[BioC] question about KEGGSOAP package

[Paul Shannon]

Hi Tijana,

I reproduced your problem, getting no results from 

    get.reactions.by.pathway("path:hsa05416" )

Interestingly, this works:

  get.reactions.by.pathway("path:eco00020")

The answer is found here:

 http://www.genome.jp/kegg/soap/

and in this paragraph in particular:

The current SOAP-based API service has not been updated for five years (see ChangeLog) and has become obsolete in certain aspects. Because the original developer is no longer with us at KEGG, we have decided to move to the new service with a much simpler design. The old service will continue to be accessible for six months, until December 31, 2012.

KEGG has further restrictions, having gone private in 2011:  all curation since last summer is available only to those who pay a licensing fee.
KEGG has been very valuable for a long time, and we are sorry to see it leave the public domain.

Could you describe your bioinformatics question -- the one that prompted you to try KEGGSOAP?  Then perhaps we can suggest alternative (and sustainable) ways to answer it.  At the very least, we wish to take your questions into consideration as Bioconductor moves ahead.

 - Paul

  

On Dec 20, 2012, at 12:45 AM, Marinkovic Tijana wrote:

> Hello,
> 
> I have a problem with using function get.reactions.by.pathway from KEGGSOAP package.
> E.g. reactions <-get.reactions.by.pathway("path:hsa05416" ) gives me output  character(0)
> while for example
> genes <-get.genes.by.pathway("path:hsa05416" ) works fine giving the list of gene identifiers.
> 
> What could be the problem?
> 
> Best regards,
> Tijana Marinkovic
> 
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> 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