|
From: Lincoln S. <ls...@cs...> - 2007-04-12 16:43:59
|
Hi Karen, I've got a working copy of the htdocs directory (so-home). Ideally I'd like to be able to make changes, cvs commit it, and have the changes appear on the live site in a day or two. Lincoln On 4/11/07, Karen Eilbeck <kei...@ge...> wrote: > > Hi Lincoln,The web pages are generated from the cvs. We could probably > mirrir from the cvs. I will look into it. > The GFF documentation is now updated. > > --Karen > > On Apr 11, 2007, at 1:41 PM, Lincoln Stein wrote: > > Hi Karen, > > Please find enclosed a new version of the GFF3 spec that discusses using > match_part/match instead of match/match_set. > > Is there a way to set up the sequenceontology.org web site such that the > gff3 spec file displayed is mirrored from the up-to-date version in CVS? > > Thanks, > > Lincoln > > On 4/11/07, Karen Eilbeck <kei...@ge...> wrote: > > > > Hi all,I will obsolete the term match_set from SO and SOFA as agreed in > > discussion below. > > Cheers, > > Karen > > > > On Apr 4, 2007, at 2:34 PM, Lincoln Stein wrote: > > > > Hi Sofia, > > > > Well, you use "protein_match" for the first one, and > > "translated_nucleotide_match" for the second one. Also, the first one uses > > nucleotide coordinates and the second uses protein coordinates. > > > > Best, > > > > Lincoln > > > > On 4/4/07, Sofia Robb < so...@ne...> wrote: > > > > > > Hi Lincoln, > > > > > > Makes sense to me. > > > I have a question, it applies to my current use of match_set and > > > protein_match / nucleotide_match and your new proposal. > > > > > > what do you do for > > > protein query against nucleotide db > > > nucleotide query against protein db > > > > > > Sofia > > > > > > > > > > > > On Apr 4, 2007, at 9:17 AM, Lincoln Stein wrote: > > > > > > Hi Sofia, > > > > > > What you're doing is what you have to do with the current SO, but it > > > isn't ideal. One has to examine the subfeatures in order to determine the > > > nature of a hit (nucleotide=>nucleotide, protein=>nucleotide, etc). Under > > > the new proposal, the match would be typed (nucleotide_match), and the > > > match_part would be generic. How does this sound to you? > > > > > > Lincoln > > > > > > On 4/2/07, Sofia Robb < so...@ne...> wrote: > > > > > > > > Hello All, > > > > i usually use > > > > match_set to represent the HIT > > > > and > > > > nucleotide_match or protein_match > > > > to represent the HSPs. > > > > > > > > sofia > > > > > > > > > > > > On Mar 29, 2007, at 2:31 AM, Richard Durbin wrote: > > > > > > > > > Karen and Lincoln's proposed solution sounds sensible and good to > > > > me. > > > > > > > > > > Richard > > > > > > > > > > Lincoln Stein wrote: > > > > >> Hi Karen, > > > > >> > > > > >> That was the solution I was hoping for. Can it be done? > > > > >> > > > > >> Lincoln > > > > >> > > > > >> On 3/28/07, *Karen Eilbeck* < kei...@ge... > > > > >> <mailto: kei...@ge...>> wrote: > > > > >> > > > > >> Hi Lincoln, > > > > >> Sorry for the delay getting back to you. I'm at a Dagstuhl at > > > > >> meeting. > > > > >> > > > > >> I think this has always been confusing and now that I look at > > > > it, > > > > >> I don't think it works as advertised. > > > > >> I think it would make logical sense if we removed match_set > > > > and > > > > >> had match_part (HSP) be part of a match. > > > > >> Then any kind of match such as EST_match could have a > > > > match_part > > > > >> But that might be too easy. > > > > >> > > > > >> -K > > > > >> > > > > >> On Mar 28, 2007, at 9:38 AM, Lincoln Stein wrote: > > > > >> > > > > >>> Hi, > > > > >>> > > > > >>> I'm trying to figure out how to represent HSPs that are part > > > > > > > > >>> of a > > > > >>> larger match. The relevant section of the DAG is enclosed, > > > > >>> and it > > > > >>> shows that "match_part" is part of "match_set" and that > > > > >>> match_set > > > > >>> ISA match. Meanwhile, expressed_sequence_match also ISA > > > > match. I > > > > >>> would like to assert that an HSP is a match_part which is > > > > then > > > > >>> PARTOF an expressed_sequence_match, but I'm not sure whether > > > > the > > > > >>> traversal rules allow this. Can anyone comment? > > > > >>> > > > > >>> Lincoln > > > > >>> > > > > >>> -- > > > > >>> Lincoln D. Stein > > > > >>> Cold Spring Harbor Laboratory > > > > >>> 1 Bungtown Road > > > > >>> Cold Spring Harbor, NY 11724 > > > > >>> (516) 367-8380 (voice) > > > > >>> (516) 367-8389 (fax) > > > > >>> FOR URGENT MESSAGES & SCHEDULING, > > > > >>> PLEASE CONTACT MY ASSISTANT, > > > > >>> SANDRA MICHELSEN, AT mic...@cs... > > > > >>> <mailto:mic...@cs... > > > > > >>> <match_question.gif> > > > > >> > > > > >> > > > > >> > > > > >> > > > > >> -- > > > > >> Lincoln D. Stein > > > > >> Cold Spring Harbor Laboratory > > > > >> 1 Bungtown Road > > > > >> Cold Spring Harbor, NY 11724 > > > > >> (516) 367-8380 (voice) > > > > >> (516) 367-8389 (fax) > > > > >> FOR URGENT MESSAGES & SCHEDULING, > > > > >> PLEASE CONTACT MY ASSISTANT, > > > > >> SANDRA MICHELSEN, AT mic...@cs... <mailto:mic...@cs...> > > > > >> > > > > --------------------------------------------------------------------- > > > > >> --- > > > > >> > > > > >> > > > > --------------------------------------------------------------------- > > > > >> ---- > > > > >> 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 > > > > > > > > > > > > > > > > -- > > > Lincoln D. Stein > > > Cold Spring Harbor Laboratory > > > 1 Bungtown Road > > > Cold Spring Harbor, NY 11724 > > > (516) 367-8380 (voice) > > > (516) 367-8389 (fax) > > > FOR URGENT MESSAGES & SCHEDULING, > > > PLEASE CONTACT MY ASSISTANT, > > > SANDRA MICHELSEN, AT mic...@cs... > > > > > > > > > > > > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > (516) 367-8380 (voice) > > (516) 367-8389 (fax) > > FOR URGENT MESSAGES & SCHEDULING, > > PLEASE CONTACT MY ASSISTANT, > > SANDRA MICHELSEN, AT mic...@cs... > > > > ------------------------------------------------------------------------- > > 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 > > > > > > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT mic...@cs... > <gff3.shtml> > > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT mic...@cs... |