Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b65 has been released
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Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b65 has been released
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From: Kam D. <kda...@lm...> - 2011-11-02 23:33:22
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Hi, Yes, sorry, that is the correct taxon ID and it should be changed. Best, Kam At 04:16 PM 11/2/2011, you wrote: >Yes, a query for the name should be doable. It will be a matter of >finding the right time/place to do it. > >Also, just to confirm, should the taxon ID be changed then to 559292? > >John David N. Dionisio, PhD >Associate Professor, Computer Science >Associate Director, University Honors Program >Loyola Marymount University > > > >On Nov 2, 2011, at 8:41 AM, Kam Dahlquist wrote: > > > Hi, > > > > Ah. So I think what happened is the same thing with E. coli, they > > made an ID for a more specific strain (in this case S288c) because > > they are sequencing more substrains of yeast. > > > > I think option 1 below is the way to go. Can't we discover what the > > name is by reading the xml? > > > > Thanks, > > Kam > > > > At 10:53 PM 11/1/2011, John David N. Dionisio wrote: > >> Greetings, > >> > >> I checked the S. cerevisiae species profile in the code and its > >> Taxon ID is 4932. Thus, you were indeed seeing a generic species > >> profile being called up to do this export because the included yeast > >> profile did not have a matching Taxon ID. > >> > >> I can change the profile to use 559292 no problem. However, this > >> scenario still reveals a bug for when the generic species profile is > >> invoked: the species name becomes null, and code that processes this > >> name crashes on that condition. > >> > >> For this latter issue, there are two ways to fix it: > >> > >> - Make the generic species profile still provide some kind of > >> species name (or make the user enter one?). > >> - Make the export code more robust by not crashing in the case where > >> the species name is null. > >> > >> I'm thinking that the former is the right way to go (the species > >> name is used to offer a default filename for the GDB, as well as for > >> various columns in the GDB schema, so its being null or blank may > >> cause issues in that aspect). > >> > >> John David N. Dionisio, PhD > >> Associate Professor, Computer Science > >> Associate Director, University Honors Program > >> Loyola Marymount University > >> > >> > >> On Nov 1, 2011, at 4:32 PM, Kam Dahlquist wrote: > >> > >>> This time with attachments. > >>> > >>> At 04:31 PM 11/1/2011, Kam Dahlquist wrote: > >>>> Hi, > >>>> > >>>> I finally had a chance to try a yeast export wtih GMB2.0b65--I > >>>> didn't get very far: > >>>> > >>>> 1. I imported the UniProt, GO, and GOA all fine. When I started > >>>> the export, the Species panel listed "Taxon ID 559292, > >>>> null". That's the correct taxon ID for the species I am > >>>> importing/exporting, but shouldn't it also tell me the species name, > >>>> not just null? or is that what happens when the generic profile is > >>>> called. There should be a Saccharomyces cerevisiae profile in > >>>> GenMAPP Builder somewhere, even though we never finished it. > >>>> > >>>> 2. In the next window, I click on the box "Save GenMAPP Database > >>>> File As..." and nothing happens. Screenshots of the console window > >>>> (parts 1 and 2, could not fit into one screen) are attached. > >>>> > >>>> 3. The title bar and notes field of the export wizard did not get > >>>> updated to gmb2.0b65. > >>>> > >>>> Thanks, > >>>> Kam > >>>> > >>>> At 11:13 PM 10/14/2011, you wrote: > >>>>> GenMAPP Builder 2.0b65 Release Notes > >>>>> > >>>>> This release of GenMAPP Builder includes a preliminary > >>>>> implementation of multi-species Gene Database exports, as well as > >>>>> user interface changes to the export wizard. This version also > >>>>> updates the Gene Ontology database library to accommodate the > >>>>> latest elements included in GO OBO XML downloads. > >>>>> > >>>>> > >>>>> > >> > ------------------------------------------------------------------------------ > >>>>> All the data continuously generated in your IT infrastructure > contains a > >>>>> definitive record of customers, application performance, security > >>>>> threats, fraudulent activity and more. Splunk takes this data and makes > >>>>> sense of it. Business sense. IT sense. 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