Query about data in graph for v-m-t for pombe

[vw253]

In these graphs http://www.esyn.org/builder.php?publishedid=232&type=Graph

which interactions are showing?The curated ones?

This would make sense (could the organism and interaction type set automatically to match the data?)

However, i couldn't figure out why vps17,29,36 an 35 has connections to itself (I don't see any recorded interactions of this type in PomBase or BioGRID)

Val

[Dan Bean]

Those are purple edges so interactions within complexes, those edges specifically come from GO:0030904 retromer complex in the pombase data

[vw253]

Hi Dan,

The self-self interactions I was looking at are orange lines

so for example here: http://www.esyn.org/builder.php?publishedid=232&type=Graph

vps17 has an orange self-self interation, but we haven't curated such an interaction with protein binding here: http://www.pombase.org/spombe/result/SPAPJ696.01c

[Dan Bean]

I see what the problem is, those edges are created because every member of the retromer complex is annotated to it twice in the complexes file, with two different evidence codes. I thought that file was a unique list of members of complexes. I'll add the extra processing of that file and those edges should go away.

[Dan Bean]

will be resolved by issue #91

[Dan Bean]

now fixed, compare

new: http://www.esyn.org/dev/builder.php?type=Graph&term=GO:0016192&interactionType=physical&source=pombase&includeInteractors=false

old: http://www.esyn.org/builder.php?publishedid=232&type=Graph

[vw253]

Thanks for that. It might make sense for us to refine the source files. I will have a think about the other users of the complex file, and the implications.