[BioC] Kegg Profile package problem

[zhao shilin]

Hi Dan,

I'm very happy to know that some other persons were using my package.
And it is the first time that some persons ask me questions about it
in the mail list.

For your question, the web page
"http://www.genome.jp/kegg/pathway/map/map00910.html" indicated that:
The biological process of the nitrogen cycle is a complex interplay
among many microorganisms catalyzing different reactions. And we can't
find human in the reference pathway tab of this page. So I think this
is not a human pathway.

And what you said about the download_KEGGfile function is right.
Because I want to download the species specific pathway map with green
background to indicate that the gene exist in this species. Maybe I
will change function as your advise in the next version.

For the find_enriched_pathway function, it used the annotation from
the package KEGG.db. I have tested the KEGG.db package and some genes
were annotated to hsa00910 pathway. I don't know why this happens.
Maybe it is because of the update of the KEGG website.

Shilin

2012/12/28 Dan Tenenbaum <dtenenba at fhcrc.org>:
> On Thu, Dec 27, 2012 at 12:58 PM, gregory voisin <voisingreg at yahoo.fr> wrote:
>>
>> In that case, can you get the pathway map you need from this link:
>> http://www.genome.jp/kegg/pathway/map/map00910.png ?
>>
>> In the automatic workflux  ( my case), it isn't very optimal
>>
>> I imagie that  download_KEGGfile function  concatenate
>> (pathway_id="00910",specis='hsa') to build the request:
>> 'http://www.genome.jp/kegg-bin/download?entry=hsa00910&format=kgml'
>>
>> Ideally the hsa could be replaced by "map".
>>
>
> I'm cc'ing the maintainer of the KEGGprofile package.
>
> Dan
>
>
>> Greg
>>
>>
>>
>> ________________________________
>> De : Dan Tenenbaum <dtenenba at fhcrc.org>
>> À : gregory voisin <voisingreg at yahoo.fr>
>> Cc : "bioconductor at r-project.org" <bioconductor at r-project.org>
>> Envoyé le : Jeudi 27 décembre 2012 14h39
>>
>> Objet : Re: [BioC] Kegg Profile package problem
>>
>> On Thu, Dec 27, 2012 at 4:30 AM, gregory voisin <voisingreg at yahoo.fr> wrote:
>>> Hi Dan ,
>>> Yes, the link associated to hsa00910 doesn't exist but the map00910
>>> (http://www.genome.jp/kegg/pathway/map/map00910.html) exists
>>>
>>> The id 00910 is a result provided by the find_enriched_pathway function().
>>>
>>
>> In that case, can you get the pathway map you need from this link:
>>
>> http://www.genome.jp/kegg/pathway/map/map00910.png
>>
>>
>> ?
>>
>> Dan
>>
>>> Greg
>>>
>>>
>>>
>>> ________________________________
>>> De : Dan Tenenbaum <dtenenba at fhcrc.org>
>>> À : gregory voisin <voisingreg at yahoo.fr>
>>> Cc : "bioconductor at r-project.org" <bioconductor at r-project.org>
>>> Envoyé le : Jeudi 27 décembre 2012 2h35
>>> Objet : Re: [BioC] Kegg Profile package problem
>>>
>>> On Wed, Dec 26, 2012 at 6:54 AM, gregory voisin <voisingreg at yahoo.fr>
>>> wrote:
>>>>
>>>>
>>>>
>>>> Hi,
>>>> I use KeggProfile in my pipeline analysis and it's efficient, but I have
>>>> problem with one pathway_ID.
>>>>
>>>> Exemple ( copy and paste):
>>>>
>>>> require(KEGGprofile)
>>>> download_KEGGfile(pathway_id="04110",specis='hsa')
>>>>
>>>> #In this case , not problem
>>>>
>>>> download_KEGGfile(pathway_id="00910",specis='hsa')
>>>
>>>
>>> I think perhaps there is no such pathway. Here's a list of all human
>>> pathways:
>>> http://rest.kegg.jp/list/pathway/hsa
>>>
>>> 04110 is included but 00910 is not.
>>>
>>> Dan
>>>
>>>
>>>>
>>>> #this pahway exits in KEGG, but the download is impossible
>>>> #[1] "Downloading files: 1/1"
>>>> #essai de l'URL
>>>> 'http://www.genome.jp/kegg-bin/download?entry=hsa00910&format=kgml'
>>>> #Content type 'text/plain' length unknown
>>>> #URL ouverte
>>>> #downloaded 1 bytes
>>>>
>>>> #essai de l'URL 'http://www.genome.jp/kegg/pathway/hsa/hsa00910.png'
>>>> #Erreur dans download.file(paste("http://www.genome.jp/kegg/pathway/",
>>>> specis,  :
>>>> #  impossible d'ouvrir l'URL
>>>> 'http://www.genome.jp/kegg/pathway/hsa/hsa00910.png'
>>>> #De plus : Message d'avis :
>>>> #In download.file(paste("http://www.genome.jp/kegg/pathway/", specis,  :
>>>> #  ouverture impossible : le statut HTTP était '404 Not Found'
>>>>
>>>>
>>>> My solution :  omit this pathway in my analysis: ponctual, fast  but not
>>>> very elegant and not professional !!
>>>>
>>>> If someone has a suggestion , comments or solution, let's go ,
>>>>
>>>> Thanks
>>>>
>>>> Greg
>>>> Montréal
>>>>
>>>>        [[alternative HTML version deleted]]
>>>>
>>>>
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>>>
>>>
>>
>>