From: Sucheta T. <su...@vb...> - 2005-02-15 18:39:53
|
Steve, You are right, parent_ids are there for some of them, but some others like transcript does not have one. I feel a parent_id needs to be there for transcript rather than genefeature. Since a transcript is derived from a gene. sucheta > sucheta- > > i *think* the answer to your question may be that features have > parent_id. this is used to build feature trees. > > steve > > Sucheta Tripathy wrote: > >> Thank you all for the response. My original question was bit premature >> and based on more of our convenience than the design of GUS per se. >> >> But these are some issues, I think the group may need to consider: >> >> By keeping different prediction outputs as different feature_ids and >> finally merging them through gene and gene_instance seems fine. But we >> need to distinguish between features within a gene and features of a >> gene. What I mean by that is a gene may have different features like >> an UTR feature , a promoter element feature etc, a cpg island feature >> and so on. which needs to be linked to a particular prediction output. >> >> For example I have gene 1 with gene_id 1 which has several >> gene_instances represented by different prediction algorithms and each >> having a different na_feature_id say: 1,2,3,4. >> >> For prediction algorithm with na_feature_id=1, I have a set of UTR >> locations and say I have feature_id 5 for UTR_5 and 6 for UTR_3 and a >> promoter feature with na_feature_id 7. Then how would I link >> na_feature_ids 1,5,6 and 7. >> >> So, for this I was thinking if one na_feature_id could represent a >> gene and its locations could have a description each with reviewer's >> status etc. And to save the geneinstances for any kind of splice >> variants or any other types of instances. >> >> Many thanks >> >> Sucheta >> >> At 09:40 AM 2/14/2005 -0500, you wrote: >> >>> This question is a bit more complex than it seems. >>> >>> All three of these may be necessary for every level of >>> analysis. first, was the overall gene prediction/feature >>> prediction reviewed and how was it algorithmically arrived at? >>> Then you can ask the same question about the locations. >>> Early locations may be provided by the same algorithm as the >>> feature, but these may be further defined later and require >>> their own review annotations. >>> >>> One thing that I think needs to be addressed, however, is how >>> these columns appear throughout the schema like mushrooms. I >>> have been told that GUS was hyper-normalized when it was first >>> written to 4N or 5N form, but that is definitely not the case >>> now. Why do you want review_status, reviewer and algorithm in >>> the feature table? Since these usually will appear in >>> clusters (i.e. running an algorithm once gives you 500 cases >>> of the same entry for all three on the same date), shouldn't >>> we have a table to collect these into an annotation_status >>> table and just have an FK to an entry in that table for every >>> table that uses these? The same goes for other SRes entries >>> such as taxon, project, etc. >>> >>> -Ed >>> >>> >>> >>> ---- Original message ---- >>> >Date: Sat, 12 Feb 2005 22:34:03 -0500 (EST) >>> >From: "Sucheta Tripathy" <su...@vb...> >>> >Subject: [Gusdev-gusdev] dots.nalocation table >>> >To: Gus...@li... >>> > >>> > >>> >Hi Group, >>> > >>> >From community annotation point of view, I was wondering if >>> it is a good >>> >idea to have is_reviewed, algorithm_id and reviewer_id in >>> dots.nalocation >>> >table. >>> > >>> >Since one na_feature_id( a transcript or a gene) may be >>> having multiple >>> >sets of nalocations, so one can easily capture them in >>> nalocation with >>> >different algorithms and with a reviewed option. >>> > >>> >In our application we need several gene calling programs to >>> have locations >>> >as well as related information registered. >>> > >>> >Sucheta >>> > >>> > >>> >-- >>> >Sucheta Tripathy >>> >Virginia Bioinformatics Institute Phase-I >>> >Washington street. >>> >Virginia Tech. >>> >Blacksburg,VA 24061-0447 >>> >phone:(540)231-8138 >>> >Fax: (540) 231-2606 >>> > >>> > >>> >------------------------------------------------------- >>> >SF email is sponsored by - The IT Product Guide >>> >Read honest & candid reviews on hundreds of IT Products from >>> real users. >>> >Discover which products truly live up to the hype. Start >>> reading now. >>> >http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >>> >_______________________________________________ >>> >Gusdev-gusdev mailing list >>> >Gus...@li... >>> >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> ----------------- >>> Ed Robinson >>> Center for Tropical and Emerging Global Diseases >>> University of Georgia, Athens, GA 30602 >>> ero...@ug.../(706)542.1447/254.8883 >>> >>> >>> ------------------------------------------------------- >>> SF email is sponsored by - The IT Product Guide >>> Read honest & candid reviews on hundreds of IT Products from real >>> users. >>> Discover which products truly live up to the hype. Start reading now. >>> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> >> >> ------------------------------------------------------- >> SF email is sponsored by - The IT Product Guide >> Read honest & candid reviews on hundreds of IT Products from real users. >> Discover which products truly live up to the hype. Start reading now. >> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > ------------------------------------------------------- > SF email is sponsored by - The IT Product Guide > Read honest & candid reviews on hundreds of IT Products from real users. > Discover which products truly live up to the hype. Start reading now. > http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > -- Sucheta Tripathy Virginia Bioinformatics Institute Phase-I Washington street. Virginia Tech. Blacksburg,VA 24061-0447 phone:(540)231-8138 Fax: (540) 231-2606 |