[Funcoup] KEGG pathways broken (?)

[Andrey Alexeyenko]

> Right, is the suggested limit of 100 to prevent excessively slow queries?
Yes, or "too big" ones if you wish...

>
> You're right that indiv. genes work with network dist = 1, but this may
> not be practical for large gene sets. Is there any reason to not allow
> it for network dist = 0 ?
The idea of the magenta box is that it is an "alternative" to finding 
neighbors at distance 1 in the normal way (although the latter is done, 
too). So 0 makes no sense. Indeed, if you want 0, why not to paste all 
genes into the yellow box?

Andrey

>
> /Erik
>
> On 10/13/2011 02:47 PM, Andrey Alexeyenko wrote:
>> Yes, they are simply not in the synonyms table yet :(
>>
>> The last time I mentioned it was related to the question:
>> how we should limit such groups as KEGG or GO?
>> I suggested that only groups with<100 genes can be queried.
>>
>> Whatever was the answer, I never was back to that, so this still has to
>> be done (together with GO, maybe something else?)
>>
>> Indiv. genes must work. Note that they never work with distance set to 0.
>>
>> Andrey
>>
>>
>> On 2011-10-13 14:44, Erik Sonnhammer wrote:
>>> Alternatively, something is broken with the magenta nodes.  Even when
>>> moving gene ids from the yellow to the magenta I get zilch magenta nodes
>>> in the output.
>>>
>>> /Erik
>>>
>>> On 10/13/2011 02:40 PM, Erik Sonnhammer wrote:
>>>> Andrey, either I forgot how to use it or it is broken, but I can't seem
>>>> to get the KEGG pathways to work on the website.  If I put any KEGG id,
>>>> e.g. KEGG00010 in the yellow box it just says.
>>>>
>>>> "The database does not contain the identifier(s) you have submitted.
>>>> Please try other synonyms. "
>>>>
>>>> If I put real queries in the yellow box and pathways I know they are
>>>> linked to in the magenta box, I get no magenta nodes.
>>>>
>>>> /Erik
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