Menu
▾
▴
Re: [SO-devel] Really basic question about mRNA and gene true path relation
|
From: Jim Hu <ji...@ta...> - 2007-04-15 19:36:47
|
Thanks Karen, The part I read in the meeting notes suggested that consensus was not actually reached on how to handle the polycitronic situation. Am I misreading? I also looked at your 2004 summary of the Cambridge meeting http://www.sequenceontology.org/meetings/SO-meeting-Cambridge.pdf From that, and poking around the ontology, it looks like your first solution (on page 6 of the pdf, which is the one that makes more sense to me, fwiw) was not adopted, since associated_with isn't in the SO relationships I see and transcribed_region is obsoleted. But then, I don't see feature_collection either. As an aside, it seems to me that the assertion that gene is not part_of polycistronic transcript is related to a difference in prokaryotic and eukaryotic usage of what a gene is (I would not assign the lac promoter/operator to lacZ; some of the older maps show the lac region as I P O Z Y A). Was there ever discussion of splitting gene into different sensu forms? I read the other reply as a yes. mRNA member_of gene is correct within SO and SOFA. But in my limited looking at sample data from Flybase it seems like it's common to use part_of when mRNAs are recorded in Chado. Perhaps that's part of what people mean by level 1 vs level 2 compliance between Chado and SO? Again, sorry if this is a rehash of ancient history and I'm just being obtuse. My basic problem is that I'm working on mapping various E. coli annotation sets to Chado but I'm new enough to both SO and Chado that I'm worrying about unforeseen problems arising from how I do it. So I'm trying to get as solid a foundation as I can...which means I'm probably overreading any ambiguity in the various sources of documentation. Jim On Apr 12, 2007, at 4:18 PM, Karen Eilbeck wrote: > Hi Jim, > The polycistronic/monocistronic debate happened at a SO meeting. > http://www.sequenceontology.org/meetings/meeting-doc.html > > Basically a gene can be thought of as a collection of transcripts. > That is what the member relationship is trying to represent. > > --Karen > > On Apr 12, 2007, at 10:07 AM, Jim Hu wrote: > >> I was browsing the ontology to try to understand the >> representation of polycistronic mRNAs and found myself wondering >> about monocitronic genes >> >> Is the relationship >> >> mRNA member_of gene >> >> via >> >> mRNA is_a processed_transcript >> is_a transcript >> is_a gene_member_region >> member_of gene >> >> or is there somewhere else that would give >> >> mRNA derives from gene >> >> or something along those lines? >> >> Presumably, how bacterial genes, mRNAs, and polypeptides should be >> represented in SO is an old discussion. Is there a FAQ or >> archived list discussion anyone can point me to? Thanks. >> >> Jim >> ===================================== >> Jim Hu >> Associate Professor >> Dept. of Biochemistry and Biophysics >> 2128 TAMU >> Texas A&M Univ. >> College Station, TX 77843-2128 >> 979-862-4054 >> >> >> --------------------------------------------------------------------- >> ---- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> opinions on IT & business topics through brief surveys-and earn cash >> http://www.techsay.com/default.php? >> page=join.php&p=sourceforge&CID=DEVDEV_______________________________ >> ________________ >> SOng-devel mailing list >> SOn...@li... >> https://lists.sourceforge.net/lists/listinfo/song-devel > > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV________________________________ > _______________ > SOng-devel mailing list > SOn...@li... > https://lists.sourceforge.net/lists/listinfo/song-devel ===================================== Jim Hu Associate Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054 |
