Re: [Gusdev-gusdev] KEEG to GUS

[Steve F. <sfi...@pc...>]

thomas-

there is definite interest in incorporating KEGG data into GUS.   I am 
hoping we can work with you and the folks at PSU (Sanger) to develop a 
GUS compliant schema for this.

steve

Thomas Otto wrote:

> Hi,
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>
> I think it is time to discuss a bit about the stuff in did so far 
> concerning Kegg to Gus.
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>
> The principle idea was to put the datas in a relations database. The 
> visualization of the pathway will not be changed.
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>
> So we did the schema for the oracle, under the namespace CLASS. Some 
> tables already exist, like pathway, OMIM, enzymeclass... (but we kept 
> it in a package). Still Trish and I are talking about the tail of the 
> pathway-table (interaction and so). Shouldn't be too difficult to 
> parse the information from the tables for the compounds, reactions and 
> enzymes to the interaction tables.
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>
> Some might say this approve is a little bit static, but at least it a 
> base of informations.
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>
> We also wrote a parser (a bit beta stage, but coming soon) to upload 
> the data in the tables. The data itself can be downloaded at 
> ftp://ftp.genome.ad.jp/pub/kegg. Further we are working on a 
> classification for protein and functions.
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>
> To use the pathways locally, we wrote some scripts to surf through the 
> pathway, the enzyme, compounds and so one, looks like under kegg, just 
> in perl (do we need this in C?), so a bit slower and not complete so 
> far (i.e. structure information). If there is interest, I will install 
> it on a webserver. (If you want to be a betatester :-))
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>
> Maybe it would be useful to talk first about the tableschema before to 
> get from alpha stage to the beta with the programms.
> We hope to get some new ideas.
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>
> Cheers,
> Thomas
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>
> PS: All stuff is in beta stage (I couldn't use the dumpSchema.pl :-(), 
> so please tell me the bugs, thanks.
>