Make examples of using ENVO for bioinformaticians

EnvironmentOntology / envo

A community-driven ontology for the representation of environments

http://www.environmentontology.org

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Make examples of using ENVO for bioinformaticians #619

Open cmungall opened 5 years ago

cmungall commented 5 years ago

R examples using rols
Python examples using ontobio
SPARQL examples against OntoBee, maybe using R (see for example this )

The above are very ontology-centric. It would be good to have some examples doing things like analyzing microbiome data, this would take a bit more work.

Another possibility is to combine with NER, e.g. using scigraph annotator

pbuttigieg commented 5 years ago

@kaiiam we could showcase some of your work through this

pbuttigieg commented 5 years ago

@cmungall These would live in our wiki, right?

cmungall commented 5 years ago

Good Q. We don't have much their right now. https://github.com/EnvironmentOntology/envo/wiki

For Jupyter notebooks, it can be useful to have a dedicated repo, easier to serve up using jupyterhub/binder.

Wikis can be hard to navigate. We should think about how we want to organize things re website vs wiki vs readthedocs

pbuttigieg commented 5 years ago

Wikis can be hard to navigate. We should think about how we want to organize things re website vs wiki vs readthedocs

Agreed - the repo and website should point to the same spot. Open to suggestions, I like the readthedocs link to repos.

For Jupyter notebooks, it can be useful to have a dedicated repo, easier to serve up using jupyterhub/binder.

True, we can build on in the ENVO org and point there from the README.Md