logical definition photoreceptor update

[JABelfiore]

logical definition photoreceptor update and update text description to match

[anitacaron]

I think this change caused the inferred equivalence, which is not allowed and it's the reason the QC is failing. :)

2024-08-01 12:28:49,500 ERROR org.obolibrary.robot.ReasonOperation - Only equivalent classes that have been asserted are allowed. Inferred equivalencies are forbidden.
2024-08-01 12:28:49,502 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: <http://purl.obolibrary.org/obo/CL_0000488> == <http://purl.obolibrary.org/obo/CL_0000210>

[AvolaAmg]

I will approve the PR after Anita's changes resolved :)

[anitacaron]

David said he fixed that in GO. We're waiting for a GO release and will update the imports then.

[dosumis]

Fixed in GO. If we are using GO nightly release, will be fixed here if we update GO in this branch on Monday.

[dosumis]

@aleixpuigb could you work with @JABelfiore to update the GO import today?

[anitacaron]

There isn't a new GO release. The last one was from June. We don't use the GO nightly releases.

[dosumis]

New GO release on 2024-09-08, so update to GO should now fix.

[dosumis]

@aleixpuigb - could you update GO Import. Should fix. Thanks!

[aleixpuigb]

#gogoeditdiff

[github-actions]

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-09-19/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-master.owl/cl-simple.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-09-19/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

eye photoreceptor cell http://purl.obolibrary.org/obo/CL_0000287

Added

• eye photoreceptor cell SubClassOf neuronal receptor cell

photoreceptor cell http://purl.obolibrary.org/obo/CL_0000210

Removed

• photoreceptor cell definition "A cell specialized to detect and transduce light."

  • database_cross_reference "MESH:D010786"

• photoreceptor cell SubClassOf neuronal receptor cell

  • is_inferred "true"

Added

• photoreceptor cell definition "A cell specialized in detecting light stimuli that are involved in visual perception."

  • database_cross_reference "MESH:D010786"

• photoreceptor cell SubClassOf sensory neuron

• photoreceptor cell SubClassOf visual system neuron

[github-actions]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
• Version IRI: None
• Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
• Version IRI: None
• Loaded from: file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

photoreceptor cell http://purl.obolibrary.org/obo/CL_0000210

Removed

• photoreceptor cell definition "A cell specialized to detect and transduce light."

  • database_cross_reference "MESH:D010786"

• photoreceptor cell EquivalentTo neuron and (capable of some detection of light stimulus involved in sensory perception)

• photoreceptor cell SubClassOf neuronal receptor cell

  • is_inferred "true"

Added

• photoreceptor cell definition "A cell specialized in detecting light stimuli that are involved in visual perception."

  • database_cross_reference "MESH:D010786"

• photoreceptor cell EquivalentTo neuron and (capable of some detection of light stimulus involved in visual perception)

• photoreceptor cell SubClassOf visual system neuron

[aleixpuigb]

It looks good to me.

[dosumis]

Good that it's finally passing, but...

@aleixpuigb - can you look into conflicts? I think definitions.owl can be resolved by choosing version on main. Maybe merged_import needs regen again? We should aim to merge down ASAP as soon as fixed. I can over-ride review requirements if needed.

[aleixpuigb]

Conflicts solved, for some reason it alway have problems with the dates.

Changes have addressed but reviewer is unable to review again