(Getting this conversation back on the list) Gabriele Sales predicts the fix for the problem reported by Hamid will be in devel before long. - Paul Begin forwarded message: > From: Gabriele Sales <gabriele.sales at="" unipd.it=""> > Subject: Re: Fwd: [BioC] edge-less pathways in graphite > Date: April 26, 2012 1:41:56 AM PDT > To: Paul Shannon <pshannon at="" fhcrc.org=""> > > Dear Paul, > > we have checked this pathway and, in fact, we have found a problem. > > Our conversion software emits the following error: > > [ERROR] in pathway "path:hsa04012": a relation references element 54 > that is either undefined or belongs to an invalid type > > This kind of error is severe enough that any further activity on the > pathway topology is aborted. The results is that no edge is emitted. > Genes (i.e. nodes) are processed in an independent step, so they still > appear in the final graph. > > Let's now turn our attention to the original cause of this problem. The > relation blocking the conversion is the following: > > <relation entry1="58" entry2="59" type="PPrel"> > <subtype name="compound" value="54"/> > </relation> > > Node 54 is defined like this: > > <entry id="54" name="path:hsa05214" type="map"> link="http://www.kegg.jp/dbget-bin/www_bget?hsa05214"> > <graphics name="Glioma" fgcolor="#000000" bgcolor="#FFFFFF"> type="roundrectangle" x="927" y="641" width="102" height="34"/> > </entry> > > As you can see it represents a pathway, but according to the relation > above it should be a compound. > > Looking at the pathway image, the relation corresponds to the chain: > > PI3K -> PIP3 -> PKB/Akt > > Therefore, it seems like that the middle node (PIP3) should really be > node 55. > > <entry id="55" name="cpd:C05981" type="compound"> link="http://www.kegg.jp/dbget-bin/www_bget?C05981"> > <graphics name="C05981" fgcolor="#000000" bgcolor="#FFFFFF"> type="circle" x="385" y="649" width="8" height="8"/> > </entry> > > This error shows that our conversion is somewhat too rigid. It should be > able to cope with this kind of problems by discarding the (single) edge, > rather than giving up completely. We are aware of this limitation and we > are already working on something better for the next graphite release. > > > Best, > g