Set up OBASK instance with basic config

[dosumis]

• [x] Set this up on a new repo - seeded using the templating mechanism in OBASK.
• [x] Configure with:
  • composite metazoan from Uberon (includes CL, Uberon, FBbt and others - need to check if this includes stage ontologies and add if not)
  • Slice of EFO needed for assays - this should be conservative: perhaps terms used + some small number of grouping terms will be sufficient? Use https://robot.obolibrary.org/extract#mireot. Suggested grouping terms - 'single cell library construction' + 'single cell RNA sequencing'. Or we might just take everything under those 2 terms a check if sufficient?
  • Assess term usage to see what else is missing?

[anitacaron]

Set this up on a new repo - seeded using the templating mechanism in OBASK.

https://github.com/EBISPOT/scxa_kg

composite metazoan from Uberon

https://github.com/EBISPOT/scxa_kg/blob/main/config/collectdata/vfb_fullontologies.txt

[anitacaron]

Slice of EFO needed for assays

Following the curation documentation (image below), only terms under single cell library construction are used, I created an EFO slice with everything under this class.

https://github.com/EBISPOT/scxa_2_cxg/blob/main/efo_slice.owl

And added to the OBASK configuration:

https://github.com/EBISPOT/scxa_kg/blob/main/config/collectdata/vfb_fullontologies.txt

[anitacaron]

After closing the issue https://github.com/EBISPOT/scxa_kg/issues/1, here can be closed.

[anitacaron]

OBASK instance is available to run locally in the repository https://github.com/EBISPOT/scxa_kg