Make schemas of sources more explicit

[cmungall]

Context: Semantic ETL manifesto

We should make this repo an exemplar of a KG ETL repo. We should formally describe upstream sources in a lightweight way and make it very transparent how things map.

We have done most of the work already here:

https://github.com/Knowledge-Graph-Hub/kg-microbe/tree/master/schemas

This describes the core trait table that is ingested. We need to switch this to use linkml first (#21), but we may add more.

We can generate markdown for this using linkml, but we need to think how this integrates with https://knowledge-graph-hub.github.io/kg-microbe/index.html

I like how dipper includes a sources section: https://dipper.readthedocs.io/en/latest/sources.html

Would it make sense to

1. generate markdown from all upstream schemas (just one so far)
2. Deposit markdown here https://github.com/Knowledge-Graph-Hub/kg-microbe/tree/master/sphinx (can markdown be mixed with rst?)
3. Publish

Alternatively we could use the generated python from the schema

[cmungall]

see also https://docs.google.com/document/d/1iEsLp9pDvjGjgWMSLArtNf6Jwan-wjMl6_viQGyTWG8/edit?ts=60c3b505#

[hrshdhgd]

Added documentation of the markdowns generated from linkml. The formatting we had decided on for the markdown files do not sit well with html.

https://knowledge-graph-hub.github.io/kg-microbe/sources/carbon_substrates.html#other-properties

Thoughts, @cmungall ?

[hrshdhgd]

[cmungall]

The formatting we had decided on for the markdown files do not sit well with html.

not sure what you mean.

it seems this is likely just a problem with linkml markdowngen. I think this ticket can be closed.

note: change the name of the class from Example to something meaningful, e.g. FooTrait, where Foo is some discrimanotor such as the paper