[BioC] edge-less pathways in graphite

[Hamid Bolouri]

Thanks very much for the reality-check Paul. For compatibility reasons, I'd like to use 'graphite' graphs if I can. 

This isn't a show-stopper. I'll proceed without the edge-less graphs for now, and keep my fingers crossed that the missing edges will become available later.

Thanks

Hamid

----- Original Message -----
From: "Paul Shannon" <pshannon at fhcrc.org>
To: "Hamid Bolouri" <hbolouri at fhcrc.org>
Cc: "Paul Shannon" <pshannon at fhcrc.org>, bioconductor at r-project.org
Sent: Wednesday, April 25, 2012 12:42:57 PM
Subject: Re: [BioC] edge-less pathways in graphite

Hello Hamid,

Thanks for the report.  

As a sanity check, I just ran some code using Jitao David Zhang's KEGGgraph package.  It retrieves a graph with what appears to have a full set of edges:

library (KEGGgraph)
library (KEGG.db)

tbl.kp = toTable (KEGGPATHID2NAME)
kegg.id.erbB = tbl.kp [grep ('erbb', tbl.kp$path_name,ignore=T),]$path_id
temp.file = 'erbB.download'
retrieveKGML (kegg.id.erbB, organism='hsa', destfile=temp.file, method='internal')
tbl.erbB = parseKGML2DataFrame (temp.file)
g.erbB = parseKGML2Graph (temp.file, expandGenes=TRUE)

head (tbl.erbB)

        from       to         subtype
  1 hsa:2885 hsa:6654      activation
  2 hsa:2885 hsa:6655      activation
  3 hsa:2885 hsa:2549      activation
  4 hsa:2066 hsa:6776      activation
  5 hsa:2066 hsa:6776 phosphorylation
  6 hsa:2066 hsa:6777      activation

g.erbB
  A graphNEL graph with directed edges
  Number of Nodes = 87
  Number of Edges = 214

Knowing now that the full graph CAN be retrieved, I will look into graphite, see what we can figure out.

 - Paul

On Apr 25, 2012, at 11:03 AM, Hamid Bolouri wrote:

> hi; I am finding that some KEGG pathway graphNELs generated by graphite have zero edges, even though the KGML description includes edges, e.g.
> 
>> kegg[["ErbB signaling pathway"]]
>  "ErbB signaling pathway" pathway from KEGG
>  Number of nodes     = 87
>  Number of edges     = 0
>  Type of identifiers = native
>  Retrieved on        = 2011-05-05
> 
> Whereas the KGML for the same pathway includes statements such as:
> 
>    <relation entry1="75" entry2="46" type="PPrel">
>        <subtype name="activation" value="-->"/>
>        <subtype name="phosphorylation" value="+p"/>
>    </relation>
> 
> Am I missing something?
> 
> Thanks for a great package, BTW! 
> 
> Hamid Bolouri 
> PS Of the 46 apparently edge-less graphite graphNELs, several have zero edges in KEGG also, e.g. kegg[["Spliceosome"]]. I am _not_ talking about those.
> 
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: i386-pc-mingw32/i386 (32-bit)
> 
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
> [5] LC_TIME=English_United States.1252    
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] graphite_1.2.0       AnnotationDbi_1.18.0 Biobase_2.16.0      
> [4] BiocGenerics_0.2.0   RSQLite_0.11.1       DBI_0.2-5           
> [7] graph_1.34.0        
> 
> loaded via a namespace (and not attached):
> [1] IRanges_1.14.2     org.Hs.eg.db_2.7.1 stats4_2.15.0      tools_2.15.0
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor