INCATools / INCATools/ontology-development-kit

Consider replacing some of the SPARQL QC checks with OAK validate

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#610 6 comments 0 reactions 2 assignees Claimed by @StroemPhi View on GitHub
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Description

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 #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
```

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