Finalise and implement queries for classification & location in context browser.

[dosumis]

Current queries here:

https://github.com/VirtualFlyBrain/geppetto-vfb/issues/542

Basic queries are in place on this ticket, but still need to discuss how upper end is anchored - by type? By template?

[dosumis]

What is X:

MATCH p=(n:Entity)-[:INSTANCEOF|:SUBCLASSOF*..]->(x) 
WHERE 'Anatomy' IN  labels(x) AND 
n.short_form = 'FBbt_00003686' 
RETURN  p, n.short_form as root

Where is X:

MATCH p=(Entity)-[:INSTANCEOF:part_of|has_synaptic_terminal_in|has_presynaptic_terminal_in|
has_postsynaptic_terminal_in|overlaps*..]->(x)
 WHERE n.short_form = 'FBbt_00003686' return  p, n.short_form as root

TBD: How to set the upper limits of terms to display in graph. We need to stop these spiralling off into abstract land.

Options:

• 1. Restrict X to upper level derived neo labels (gross typing). Problem: these are not currently comprehensive. We'll have some cases where no graph is displayed. However, this is probably good enough for cells and the nervous system.
• 2. Restrict X to a set of preferred roots. This will result in less fragmented graphs being returned. Potential problem: Is the ontology complete enough?

[dosumis]

@Robbie1977 to update queries (see below) and add to Geppetto config.

List of labels to use for restriction for now: Cell, Synaptic_neuropil, Ganglion, Neuron_projection_bundle

Example query with this type of restriction on:

MATCH p=(n:Entity)-[:SUBCLASSOF*..]->(x) 
WHERE (('Cell' IN  labels(x)) or ('synaptic neuropil' IN labels(x))) 
AND n.short_form = 'FBbt_00003686' return  p, n.short_form as root

Test - and expand list as needed later (probably need Sensory_organ, Tagma, segment, Neuromere)

Use APOC for list to list restriction.

[dosumis]

Any progress? Is above description sufficient?

[Robbie1977]

https://github.com/VirtualFlyBrain/geppetto-vfb/blob/pipeline2/components/configuration/VFBGraph/graphConfiguration.js