Oddities in folding in graph display

[cmungall]

See: http://create.monarchinitiative.org/editor/graph/gomodel:5797c67200000016

The underlying edge is

[a ParkinsonDisease] --has_part--> [a Tremor]

When folding a relationship, the directionality must be preserved. ie this should be shown as:

PD 
has_part(Tremor)

however, it is inverting it:

Tremor
has_part(PD)

it is never semantically correct to do this, unless R is replaced with InverseOf(R). This is the same as translating the base graph to the equivalent:

[a Tremor] --part_of--> [a ParkinsonDisease]

based on the inverse properties declaration

(although a generic graph editor issue this is only affecting monarch so far)

[kltm]

As I mentioned, this smells a lot like a fold configuration issue; I've, so far, been unable to create anything like this in GO Noctua. Semantics have no part if there is a raw override in the configuration of the folding order. Where is the startup.yaml for Monarch being kept? I'd like to first check the settings of COLLAPSIBLE_REVERSE_RELATIONS.

[cmungall]

COLLAPSIBLE_REVERSE_RELATIONS sounds like the kind of configuration parameter that should be eliminated. I believe this was introduced for protein complexes, but the original implementation was incorrect. Remember this one? https://github.com/geneontology/noctua/issues/265

On 27 Jul 2016, at 0:51, kltm wrote:

As I mentioned, this smells a lot like a fold configuration issue; I've, so far, been unable to create anything like this in GO Noctua. Semantics have no part if there is a raw override in the configuration of the folding order. Where is the startup.yaml for Monarch being kept? I'd like to first check the settings of COLLAPSIBLE_REVERSE_RELATIONS.

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[kltm]

Either way, we need to see the current configuration to make sure that this is what's going on.