Closed ukemi closed 8 years ago
http://amigo.geneontology.org/amigo/term/GO:1903293#display-lineage-tab
View from parent term shows child with only "capable_of": http://amigo.geneontology.org/amigo/term/GO:0016791#display-lineage-tab
Nuts, I get the "correct" answer using the JS browser: http://nakama.berkeleybop.org/amigo/browse There is almost certainly a bug in the perl engine then.
I'm thinking that I'd rather drop the perl version altogether and just have a form of the JS one in its place--I do not want to have to keep aligning these two codebases.
@ukemi , you like the current tree behavior with jumping between pages, right?
Ugh, or maybe not--there is also the [Ancestors and children] view.
Duplicated locally.
Technically it's not wrong, it's just imprecise (as capable-of-part-of is the parent relation). However, it is confusing. We should show the more specific capable-of.
Okay, I see where this is going. In the transitivity closure, we have the following relations:
{
"sub": "GO:1903293",
"obj": "GO:0016791",
"pred": "capable of"
},
and
{
"sub": "GO:1903293",
"obj": "GO:0016791",
"pred": "capable of part of"
},
Both are, of course, right. This looks like the shadow of #161, with the JS grabbing one, and perl the other. This could be "solved" by adding these relations to the weighing system.
Bit ad-hoc, would be better to have better redundancy filtering upstream, but the weighting is at least a good and easy fallback
On 3 Mar 2016, at 15:15, kltm wrote:
Okay, I see where this is going. In the transitivity closure, we have the following relations:
{ "sub": "GO:1903293", "obj": "GO:0016791", "pred": "capable of" },
and
{ "sub": "GO:1903293", "obj": "GO:0016791", "pred": "capable of part of" },
Both are, of course, right. This looks like the shadow of #161, with the JS grabbing one, and perl the other. This could be "solved" by adding these relations to the weighing system.
Reply to this email directly or view it on GitHub: https://github.com/geneontology/amigo/issues/316#issuecomment-192013346
I think there is a bug in displaying relations in the inferred tree view for a GO term. If you search on the ontology term 'phosphatase complex (GO:1903293)' and display the inferred tree, the relation displayed between 'phosphatase complex' and 'phosphatase activity' is 'capable_of part of'. It should be 'capable_of'.