Re: [SO-devel] Matches and match parts

SourceForge Headquarters 1320 Columbia Street Suite 310 San Diego, CA 92101 +1 (858) 422-6466

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...