"Inferred fatal relation" for GO:0000124

[raymond91125]

in the inferred tree view for term GO:0000124 SAGA complex, there are a number of [Inferred fatal relation]. AmiGO 1 does not have these. no other term in the tree show this relation.

perhaps related issue, GO:0000124 should have a relationship: has_part GO:0071819. i don't see this relationship on either terms' pages, except under Graph Views of GO:0071819.

i hope this is a 'New' issue. i can't figure out how to search issues.

[kltm]

In this case (I haven't been able to find another), while the topology graph seems to be correct, the transitivity graph seem to be missing the nodes/edges and that hits the "fatal" relation, which for some reason looks like a normal--non-error--case in the code with no real comment.

[kltm]

Transitivity graph: {"nodes":[{"id":"GO:0032991","lbl":"macromolecular complex"},{"id":"GO:0000123","lbl":"histone acetyltransferase complex"},{"id":"GO:0044451","lbl":"nucleoplasm part"},{"id":"GO:0044464","lbl":"cell part"},{"id":"GO:0005575","lbl":"cellular_component"},{"id":"GO:0044422","lbl":"organelle part"},{"id":"GO:0070461","lbl":"SAGA-type complex"},{"id":"GO:0000124","lbl":"SAGA complex"},{"id":"GO:0044424","lbl":"intracellular part"},{"id":"GO:0005634","lbl":"nucleus"},{"id":"GO:0043234","lbl":"protein complex"},{"id":"GO:0043229","lbl":"intracellular organelle"},{"id":"GO:0044446","lbl":"intracellular organelle part"},{"id":"GO:0005623","lbl":"cell"},{"id":"GO:0044428","lbl":"nuclear part"},{"id":"GO:0043226","lbl":"organelle"},{"id":"GO:0005622","lbl":"intracellular"},{"id":"GO:0005654","lbl":"nucleoplasm"}],"edges":[{"sub":"GO:0000124","obj":"GO:0070461","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0043229","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0000123","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0005623","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0005634","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0044424","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0043226","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0005654","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0032991","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0043234","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0044446","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0005575","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0044451","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0044464","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0005622","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0044428","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0044422","pred":"is_a"}]}

[kltm]

Topology graph: {"nodes":[{"id":"GO:0032991","lbl":"macromolecular complex"},{"id":"GO:0000123","lbl":"histone acetyltransferase complex"},{"id":"GO:0044451","lbl":"nucleoplasm part"},{"id":"GO:0044464","lbl":"cell part"},{"id":"GO:0031974","lbl":"membrane-enclosed lumen"},{"id":"GO:0043231","lbl":"intracellular membrane-bounded organelle"},{"id":"GO:0031981","lbl":"nuclear lumen"},{"id":"GO:0005575","lbl":"cellular_component"},{"id":"GO:0044422","lbl":"organelle part"},{"id":"GO:0070013","lbl":"intracellular organelle lumen"},{"id":"GO:0000124","lbl":"SAGA complex"},{"id":"GO:0070461","lbl":"SAGA-type complex"},{"id":"GO:0044424","lbl":"intracellular part"},{"id":"GO:0043234","lbl":"protein complex"},{"id":"GO:0005634","lbl":"nucleus"},{"id":"GO:0043229","lbl":"intracellular organelle"},{"id":"GO:0043233","lbl":"organelle lumen"},{"id":"GO:0044446","lbl":"intracellular organelle part"},{"id":"GO:0043227","lbl":"membrane-bounded organelle"},{"id":"GO:0005623","lbl":"cell"},{"id":"GO:0044428","lbl":"nuclear part"},{"id":"GO:0043226","lbl":"organelle"},{"id":"GO:0005622","lbl":"intracellular"},{"id":"GO:0005654","lbl":"nucleoplasm"}],"edges":[{"sub":"GO:0043234","obj":"GO:0032991","pred":"is_a"},{"sub":"GO:0000124","obj":"GO:0070461","pred":"is_a"},{"sub":"GO:0070013","obj":"GO:0043233","pred":"is_a"},{"sub":"GO:0044428","obj":"GO:0005634","pred":"part_of"},{"sub":"GO:0044446","obj":"GO:0043229","pred":"part_of"},{"sub":"GO:0044464","obj":"GO:0005575","pred":"is_a"},{"sub":"GO:0044451","obj":"GO:0044428","pred":"is_a"},{"sub":"GO:0005634","obj":"GO:0043231","pred":"is_a"},{"sub":"GO:0044464","obj":"GO:0005623","pred":"part_of"},{"sub":"GO:0043226","obj":"GO:0005575","pred":"is_a"},{"sub":"GO:0000123","obj":"GO:0043234","pred":"is_a"},{"sub":"GO:0043229","obj":"GO:0043226","pred":"is_a"},{"sub":"GO:0005654","obj":"GO:0044428","pred":"is_a"},{"sub":"GO:0043231","obj":"GO:0043227","pred":"is_a"},{"sub":"GO:0032991","obj":"GO:0005575","pred":"is_a"},{"sub":"GO:0044446","obj":"GO:0044424","pred":"is_a"},{"sub":"GO:0031981","obj":"GO:0044428","pred":"is_a"},{"sub":"GO:0070461","obj":"GO:0000123","pred":"is_a"},{"sub":"GO:0043233","obj":"GO:0044422","pred":"is_a"},{"sub":"GO:0044424","obj":"GO:0005622","pred":"part_of"},{"sub":"GO:0044451","obj":"GO:0005654","pred":"part_of"},{"sub":"GO:0005623","obj":"GO:0005575","pred":"is_a"},{"sub":"GO:0044424","obj":"GO:0005575","pred":"is_a"},{"sub":"GO:0044446","obj":"GO:0044422","pred":"is_a"},{"sub":"GO:0044422","obj":"GO:0005575","pred":"is_a"},{"sub":"GO:0043231","obj":"GO:0043229","pred":"is_a"},{"sub":"GO:0044428","obj":"GO:0005575","pred":"is_a"},{"sub":"GO:0031981","obj":"GO:0070013","pred":"is_a"},{"sub":"GO:0031974","obj":"GO:0005575","pred":"is_a"},{"sub":"GO:0043229","obj":"GO:0044424","pred":"is_a"},{"sub":"GO:0070013","obj":"GO:0044446","pred":"is_a"},{"sub":"GO:0043227","obj":"GO:0043226","pred":"is_a"},{"sub":"GO:0044451","obj":"GO:0005575","pred":"is_a"},{"sub":"GO:0044428","obj":"GO:0044446","pred":"is_a"},{"sub":"GO:0044424","obj":"GO:0044464","pred":"is_a"},{"sub":"GO:0005654","obj":"GO:0031981","pred":"part_of"},{"sub":"GO:0043233","obj":"GO:0031974","pred":"is_a"},{"sub":"GO:0000123","obj":"GO:0044451","pred":"is_a"},{"sub":"GO:0005622","obj":"GO:0044464","pred":"is_a"},{"sub":"GO:0044422","obj":"GO:0043226","pred":"part_of"}]}

[kltm]

This naturally also breaks the browse widget in this case.

[kltm]

This is an OWLTools problem then, not an issue with this codebase. I'll keep the bug here for now as a placeholder since it directly affects current "production" code.

[kltm]

This appears to be a bug in a bit of code that we'll be rewriting soon (around getOutgoingEdgesClosure in OWLTools). After conferring with Heiko about this, we'll not be tracking this down unless this continues to be in an issue in the new method that we'll be using (which will happen in conjunction with some changes we'll be making to get IEAs fully loaded). Since this appears in the perl version and can safely be used in spite of the underlying data error, this only rates as a C-type bug in my book. Also, "revisit" since it cannot be fixed from within this code base.

[kltm]

A (currently deactivated) test case was written for OWLTools, which exposed some other weird stuff. Possibly a very interesting bug.

[kltm]

This needs to have some kind of fix immediately. The proposed path above is not going to cut it time-wise, so we're going to add a "related_to" relationship that is generic and true.

[kltm]

Another example (from rama): http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/GO:0016592

[kltm]

Looking at the version I have and the current loaded beta version, the introduction of has_part seem to have caused (at least some of) the disruption.