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Provide graph view over GCIs #45

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ShahimEssaid opened this issue Feb 2, 2015 · 4 comments
Open

Provide graph view over GCIs #45

ShahimEssaid opened this issue Feb 2, 2015 · 4 comments

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@ShahimEssaid
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From cmung...@gmail.com on January 24, 2013 17:15:48

OWLGraphView provides a graph view of an ontology, with edges formed by axioms such as

X SubClassOf R Some Y
==>

Ontologies such as Uberon have taxon-specific relationships which have OWL semantics

(X and part_of some Taxon) SubClassOf R some Y

these are "invisible" in the graph view, as the subject is not a named class.

Some options:

  1. Add something to materialize the class expressions on the LHS. In the above you would get a graph

{{{
Taxon X
^ /
| /
[p] [i]
| /
NewClass---[R]-->Y
}}}

  1. Fold the GCI conditions into the edge label. E.g.

    X---[R,Taxon]---->Y

This is potentially dangerous, so it would be done only if the API user asks for this.

Any other options?

[Reported by Frederic Bastian]

Original issue: http://code.google.com/p/owltools/issues/detail?id=45

@ShahimEssaid
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From cmung...@gmail.com on January 30, 2013 16:32:41

Note: should be possible to use uberon as example:

Query:
how does the lineage of the paraythroid gland vary across species?

Answer:
dorsal part of pouch 3+4 (mammals)
ventral part of pouch 3-4 (aves)

(need to check these are present in the ontology)

@ShahimEssaid
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From cmung...@gmail.com on January 30, 2013 16:42:08

Just a note here to keep things in one place: the manually curated GCIs are missing from uberon/composite-* ontologies.

This isn't an owltools problem, but if we switch to owltools to generate the auto-GCIs the problem should go away

@ShahimEssaid
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From cmung...@gmail.com on May 02, 2013 13:29:51

SpeciesMergeUtil now being used, fixes GCI issue

@ShahimEssaid
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From frederic...@gmail.com on November 28, 2014 05:49:27

Solution 2 has been implemented, see issue #102 . OWLGraphEdge now has gci_relation and gci_filler attributes. OWLGraphWrapperEdgesExtended implements many methods reproducing behavior of OWLGraphWrapperEdges methods, but taking into account GCI relations. The ticket might be closed.

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