Create documentation

[jennifer-bowser]

Here's the documentation I've created for the demo site to explain to grant reviewers how to use VarCat. The files are numbered to indicate the order in which they are designed to be read.

I'd LOVE feedback, especially on the following:

• Is any information missing?
• Are any parts too verbose and/or repetitive?
• Does the way in which the information is organized make sense?
  • e.g., splitting the info into 2 documents, the flow of information within each document individually, etc.
• Presentation: does it make sense to leave these as markdown files, or should I use something like mkdocs to create a small read-the-docs-type website à la the gkm starter kit?

[korikuzma]

@jennifer-bowser Could you put a priority label on this (asking so I know when I need to review by)

[korikuzma]

Presentation: does it make sense to leave these as markdown files, or should I use something like mkdocs to create a small read-the-docs-type website à la the gkm starter kit?

I haven't done a deep dive on what you wrote, but I would recommend linking to these files in the repo README if you don't want to go the mkdocs route. I would guess most people would not look in the documentation folder

[korikuzma]

Great first pass @jennifer-bowser ! Made some suggestions on things that could be added to make the tutorial more thorough.

IMO, I would prefer a GH pages site using Zensical (apparently mkdocs is no longer maintained). GKM-Starter Kit has been updated with this migration.

[ahwagner]

Overall a great start to our documentation, nice work!

In addition to a few minor comments below, we might consider restructuring the first page to bring the visual / anatomy content to the top. It might be too jarring an intro for people to jump immediately into a concept dictionary. Maybe put the anatomy stuff at the top and add in some references to concept definitions later on the page where the concepts are defined in detail.

[jennifer-bowser]

I envision the first two pages as that content that all users should read before using VarCat; but this page is something that only needs to be used as a reference while users are actively working on adding manual evidence to an assertion.