You've got to give me Model SEED compound and media IDs for now though. We can move to KBase IDs later once the prototype services are up (which will be very soon). Don’t give me compound names. We will eventually have a separate service that returns compound IDs given input names. -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Ben Bowen Sent: Thursday, April 19, 2012 12:08 PM To: KBase Microbes List; Brettin, Thomas S.; Ross Overbeek; KBase developers at LBL/UCB; [email protected] Subject: Re: [Microbe] Phenotype Exchange Data v0.1 Hi All, Regarding the previous mail, thanks to those who have given feedback. Somethings that have come up are which gene & organism ids to use and how to specify the non-obvious waste & utilization reactions in the FBA growth condition description. Issues like requires chloride ions, must dispose of CO2, H2O, etc have been raised. Thoughts? Ben ----------------------------- Email: [email protected] Office: 510-486-5138 MS 84RO171, Lawrence Berkeley Lab Web: ms.lbl.gov On Wed, Apr 18, 2012 at 5:39 PM, Ben Bowen <[email protected]> wrote:

Hi All,

Attached is the following 1) rationale for the minimum schema necessary to capture phenotype data 2) what we think example data would look like 3) a file that helps to better understand the growth media

Please advise us on what next steps should be.  We are not clear on the best organism IDs to use, gene ids, or how to supply the description of growth media.  In other words, we don't know if there is a requirement for a given format or if it is okay to send whatever we have.  This table is a minimal derivation of how we were already working with the data.

Thanks,

Ben

----------------------------- Email: [email protected] Office: 510-486-5138 MS 84RO171, Lawrence Berkeley Lab Web: ms.lbl.gov