Add instructions on how to set up an ubergraph instance with a custom set of ontologies

INCATools / ubergraph

Integrated OBO ontology store

BSD 3-Clause "New" or "Revised" License

42 stars 3 forks source link

Add instructions on how to set up an ubergraph instance with a custom set of ontologies #12

Open cmungall opened 3 years ago

cmungall commented 3 years ago

We would like an ubergraph instance with ENVO, PO, perhaps FOODON - and maybe also the LinkML OWL translations of MIxS (@hrshdhgd we will make this correspond with our OLS instance)

Should we set up our own instance and run on AWS? Or can we put into the main instance?

If we set up our own instance it looks like we should be able to figure from the Makefile, we can contribute back docs later

cc @turbomam @wdduncan @hrshdhgd

balhoff commented 3 years ago

I'm inclined to grow this Ubergraph as large as possible, at least adding ENVO, PO, and FOODON. I know less about MIxS, but if you think it's a good idea then probably so.

balhoff commented 3 years ago

@cmungall PO doesn't seem to have a base file, do you think they can make one? cc @matentzn

balhoff commented 3 years ago

Same for FOODON.

turbomam commented 3 years ago

@balhoff Is PO in this context the protein ontology? What's a base file in this context?

balhoff commented 3 years ago

@turbomam PO is Plant Ontology. Coincidentally Protein Ontology also doesn't provide a base file, but I am simulating one: https://github.com/NCATS-Tangerine/ubergraph/blob/8e1a2938e4dcc1c1a104dcd0cbcd375e65a3a1a8/Makefile#L18-L24

I can temporarily do that for PO and FOODON as well. I will send you a link to my base file manifesto. 😉

turbomam commented 3 years ago

I WILL READ THE MANIFESTO, SIR!

cmungall commented 3 years ago

and https://github.com/INCATools/ontology-development-kit/issues/411