Anita Caron

Cases where `comment` tag text using quotes

1

**Uberon term** One of the cases: UBERON:0006428 **Bug description** Term in OBO ``` [Term] id: UBERON:0006428 name: basisphenoid bone def: "Part of the base of the cranium between the basioccipital...

Download component from source url workflow can't find file to copy

7

When the component is different, it copies from the tmp folder, but when it's downloading for the first time, it shouldn't try to copy. Error on test [PR](https://github.com/obophenotype/uberon/pull/2975) https://github.com/obophenotype/uberon/actions/runs/8389532879/job/22975944727 ![Screenshot...

The default can stay full, but it would be good also to give the option to choose other lighter versions, e.g. base.

`Deprecate entity` using GO profile is adding axioms into an imported file

1

I tested the functionality using CL Ontology. As you can see in the screenshot below, the annotations added as part of the deprecation workflow are added to the `cellxgene_subset` instead...

Remove all SubClassOf axioms annotated with is_inferred:true

8

Fixes #2426

- [ ] Remove the message if there isn't invalid IRIs - [ ] Add the invalid ontology iri to the URI report

This will make it easier to install on ODK without worrying about its dependencies.

Using jq in makefile, but it isn't installed

1

This is not completing the assertion on OBOMD version https://github.com/OBOFoundry/OBO-Dashboard/blob/ca7061b6ba6e3d6f0b78bbcc1abb4a258d8e5d8e/Makefile#L139 ```bash jq: command not found % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total...

Reduce overuse of ROBOT commands for efficiency

4

There's a function to generate a ROBOT command that has many commands in a chain, which may be unnecessary. It can be time-consuming and memory-consuming for large ontologies, e.g., NCBITaxon,...

Yeah that is a good idea. We could: - Include all ERROR (these are typically few) - Increase the number of rows to 1000 - Strip out owlclassexpression hashcodes to...