[Funcoup] KEGG pathways broken (?)

[Erik Sonnhammer]

On 10/13/2011 03:39 PM, Andrey Alexeyenko wrote:
>> Right, is the suggested limit of 100 to prevent excessively slow queries?
> Yes, or "too big" ones if you wish...

OK, 100 seems fine to me, I guess very few KEGG are > 100 anyway.  But 
please indicate which ones have been disallowed, and why, rather than 
just deleting them.

>> 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?

A typical example is when the user has 2 gene lists and want to check 
how they are connected but showing list membership.

Unfortunately many users have more than 2 gene lists and would like to 
do the same for up to maybe 10 gene lists.  We should think about ways 
to enable this. If one could set a feature (color/shape) for each gene 
somehow in the query box that would do it.

/Erik

>
> 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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