this is something that is supported by the API now. But not fast.

The query is one of the uses cases we are re-designing the search for MG-RAST for. We expect it to be done in a couple (read 2) of weeks.

once that is done, we will implement simple searches in MG-RAST like which taxon is present in which geographic region etc.

currently it is very slow. you are going 90 degrees to the way the system is optimized

Best,
Folker

On May 16, 2013, at 3:17 PM, Paramvir Dehal <psdehal@lbl.gov> wrote:

> Yeah, those methods would work, I just need to know the function call and how to execute it.
>
>
> On Thu, May 16, 2013 at 3:14 PM, Rick stevens <stevens@anl.gov> wrote:
> For isolate genomes we can use metadata and 16s precomputed mapping.
>
> For WGS  and WGS contigs we need to workout precisely what you mean by assign to a taxon grouping.
>
>
>
>
> Sent from my iPad
>
> On May 16, 2013, at 2:58 PM, Rick stevens <stevens@anl.gov> wrote:
>
>> Dylan
>>
>> I'm trying Ti understand what you want to build.
>>
>> I think you want some way to have some one select a taxon and bring up in a taxon page all genomes and metagenomes and metagenome derived contigs associated with that taxon..
>>
>> Is that correct ?
>>
>> Sent from my iPad
>>
>> On May 16, 2013, at 2:26 PM, Dylan Chivian <dcchivian@lbl.gov> wrote:
>>
>>> I'm confused.  Isn't this week a joint hack-a-thon?  My guys flew out there to work with your guys.  Is that not happening?
>>>
>>> Thanks,
>>> - Dylan
>>>
>>>
>>>
>>>
>>>
>>> On Thu, May 16, 2013 at 12:21 PM, Folker Meyer <folker@mcs.anl.gov> wrote:
>>> We are super busy right now. Can we do this next week over the phone. I still need some input on the actual goals of this.
>>>
>>>
>>> --
>>> Sent from mobile device
>>>
>>> On May 16, 2013, at 14:14, Matthew Henderson <mhenderson@lbl.gov> wrote:
>>>
>>>> Paramvir, Mike and I are at Freund Lodge currently, and you guys (Andreas?) are welcome to come over and be part of the excitement of the KBase build and "stuff".  Mike and I will also be here tomorrow morning, but will have to leave around lunchtime to get back to the airport for the trip back home.
>>>>
>>>> Paramvir is less concerned at the moment about thresholding and just wants to see some functionality.
>>>>
>>>> Alternatively, if you are not feeling Freundlich, an email pointing us in the proper direction would also be appreciated.
>>>>
>>>> Thanks,
>>>> Matt
>>>>
>>>>
>>>> On Thu, May 16, 2013 at 1:28 PM, Dylan Chivian <dcchivian@lbl.gov> wrote:
>>>> Paramvir is a stakeholder here, so we should get his input, including on which identity thresholds he'd like to see.
>>>>
>>>> Thanks,
>>>> - Dylan
>>>>
>>>>
>>>> On Thu, May 16, 2013 at 11:10 AM, Dylan Chivian <dcchivian@lbl.gov> wrote:
>>>> Hi guys,
>>>>
>>>> instead of the call today, probably the time would be best spent with Folker and Andreas working with Matt and Mike directly on the metagenomics species search functionality for the Taxon pages.  I expect it is an expensive operation, so it is probably something that should be a one-time compute and stored somewhere associated with each taxon rather than on-the-fly when someone calls up the Taxon page.  There should probably also be separate lists for 99% identity and 97% identity (not sure other thresholds make any sense).
>>>>
>>>> Thoughts?  Are there other things to discuss and we should have the call anyway?
>>>>
>>>> Thanks,
>>>> - Dylan
>>>>
>>>>
>>>>
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