Skip to content

Consider replacing some of the SPARQL QC checks with OAK validate #610

@matentzn

Description

@matentzn

OAK has a new but very experimental validation interface:

https://incatools.github.io/ontology-access-kit/interfaces/validator.html

We should start exploring that for QC rather than adding sparql. Good first issue:

#587

@anitacaron would this be an issue you'd be interested in? For starters, the only thing we need is:

  1. An example of a working OAK command (CLI) which takes in an ontology and validates it.
  2. An implementation of Please incorporate checks for the dateTime property  #587 extending the ontology metadata schema provided by OAK (we will maintain our own here for now).
  3. A make goal in Makefile.jinja2 that runs the validation on $(ONT).owl.
  4. We should build-in support for multiple profiles. @StroemPhi rather than extending existing profiles, I would suggest exploring their composition. Maybe the ODK config should get this option:
oak_validate:
    profiles:
        - filename: profile1.yml
           description: Monarch validation (Monarch QC)
           mirror_from: 'http://...'
         - filename: profile2.yml
           description: OMO validation (OBO QC)
           mirror_from: 'http://...'

This will result in a make goal like this:

reports/profile1.tsv: $(FILE) tmp/profile1.yml
    oak validate $< --profile  tmp/profile1.yml -o $@

reports/profile2.tsv: $(FILE) tmp/profile2.yml
    oak validate $< --profile  tmp/profile2.yml -o $@

oak_validate:
    $(MAKE_FAST) reports/profile1.tsv reports/profile2.tsv

Metadata

Metadata

Labels

No labels
No labels

Type

No type

Projects

No projects

Relationships

None yet

Development

No branches or pull requests

Issue actions