From ranjana at caltech.edu Mon Jun 2 08:21:23 2008 From: ranjana at caltech.edu (Ranjana Kishore) Date: Mon, 02 Jun 2008 08:21:23 -0700 Subject: [Annotation] Curator Discussion - June 2nd - 11A EDT [corrected date] In-Reply-To: <2259727D-F6EC-491C-8BC1-1D36DC9B686E@stanford.edu> References: <2259727D-F6EC-491C-8BC1-1D36DC9B686E@stanford.edu> Message-ID: <48440FF3.5050407@caltech.edu> WormBase has phoned in and nothing is happening, has something changed? It is 8.21 am. Cheers Ranjana Mike Cherry wrote: > Of course that is June 2nd. > > -Mike > > On May 22, 2008, at 3:09 AM, Mike Cherry wrote: > >> The next Curation Discussion teleconference will be at 11:00A EDT on >> May 2nd. This was the second most popular time on the doodle >> survey. There has been consistent requires to start at earlier time >> by our colleagues in the UK. >> >> The access codes are the same as previous calls. >> >> US: 866-365-4406 >> UK: 08004960580 >> access code: 7237541 >> >> >> _______________________________________________ >> Annotation mailing list >> Annotation at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/annotation > > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation From shimoyama at mcw.edu Mon Jun 2 08:27:50 2008 From: shimoyama at mcw.edu (Shimoyama, Mary) Date: Mon, 2 Jun 2008 10:27:50 -0500 Subject: [Annotation] Curator Discussion - June 2nd - 11A EDT [corrected date] In-Reply-To: <48440FF3.5050407@caltech.edu> References: <2259727D-F6EC-491C-8BC1-1D36DC9B686E@stanford.edu> <48440FF3.5050407@caltech.edu> Message-ID: <1448A38A42714048B9C53E473E13CCF00150C399@davis.hmgc.mcw.edu> We phoned in too and finally just gave up Mary Shimoyama Program Manager Rat Genome Database Human and Molecular Genetics Center Medical College of Wisconsin shimoyama at mcw.edu Tel: 414-456-7505 Fax: 414-456-6595 http://rgd.mcw.edu -----Original Message----- From: annotation-bounces at genome.stanford.edu [mailto:annotation-bounces at genome.stanford.edu] On Behalf Of Ranjana Kishore Sent: Monday, June 02, 2008 10:21 AM To: Mike Cherry Cc: biocurator at tairgroup.org; annotation at genome.stanford.edu Subject: Re: [Annotation] Curator Discussion - June 2nd - 11A EDT [corrected date] WormBase has phoned in and nothing is happening, has something changed? It is 8.21 am. Cheers Ranjana Mike Cherry wrote: > Of course that is June 2nd. > > -Mike > > On May 22, 2008, at 3:09 AM, Mike Cherry wrote: > >> The next Curation Discussion teleconference will be at 11:00A EDT on >> May 2nd. This was the second most popular time on the doodle >> survey. There has been consistent requires to start at earlier time >> by our colleagues in the UK. >> >> The access codes are the same as previous calls. >> >> US: 866-365-4406 >> UK: 08004960580 >> access code: 7237541 >> >> >> _______________________________________________ >> Annotation mailing list >> Annotation at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/annotation > > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation _______________________________________________ Annotation mailing list Annotation at geneontology.org http://fafner.stanford.edu/mailman/listinfo/annotation From hjd at informatics.jax.org Mon Jun 2 08:51:53 2008 From: hjd at informatics.jax.org (Harold Drabkin) Date: Mon, 02 Jun 2008 11:51:53 -0400 Subject: [Annotation] Curator Discussion - June 2nd - 11A EDT [corrected date] In-Reply-To: <1448A38A42714048B9C53E473E13CCF00150C399@davis.hmgc.mcw.edu> References: <2259727D-F6EC-491C-8BC1-1D36DC9B686E@stanford.edu> <48440FF3.5050407@caltech.edu> <1448A38A42714048B9C53E473E13CCF00150C399@davis.hmgc.mcw.edu> Message-ID: <48441719.1070807@informatics.jax.org> same here in mouseland Shimoyama, Mary wrote: > We phoned in too and finally just gave up > > Mary Shimoyama > Program Manager > Rat Genome Database > Human and Molecular Genetics Center > Medical College of Wisconsin > shimoyama at mcw.edu > Tel: 414-456-7505 > Fax: 414-456-6595 > http://rgd.mcw.edu > > > -----Original Message----- > From: annotation-bounces at genome.stanford.edu > [mailto:annotation-bounces at genome.stanford.edu] On Behalf Of Ranjana > Kishore > Sent: Monday, June 02, 2008 10:21 AM > To: Mike Cherry > Cc: biocurator at tairgroup.org; annotation at genome.stanford.edu > Subject: Re: [Annotation] Curator Discussion - June 2nd - 11A EDT > [corrected date] > > WormBase has phoned in and nothing is happening, has something changed? > > It is 8.21 am. > Cheers > Ranjana > > Mike Cherry wrote: > >> Of course that is June 2nd. >> >> -Mike >> >> On May 22, 2008, at 3:09 AM, Mike Cherry wrote: >> >> >>> The next Curation Discussion teleconference will be at 11:00A EDT on >>> May 2nd. This was the second most popular time on the doodle >>> survey. There has been consistent requires to start at earlier time >>> by our colleagues in the UK. >>> >>> The access codes are the same as previous calls. >>> >>> US: 866-365-4406 >>> UK: 08004960580 >>> access code: 7237541 >>> >>> >>> _______________________________________________ >>> Annotation mailing list >>> Annotation at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/annotation >>> >> _______________________________________________ >> Annotation mailing list >> Annotation at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/annotation >> > > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation > > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation > From cherry at stanford.edu Mon Jun 2 08:57:31 2008 From: cherry at stanford.edu (Mike Cherry) Date: Mon, 2 Jun 2008 08:57:31 -0700 Subject: [Annotation] Curator Discussion - June 2nd - 11A EDT [corrected date] In-Reply-To: <48441719.1070807@informatics.jax.org> References: <2259727D-F6EC-491C-8BC1-1D36DC9B686E@stanford.edu> <48440FF3.5050407@caltech.edu> <1448A38A42714048B9C53E473E13CCF00150C399@davis.hmgc.mcw.edu> <48441719.1070807@informatics.jax.org> Message-ID: <64DC64C4-9A42-4A42-BE22-5AA87FFCCD56@stanford.edu> I'm really sorry about this. This weekend I got worried about a grant and several other things on my plate. I woke up focused on those things and completely forgot about the call. I guess we'll just forego the call this month and I'll schedule something for July. Sorry for wasting your time this morning. I remembered the call last Friday and it was on my calendar, I just blew it. -Mike On Jun 2, 2008, at 8:51 AM, Harold Drabkin wrote: > same here in mouseland > > > Shimoyama, Mary wrote: >> We phoned in too and finally just gave up >> >> Mary Shimoyama >> Program Manager >> Rat Genome Database >> Human and Molecular Genetics Center >> Medical College of Wisconsin >> shimoyama at mcw.edu >> Tel: 414-456-7505 >> Fax: 414-456-6595 >> http://rgd.mcw.edu >> >> -----Original Message----- >> From: annotation-bounces at genome.stanford.edu >> [mailto:annotation-bounces at genome.stanford.edu] On Behalf Of Ranjana >> Kishore >> Sent: Monday, June 02, 2008 10:21 AM >> To: Mike Cherry >> Cc: biocurator at tairgroup.org; annotation at genome.stanford.edu >> Subject: Re: [Annotation] Curator Discussion - June 2nd - 11A EDT >> [corrected date] >> >> WormBase has phoned in and nothing is happening, has something >> changed? >> >> It is 8.21 am. >> Cheers >> Ranjana >> >> Mike Cherry wrote: >> >>> Of course that is June 2nd. >>> >>> -Mike >>> >>> On May 22, 2008, at 3:09 AM, Mike Cherry wrote: >>> >>> >>>> The next Curation Discussion teleconference will be at 11:00A EDT >>>> on May 2nd. This was the second most popular time on the doodle >>>> survey. There has been consistent requires to start at earlier >>>> time by our colleagues in the UK. >>>> >>>> The access codes are the same as previous calls. >>>> >>>> US: 866-365-4406 >>>> UK: 08004960580 >>>> access code: 7237541 >>>> >>>> >>>> _______________________________________________ >>>> Annotation mailing list >>>> Annotation at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/annotation >>>> >>> _______________________________________________ >>> Annotation mailing list >>> Annotation at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/annotation >>> >> >> _______________________________________________ >> Annotation mailing list >> Annotation at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/annotation >> >> _______________________________________________ >> Annotation mailing list >> Annotation at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/annotation >> From shimoyama at mcw.edu Mon Jun 2 09:19:44 2008 From: shimoyama at mcw.edu (Shimoyama, Mary) Date: Mon, 2 Jun 2008 11:19:44 -0500 Subject: [Annotation] Curator Discussion - June 2nd - 11A EDT [correcteddate] In-Reply-To: <64DC64C4-9A42-4A42-BE22-5AA87FFCCD56@stanford.edu> References: <2259727D-F6EC-491C-8BC1-1D36DC9B686E@stanford.edu> <48440FF3.5050407@caltech.edu><1448A38A42714048B9C53E473E13CCF00150C399@davis.hmgc.mcw.edu><48441719.1070807@informatics.jax.org> <64DC64C4-9A42-4A42-BE22-5AA87FFCCD56@stanford.edu> Message-ID: <1448A38A42714048B9C53E473E13CCF00150C39C@davis.hmgc.mcw.edu> It's ok Mike - we've all been there, done that. -----Original Message----- From: annotation-bounces at genome.stanford.edu [mailto:annotation-bounces at genome.stanford.edu] On Behalf Of Mike Cherry Sent: Monday, June 02, 2008 10:58 AM To: biocurator at tairgroup.org; GO Annotation list Subject: Re: [Annotation] Curator Discussion - June 2nd - 11A EDT [correcteddate] I'm really sorry about this. This weekend I got worried about a grant and several other things on my plate. I woke up focused on those things and completely forgot about the call. I guess we'll just forego the call this month and I'll schedule something for July. Sorry for wasting your time this morning. I remembered the call last Friday and it was on my calendar, I just blew it. -Mike On Jun 2, 2008, at 8:51 AM, Harold Drabkin wrote: > same here in mouseland > > > Shimoyama, Mary wrote: >> We phoned in too and finally just gave up >> >> Mary Shimoyama >> Program Manager >> Rat Genome Database >> Human and Molecular Genetics Center >> Medical College of Wisconsin >> shimoyama at mcw.edu >> Tel: 414-456-7505 >> Fax: 414-456-6595 >> http://rgd.mcw.edu >> >> -----Original Message----- >> From: annotation-bounces at genome.stanford.edu >> [mailto:annotation-bounces at genome.stanford.edu] On Behalf Of Ranjana >> Kishore >> Sent: Monday, June 02, 2008 10:21 AM >> To: Mike Cherry >> Cc: biocurator at tairgroup.org; annotation at genome.stanford.edu >> Subject: Re: [Annotation] Curator Discussion - June 2nd - 11A EDT >> [corrected date] >> >> WormBase has phoned in and nothing is happening, has something >> changed? >> >> It is 8.21 am. >> Cheers >> Ranjana >> >> Mike Cherry wrote: >> >>> Of course that is June 2nd. >>> >>> -Mike >>> >>> On May 22, 2008, at 3:09 AM, Mike Cherry wrote: >>> >>> >>>> The next Curation Discussion teleconference will be at 11:00A EDT >>>> on May 2nd. This was the second most popular time on the doodle >>>> survey. There has been consistent requires to start at earlier >>>> time by our colleagues in the UK. >>>> >>>> The access codes are the same as previous calls. >>>> >>>> US: 866-365-4406 >>>> UK: 08004960580 >>>> access code: 7237541 >>>> >>>> >>>> _______________________________________________ >>>> Annotation mailing list >>>> Annotation at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/annotation >>>> >>> _______________________________________________ >>> Annotation mailing list >>> Annotation at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/annotation >>> >> >> _______________________________________________ >> Annotation mailing list >> Annotation at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/annotation >> >> _______________________________________________ >> Annotation mailing list >> Annotation at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/annotation >> _______________________________________________ Annotation mailing list Annotation at geneontology.org http://fafner.stanford.edu/mailman/listinfo/annotation From rama at genome.stanford.edu Tue Jun 3 12:05:16 2008 From: rama at genome.stanford.edu (Rama Balakrishnan) Date: Tue, 3 Jun 2008 12:05:16 -0700 Subject: [Annotation] Fwd: [Evidence] ISS/ISA from Southerns? References: Message-ID: <38F4156F-A491-4107-9006-3FF53967001C@genome.stanford.edu> I haven't heard from anybody on this so far. Is it okay if we add 'southern analysis' as an acceptable evidence to the ISS documentation? Thanks, Rama Begin forwarded message: > From: Rama Balakrishnan > Date: May 9, 2008 5:18:06 PM PDT > To: Evidence Code Group > Cc: GO Annotation list > Subject: [Evidence] ISS/ISA from Southerns? > > Reposting... > I am dealing with a similar situation like the one Julie has > mentioned below. > > Thanks, > > Rama > > > Begin forwarded message: >> From: Julie Park >> Date: April 23, 2008 3:57:22 PM PDT >> To: evidence at genome.stanford.edu >> Subject: [Evidence] ISS/ISA from Southerns? >> >> Dear evidence code group, >> >> I had a question about whether Southern analysis alone can be used as >> evidence for an annotation. >> >> In S. cerevisiae, MEL2-10 are annotated by ISS to alpha-galactosidase >> activity. There is no sequence alignment or information (older >> literature, pre-genome sequencing), instead the authors infer >> homology/ >> sequence similarity from a Southern hybridization using a MEL1 probe. >> Southern analysis was listed in the old ISS documentation but the >> only >> mention of Southerns in the new documentation is under ISA in >> conjunction with a sequence alignment. >> >> Is ISS by Southern only no longer allowed or did it just get left out >> of the current documentation? >> If allowed, would I leave these annotations as ISS or would it be >> okay >> to ISA w/ MEL1? >> >> thanks, >> Julie >> >> **************************************************************** >> Julie Park, Ph.D., Scientific Curator >> Saccharomyces Genome Database >> Department of Genetics >> Stanford University School of Medicine >> Stanford, CA 94305-5120 USA >> phone: (650)724-9959 fax: (650)725-1534 >> http://www.yeastgenome.org >> ***************************************************************** >> _______________________________________________ >> Evidence mailing list >> Evidence at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/evidence > > _______________________________________________ > Evidence mailing list > Evidence at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/evidence -------------- next part -------------- An HTML attachment was scrubbed... URL: From sart2 at gen.cam.ac.uk Wed Jun 4 02:17:01 2008 From: sart2 at gen.cam.ac.uk (Susan Tweedie) Date: Wed, 04 Jun 2008 10:17:01 +0100 Subject: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? In-Reply-To: <38F4156F-A491-4107-9006-3FF53967001C@genome.stanford.edu> References: <38F4156F-A491-4107-9006-3FF53967001C@genome.stanford.edu> Message-ID: <1212571021.14618.17.camel@paul.gen.cam.ac.uk> One thing we'd have to consider if we added this (back?) to ISS is that the new classification of evidence codes groups ISS, ISA etc as 'computational analysis evidence codes' - that wouldn't be strictly true if Southerns were included. I am uneasy about mixing together cases where the sequence is known with those that aren't - no review of the evidence is possible in the latter case. Personally, I would be reluctant to make an annotation based on a cross-hybridisation expt but maybe I just remember too many spurious bands from my time in the lab. Are there really that many cases these days where sequencing is so stnadard where this is the only evidence to support a term? Maybe I'm just spolit working on a species with complete genome sequence... Cheers, Susan On Tue, 2008-06-03 at 12:05 -0700, Rama Balakrishnan wrote: > I haven't heard from anybody on this so far. Is it okay if we add > 'southern analysis' as an acceptable evidence to the ISS > documentation? > > > Thanks, > > > Rama > > > Begin forwarded message: > > > From: Rama Balakrishnan > > Date: May 9, 2008 5:18:06 PM PDT > > To: Evidence Code Group > > Cc: GO Annotation list > > Subject: [Evidence] ISS/ISA from Southerns? > > > > > > Reposting... > > I am dealing with a similar situation like the one Julie has > > mentioned below. > > > > > > Thanks, > > > > > > Rama > > > > > > Begin forwarded message: > > > From: Julie Park > > > Date: April 23, 2008 3:57:22 PM PDT > > > To: evidence at genome.stanford.edu > > > Subject: [Evidence] ISS/ISA from Southerns? > > > > > > > > > Dear evidence code group, > > > > > > I had a question about whether Southern analysis alone can be used > > > as > > > evidence for an annotation. > > > > > > In S. cerevisiae, MEL2-10 are annotated by ISS to > > > alpha-galactosidase > > > activity. There is no sequence alignment or information (older > > > literature, pre-genome sequencing), instead the authors infer > > > homology/ > > > sequence similarity from a Southern hybridization using a MEL1 > > > probe. > > > Southern analysis was listed in the old ISS documentation but the > > > only > > > mention of Southerns in the new documentation is under ISA in > > > conjunction with a sequence alignment. > > > > > > Is ISS by Southern only no longer allowed or did it just get left > > > out > > > of the current documentation? > > > If allowed, would I leave these annotations as ISS or would it be > > > okay > > > to ISA w/ MEL1? > > > > > > thanks, > > > Julie > > > > > > **************************************************************** > > > Julie Park, Ph.D., Scientific Curator > > > Saccharomyces Genome Database > > > Department of Genetics > > > Stanford University School of Medicine > > > Stanford, CA 94305-5120 USA > > > phone: (650)724-9959 fax: (650)725-1534 > > > http://www.yeastgenome.org > > > ***************************************************************** > > > _______________________________________________ > > > Evidence mailing list > > > Evidence at geneontology.org > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > _______________________________________________ > > Evidence mailing list > > Evidence at geneontology.org > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > _______________________________________________ > Evidence mailing list > Evidence at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/evidence From mgiglio at SOM.UMARYLAND.EDU Wed Jun 4 21:37:36 2008 From: mgiglio at SOM.UMARYLAND.EDU (MICHELLE GIGLIO) Date: Thu, 5 Jun 2008 00:37:36 -0400 Subject: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? References: <38F4156F-A491-4107-9006-3FF53967001C@genome.stanford.edu> <1212571021.14618.17.camel@paul.gen.cam.ac.uk> Message-ID: <124A5002E66E5647AEB8D0146B9B2E2E077B0FD4@someven.som.umaryland.edu> Hi Rama, I agree with Susan. I am reluctant to add this back to ISS. However, I don't know where it would go instead. If it does come back to the ISS family (if we can not think of another alternative) then it definitely can NOT go under ISA as there is no alignment in this situation. It would have to be plain ISS. (But I still don't like it there.) Could it possibly be an IPI? Michelle -----Original Message----- From: evidence-bounces at genome.stanford.edu on behalf of Susan Tweedie Sent: Wed 6/4/2008 5:17 AM To: Rama Balakrishnan Cc: Evidence Code Group; GO Annotation list Subject: Re: [Evidence] Fwd: ISS/ISA from Southerns? One thing we'd have to consider if we added this (back?) to ISS is that the new classification of evidence codes groups ISS, ISA etc as 'computational analysis evidence codes' - that wouldn't be strictly true if Southerns were included. I am uneasy about mixing together cases where the sequence is known with those that aren't - no review of the evidence is possible in the latter case. Personally, I would be reluctant to make an annotation based on a cross-hybridisation expt but maybe I just remember too many spurious bands from my time in the lab. Are there really that many cases these days where sequencing is so stnadard where this is the only evidence to support a term? Maybe I'm just spolit working on a species with complete genome sequence... Cheers, Susan On Tue, 2008-06-03 at 12:05 -0700, Rama Balakrishnan wrote: > I haven't heard from anybody on this so far. Is it okay if we add > 'southern analysis' as an acceptable evidence to the ISS > documentation? > > > Thanks, > > > Rama > > > Begin forwarded message: > > > From: Rama Balakrishnan > > Date: May 9, 2008 5:18:06 PM PDT > > To: Evidence Code Group > > Cc: GO Annotation list > > Subject: [Evidence] ISS/ISA from Southerns? > > > > > > Reposting... > > I am dealing with a similar situation like the one Julie has > > mentioned below. > > > > > > Thanks, > > > > > > Rama > > > > > > Begin forwarded message: > > > From: Julie Park > > > Date: April 23, 2008 3:57:22 PM PDT > > > To: evidence at genome.stanford.edu > > > Subject: [Evidence] ISS/ISA from Southerns? > > > > > > > > > Dear evidence code group, > > > > > > I had a question about whether Southern analysis alone can be used > > > as > > > evidence for an annotation. > > > > > > In S. cerevisiae, MEL2-10 are annotated by ISS to > > > alpha-galactosidase > > > activity. There is no sequence alignment or information (older > > > literature, pre-genome sequencing), instead the authors infer > > > homology/ > > > sequence similarity from a Southern hybridization using a MEL1 > > > probe. > > > Southern analysis was listed in the old ISS documentation but the > > > only > > > mention of Southerns in the new documentation is under ISA in > > > conjunction with a sequence alignment. > > > > > > Is ISS by Southern only no longer allowed or did it just get left > > > out > > > of the current documentation? > > > If allowed, would I leave these annotations as ISS or would it be > > > okay > > > to ISA w/ MEL1? > > > > > > thanks, > > > Julie > > > > > > **************************************************************** > > > Julie Park, Ph.D., Scientific Curator > > > Saccharomyces Genome Database > > > Department of Genetics > > > Stanford University School of Medicine > > > Stanford, CA 94305-5120 USA > > > phone: (650)724-9959 fax: (650)725-1534 > > > http://www.yeastgenome.org > > > ***************************************************************** > > > _______________________________________________ > > > Evidence mailing list > > > Evidence at geneontology.org > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > _______________________________________________ > > Evidence mailing list > > Evidence at geneontology.org > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > _______________________________________________ > Evidence mailing list > Evidence at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/evidence _______________________________________________ Evidence mailing list Evidence at geneontology.org http://fafner.stanford.edu/mailman/listinfo/evidence -------------- next part -------------- An HTML attachment was scrubbed... URL: From val at sanger.ac.uk Thu Jun 5 00:03:20 2008 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 05 Jun 2008 08:03:20 +0100 Subject: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? In-Reply-To: <124A5002E66E5647AEB8D0146B9B2E2E077B0FD4@someven.som.umaryland.edu> References: <38F4156F-A491-4107-9006-3FF53967001C@genome.stanford.edu> <1212571021.14618.17.camel@paul.gen.cam.ac.uk> <124A5002E66E5647AEB8D0146B9B2E2E077B0FD4@someven.som.umaryland.edu> Message-ID: <48478FB8.9010308@sanger.ac.uk> I prefer IPI with the accession of the DNA molecule Val MICHELLE GIGLIO wrote: > > > Hi Rama, > > I agree with Susan. I am reluctant to add this back to ISS. However, > I don't know where it would go instead. > > If it does come back to the ISS family (if we can not think of another > alternative) then it definitely can NOT go under ISA as there is no > alignment in this situation. It would have to be plain ISS. (But I > still don't like it there.) > > Could it possibly be an IPI? > > Michelle > > > > > -----Original Message----- > From: evidence-bounces at genome.stanford.edu on behalf of Susan Tweedie > Sent: Wed 6/4/2008 5:17 AM > To: Rama Balakrishnan > Cc: Evidence Code Group; GO Annotation list > Subject: Re: [Evidence] Fwd: ISS/ISA from Southerns? > > One thing we'd have to consider if we added this (back?) to ISS is that > the new classification of evidence codes groups ISS, ISA etc as > 'computational analysis evidence codes' - that wouldn't be strictly true > if Southerns were included. > > I am uneasy about mixing together cases where the sequence is known with > those that aren't - no review of the evidence is possible in the latter > case. Personally, I would be reluctant to make an annotation based on a > cross-hybridisation expt but maybe I just remember too many spurious > bands from my time in the lab. > > Are there really that many cases these days where sequencing is so > stnadard where this is the only evidence to support a term? Maybe I'm > just spolit working on a species with complete genome sequence... > > Cheers, > > Susan > > > > > > On Tue, 2008-06-03 at 12:05 -0700, Rama Balakrishnan wrote: > > I haven't heard from anybody on this so far. Is it okay if we add > > 'southern analysis' as an acceptable evidence to the ISS > > documentation? > > > > > > Thanks, > > > > > > Rama > > > > > > Begin forwarded message: > > > > > From: Rama Balakrishnan > > > Date: May 9, 2008 5:18:06 PM PDT > > > To: Evidence Code Group > > > Cc: GO Annotation list > > > Subject: [Evidence] ISS/ISA from Southerns? > > > > > > > > > Reposting... > > > I am dealing with a similar situation like the one Julie has > > > mentioned below. > > > > > > > > > Thanks, > > > > > > > > > Rama > > > > > > > > > Begin forwarded message: > > > > From: Julie Park > > > > Date: April 23, 2008 3:57:22 PM PDT > > > > To: evidence at genome.stanford.edu > > > > Subject: [Evidence] ISS/ISA from Southerns? > > > > > > > > > > > > Dear evidence code group, > > > > > > > > I had a question about whether Southern analysis alone can be used > > > > as > > > > evidence for an annotation. > > > > > > > > In S. cerevisiae, MEL2-10 are annotated by ISS to > > > > alpha-galactosidase > > > > activity. There is no sequence alignment or information (older > > > > literature, pre-genome sequencing), instead the authors infer > > > > homology/ > > > > sequence similarity from a Southern hybridization using a MEL1 > > > > probe. > > > > Southern analysis was listed in the old ISS documentation but the > > > > only > > > > mention of Southerns in the new documentation is under ISA in > > > > conjunction with a sequence alignment. > > > > > > > > Is ISS by Southern only no longer allowed or did it just get left > > > > out > > > > of the current documentation? > > > > If allowed, would I leave these annotations as ISS or would it be > > > > okay > > > > to ISA w/ MEL1? > > > > > > > > thanks, > > > > Julie > > > > > > > > **************************************************************** > > > > Julie Park, Ph.D., Scientific Curator > > > > Saccharomyces Genome Database > > > > Department of Genetics > > > > Stanford University School of Medicine > > > > Stanford, CA 94305-5120 USA > > > > phone: (650)724-9959 fax: (650)725-1534 > > > > http://www.yeastgenome.org > > > > ***************************************************************** > > > > _______________________________________________ > > > > Evidence mailing list > > > > Evidence at geneontology.org > > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > > > > _______________________________________________ > > > Evidence mailing list > > > Evidence at geneontology.org > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > _______________________________________________ > > Evidence mailing list > > Evidence at geneontology.org > > http://fafner.stanford.edu/mailman/listinfo/evidence > > _______________________________________________ > Evidence mailing list > Evidence at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/evidence > > ------------------------------------------------------------------------ > > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation > -- --------------------------------------------------------------------------- Valerie Wood Tel: 01223 496909 S. pombe Genome Project Fax: 01223 494919 Wellcome Trust Sanger Institute email: val at sanger.ac.uk Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From jblake at informatics.jax.org Thu Jun 5 04:38:06 2008 From: jblake at informatics.jax.org (Judith Blake) Date: Thu, 05 Jun 2008 07:38:06 -0400 Subject: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? In-Reply-To: <124A5002E66E5647AEB8D0146B9B2E2E077B0FD4@someven.som.umaryland.edu> References: <38F4156F-A491-4107-9006-3FF53967001C@genome.stanford.edu> <1212571021.14618.17.camel@paul.gen.cam.ac.uk> <124A5002E66E5647AEB8D0146B9B2E2E077B0FD4@someven.som.umaryland.edu> Message-ID: <4847D01E.5080509@informatics.jax.org> I agree too. This is too far from ISS as now employed. aren't these from older papers? Isn't there better evidence available now? if so, why include them? if not, what about EXP? judy MICHELLE GIGLIO wrote: > > > Hi Rama, > > I agree with Susan. I am reluctant to add this back to ISS. However, > I don't know where it would go instead. > > If it does come back to the ISS family (if we can not think of another > alternative) then it definitely can NOT go under ISA as there is no > alignment in this situation. It would have to be plain ISS. (But I > still don't like it there.) > > Could it possibly be an IPI? > > Michelle > > > > > -----Original Message----- > From: evidence-bounces at genome.stanford.edu on behalf of Susan Tweedie > Sent: Wed 6/4/2008 5:17 AM > To: Rama Balakrishnan > Cc: Evidence Code Group; GO Annotation list > Subject: Re: [Evidence] Fwd: ISS/ISA from Southerns? > > One thing we'd have to consider if we added this (back?) to ISS is that > the new classification of evidence codes groups ISS, ISA etc as > 'computational analysis evidence codes' - that wouldn't be strictly true > if Southerns were included. > > I am uneasy about mixing together cases where the sequence is known with > those that aren't - no review of the evidence is possible in the latter > case. Personally, I would be reluctant to make an annotation based on a > cross-hybridisation expt but maybe I just remember too many spurious > bands from my time in the lab. > > Are there really that many cases these days where sequencing is so > stnadard where this is the only evidence to support a term? Maybe I'm > just spolit working on a species with complete genome sequence... > > Cheers, > > Susan > > > > > > On Tue, 2008-06-03 at 12:05 -0700, Rama Balakrishnan wrote: > > I haven't heard from anybody on this so far. Is it okay if we add > > 'southern analysis' as an acceptable evidence to the ISS > > documentation? > > > > > > Thanks, > > > > > > Rama > > > > > > Begin forwarded message: > > > > > From: Rama Balakrishnan > > > Date: May 9, 2008 5:18:06 PM PDT > > > To: Evidence Code Group > > > Cc: GO Annotation list > > > Subject: [Evidence] ISS/ISA from Southerns? > > > > > > > > > Reposting... > > > I am dealing with a similar situation like the one Julie has > > > mentioned below. > > > > > > > > > Thanks, > > > > > > > > > Rama > > > > > > > > > Begin forwarded message: > > > > From: Julie Park > > > > Date: April 23, 2008 3:57:22 PM PDT > > > > To: evidence at genome.stanford.edu > > > > Subject: [Evidence] ISS/ISA from Southerns? > > > > > > > > > > > > Dear evidence code group, > > > > > > > > I had a question about whether Southern analysis alone can be used > > > > as > > > > evidence for an annotation. > > > > > > > > In S. cerevisiae, MEL2-10 are annotated by ISS to > > > > alpha-galactosidase > > > > activity. There is no sequence alignment or information (older > > > > literature, pre-genome sequencing), instead the authors infer > > > > homology/ > > > > sequence similarity from a Southern hybridization using a MEL1 > > > > probe. > > > > Southern analysis was listed in the old ISS documentation but the > > > > only > > > > mention of Southerns in the new documentation is under ISA in > > > > conjunction with a sequence alignment. > > > > > > > > Is ISS by Southern only no longer allowed or did it just get left > > > > out > > > > of the current documentation? > > > > If allowed, would I leave these annotations as ISS or would it be > > > > okay > > > > to ISA w/ MEL1? > > > > > > > > thanks, > > > > Julie > > > > > > > > **************************************************************** > > > > Julie Park, Ph.D., Scientific Curator > > > > Saccharomyces Genome Database > > > > Department of Genetics > > > > Stanford University School of Medicine > > > > Stanford, CA 94305-5120 USA > > > > phone: (650)724-9959 fax: (650)725-1534 > > > > http://www.yeastgenome.org > > > > ***************************************************************** > > > > _______________________________________________ > > > > Evidence mailing list > > > > Evidence at geneontology.org > > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > > > > _______________________________________________ > > > Evidence mailing list > > > Evidence at geneontology.org > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > _______________________________________________ > > Evidence mailing list > > Evidence at geneontology.org > > http://fafner.stanford.edu/mailman/listinfo/evidence > > _______________________________________________ > Evidence mailing list > Evidence at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/evidence > > ------------------------------------------------------------------------ > > _______________________________________________ > Evidence mailing list > Evidence at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/evidence > From edimmer at ebi.ac.uk Thu Jun 5 04:56:56 2008 From: edimmer at ebi.ac.uk (Emily Dimmer) Date: Thu, 05 Jun 2008 12:56:56 +0100 Subject: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? In-Reply-To: <4847D01E.5080509@informatics.jax.org> References: <38F4156F-A491-4107-9006-3FF53967001C@genome.stanford.edu> <1212571021.14618.17.camel@paul.gen.cam.ac.uk> <124A5002E66E5647AEB8D0146B9B2E2E077B0FD4@someven.som.umaryland.edu> <4847D01E.5080509@informatics.jax.org> Message-ID: <4847D488.6040409@ebi.ac.uk> I like the idea of using IPI. At the moment all experimental annotations should be able to be described by one of the child codes of EXP, the only annotations which directly use this code are those which do meet the criteria of the child experimental codes, but cannot be retrofitted by the submitting group. It might be nice to keep it this way, rather than allow EXP to be used for undocumented experimental methods - otherwise EXP could potentially end up as a dumping ground for a diverse range of annotations where the curator is not sure which of the child experimental codes is appropriate. Emily Judith Blake wrote: > I agree too. This is too far from ISS as now employed. > > aren't these from older papers? Isn't there better evidence available > now? if so, why include them? if not, what about EXP? > > judy > > MICHELLE GIGLIO wrote: >> >> >> Hi Rama, >> >> I agree with Susan. I am reluctant to add this back to ISS. >> However, I don't know where it would go instead. >> >> If it does come back to the ISS family (if we can not think of >> another alternative) then it definitely can NOT go under ISA as there >> is no alignment in this situation. It would have to be plain ISS. >> (But I still don't like it there.) >> >> Could it possibly be an IPI? >> >> Michelle >> >> >> >> >> -----Original Message----- >> From: evidence-bounces at genome.stanford.edu on behalf of Susan Tweedie >> Sent: Wed 6/4/2008 5:17 AM >> To: Rama Balakrishnan >> Cc: Evidence Code Group; GO Annotation list >> Subject: Re: [Evidence] Fwd: ISS/ISA from Southerns? >> >> One thing we'd have to consider if we added this (back?) to ISS is that >> the new classification of evidence codes groups ISS, ISA etc as >> 'computational analysis evidence codes' - that wouldn't be strictly true >> if Southerns were included. >> >> I am uneasy about mixing together cases where the sequence is known with >> those that aren't - no review of the evidence is possible in the latter >> case. Personally, I would be reluctant to make an annotation based on a >> cross-hybridisation expt but maybe I just remember too many spurious >> bands from my time in the lab. >> Are there really that many cases these days where sequencing is so >> stnadard where this is the only evidence to support a term? Maybe I'm >> just spolit working on a species with complete genome sequence... >> >> Cheers, >> >> Susan >> >> >> >> >> >> On Tue, 2008-06-03 at 12:05 -0700, Rama Balakrishnan wrote: >> > I haven't heard from anybody on this so far. Is it okay if we add >> > 'southern analysis' as an acceptable evidence to the ISS >> > documentation? >> > >> > >> > Thanks, >> > >> > >> > Rama >> > >> > >> > Begin forwarded message: >> > >> > > From: Rama Balakrishnan >> > > Date: May 9, 2008 5:18:06 PM PDT >> > > To: Evidence Code Group >> > > Cc: GO Annotation list >> > > Subject: [Evidence] ISS/ISA from Southerns? >> > > >> > > >> > > Reposting... >> > > I am dealing with a similar situation like the one Julie has >> > > mentioned below. >> > > >> > > >> > > Thanks, >> > > >> > > >> > > Rama >> > > >> > > >> > > Begin forwarded message: >> > > > From: Julie Park >> > > > Date: April 23, 2008 3:57:22 PM PDT >> > > > To: evidence at genome.stanford.edu >> > > > Subject: [Evidence] ISS/ISA from Southerns? >> > > > >> > > > >> > > > Dear evidence code group, >> > > > >> > > > I had a question about whether Southern analysis alone can be used >> > > > as > > > evidence for an annotation. >> > > > >> > > > In S. cerevisiae, MEL2-10 are annotated by ISS to >> > > > alpha-galactosidase > > > activity. There is no sequence >> alignment or information (older > > > literature, pre-genome >> sequencing), instead the authors infer >> > > > homology/ >> > > > sequence similarity from a Southern hybridization using a MEL1 >> > > > probe. > > > Southern analysis was listed in the old ISS >> documentation but the >> > > > only > > > mention of Southerns in the new documentation is >> under ISA in > > > conjunction with a sequence alignment. >> > > > >> > > > Is ISS by Southern only no longer allowed or did it just get left >> > > > out > > > of the current documentation? >> > > > If allowed, would I leave these annotations as ISS or would it be >> > > > okay > > > to ISA w/ MEL1? >> > > > >> > > > thanks, >> > > > Julie >> > > > >> > > > **************************************************************** >> > > > Julie Park, Ph.D., Scientific Curator >> > > > Saccharomyces Genome Database >> > > > Department of Genetics >> > > > Stanford University School of Medicine >> > > > Stanford, CA 94305-5120 USA >> > > > phone: (650)724-9959 fax: (650)725-1534 >> > > > http://www.yeastgenome.org >> > > > ***************************************************************** >> > > > _______________________________________________ >> > > > Evidence mailing list >> > > > Evidence at geneontology.org >> > > > http://fafner.stanford.edu/mailman/listinfo/evidence >> > > >> > > >> > > _______________________________________________ >> > > Evidence mailing list >> > > Evidence at geneontology.org >> > > http://fafner.stanford.edu/mailman/listinfo/evidence >> > >> > >> > _______________________________________________ >> > Evidence mailing list >> > Evidence at geneontology.org >> > http://fafner.stanford.edu/mailman/listinfo/evidence >> >> _______________________________________________ >> Evidence mailing list >> Evidence at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/evidence >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Evidence mailing list >> Evidence at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/evidence >> > > > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation -- Do you need any additional GO annotation resources? Which proteins would you like annotated with GO? Let us know in the GOA User Survey, available at: http://www.ebi.ac.uk/GOA/contactus.html ------------------------------------------------------------------ Emily Dimmer Ph.D. GOA Coordinator EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD, U.K. Tel: +44 1223 494654 Fax: +44 1223 494468 email: edimmer at ebi.ac.uk URL: http://www.ebi.ac.uk/goa From juliep at genome.stanford.edu Thu Jun 5 12:58:49 2008 From: juliep at genome.stanford.edu (Julie Park) Date: Thu, 5 Jun 2008 12:58:49 -0700 Subject: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? In-Reply-To: References: <4847D488.6040409@ebi.ac.uk> Message-ID: <960463BA-B506-4665-8134-3E1757195212@genome.stanford.edu> Thanks all for your input. Unfortunately there is no other evidence for these annotations and all subsequent papers that discuss these genes reference the original Southern experiments. The curators here agree with Emily's reasoning for not using EXP. We also are against using IPI. Since both interacting parties are DNA molecules and not gene products it is both misleading and non- compliant with the IPI criteria. We at SGD have decided that given the changes to the ISS evidence code, we'll change these annotations to use the evidence code NAS and still use the Southern paper as the reference. Thanks again, -Julie > >> From: Emily Dimmer >> Date: June 5, 2008 4:56:56 AM PDT >> To: Evidence Code Group >> Cc: GO Annotation list >> Subject: Re: [Evidence] [Annotation] Fwd: ISS/ISA from Southerns? >> >> I like the idea of using IPI. >> >> At the moment all experimental annotations should be able to be >> described by one of the child codes of EXP, the only annotations >> which directly use this code are those which do meet the criteria >> of the child experimental codes, but cannot be retrofitted by the >> submitting group. >> It might be nice to keep it this way, rather than allow EXP to be >> used for undocumented experimental methods - otherwise EXP could >> potentially end up as a dumping ground for a diverse range of >> annotations where the curator is not sure which of the child >> experimental codes is appropriate. >> >> Emily >> >> >> >> Judith Blake wrote: >>> I agree too. This is too far from ISS as now employed. >>> >>> aren't these from older papers? Isn't there better evidence >>> available now? if so, why include them? if not, what about EXP? >>> >>> judy >>> >>> MICHELLE GIGLIO wrote: >>>> >>>> >>>> Hi Rama, >>>> >>>> I agree with Susan. I am reluctant to add this back to ISS. >>>> However, I don't know where it would go instead. >>>> >>>> If it does come back to the ISS family (if we can not think of >>>> another alternative) then it definitely can NOT go under ISA as >>>> there is no alignment in this situation. It would have to be >>>> plain ISS. (But I still don't like it there.) >>>> >>>> Could it possibly be an IPI? >>>> >>>> Michelle >>>> >>>> >>>> >>>> >>>> -----Original Message----- >>>> From: evidence-bounces at genome.stanford.edu on behalf of Susan >>>> Tweedie >>>> Sent: Wed 6/4/2008 5:17 AM >>>> To: Rama Balakrishnan >>>> Cc: Evidence Code Group; GO Annotation list >>>> Subject: Re: [Evidence] Fwd: ISS/ISA from Southerns? >>>> >>>> One thing we'd have to consider if we added this (back?) to ISS >>>> is that >>>> the new classification of evidence codes groups ISS, ISA etc as >>>> 'computational analysis evidence codes' - that wouldn't be >>>> strictly true >>>> if Southerns were included. >>>> >>>> I am uneasy about mixing together cases where the sequence is >>>> known with >>>> those that aren't - no review of the evidence is possible in the >>>> latter >>>> case. Personally, I would be reluctant to make an annotation >>>> based on a >>>> cross-hybridisation expt but maybe I just remember too many >>>> spurious >>>> bands from my time in the lab. >>>> Are there really that many cases these days where sequencing is so >>>> stnadard where this is the only evidence to support a term? Maybe >>>> I'm >>>> just spolit working on a species with complete genome sequence... >>>> >>>> Cheers, >>>> >>>> Susan >>>> >>>> >>>> >>>> >>>> >>>> On Tue, 2008-06-03 at 12:05 -0700, Rama Balakrishnan wrote: >>>> > I haven't heard from anybody on this so far. Is it okay if we add >>>> > 'southern analysis' as an acceptable evidence to the ISS >>>> > documentation? >>>> > >>>> > >>>> > Thanks, >>>> > >>>> > >>>> > Rama >>>> > >>>> > >>>> > Begin forwarded message: >>>> > >>>> > > From: Rama Balakrishnan >>>> > > Date: May 9, 2008 5:18:06 PM PDT >>>> > > To: Evidence Code Group >>>> > > Cc: GO Annotation list >>>> > > Subject: [Evidence] ISS/ISA from Southerns? >>>> > > >>>> > > >>>> > > Reposting... >>>> > > I am dealing with a similar situation like the one Julie has >>>> > > mentioned below. >>>> > > >>>> > > >>>> > > Thanks, >>>> > > >>>> > > >>>> > > Rama >>>> > > >>>> > > >>>> > > Begin forwarded message: >>>> > > > From: Julie Park >>>> > > > Date: April 23, 2008 3:57:22 PM PDT >>>> > > > To: evidence at genome.stanford.edu >>>> > > > Subject: [Evidence] ISS/ISA from Southerns? >>>> > > > >>>> > > > >>>> > > > Dear evidence code group, >>>> > > > >>>> > > > I had a question about whether Southern analysis alone can >>>> be used >>>> > > > as > > > evidence for an annotation. >>>> > > > >>>> > > > In S. cerevisiae, MEL2-10 are annotated by ISS to >>>> > > > alpha-galactosidase > > > activity. There is no sequence >>>> alignment or information (older > > > literature, pre-genome >>>> sequencing), instead the authors infer >>>> > > > homology/ >>>> > > > sequence similarity from a Southern hybridization using a >>>> MEL1 >>>> > > > probe. > > > Southern analysis was listed in the old ISS >>>> documentation but the >>>> > > > only > > > mention of Southerns in the new documentation is >>>> under ISA in > > > conjunction with a sequence alignment. >>>> > > > >>>> > > > Is ISS by Southern only no longer allowed or did it just >>>> get left >>>> > > > out > > > of the current documentation? >>>> > > > If allowed, would I leave these annotations as ISS or would >>>> it be >>>> > > > okay > > > to ISA w/ MEL1? >>>> > > > >>>> > > > thanks, >>>> > > > Julie >>>> > > > >>>> > > > >>>> **************************************************************** >>>> > > > Julie Park, Ph.D., Scientific Curator >>>> > > > Saccharomyces Genome Database >>>> > > > Department of Genetics >>>> > > > Stanford University School of Medicine >>>> > > > Stanford, CA 94305-5120 USA >>>> > > > phone: (650)724-9959 fax: (650)725-1534 >>>> > > > http://www.yeastgenome.org >>>> > > > >>>> ***************************************************************** >>>> > > > _______________________________________________ >>>> > > > Evidence mailing list >>>> > > > Evidence at geneontology.org >>>> > > > http://fafner.stanford.edu/mailman/listinfo/evidence >>>> > > >>>> > > >>>> > > _______________________________________________ >>>> > > Evidence mailing list >>>> > > Evidence at geneontology.org >>>> > > http://fafner.stanford.edu/mailman/listinfo/evidence >>>> > >>>> > >>>> > _______________________________________________ >>>> > Evidence mailing list >>>> > Evidence at geneontology.org >>>> > http://fafner.stanford.edu/mailman/listinfo/evidence >>>> >>>> _______________________________________________ >>>> Evidence mailing list >>>> Evidence at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/evidence >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> Evidence mailing list >>>> Evidence at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/evidence >>>> >>> >>> >>> _______________________________________________ >>> Annotation mailing list >>> Annotation at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/annotation >> >> >> -- >> >> >> Do you need any additional GO annotation resources? >> Which proteins would you like annotated with GO? >> >> Let us know in the GOA User Survey, available at: http://www.ebi.ac.uk/GOA/contactus.html >> >> ------------------------------------------------------------------ >> Emily Dimmer Ph.D. >> GOA Coordinator >> EMBL-EBI >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD, U.K. >> Tel: +44 1223 494654 >> Fax: +44 1223 494468 >> email: edimmer at ebi.ac.uk >> URL: http://www.ebi.ac.uk/goa >> >> _______________________________________________ >> Evidence mailing list >> Evidence at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/evidence > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pgaudet at northwestern.edu Thu Jun 5 13:10:47 2008 From: pgaudet at northwestern.edu (Pascale Gaudet) Date: Thu, 05 Jun 2008 16:10:47 -0400 Subject: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? In-Reply-To: <960463BA-B506-4665-8134-3E1757195212@genome.stanford.edu> References: <4847D488.6040409@ebi.ac.uk> <960463BA-B506-4665-8134-3E1757195212@genome.stanford.edu> Message-ID: <48484847.2080101@northwestern.edu> An HTML attachment was scrubbed... URL: From kchris at genome.stanford.edu Thu Jun 5 13:53:45 2008 From: kchris at genome.stanford.edu (Karen Christie) Date: Thu, 5 Jun 2008 13:53:45 -0700 (PDT) Subject: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? In-Reply-To: <48484847.2080101@northwestern.edu> References: <4847D488.6040409@ebi.ac.uk> <960463BA-B506-4665-8134-3E1757195212@genome.stanford.edu> <48484847.2080101@northwestern.edu> Message-ID: How could we cite SGD? We didn't do any sequence similarity comparisons. Also, why do you think the Southern evidence is dubious? High stringency Southerns are actually quite strong evidence. -Karen On Thu, 5 Jun 2008, Pascale Gaudet wrote: > Another suggestion: How about making the annotation citing SGD rather than the paper? Is the sequence similarity good enough to do that? > > It seems to me that Southern evidence is pretty dubious anyway, I know it's nice to capture all information we can get from papers, but that seems > rather low quality? > > Pascale > > Julie Park wrote: > Thanks all for your input. > > Unfortunately there is no other evidence for these annotations and all subsequent papers that discuss these genes reference the original Southern > experiments. > > The curators here agree with Emily's reasoning for not using EXP. We also are against using IPI. Since both interacting parties are DNA > molecules and not gene products it is both misleading and non-compliant with the IPI criteria. > > We at SGD have decided that given the changes to the ISS evidence code, we'll change these annotations to use the evidence code NAS and still use > the Southern paper as the reference. > > Thanks again, > -Julie > > > > From: Emily Dimmer > Date: June 5, 2008 4:56:56 AM PDT > To: Evidence Code Group > Cc: GO Annotation list > Subject: Re: [Evidence] [Annotation] Fwd: ISS/ISA from Southerns? > > I like the idea of using IPI. > > At the moment all experimental annotations should be able to be described by one of the child codes of EXP, the only annotations > which directly use this code are those which do meet the criteria of the child experimental codes, but cannot be retrofitted by the > submitting group. > It might be nice to keep it this way, rather than allow EXP to be used for undocumented experimental methods - otherwise EXP could > potentially end up as a dumping ground for a diverse range of annotations where the curator is not sure which of the child > experimental codes is appropriate. > > Emily > > > > Judith Blake wrote: > I agree too. This is too far from ISS as now employed. > > > aren't these from older papers? Isn't there better evidence available now? if so, why include them? if not, what about > EXP? > > > judy > > > MICHELLE GIGLIO wrote: > > > > Hi Rama, > > > I agree with Susan. I am reluctant to add this back to ISS. However, I don't know where it would go > instead. > > > If it does come back to the ISS family (if we can not think of another alternative) then it definitely can > NOT go under ISA as there is no alignment in this situation. It would have to be plain ISS. (But I still > don't like it there.) > > > Could it possibly be an IPI? > > > Michelle > > > > > > -----Original Message----- > > From: evidence-bounces at genome.stanford.edu on behalf of Susan Tweedie > > Sent: Wed 6/4/2008 5:17 AM > > To: Rama Balakrishnan > > Cc: Evidence Code Group; GO Annotation list > > Subject: Re: [Evidence] Fwd: ISS/ISA from Southerns? > > > One thing we'd have to consider if we added this (back?) to ISS is that > > the new classification of evidence codes groups ISS, ISA etc as > > 'computational analysis evidence codes' - that wouldn't be strictly true > > if Southerns were included. > > > I am uneasy about mixing together cases where the sequence is known with > > those that aren't - no review of the evidence is possible in the latter > > case. Personally, I would be reluctant to make an annotation based on a > > cross-hybridisation expt but maybe I just remember too many spurious > > bands from my time in the lab. > > Are there really that many cases these days where sequencing is so > > stnadard where this is the only evidence to support a term? Maybe I'm > > just spolit working on a species with complete genome sequence... > > > Cheers, > > > Susan > > > > > > > On Tue, 2008-06-03 at 12:05 -0700, Rama Balakrishnan wrote: > > > I haven't heard from anybody on this so far. Is it okay if we add > > > 'southern analysis' as an acceptable evidence to the ISS > > > documentation? > > > > > > > > > Thanks, > > > > > > > > > Rama > > > > > > > > > Begin forwarded message: > > > > > > > From: Rama Balakrishnan > > > > Date: May 9, 2008 5:18:06 PM PDT > > > > To: Evidence Code Group > > > > Cc: GO Annotation list > > > > Subject: [Evidence] ISS/ISA from Southerns? > > > > > > > > > > > > Reposting... > > > > I am dealing with a similar situation like the one Julie has > > > > mentioned below. > > > > > > > > > > > > Thanks, > > > > > > > > > > > > Rama > > > > > > > > > > > > Begin forwarded message: > > > > > From: Julie Park > > > > > Date: April 23, 2008 3:57:22 PM PDT > > > > > To: evidence at genome.stanford.edu > > > > > Subject: [Evidence] ISS/ISA from Southerns? > > > > > > > > > > > > > > > Dear evidence code group, > > > > > > > > > > I had a question about whether Southern analysis alone can be used > > > > > as > > > evidence for an annotation. > > > > > > > > > > In S. cerevisiae, MEL2-10 are annotated by ISS to > > > > > alpha-galactosidase > > > activity. There is no sequence alignment or information (older > > > > literature, pre-genome sequencing), instead the authors infer > > > > > homology/ > > > > > sequence similarity from a Southern hybridization using a MEL1 > > > > > probe. > > > Southern analysis was listed in the old ISS documentation but the > > > > > only > > > mention of Southerns in the new documentation is under ISA in > > > conjunction with a > sequence alignment. > > > > > > > > > > Is ISS by Southern only no longer allowed or did it just get left > > > > > out > > > of the current documentation? > > > > > If allowed, would I leave these annotations as ISS or would it be > > > > > okay > > > to ISA w/ MEL1? > > > > > > > > > > thanks, > > > > > Julie > > > > > > > > > > **************************************************************** > > > > > Julie Park, Ph.D., Scientific Curator > > > > > Saccharomyces Genome Database > > > > > Department of Genetics > > > > > Stanford University School of Medicine > > > > > Stanford, CA 94305-5120 USA > > > > > phone: (650)724-9959 fax: (650)725-1534 > > > > > http://www.yeastgenome.org > > > > > ***************************************************************** > > > > > _______________________________________________ > > > > > Evidence mailing list > > > > > Evidence at geneontology.org > > > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > > > > > > > _______________________________________________ > > > > Evidence mailing list > > > > Evidence at geneontology.org > > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > > > > _______________________________________________ > > > Evidence mailing list > > > Evidence at geneontology.org > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > _______________________________________________ > > Evidence mailing list > > Evidence at geneontology.org > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > ------------------------------------------------------------------------ > > > _______________________________________________ > > Evidence mailing list > > Evidence at geneontology.org > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > _______________________________________________ > > Annotation mailing list > > Annotation at geneontology.org > > http://fafner.stanford.edu/mailman/listinfo/annotation > > > > -- > > > Do you need any additional GO annotation resources? > Which proteins would you like annotated with GO? > > Let us know in the GOA User Survey, available at: http://www.ebi.ac.uk/GOA/contactus.html > > ------------------------------------------------------------------ > Emily Dimmer Ph.D. > GOA Coordinator > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD, U.K. > Tel: +44 1223 494654 > Fax: +44 1223 494468 > email: edimmer at ebi.ac.uk > URL: http://www.ebi.ac.uk/goa > > _______________________________________________ > Evidence mailing list > Evidence at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > ______________________________________________________________________________________________________________________________________________ > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation > > > > From mgiglio at SOM.UMARYLAND.EDU Thu Jun 5 15:37:00 2008 From: mgiglio at SOM.UMARYLAND.EDU (MICHELLE GIGLIO) Date: Thu, 5 Jun 2008 18:37:00 -0400 Subject: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? References: <4847D488.6040409@ebi.ac.uk><960463BA-B506-4665-8134-3E1757195212@genome.stanford.edu><48484847.2080101@northwestern.edu> Message-ID: <124A5002E66E5647AEB8D0146B9B2E2E077B0FD6@someven.som.umaryland.edu> Hi, Should we explore the option of expanding the scope of IPI? A Southern is an experiment that looks for a physical interaction. But if folks don't want to do that, then I think it would be TAS, not NAS. It is traceable to the Southern. Michelle -----Original Message----- From: annotation-bounces at genome.stanford.edu on behalf of Karen Christie Sent: Thu 6/5/2008 4:53 PM To: Pascale Gaudet Cc: GO Annotation list; Julie Park; evidence at genome.stanford.edu Subject: Re: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? How could we cite SGD? We didn't do any sequence similarity comparisons. Also, why do you think the Southern evidence is dubious? High stringency Southerns are actually quite strong evidence. -Karen On Thu, 5 Jun 2008, Pascale Gaudet wrote: > Another suggestion: How about making the annotation citing SGD rather than the paper? Is the sequence similarity good enough to do that? > > It seems to me that Southern evidence is pretty dubious anyway, I know it's nice to capture all information we can get from papers, but that seems > rather low quality? > > Pascale > > Julie Park wrote: > Thanks all for your input. > > Unfortunately there is no other evidence for these annotations and all subsequent papers that discuss these genes reference the original Southern > experiments. > > The curators here agree with Emily's reasoning for not using EXP. We also are against using IPI. Since both interacting parties are DNA > molecules and not gene products it is both misleading and non-compliant with the IPI criteria. > > We at SGD have decided that given the changes to the ISS evidence code, we'll change these annotations to use the evidence code NAS and still use > the Southern paper as the reference. > > Thanks again, > -Julie > > > > From: Emily Dimmer > Date: June 5, 2008 4:56:56 AM PDT > To: Evidence Code Group > Cc: GO Annotation list > Subject: Re: [Evidence] [Annotation] Fwd: ISS/ISA from Southerns? > > I like the idea of using IPI. > > At the moment all experimental annotations should be able to be described by one of the child codes of EXP, the only annotations > which directly use this code are those which do meet the criteria of the child experimental codes, but cannot be retrofitted by the > submitting group. > It might be nice to keep it this way, rather than allow EXP to be used for undocumented experimental methods - otherwise EXP could > potentially end up as a dumping ground for a diverse range of annotations where the curator is not sure which of the child > experimental codes is appropriate. > > Emily > > > > Judith Blake wrote: > I agree too. This is too far from ISS as now employed. > > > aren't these from older papers? Isn't there better evidence available now? if so, why include them? if not, what about > EXP? > > > judy > > > MICHELLE GIGLIO wrote: > > > > Hi Rama, > > > I agree with Susan. I am reluctant to add this back to ISS. However, I don't know where it would go > instead. > > > If it does come back to the ISS family (if we can not think of another alternative) then it definitely can > NOT go under ISA as there is no alignment in this situation. It would have to be plain ISS. (But I still > don't like it there.) > > > Could it possibly be an IPI? > > > Michelle > > > > > > -----Original Message----- > > From: evidence-bounces at genome.stanford.edu on behalf of Susan Tweedie > > Sent: Wed 6/4/2008 5:17 AM > > To: Rama Balakrishnan > > Cc: Evidence Code Group; GO Annotation list > > Subject: Re: [Evidence] Fwd: ISS/ISA from Southerns? > > > One thing we'd have to consider if we added this (back?) to ISS is that > > the new classification of evidence codes groups ISS, ISA etc as > > 'computational analysis evidence codes' - that wouldn't be strictly true > > if Southerns were included. > > > I am uneasy about mixing together cases where the sequence is known with > > those that aren't - no review of the evidence is possible in the latter > > case. Personally, I would be reluctant to make an annotation based on a > > cross-hybridisation expt but maybe I just remember too many spurious > > bands from my time in the lab. > > Are there really that many cases these days where sequencing is so > > stnadard where this is the only evidence to support a term? Maybe I'm > > just spolit working on a species with complete genome sequence... > > > Cheers, > > > Susan > > > > > > > On Tue, 2008-06-03 at 12:05 -0700, Rama Balakrishnan wrote: > > > I haven't heard from anybody on this so far. Is it okay if we add > > > 'southern analysis' as an acceptable evidence to the ISS > > > documentation? > > > > > > > > > Thanks, > > > > > > > > > Rama > > > > > > > > > Begin forwarded message: > > > > > > > From: Rama Balakrishnan > > > > Date: May 9, 2008 5:18:06 PM PDT > > > > To: Evidence Code Group > > > > Cc: GO Annotation list > > > > Subject: [Evidence] ISS/ISA from Southerns? > > > > > > > > > > > > Reposting... > > > > I am dealing with a similar situation like the one Julie has > > > > mentioned below. > > > > > > > > > > > > Thanks, > > > > > > > > > > > > Rama > > > > > > > > > > > > Begin forwarded message: > > > > > From: Julie Park > > > > > Date: April 23, 2008 3:57:22 PM PDT > > > > > To: evidence at genome.stanford.edu > > > > > Subject: [Evidence] ISS/ISA from Southerns? > > > > > > > > > > > > > > > Dear evidence code group, > > > > > > > > > > I had a question about whether Southern analysis alone can be used > > > > > as > > > evidence for an annotation. > > > > > > > > > > In S. cerevisiae, MEL2-10 are annotated by ISS to > > > > > alpha-galactosidase > > > activity. There is no sequence alignment or information (older > > > > literature, pre-genome sequencing), instead the authors infer > > > > > homology/ > > > > > sequence similarity from a Southern hybridization using a MEL1 > > > > > probe. > > > Southern analysis was listed in the old ISS documentation but the > > > > > only > > > mention of Southerns in the new documentation is under ISA in > > > conjunction with a > sequence alignment. > > > > > > > > > > Is ISS by Southern only no longer allowed or did it just get left > > > > > out > > > of the current documentation? > > > > > If allowed, would I leave these annotations as ISS or would it be > > > > > okay > > > to ISA w/ MEL1? > > > > > > > > > > thanks, > > > > > Julie > > > > > > > > > > **************************************************************** > > > > > Julie Park, Ph.D., Scientific Curator > > > > > Saccharomyces Genome Database > > > > > Department of Genetics > > > > > Stanford University School of Medicine > > > > > Stanford, CA 94305-5120 USA > > > > > phone: (650)724-9959 fax: (650)725-1534 > > > > > http://www.yeastgenome.org > > > > > ***************************************************************** > > > > > _______________________________________________ > > > > > Evidence mailing list > > > > > Evidence at geneontology.org > > > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > > > > > > > _______________________________________________ > > > > Evidence mailing list > > > > Evidence at geneontology.org > > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > > > > _______________________________________________ > > > Evidence mailing list > > > Evidence at geneontology.org > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > _______________________________________________ > > Evidence mailing list > > Evidence at geneontology.org > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > ------------------------------------------------------------------------ > > > _______________________________________________ > > Evidence mailing list > > Evidence at geneontology.org > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > _______________________________________________ > > Annotation mailing list > > Annotation at geneontology.org > > http://fafner.stanford.edu/mailman/listinfo/annotation > > > > -- > > > Do you need any additional GO annotation resources? > Which proteins would you like annotated with GO? > > Let us know in the GOA User Survey, available at: http://www.ebi.ac.uk/GOA/contactus.html > > ------------------------------------------------------------------ > Emily Dimmer Ph.D. > GOA Coordinator > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD, U.K. > Tel: +44 1223 494654 > Fax: +44 1223 494468 > email: edimmer at ebi.ac.uk > URL: http://www.ebi.ac.uk/goa > > _______________________________________________ > Evidence mailing list > Evidence at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > ______________________________________________________________________________________________________________________________________________ > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation > > > > _______________________________________________ Annotation mailing list Annotation at geneontology.org http://fafner.stanford.edu/mailman/listinfo/annotation -------------- next part -------------- An HTML attachment was scrubbed... URL: From stacia at genome.stanford.edu Thu Jun 5 15:44:26 2008 From: stacia at genome.stanford.edu (Stacia Engel) Date: Thu, 5 Jun 2008 15:44:26 -0700 Subject: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? In-Reply-To: <124A5002E66E5647AEB8D0146B9B2E2E077B0FD6@someven.som.umaryland.edu> References: <4847D488.6040409@ebi.ac.uk><960463BA-B506-4665-8134-3E1757195212@genome.stanford.edu><48484847.2080101@northwestern.edu> <124A5002E66E5647AEB8D0146B9B2E2E077B0FD6@someven.som.umaryland.edu> Message-ID: I agree that it should be TAS with the paper that does the Southern. NAS doesn't make much sense. stacia On Jun 5, 2008, at 3:37 PM, MICHELLE GIGLIO wrote: > > > Hi, > > Should we explore the option of expanding the scope of IPI? A > Southern is an experiment that looks for a physical interaction. > > But if folks don't want to do that, then I think it would be TAS, > not NAS. It is traceable to the Southern. > > Michelle > > > > > > -----Original Message----- > From: annotation-bounces at genome.stanford.edu on behalf of Karen > Christie > Sent: Thu 6/5/2008 4:53 PM > To: Pascale Gaudet > Cc: GO Annotation list; Julie Park; evidence at genome.stanford.edu > Subject: Re: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? > > How could we cite SGD? We didn't do any sequence similarity > comparisons. > > Also, why do you think the Southern evidence is dubious? High > stringency > Southerns are actually quite strong evidence. > > -Karen > > On Thu, 5 Jun 2008, Pascale Gaudet wrote: > > > Another suggestion: How about making the annotation citing SGD > rather than the paper? Is the sequence similarity good enough to do > that? > > > > It seems to me that Southern evidence is pretty dubious anyway, I > know it's nice to capture all information we can get from papers, > but that seems > > rather low quality? > > > > Pascale > > > > Julie Park wrote: > > Thanks all for your input. > > > > Unfortunately there is no other evidence for these annotations > and all subsequent papers that discuss these genes reference the > original Southern > > experiments. > > > > The curators here agree with Emily's reasoning for not using > EXP. We also are against using IPI. Since both interacting > parties are DNA > > molecules and not gene products it is both misleading and non- > compliant with the IPI criteria. > > > > We at SGD have decided that given the changes to the ISS evidence > code, we'll change these annotations to use the evidence code NAS > and still use > > the Southern paper as the reference. > > > > Thanks again, > > -Julie > > > > > > > > From: Emily Dimmer > > Date: June 5, 2008 4:56:56 AM PDT > > To: Evidence Code Group > > Cc: GO Annotation list > > Subject: Re: [Evidence] [Annotation] Fwd: ISS/ISA from Southerns? > > > > I like the idea of using IPI. > > > > At the moment all experimental annotations should be able to be > described by one of the child codes of EXP, the only annotations > > which directly use this code are those which do meet the criteria > of the child experimental codes, but cannot be retrofitted by the > > submitting group. > > It might be nice to keep it this way, rather than allow EXP to be > used for undocumented experimental methods - otherwise EXP could > > potentially end up as a dumping ground for a diverse range of > annotations where the curator is not sure which of the child > > experimental codes is appropriate. > > > > Emily > > > > > > > > Judith Blake wrote: > > I agree too. This is too far from ISS as now employed. > > > > > > aren't these from older papers? Isn't there better > evidence available now? if so, why include them? if not, what about > > EXP? > > > > > > judy > > > > > > MICHELLE GIGLIO wrote: > > > > > > > > Hi Rama, > > > > > > I agree with Susan. I am reluctant to add this back > to ISS. However, I don't know where it would go > > instead. > > > > > > If it does come back to the ISS family (if we can not > think of another alternative) then it definitely can > > NOT go under ISA as there is no alignment in this > situation. It would have to be plain ISS. (But I still > > don't like it there.) > > > > > > Could it possibly be an IPI? > > > > > > Michelle > > > > > > > > > > > > -----Original Message----- > > > > From: evidence-bounces at genome.stanford.edu on behalf > of Susan Tweedie > > > > Sent: Wed 6/4/2008 5:17 AM > > > > To: Rama Balakrishnan > > > > Cc: Evidence Code Group; GO Annotation list > > > > Subject: Re: [Evidence] Fwd: ISS/ISA from Southerns? > > > > > > One thing we'd have to consider if we added this > (back?) to ISS is that > > > > the new classification of evidence codes groups ISS, > ISA etc as > > > > 'computational analysis evidence codes' - that > wouldn't be strictly true > > > > if Southerns were included. > > > > > > I am uneasy about mixing together cases where the > sequence is known with > > > > those that aren't - no review of the evidence is > possible in the latter > > > > case. Personally, I would be reluctant to make an > annotation based on a > > > > cross-hybridisation expt but maybe I just remember > too many spurious > > > > bands from my time in the lab. > > > > Are there really that many cases these days where > sequencing is so > > > > stnadard where this is the only evidence to support a > term? Maybe I'm > > > > just spolit working on a species with complete genome > sequence... > > > > > > Cheers, > > > > > > Susan > > > > > > > > > > > > > > On Tue, 2008-06-03 at 12:05 -0700, Rama Balakrishnan > wrote: > > > > > I haven't heard from anybody on this so far. Is it > okay if we add > > > > > 'southern analysis' as an acceptable evidence to > the ISS > > > > > documentation? > > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > > Rama > > > > > > > > > > > > > > > Begin forwarded message: > > > > > > > > > > > From: Rama Balakrishnan > > > > > > Date: May 9, 2008 5:18:06 PM PDT > > > > > > To: Evidence Code Group > > > > > > > Cc: GO Annotation list > > > > > > > Subject: [Evidence] ISS/ISA from Southerns? > > > > > > > > > > > > > > > > > > Reposting... > > > > > > I am dealing with a similar situation like the > one Julie has > > > > > > mentioned below. > > > > > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > > > > > Rama > > > > > > > > > > > > > > > > > > Begin forwarded message: > > > > > > > From: Julie Park > > > > > > > Date: April 23, 2008 3:57:22 PM PDT > > > > > > > To: evidence at genome.stanford.edu > > > > > > > Subject: [Evidence] ISS/ISA from Southerns? > > > > > > > > > > > > > > > > > > > > > Dear evidence code group, > > > > > > > > > > > > > > I had a question about whether Southern > analysis alone can be used > > > > > > > as > > > evidence for an annotation. > > > > > > > > > > > > > > In S. cerevisiae, MEL2-10 are annotated by ISS to > > > > > > > alpha-galactosidase > > > activity. There is > no sequence alignment or information (older > > > > > literature, pre-genome sequencing), instead the > authors infer > > > > > > > homology/ > > > > > > > sequence similarity from a Southern > hybridization using a MEL1 > > > > > > > probe. > > > Southern analysis was listed in > the old ISS documentation but the > > > > > > > only > > > mention of Southerns in the new > documentation is under ISA in > > > conjunction with a > > sequence alignment. > > > > > > > > > > > > > > Is ISS by Southern only no longer allowed or > did it just get left > > > > > > > out > > > of the current documentation? > > > > > > > If allowed, would I leave these annotations as > ISS or would it be > > > > > > > okay > > > to ISA w/ MEL1? > > > > > > > > > > > > > > thanks, > > > > > > > Julie > > > > > > > > > > > > > > > **************************************************************** > > > > > > > Julie Park, Ph.D., Scientific Curator > > > > > > > Saccharomyces Genome Database > > > > > > > Department of Genetics > > > > > > > Stanford University School of Medicine > > > > > > > Stanford, CA 94305-5120 USA > > > > > > > phone: (650)724-9959 fax: (650)725-1534 > > > > > > > http://www.yeastgenome.org > > > > > > > > ***************************************************************** > > > > > > > _______________________________________________ > > > > > > > Evidence mailing list > > > > > > > Evidence at geneontology.org > > > > > > > http://fafner.stanford.edu/mailman/listinfo/ > evidence > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Evidence mailing list > > > > > > Evidence at geneontology.org > > > > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > > > > > > > > > > _______________________________________________ > > > > > Evidence mailing list > > > > > Evidence at geneontology.org > > > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > _______________________________________________ > > > > Evidence mailing list > > > > Evidence at geneontology.org > > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > > ---------------------------------------------------------------------- > -- > > > > > > _______________________________________________ > > > > Evidence mailing list > > > > Evidence at geneontology.org > > > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > > > > > > > _______________________________________________ > > > > Annotation mailing list > > > > Annotation at geneontology.org > > > > http://fafner.stanford.edu/mailman/listinfo/annotation > > > > > > > > -- > > > > > > Do you need any additional GO annotation resources? > > Which proteins would you like annotated with GO? > > > > Let us know in the GOA User Survey, available at: http:// > www.ebi.ac.uk/GOA/contactus.html > > > > ------------------------------------------------------------------ > > Emily Dimmer Ph.D. > > GOA Coordinator > > EMBL-EBI > > Wellcome Trust Genome Campus > > Hinxton > > Cambridge CB10 1SD, U.K. > > Tel: +44 1223 494654 > > Fax: +44 1223 494468 > > email: edimmer at ebi.ac.uk > > URL: http://www.ebi.ac.uk/goa > > > > _______________________________________________ > > Evidence mailing list > > Evidence at geneontology.org > > http://fafner.stanford.edu/mailman/listinfo/evidence > > > > > > > > > ______________________________________________________________________ > ______________________________________________________________________ > __ > > _______________________________________________ > > Annotation mailing list > > Annotation at geneontology.org > > http://fafner.stanford.edu/mailman/listinfo/annotation > > > > > > > > > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation > > > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation -------------- next part -------------- An HTML attachment was scrubbed... URL: From kchris at genome.stanford.edu Thu Jun 5 15:50:49 2008 From: kchris at genome.stanford.edu (Karen Christie) Date: Thu, 5 Jun 2008 15:50:49 -0700 (PDT) Subject: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? In-Reply-To: References: <4847D488.6040409@ebi.ac.uk><960463BA-B506-4665-8134-3E1757195212@genome.stanford.edu><48484847.2080101@northwestern.edu> <124A5002E66E5647AEB8D0146B9B2E2E077B0FD6@someven.som.umaryland.edu> Message-ID: Our new documentation for the distinction between TAS and NAS is very simple. If they cite another paper, it is TAS. If it isn't tracable to another publication, then it isn't TAS. Here's what we have on the web in the current documentation: TAS Any statement in an article where the original evidence (experimental results, sequence comparison, etc.) is not directly shown, but is referenced in the article and therefore can be traced to another source. NAS Statements in papers (abstract, introduction, or discussion) that a curator cannot trace to another publication -Karen On Thu, 5 Jun 2008, Stacia Engel wrote: > I agree that it should be TAS with the paper that does the Southern. NAS > doesn't make much sense. > > stacia > > > On Jun 5, 2008, at 3:37 PM, MICHELLE GIGLIO wrote: > >> >> >> Hi, >> >> Should we explore the option of expanding the scope of IPI? A Southern is >> an experiment that looks for a physical interaction. >> >> But if folks don't want to do that, then I think it would be TAS, not NAS. >> It is traceable to the Southern. >> >> Michelle >> >> >> >> >> >> -----Original Message----- >> From: annotation-bounces at genome.stanford.edu on behalf of Karen Christie >> Sent: Thu 6/5/2008 4:53 PM >> To: Pascale Gaudet >> Cc: GO Annotation list; Julie Park; evidence at genome.stanford.edu >> Subject: Re: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? >> >> How could we cite SGD? We didn't do any sequence similarity comparisons. >> >> Also, why do you think the Southern evidence is dubious? High stringency >> Southerns are actually quite strong evidence. >> >> -Karen >> >> On Thu, 5 Jun 2008, Pascale Gaudet wrote: >> >>> Another suggestion: How about making the annotation citing SGD rather than >>> the paper? Is the sequence similarity good enough to do that? >>> >>> It seems to me that Southern evidence is pretty dubious anyway, I know >>> it's nice to capture all information we can get from papers, but that >>> seems >>> rather low quality? >>> >>> Pascale >>> >>> Julie Park wrote: >>> Thanks all for your input. >>> >>> Unfortunately there is no other evidence for these annotations and all >>> subsequent papers that discuss these genes reference the original Southern >>> experiments. >>> >>> The curators here agree with Emily's reasoning for not using EXP. We also >>> are against using IPI. Since both interacting parties are DNA >>> molecules and not gene products it is both misleading and non-compliant >>> with the IPI criteria. >>> >>> We at SGD have decided that given the changes to the ISS evidence code, >>> we'll change these annotations to use the evidence code NAS and still use >>> the Southern paper as the reference. >>> >>> Thanks again, >>> -Julie >>> >>> >>> >>> From: Emily Dimmer >>> Date: June 5, 2008 4:56:56 AM PDT >>> To: Evidence Code Group >>> Cc: GO Annotation list >>> Subject: Re: [Evidence] [Annotation] Fwd: ISS/ISA from Southerns? >>> >>> I like the idea of using IPI. >>> >>> At the moment all experimental annotations should be able to be described >>> by one of the child codes of EXP, the only annotations >>> which directly use this code are those which do meet the criteria of the >>> child experimental codes, but cannot be retrofitted by the >>> submitting group. >>> It might be nice to keep it this way, rather than allow EXP to be used for >>> undocumented experimental methods - otherwise EXP could >>> potentially end up as a dumping ground for a diverse range of annotations >>> where the curator is not sure which of the child >>> experimental codes is appropriate. >>> >>> Emily >>> >>> >>> >>> Judith Blake wrote: >>> I agree too. This is too far from ISS as now employed. >>> >>> >>> aren't these from older papers? Isn't there better evidence >>> available now? if so, why include them? if not, what about >>> EXP? >>> >>> >>> judy >>> >>> >>> MICHELLE GIGLIO wrote: >>> >>> >>> >>> Hi Rama, >>> >>> >>> I agree with Susan. I am reluctant to add this back to ISS. >>> However, I don't know where it would go >>> instead. >>> >>> >>> If it does come back to the ISS family (if we can not think of >>> another alternative) then it definitely can >>> NOT go under ISA as there is no alignment in this situation. >>> It would have to be plain ISS. (But I still >>> don't like it there.) >>> >>> >>> Could it possibly be an IPI? >>> >>> >>> Michelle >>> >>> >>> >>> >>> >>> -----Original Message----- >>> >>> From: evidence-bounces at genome.stanford.edu on behalf of Susan >>> Tweedie >>> >>> Sent: Wed 6/4/2008 5:17 AM >>> >>> To: Rama Balakrishnan >>> >>> Cc: Evidence Code Group; GO Annotation list >>> >>> Subject: Re: [Evidence] Fwd: ISS/ISA from Southerns? >>> >>> >>> One thing we'd have to consider if we added this (back?) to >>> ISS is that >>> >>> the new classification of evidence codes groups ISS, ISA etc >>> as >>> >>> 'computational analysis evidence codes' - that wouldn't be >>> strictly true >>> >>> if Southerns were included. >>> >>> >>> I am uneasy about mixing together cases where the sequence is >>> known with >>> >>> those that aren't - no review of the evidence is possible in >>> the latter >>> >>> case. Personally, I would be reluctant to make an annotation >>> based on a >>> >>> cross-hybridisation expt but maybe I just remember too many >>> spurious >>> >>> bands from my time in the lab. >>> >>> Are there really that many cases these days where sequencing >>> is so >>> >>> stnadard where this is the only evidence to support a term? >>> Maybe I'm >>> >>> just spolit working on a species with complete genome >>> sequence... >>> >>> >>> Cheers, >>> >>> >>> Susan >>> >>> >>> >>> >>> >>> >>> On Tue, 2008-06-03 at 12:05 -0700, Rama Balakrishnan wrote: >>> >>> > I haven't heard from anybody on this so far. Is it okay if >>> we add >>> >>> > 'southern analysis' as an acceptable evidence to the ISS >>> >>> > documentation? >>> >>> > >>> >>> > >>> >>> > Thanks, >>> >>> > >>> >>> > >>> >>> > Rama >>> >>> > >>> >>> > >>> >>> > Begin forwarded message: >>> >>> > >>> >>> > > From: Rama Balakrishnan >>> >>> > > Date: May 9, 2008 5:18:06 PM PDT >>> >>> > > To: Evidence Code Group >>> >>> > > Cc: GO Annotation list >>> >>> > > Subject: [Evidence] ISS/ISA from Southerns? >>> >>> > > >>> >>> > > >>> >>> > > Reposting... >>> >>> > > I am dealing with a similar situation like the one Julie >>> has >>> >>> > > mentioned below. >>> >>> > > >>> >>> > > >>> >>> > > Thanks, >>> >>> > > >>> >>> > > >>> >>> > > Rama >>> >>> > > >>> >>> > > >>> >>> > > Begin forwarded message: >>> >>> > > > From: Julie Park >>> >>> > > > Date: April 23, 2008 3:57:22 PM PDT >>> >>> > > > To: evidence at genome.stanford.edu >>> >>> > > > Subject: [Evidence] ISS/ISA from Southerns? >>> >>> > > > >>> >>> > > > >>> >>> > > > Dear evidence code group, >>> >>> > > > >>> >>> > > > I had a question about whether Southern analysis alone >>> can be used >>> >>> > > > as > > > evidence for an annotation. >>> >>> > > > >>> >>> > > > In S. cerevisiae, MEL2-10 are annotated by ISS to >>> >>> > > > alpha-galactosidase > > > activity. There is no >>> sequence alignment or information (older > > > >>> literature, pre-genome sequencing), instead the authors infer >>> >>> > > > homology/ >>> >>> > > > sequence similarity from a Southern hybridization using >>> a MEL1 >>> >>> > > > probe. > > > Southern analysis was listed in the old >>> ISS documentation but the >>> >>> > > > only > > > mention of Southerns in the new documentation >>> is under ISA in > > > conjunction with a >>> sequence alignment. >>> >>> > > > >>> >>> > > > Is ISS by Southern only no longer allowed or did it just >>> get left >>> >>> > > > out > > > of the current documentation? >>> >>> > > > If allowed, would I leave these annotations as ISS or >>> would it be >>> >>> > > > okay > > > to ISA w/ MEL1? >>> >>> > > > >>> >>> > > > thanks, >>> >>> > > > Julie >>> >>> > > > >>> >>> > > > >>> **************************************************************** >>> >>> > > > Julie Park, Ph.D., Scientific Curator >>> >>> > > > Saccharomyces Genome Database >>> >>> > > > Department of Genetics >>> >>> > > > Stanford University School of Medicine >>> >>> > > > Stanford, CA 94305-5120 USA >>> >>> > > > phone: (650)724-9959 fax: (650)725-1534 >>> >>> > > > http://www.yeastgenome.org >>> >>> > > > >>> ***************************************************************** >>> >>> > > > _______________________________________________ >>> >>> > > > Evidence mailing list >>> >>> > > > Evidence at geneontology.org >>> >>> > > > http://fafner.stanford.edu/mailman/listinfo/evidence >>> >>> > > >>> >>> > > >>> >>> > > _______________________________________________ >>> >>> > > Evidence mailing list >>> >>> > > Evidence at geneontology.org >>> >>> > > http://fafner.stanford.edu/mailman/listinfo/evidence >>> >>> > >>> >>> > >>> >>> > _______________________________________________ >>> >>> > Evidence mailing list >>> >>> > Evidence at geneontology.org >>> >>> > http://fafner.stanford.edu/mailman/listinfo/evidence >>> >>> >>> _______________________________________________ >>> >>> Evidence mailing list >>> >>> Evidence at geneontology.org >>> >>> http://fafner.stanford.edu/mailman/listinfo/evidence >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> >>> Evidence mailing list >>> >>> Evidence at geneontology.org >>> >>> http://fafner.stanford.edu/mailman/listinfo/evidence >>> >>> >>> >>> >>> >>> _______________________________________________ >>> >>> Annotation mailing list >>> >>> Annotation at geneontology.org >>> >>> http://fafner.stanford.edu/mailman/listinfo/annotation >>> >>> >>> >>> -- >>> >>> >>> Do you need any additional GO annotation resources? >>> Which proteins would you like annotated with GO? >>> >>> Let us know in the GOA User Survey, available at: >>> http://www.ebi.ac.uk/GOA/contactus.html >>> >>> ------------------------------------------------------------------ >>> Emily Dimmer Ph.D. >>> GOA Coordinator >>> EMBL-EBI >>> Wellcome Trust Genome Campus >>> Hinxton >>> Cambridge CB10 1SD, U.K. >>> Tel: +44 1223 494654 >>> Fax: +44 1223 494468 >>> email: edimmer at ebi.ac.uk >>> URL: http://www.ebi.ac.uk/goa >>> >>> _______________________________________________ >>> Evidence mailing list >>> Evidence at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/evidence >>> >>> >>> >>> ______________________________________________________________________________________________________________________________________________ >>> _______________________________________________ >>> Annotation mailing list >>> Annotation at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/annotation >>> >>> >>> >>> >> _______________________________________________ >> Annotation mailing list >> Annotation at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/annotation >> >> >> _______________________________________________ >> Annotation mailing list >> Annotation at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/annotation > From stacia at genome.stanford.edu Thu Jun 5 15:57:53 2008 From: stacia at genome.stanford.edu (Stacia Engel) Date: Thu, 5 Jun 2008 15:57:53 -0700 Subject: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? In-Reply-To: References: <4847D488.6040409@ebi.ac.uk><960463BA-B506-4665-8134-3E1757195212@genome.stanford.edu><48484847.2080101@northwestern.edu> <124A5002E66E5647AEB8D0146B9B2E2E077B0FD6@someven.som.umaryland.edu> Message-ID: <808E68C0-6AEE-44DB-8355-8D59BE9BDFD9@genome.stanford.edu> yes, very good. the documentation also says this: "The NAS evidence code should be used in all cases where the author makes a statement that a curator wants to capture but for which there are neither results presented nor a specific reference cited in the source used to make the annotation." see http://www.geneontology.org/GO.evidence.shtml#nas There are results presented from a Southern hybridization, so NAS still doesn't make sense in this case. i'm not sure what the right answer is, but i don't think NAS is it. stacia On Jun 5, 2008, at 3:50 PM, Karen Christie wrote: > > Our new documentation for the distinction between TAS and NAS is > very simple. If they cite another paper, it is TAS. If it isn't > tracable to another publication, then it isn't TAS. > > Here's what we have on the web in the current documentation: > > TAS > Any statement in an article where the original evidence > (experimental results, sequence comparison, etc.) is not directly > shown, but is referenced in the article and therefore can be traced > to another source. > > NAS > Statements in papers (abstract, introduction, or discussion) that a > curator cannot trace to another publication > > -Karen > > > On Thu, 5 Jun 2008, Stacia Engel wrote: > >> I agree that it should be TAS with the paper that does the >> Southern. NAS doesn't make much sense. >> >> stacia >> >> >> On Jun 5, 2008, at 3:37 PM, MICHELLE GIGLIO wrote: >> >>> Hi, >>> Should we explore the option of expanding the scope of IPI? A >>> Southern is an experiment that looks for a physical interaction. >>> But if folks don't want to do that, then I think it would be TAS, >>> not NAS. It is traceable to the Southern. >>> Michelle >>> -----Original Message----- >>> From: annotation-bounces at genome.stanford.edu on behalf of Karen >>> Christie >>> Sent: Thu 6/5/2008 4:53 PM >>> To: Pascale Gaudet >>> Cc: GO Annotation list; Julie Park; evidence at genome.stanford.edu >>> Subject: Re: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? >>> How could we cite SGD? We didn't do any sequence similarity >>> comparisons. >>> Also, why do you think the Southern evidence is dubious? High >>> stringency >>> Southerns are actually quite strong evidence. >>> -Karen >>> On Thu, 5 Jun 2008, Pascale Gaudet wrote: >>>> Another suggestion: How about making the annotation citing SGD >>>> rather than the paper? Is the sequence similarity good enough to >>>> do that? >>>> It seems to me that Southern evidence is pretty dubious anyway, >>>> I know it's nice to capture all information we can get from >>>> papers, but that seems >>>> rather low quality? >>>> Pascale >>>> Julie Park wrote: >>>> Thanks all for your input. >>>> Unfortunately there is no other evidence for these annotations >>>> and all subsequent papers that discuss these genes reference the >>>> original Southern >>>> experiments. >>>> The curators here agree with Emily's reasoning for not using >>>> EXP. We also are against using IPI. Since both interacting >>>> parties are DNA >>>> molecules and not gene products it is both misleading and non- >>>> compliant with the IPI criteria. >>>> We at SGD have decided that given the changes to the ISS >>>> evidence code, we'll change these annotations to use the >>>> evidence code NAS and still use >>>> the Southern paper as the reference. >>>> Thanks again, >>>> -Julie >>>> >>>> From: Emily Dimmer >>>> Date: June 5, 2008 4:56:56 AM PDT >>>> To: Evidence Code Group >>>> Cc: GO Annotation list >>>> Subject: Re: [Evidence] [Annotation] Fwd: ISS/ISA from Southerns? >>>> I like the idea of using IPI. >>>> At the moment all experimental annotations should be able to be >>>> described by one of the child codes of EXP, the only annotations >>>> which directly use this code are those which do meet the >>>> criteria of the child experimental codes, but cannot be >>>> retrofitted by the >>>> submitting group. >>>> It might be nice to keep it this way, rather than allow EXP to >>>> be used for undocumented experimental methods - otherwise EXP >>>> could >>>> potentially end up as a dumping ground for a diverse range of >>>> annotations where the curator is not sure which of the child >>>> experimental codes is appropriate. >>>> Emily >>>> Judith Blake wrote: >>>> I agree too. This is too far from ISS as now employed. >>>> >>>> aren't these from older papers? Isn't there better >>>> evidence available now? if so, why include them? if not, what >>>> about >>>> EXP? >>>> >>>> judy >>>> >>>> MICHELLE GIGLIO wrote: >>>> >>>> Hi Rama, >>>> >>>> I agree with Susan. I am reluctant to add this back >>>> to ISS. However, I don't know where it would go >>>> instead. >>>> >>>> If it does come back to the ISS family (if we can >>>> not think of another alternative) then it definitely can >>>> NOT go under ISA as there is no alignment in this >>>> situation. It would have to be plain ISS. (But I still >>>> don't like it there.) >>>> >>>> Could it possibly be an IPI? >>>> >>>> Michelle >>>> >>>> -----Original Message----- >>>> >>>> From: evidence-bounces at genome.stanford.edu on behalf >>>> of Susan Tweedie >>>> >>>> Sent: Wed 6/4/2008 5:17 AM >>>> >>>> To: Rama Balakrishnan >>>> >>>> Cc: Evidence Code Group; GO Annotation list >>>> >>>> Subject: Re: [Evidence] Fwd: ISS/ISA from Southerns? >>>> >>>> One thing we'd have to consider if we added this >>>> (back?) to ISS is that >>>> >>>> the new classification of evidence codes groups ISS, >>>> ISA etc as >>>> >>>> 'computational analysis evidence codes' - that >>>> wouldn't be strictly true >>>> >>>> if Southerns were included. >>>> >>>> I am uneasy about mixing together cases where the >>>> sequence is known with >>>> >>>> those that aren't - no review of the evidence is >>>> possible in the latter >>>> >>>> case. Personally, I would be reluctant to make an >>>> annotation based on a >>>> >>>> cross-hybridisation expt but maybe I just remember >>>> too many spurious >>>> >>>> bands from my time in the lab. >>>> >>>> Are there really that many cases these days where >>>> sequencing is so >>>> >>>> stnadard where this is the only evidence to support >>>> a term? Maybe I'm >>>> >>>> just spolit working on a species with complete >>>> genome sequence... >>>> >>>> Cheers, >>>> >>>> Susan >>>> >>>> On Tue, 2008-06-03 at 12:05 -0700, Rama Balakrishnan >>>> wrote: >>>> >>>> > I haven't heard from anybody on this so far. Is it >>>> okay if we add >>>> >>>> > 'southern analysis' as an acceptable evidence to >>>> the ISS >>>> >>>> > documentation? >>>> >>>> > >>>> >>>> > >>>> >>>> > Thanks, >>>> >>>> > >>>> >>>> > >>>> >>>> > Rama >>>> >>>> > >>>> >>>> > >>>> >>>> > Begin forwarded message: >>>> >>>> > >>>> >>>> > > From: Rama Balakrishnan >>>> >>>> > > Date: May 9, 2008 5:18:06 PM PDT >>>> >>>> > > To: Evidence Code Group >>>> >>>> >>>> > > Cc: GO Annotation list >>>> >>>> >>>> > > Subject: [Evidence] ISS/ISA from Southerns? >>>> >>>> > > >>>> >>>> > > >>>> >>>> > > Reposting... >>>> >>>> > > I am dealing with a similar situation like the >>>> one Julie has >>>> >>>> > > mentioned below. >>>> >>>> > > >>>> >>>> > > >>>> >>>> > > Thanks, >>>> >>>> > > >>>> >>>> > > >>>> >>>> > > Rama >>>> >>>> > > >>>> >>>> > > >>>> >>>> > > Begin forwarded message: >>>> >>>> > > > From: Julie Park >>>> >>>> > > > Date: April 23, 2008 3:57:22 PM PDT >>>> >>>> > > > To: evidence at genome.stanford.edu >>>> >>>> > > > Subject: [Evidence] ISS/ISA from Southerns? >>>> >>>> > > > >>>> >>>> > > > >>>> >>>> > > > Dear evidence code group, >>>> >>>> > > > >>>> >>>> > > > I had a question about whether Southern >>>> analysis alone can be used >>>> >>>> > > > as > > > evidence for an annotation. >>>> >>>> > > > >>>> >>>> > > > In S. cerevisiae, MEL2-10 are annotated by ISS to >>>> >>>> > > > alpha-galactosidase > > > activity. There is >>>> no sequence alignment or information (older > > > >>>> literature, pre-genome sequencing), instead the >>>> authors infer >>>> >>>> > > > homology/ >>>> >>>> > > > sequence similarity from a Southern >>>> hybridization using a MEL1 >>>> >>>> > > > probe. > > > Southern analysis was listed in >>>> the old ISS documentation but the >>>> >>>> > > > only > > > mention of Southerns in the new >>>> documentation is under ISA in > > > conjunction with a >>>> sequence alignment. >>>> >>>> > > > >>>> >>>> > > > Is ISS by Southern only no longer allowed or >>>> did it just get left >>>> >>>> > > > out > > > of the current documentation? >>>> >>>> > > > If allowed, would I leave these annotations as >>>> ISS or would it be >>>> >>>> > > > okay > > > to ISA w/ MEL1? >>>> >>>> > > > >>>> >>>> > > > thanks, >>>> >>>> > > > Julie >>>> >>>> > > > >>>> >>>> > > > >>>> **************************************************************** >>>> >>>> > > > Julie Park, Ph.D., Scientific Curator >>>> >>>> > > > Saccharomyces Genome Database >>>> >>>> > > > Department of Genetics >>>> >>>> > > > Stanford University School of Medicine >>>> >>>> > > > Stanford, CA 94305-5120 USA >>>> >>>> > > > phone: (650)724-9959 fax: (650)725-1534 >>>> >>>> > > > http://www.yeastgenome.org >>>> >>>> > > > >>>> ***************************************************************** >>>> >>>> > > > _______________________________________________ >>>> >>>> > > > Evidence mailing list >>>> >>>> > > > Evidence at geneontology.org >>>> >>>> > > > http://fafner.stanford.edu/mailman/listinfo/ >>>> evidence >>>> >>>> > > >>>> >>>> > > >>>> >>>> > > _______________________________________________ >>>> >>>> > > Evidence mailing list >>>> >>>> > > Evidence at geneontology.org >>>> >>>> > > http://fafner.stanford.edu/mailman/listinfo/ >>>> evidence >>>> >>>> > >>>> >>>> > >>>> >>>> > _______________________________________________ >>>> >>>> > Evidence mailing list >>>> >>>> > Evidence at geneontology.org >>>> >>>> > http://fafner.stanford.edu/mailman/listinfo/evidence >>>> >>>> _______________________________________________ >>>> >>>> Evidence mailing list >>>> >>>> Evidence at geneontology.org >>>> >>>> http://fafner.stanford.edu/mailman/listinfo/evidence >>>> >>>> >>>> ------------------------------------------------------------------- >>>> ----- >>>> >>>> _______________________________________________ >>>> >>>> Evidence mailing list >>>> >>>> Evidence at geneontology.org >>>> >>>> http://fafner.stanford.edu/mailman/listinfo/evidence >>>> >>>> _______________________________________________ >>>> >>>> Annotation mailing list >>>> >>>> Annotation at geneontology.org >>>> >>>> http://fafner.stanford.edu/mailman/listinfo/annotation >>>> -- >>>> Do you need any additional GO annotation resources? >>>> Which proteins would you like annotated with GO? >>>> Let us know in the GOA User Survey, available at: http:// >>>> www.ebi.ac.uk/GOA/contactus.html >>>> ------------------------------------------------------------------ >>>> Emily Dimmer Ph.D. >>>> GOA Coordinator >>>> EMBL-EBI >>>> Wellcome Trust Genome Campus >>>> Hinxton >>>> Cambridge CB10 1SD, U.K. >>>> Tel: +44 1223 494654 >>>> Fax: +44 1223 494468 >>>> email: edimmer at ebi.ac.uk >>>> URL: http://www.ebi.ac.uk/goa >>>> _______________________________________________ >>>> Evidence mailing list >>>> Evidence at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/evidence >>>> >>>> >>>> ___________________________________________________________________ >>>> ___________________________________________________________________ >>>> ________ >>>> _______________________________________________ >>>> Annotation mailing list >>>> Annotation at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/annotation >>> _______________________________________________ >>> Annotation mailing list >>> Annotation at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/annotation >>> _______________________________________________ >>> Annotation mailing list >>> Annotation at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/annotation >> From midori at ebi.ac.uk Thu Jun 5 16:00:06 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 5 Jun 2008 23:00:06 UT Subject: [Annotation] SourceForge Annotation Tracker Update Message-ID: <200806052300.m55N07S1170551@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From jblake at informatics.jax.org Fri Jun 6 05:10:02 2008 From: jblake at informatics.jax.org (Judith Blake) Date: Fri, 06 Jun 2008 08:10:02 -0400 Subject: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? In-Reply-To: <808E68C0-6AEE-44DB-8355-8D59BE9BDFD9@genome.stanford.edu> References: <4847D488.6040409@ebi.ac.uk><960463BA-B506-4665-8134-3E1757195212@genome.stanford.edu><48484847.2080101@northwestern.edu> <124A5002E66E5647AEB8D0146B9B2E2E077B0FD6@someven.som.umaryland.edu> <808E68C0-6AEE-44DB-8355-8D59BE9BDFD9@genome.stanford.edu> Message-ID: <4849291A.1090208@informatics.jax.org> TAS would work....Author says (incidently, he has a Southern result in the paper) judy Stacia Engel wrote: > yes, very good. the documentation also says this: > "The NAS evidence code should be used in all cases where the author > makes a statement that a curator wants to capture but for which there > are neither results presented nor a specific reference cited in the > source used to make the annotation." > > see http://www.geneontology.org/GO.evidence.shtml#nas > > There are results presented from a Southern hybridization, so NAS > still doesn't make sense in this case. > > i'm not sure what the right answer is, but i don't think NAS is it. > > > > stacia > > > On Jun 5, 2008, at 3:50 PM, Karen Christie wrote: > >> >> Our new documentation for the distinction between TAS and NAS is very >> simple. If they cite another paper, it is TAS. If it isn't tracable >> to another publication, then it isn't TAS. >> >> Here's what we have on the web in the current documentation: >> >> TAS >> Any statement in an article where the original evidence (experimental >> results, sequence comparison, etc.) is not directly shown, but is >> referenced in the article and therefore can be traced to another source. >> >> NAS >> Statements in papers (abstract, introduction, or discussion) that a >> curator cannot trace to another publication >> >> -Karen >> >> >> On Thu, 5 Jun 2008, Stacia Engel wrote: >> >>> I agree that it should be TAS with the paper that does the >>> Southern. NAS doesn't make much sense. >>> >>> stacia >>> >>> >>> On Jun 5, 2008, at 3:37 PM, MICHELLE GIGLIO wrote: >>> >>>> Hi, >>>> Should we explore the option of expanding the scope of IPI? A >>>> Southern is an experiment that looks for a physical interaction. >>>> But if folks don't want to do that, then I think it would be TAS, >>>> not NAS. It is traceable to the Southern. >>>> Michelle >>>> -----Original Message----- >>>> From: annotation-bounces at genome.stanford.edu on behalf of Karen >>>> Christie >>>> Sent: Thu 6/5/2008 4:53 PM >>>> To: Pascale Gaudet >>>> Cc: GO Annotation list; Julie Park; evidence at genome.stanford.edu >>>> Subject: Re: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns? >>>> How could we cite SGD? We didn't do any sequence similarity >>>> comparisons. >>>> Also, why do you think the Southern evidence is dubious? High >>>> stringency >>>> Southerns are actually quite strong evidence. >>>> -Karen >>>> On Thu, 5 Jun 2008, Pascale Gaudet wrote: >>>>> Another suggestion: How about making the annotation citing SGD >>>>> rather than the paper? Is the sequence similarity good enough to >>>>> do that? >>>>> It seems to me that Southern evidence is pretty dubious anyway, I >>>>> know it's nice to capture all information we can get from papers, >>>>> but that seems >>>>> rather low quality? >>>>> Pascale >>>>> Julie Park wrote: >>>>> Thanks all for your input. >>>>> Unfortunately there is no other evidence for these annotations and >>>>> all subsequent papers that discuss these genes reference the >>>>> original Southern >>>>> experiments. >>>>> The curators here agree with Emily's reasoning for not using EXP. >>>>> We also are against using IPI. Since both interacting parties are >>>>> DNA >>>>> molecules and not gene products it is both misleading and >>>>> non-compliant with the IPI criteria. >>>>> We at SGD have decided that given the changes to the ISS evidence >>>>> code, we'll change these annotations to use the evidence code NAS >>>>> and still use >>>>> the Southern paper as the reference. >>>>> Thanks again, >>>>> -Julie >>>>> >>>>> From: Emily Dimmer >>>>> Date: June 5, 2008 4:56:56 AM PDT >>>>> To: Evidence Code Group >>>>> Cc: GO Annotation list >>>>> Subject: Re: [Evidence] [Annotation] Fwd: ISS/ISA from Southerns? >>>>> I like the idea of using IPI. >>>>> At the moment all experimental annotations should be able to be >>>>> described by one of the child codes of EXP, the only annotations >>>>> which directly use this code are those which do meet the criteria >>>>> of the child experimental codes, but cannot be retrofitted by the >>>>> submitting group. >>>>> It might be nice to keep it this way, rather than allow EXP to be >>>>> used for undocumented experimental methods - otherwise EXP could >>>>> potentially end up as a dumping ground for a diverse range of >>>>> annotations where the curator is not sure which of the child >>>>> experimental codes is appropriate. >>>>> Emily >>>>> Judith Blake wrote: >>>>> I agree too. This is too far from ISS as now employed. >>>>> >>>>> aren't these from older papers? Isn't there better evidence >>>>> available now? if so, why include them? if not, what about >>>>> EXP? >>>>> >>>>> judy >>>>> >>>>> MICHELLE GIGLIO wrote: >>>>> >>>>> Hi Rama, >>>>> >>>>> I agree with Susan. I am reluctant to add this back >>>>> to ISS. However, I don't know where it would go >>>>> instead. >>>>> >>>>> If it does come back to the ISS family (if we can not >>>>> think of another alternative) then it definitely can >>>>> NOT go under ISA as there is no alignment in this >>>>> situation. It would have to be plain ISS. (But I still >>>>> don't like it there.) >>>>> >>>>> Could it possibly be an IPI? >>>>> >>>>> Michelle >>>>> >>>>> -----Original Message----- >>>>> >>>>> From: evidence-bounces at genome.stanford.edu on behalf >>>>> of Susan Tweedie >>>>> >>>>> Sent: Wed 6/4/2008 5:17 AM >>>>> >>>>> To: Rama Balakrishnan >>>>> >>>>> Cc: Evidence Code Group; GO Annotation list >>>>> >>>>> Subject: Re: [Evidence] Fwd: ISS/ISA from Southerns? >>>>> >>>>> One thing we'd have to consider if we added this >>>>> (back?) to ISS is that >>>>> >>>>> the new classification of evidence codes groups ISS, >>>>> ISA etc as >>>>> >>>>> 'computational analysis evidence codes' - that >>>>> wouldn't be strictly true >>>>> >>>>> if Southerns were included. >>>>> >>>>> I am uneasy about mixing together cases where the >>>>> sequence is known with >>>>> >>>>> those that aren't - no review of the evidence is >>>>> possible in the latter >>>>> >>>>> case. Personally, I would be reluctant to make an >>>>> annotation based on a >>>>> >>>>> cross-hybridisation expt but maybe I just remember too >>>>> many spurious >>>>> >>>>> bands from my time in the lab. >>>>> >>>>> Are there really that many cases these days where >>>>> sequencing is so >>>>> >>>>> stnadard where this is the only evidence to support a >>>>> term? Maybe I'm >>>>> >>>>> just spolit working on a species with complete genome >>>>> sequence... >>>>> >>>>> Cheers, >>>>> >>>>> Susan >>>>> >>>>> On Tue, 2008-06-03 at 12:05 -0700, Rama Balakrishnan >>>>> wrote: >>>>> >>>>> > I haven't heard from anybody on this so far. Is it >>>>> okay if we add >>>>> >>>>> > 'southern analysis' as an acceptable evidence to the >>>>> ISS >>>>> >>>>> > documentation? >>>>> >>>>> > >>>>> >>>>> > >>>>> >>>>> > Thanks, >>>>> >>>>> > >>>>> >>>>> > >>>>> >>>>> > Rama >>>>> >>>>> > >>>>> >>>>> > >>>>> >>>>> > Begin forwarded message: >>>>> >>>>> > >>>>> >>>>> > > From: Rama Balakrishnan >>>>> >>>>> > > Date: May 9, 2008 5:18:06 PM PDT >>>>> >>>>> > > To: Evidence Code Group >>>>> >>>>> >>>>> > > Cc: GO Annotation list >>>>> >>>>> >>>>> > > Subject: [Evidence] ISS/ISA from Southerns? >>>>> >>>>> > > >>>>> >>>>> > > >>>>> >>>>> > > Reposting... >>>>> >>>>> > > I am dealing with a similar situation like the one >>>>> Julie has >>>>> >>>>> > > mentioned below. >>>>> >>>>> > > >>>>> >>>>> > > >>>>> >>>>> > > Thanks, >>>>> >>>>> > > >>>>> >>>>> > > >>>>> >>>>> > > Rama >>>>> >>>>> > > >>>>> >>>>> > > >>>>> >>>>> > > Begin forwarded message: >>>>> >>>>> > > > From: Julie Park >>>>> >>>>> > > > Date: April 23, 2008 3:57:22 PM PDT >>>>> >>>>> > > > To: evidence at genome.stanford.edu >>>>> >>>>> > > > Subject: [Evidence] ISS/ISA from Southerns? >>>>> >>>>> > > > >>>>> >>>>> > > > >>>>> >>>>> > > > Dear evidence code group, >>>>> >>>>> > > > >>>>> >>>>> > > > I had a question about whether Southern analysis >>>>> alone can be used >>>>> >>>>> > > > as > > > evidence for an annotation. >>>>> >>>>> > > > >>>>> >>>>> > > > In S. cerevisiae, MEL2-10 are annotated by ISS to >>>>> >>>>> > > > alpha-galactosidase > > > activity. There is no >>>>> sequence alignment or information (older > > > >>>>> literature, pre-genome sequencing), instead the >>>>> authors infer >>>>> >>>>> > > > homology/ >>>>> >>>>> > > > sequence similarity from a Southern >>>>> hybridization using a MEL1 >>>>> >>>>> > > > probe. > > > Southern analysis was listed in >>>>> the old ISS documentation but the >>>>> >>>>> > > > only > > > mention of Southerns in the new >>>>> documentation is under ISA in > > > conjunction with a >>>>> sequence alignment. >>>>> >>>>> > > > >>>>> >>>>> > > > Is ISS by Southern only no longer allowed or did >>>>> it just get left >>>>> >>>>> > > > out > > > of the current documentation? >>>>> >>>>> > > > If allowed, would I leave these annotations as >>>>> ISS or would it be >>>>> >>>>> > > > okay > > > to ISA w/ MEL1? >>>>> >>>>> > > > >>>>> >>>>> > > > thanks, >>>>> >>>>> > > > Julie >>>>> >>>>> > > > >>>>> >>>>> > > > >>>>> **************************************************************** >>>>> >>>>> > > > Julie Park, Ph.D., Scientific Curator >>>>> >>>>> > > > Saccharomyces Genome Database >>>>> >>>>> > > > Department of Genetics >>>>> >>>>> > > > Stanford University School of Medicine >>>>> >>>>> > > > Stanford, CA 94305-5120 USA >>>>> >>>>> > > > phone: (650)724-9959 fax: (650)725-1534 >>>>> >>>>> > > > http://www.yeastgenome.org >>>>> >>>>> > > > >>>>> ***************************************************************** >>>>> >>>>> > > > _______________________________________________ >>>>> >>>>> > > > Evidence mailing list >>>>> >>>>> > > > Evidence at geneontology.org >>>>> >>>>> > > > >>>>> http://fafner.stanford.edu/mailman/listinfo/evidence >>>>