

The current doc system is described here URL: http://purl.obolibrary.org/obo/uberon/references/reference_0000000

Issues:

• Not friendly to web-based editing of manual pages, design patterns etc
• Editor must edit from within Protege, no native markdown support, no way to see formatted changes
• Individual articles not versioned
• numeric ordering by ID not necessarily the most intuitive
• we end up re-inventing our own CMS

Suggested replacement:

• use github wiki system
• continue to use md as format
• individual page per article
• directory contents can still be slurped into owl for importation and linking within protege
• can clone git@github.com:cmungall/uberon.wiki.git and edit md files just like a stanard git repo

Advantages:

• multiple people can contribute by editing via github wiki
• per-article versioning
• can provide TOC easily
• integrated with rest of project

Possible extensions:

• automated job that replaces LABEL syntax with MD links to PURLs

[cmungall]

Completed

[cmungall]

Although marked completed, the "about" page for the documentation describes the pre-refactored system

[cmungall]

Note: we have not necessarily abandoned the idea of the documentation being semantic.

We should have conventions for embedding metadata in the markdown (a kind of RDFa for markdown if you will).

At the moment we have lines such as:

Status: [intermediate draft](http://purl.org/spar/pso/intermediate-draft)

There's kind of implicitly a JSON-LD-like-context entity that maps this to the property that was used originally in the owl version of the docs. Conversion back to RDF should not be hard if conventions are followed. Easy to fall into a rabbit hole here but may be useful in the future.

[cmungall]

Original page moved here and changed status to a proposal
https://github.com/obophenotype/uberon/wiki/Documentation-metamodel

New about page here:
https://github.com/obophenotype/uberon/wiki/About-documentation

This should clarify #333