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Re: [SO-devel] Really basic question about mRNA and gene true path relation
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From: Jim Hu <ji...@ta...> - 2007-04-16 00:15:54
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Hi Karen, I actually started from the GFF3 docs (I'm on sabbatical in Lincoln's lab right now and have also been discussing this with people there and on the GMOD conf calls) so this kind of brings me full circle. I just wasn't sure from that if the SO representation was the same as the GFF3 representation (esp. wrt Chado) or if there is a data transformation between GFF3 and SO/Chado. For example, the Chado docs suggest that CDS is not explicitly in the feature graph for Chado, but is inferred from polypeptides + exons. But I see that for polycistronic genes we need explicit CDS features because otherwise we don't get the intergenic bits...unless we use a CDS only gene model. Thanks! Jim On Apr 15, 2007, at 7:00 PM, Karen Eilbeck wrote: > Hi Jim, > I'm sorry, I should have pointed you to the gff3 documentation in > the first place. > http://www.sequenceontology.org/gff3.shtml > > f) An operon > > A classic operon occurs when the genes in a polycistronic transcript > are co-regulated by cis-regulatory element(s): > > regulatory element > * ================================================> operon > ----->XXXXXXX*-->BBBBBB*--->ZZZZ*-->AAAAAA*----- > > It can be indicated in GFF3 in this way: > > ChrX . operon XXXX YYYY . + . ID=operon01;name=my_operon > ChrX . promoter XXXX YYYY . + . Parent=operon01 > ChrX . gene XXXX YYYY . + . > ID=gene01;Parent=operon01;name=resA > ChrX . gene XXXX YYYY . + . > ID=gene02;Parent=operon01;name=resB > ChrX . gene XXXX YYYY . + . > ID=gene03;Parent=operon01;name=resX > ChrX . gene XXXX YYYY . + . > ID=gene04;Parent=operon01;name=resZ > ChrX . mRNA XXXX YYYY . + . > ID=tran01;Parent=gene01,gene02,gene03,gene04 > ChrX . exon XXXX YYYY . + . ID=exon00001;Parent=tran01 > ChrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene01 > ChrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene02 > ChrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene03 > ChrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene04 > > Hope this helps, > Karen > > > On Apr 15, 2007, at 1:36 PM, Jim Hu wrote: > >> 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 >> >> > ===================================== Jim Hu Associate Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054 |
