neo node labelling should label equivalent classes as well as subclasses.

[dosumis]

labels specified by class expressions under neo4j2owl-config.neo_node_labelling should be applied to equivalent classes as well as subclasses.

[dosumis]

Hi @hkir-dev - could you make this a priority? It's an issue for both BDS and VFB (esp for VFB_connect queries) Would be great go have a fix in place and run through the pipeline before our next workshop on May 4th.

CC @Clare72

[matentzn]

(sorry to barge in, its of interest to me) I just reviewed the old code - they are! You have a case of a class A = R some C with R some C being labelled as Label A and that label not appearing in prod?

[dosumis]

Try

MATCH (n:Motor_neuron) where n.label = 'motor neuron' return n

On http://pdb.virtualflybrain.org/browser/

[dosumis]

I'm not sure we have any cases with anonymous class expressions.

[hkir-dev]

After talking with Nico, I tried to find a case in BDS but in neo4j we don't have any "equivalent class" relation. Should we label them without connecting them

[dosumis]

As I understand it, this is entirely driven by OWL (DL) queries - creating AP axioms which are then converted into Neo4J labels on loading. We just need those OWL queries to return Equivalent classes as well as subclasses (probably need two queries).

[dosumis]

We have plenty of cases in BDS: e.g. CL:astrocyte doesn't get the Astrocyte label, only subclasses of CL:astrocyte do.

[dosumis]

@matentzn - could you point to code that uses this?

[hkir-dev]

https://github.com/VirtualFlyBrain/neo4j2owl/blob/eb06b662730b3e4cc095b8d31e285bc1fc604c43/src/main/java/ebi/spot/neo4j2owl/importer/N2OOntologyLoader.java#L90
https://github.com/VirtualFlyBrain/neo4j2owl/blob/eb06b662730b3e4cc095b8d31e285bc1fc604c43/src/main/java/ebi/spot/neo4j2owl/importer/N2OOntologyLoader.java#L72
this seems to handle equivalent classes also but probably not working with existential restrictions

[dosumis]

Is it possible that the equivalent (query) class gets removed here:

https://github.com/VirtualFlyBrain/neo4j2owl/blob/eb06b662730b3e4cc095b8d31e285bc1fc604c43/src/main/java/ebi/spot/neo4j2owl/importer/N2OOntologyLoader.java#L95 ?

[matentzn]

Alright, there are two issues here:

1. In our initial design, we explicitly excluded the class itself from the tagging. This is easy to fix: just remove the

if (e.isClassExpressionLiteral()) {
            subclasses.remove(e.asOWLClass());
}

But note that we did put some thought into this when we designed it, so you should consider the ramifications (sometimes, you want only the instances to be tagged, not the super class).
2. The jar that generates the labels outside of neo is standalone. It was never meant to be changed, because it has such a singular purpose, but if you decide that you really want to go down that route as you say here, I will create a separate repo for you and move it into the VFB space, then you can continue to edit it (right now, its part of my phenotype utils).

If you still want to go ahead with this decision, I will move the VFBExpressionAnnotator into a separate repo under VFB guardianship.

[matentzn]

Just in case I moved 2. into the VFB space to give you full control: https://github.com/VirtualFlyBrain/vfb_expression_annotator

[dosumis]

Re point 1. Don't recall the decision. Differs from previous implementation. Will be v.useful to change back for both BDS and VFB_connect use cases.

Re point 2: Must have been some misunderstanding on this. Needs to be core part of the pipelines. Can you move to a VFB repo?

Thanks