Hi Gilbert,

2011/2/3 Gilbert Feng <g-feng@northwestern.edu>

> Hi, Laurent
>
> Basically, GeneAnswers is designed for enrichment test based on different
> annotation libraries. In your case, if you just want to retrieve one or
> several NCI pathways, you can use standard xml query to obtain them from
> caBIO site. Then reconstruct the pathway by yourself (GeneAnswers also
> contains filtered gene/protein interaction dataframes for human, mouse and
> rat from NCBI). But if you want to retrieve a lot of NCI pathways, xml query
> might take a long time and it's better to ask NCI or caBIO people to
> generate a flat text for you.


Ok thanks for the suggestion. The tricky part is to systematically parse the
xml to a graphNEL. Paul Shannon kindly suggested another workaround using
Cytoscape and RCytoscape, I'll let everyone know how it went.

Also, caBIO doesn't includes only NCI, but also old BioCarta and Reactome
> pathways.
>

Actually the Biocarta and Reactome pathways are all available in BioPAX
format on the NCI website http://pid.nci.nih.gov/download.shtml so I should
be fine if I manage to convert BioPAX files to graphNEL objects.

Cheers,

Laurent

-- 
Laurent Jacob
Department of Statistics
UC Berkeley
http://cbio.ensmp.fr/~ljacob

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