Implement transitive reduction in hierarchy views and graph views

[cmungall]

This is unintuitive to many users:

• http://amigo.geneontology.org/amigo/term/GO:0044767#display-lineage-tab
• http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0044767

We can see a long list of direct subclasses.

Formally it's correct, these are all the most specific subclasses of [http://amigo.geneontology.org/amigo/term/GO:0044767](single-organism development). However, many of the classes are highly specific,, as be seen clearly if we click on a child like [http://amigo.geneontology.org/amigo/term/GO:0021694](cerebellar Purkinje cell layer formation):

• http://amigo.geneontology.org/amigo/term/GO:0021694#display-lineage-tab

See:

We should discuss using some kind of transitive reduction (e.g. same as what @fbastian implemented in owltools) to eliminate these. This should be custmizable, so best done on the client side.

[kltm]

If I'm understanding correctly, I'm skeptical of this taking place on the client side as things currently stand.

The current return is a transitivity graph (essentially the relation of the target node to its neighbors) and a topology graph (how its connected to its neighbors). They are then merged into the current view. To make this work we need different returns and calculations, that I believe would need to be done on the server to maintain our speed.

We should talk out of thread about the details and add the results when we want to implement.

[kltm]

After a talk, for the first iteration we'd likely do something along the lines of create a new field like topology_reduced_graph_json (or whatever) and populate it with the reduction. This would be a server-side solution. Possibly easy enough to implement when we start the Java/server-side work again.

[fbastian]

Hi, I run the fake relation reduction (considering is_a and part_of equivalent) over go-basic, it removed 2539 relations, result can be found here: http://bgee.unil.ch/download/go-basic-reduced.obo

The result for GO:0021694:
Before:

[Term]
id: GO:0021694
name: cerebellar Purkinje cell layer formation
...
is_a: GO:0044767 ! single-organism developmental process
is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
relationship: part_of GO:0021692 ! cerebellar Purkinje cell layer morphogenesis
relationship: part_of GO:0021697 ! cerebellar cortex formation

After:

[Term]
id: GO:0021694
name: cerebellar Purkinje cell layer formation
...
relationship: part_of GO:0021692 ! cerebellar Purkinje cell layer morphogenesis
relationship: part_of GO:0021697 ! cerebellar cortex formation

On a side note, the reduction over super-properties also removed 711 relations.