From midori at ebi.ac.uk Thu Mar 1 02:21:37 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 1 Mar 2007 10:21:37 +0000 (GMT) Subject: HGNC database like In-Reply-To: <74DD2BCC-2D97-4686-9BA2-374CC5D2F38D@fruitfly.org> References: <20070226104741.J33706@diamond.gene.ucl.ac.uk> <6479DEEE-312C-4023-983B-72F0F61C40EB@fruitfly.org> <74DD2BCC-2D97-4686-9BA2-374CC5D2F38D@fruitfly.org> Message-ID: On Wed, 28 Feb 2007, Chris Mungall wrote: > > On Feb 28, 2007, at 1:11 PM, Midori Harris wrote: > >> So would you use two entries, HGNC as in HGNC:29, and HGNC_gene for ABCA1? > > yes, I think so. We designate the first as the primary one through the > 'object' field in the metadata; this should presumably be the stable ID, > whereas the second one is useful for making links I'm not sure I'm following this, but OK as long as annotation providers know that they have to use the IDs, not the gene names, with the 'HGNC' prefix -- i.e. some of the gene_association.goa* files (and maybe a few others?) need to be updated. m >> On Wed, 28 Feb 2007, Chris Mungall wrote: >> >>> I think we should make the prefix for the IDs HGNC, and add suffixes for >>> non-ID retrieval (otherwise we should have FlyBase_id, GO_id, etc). >>> There's no need for an HGNC_id entry. >>> From midori at ebi.ac.uk Thu Mar 1 02:24:11 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 1 Mar 2007 10:24:11 +0000 (GMT) Subject: HGNC database like In-Reply-To: <74DD2BCC-2D97-4686-9BA2-374CC5D2F38D@fruitfly.org> References: <20070226104741.J33706@diamond.gene.ucl.ac.uk> <6479DEEE-312C-4023-983B-72F0F61C40EB@fruitfly.org> <74DD2BCC-2D97-4686-9BA2-374CC5D2F38D@fruitfly.org> Message-ID: So the latest suggestion is: abbreviation: HGNC database: HUGO Gene Nomenclature Committee object: Identifier example_id: HGNC:29 generic_url: http://www.gene.ucl.ac.uk/nomenclature/ url_syntax: http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id= url_example: http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id=HGNC:29 abbreviation: HGNC_gene database: HUGO Gene Nomenclature Committee object: Gene symbol example_id: HGNC:ABCA1 generic_url: http://www.gene.ucl.ac.uk/nomenclature/ url_syntax: http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?app_sym= url_example: http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?app_sym=ABCA1 (with a comment warning that gene symbols may change) OK? From cjm at fruitfly.org Thu Mar 1 08:35:36 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Thu, 1 Mar 2007 08:35:36 -0800 Subject: HGNC database like In-Reply-To: References: <20070226104741.J33706@diamond.gene.ucl.ac.uk> <6479DEEE-312C-4023-983B-72F0F61C40EB@fruitfly.org> <74DD2BCC-2D97-4686-9BA2-374CC5D2F38D@fruitfly.org> Message-ID: <42BD2FEB-C06D-4A23-BFBE-B2C5D96E21E6@fruitfly.org> On Mar 1, 2007, at 2:24 AM, Midori Harris wrote: > So the latest suggestion is: > > abbreviation: HGNC > database: HUGO Gene Nomenclature Committee > object: Identifier > example_id: HGNC:29 > generic_url: http://www.gene.ucl.ac.uk/nomenclature/ > url_syntax: > http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id= > url_example: > http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php? > hgnc_id=HGNC:29 > > abbreviation: HGNC_gene > database: HUGO Gene Nomenclature Committee > object: Gene symbol > example_id: HGNC:ABCA1 surely HGNC_gene:ABCA1 ? cheers c > generic_url: http://www.gene.ucl.ac.uk/nomenclature/ > url_syntax: > http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?app_sym= > url_example: > http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php? > app_sym=ABCA1 > > (with a comment warning that gene symbols may change) > > OK? > From midori at ebi.ac.uk Thu Mar 1 08:38:45 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 1 Mar 2007 16:38:45 +0000 (GMT) Subject: HGNC database like In-Reply-To: <42BD2FEB-C06D-4A23-BFBE-B2C5D96E21E6@fruitfly.org> References: <20070226104741.J33706@diamond.gene.ucl.ac.uk> <6479DEEE-312C-4023-983B-72F0F61C40EB@fruitfly.org> <74DD2BCC-2D97-4686-9BA2-374CC5D2F38D@fruitfly.org> <42BD2FEB-C06D-4A23-BFBE-B2C5D96E21E6@fruitfly.org> Message-ID: > > surely > > HGNC_gene:ABCA1 > > ? oops, yes! m From midori at ebi.ac.uk Thu Mar 1 16:00:06 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 2 Mar 2007 00:00:06 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200703020000.l22006I1302759@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070302/e8b05f5d/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070302/e8b05f5d/attachment.pl From tberardi at acoma.Stanford.EDU Tue Mar 6 17:58:01 2007 From: tberardi at acoma.Stanford.EDU (Tanya Berardini) Date: Tue, 6 Mar 2007 17:58:01 -0800 Subject: Fwd: question concerning annotations based on motif recognition References: <1f70cc570703061650k1864d8f9ue3a418d58bb44548@mail.gmail.com> Message-ID: <03ECCDB4-5A42-431A-B502-8076C693C626@acoma.stanford.edu> Am forwarding this on behalf of Chris, another curator here at TAIR. We'd appreciate your thoughts. Tanya Begin forwarded message: > From: "Christophe Tissier" > Date: March 6, 2007 4:50:02 PM PST > To: "Tanya Berardini" > Subject: Fwd: question concerning annotations based on motif > recognition > > hey, did you ever receive this email through the discussion group? > I never received a single answer! > > Chris > > ---------- Forwarded message ---------- > From: Christophe Tissier > Date: Mar 2, 2007 10:35 AM > Subject: question concerning annotations based on motif recognition > To: annotation at genome.stanford.edu > > Hi, > > should we annotate to motif? For example, I have a paper with ATP- > and GTP-binding motifs. Often when these results are presented no > specific method is given as they are often considered common > knowledge. Should we annotate and if so, to what? I guess RCA might > fit the bill, it is afterall based on sequence alignments. > > Thanks your help > > Christophe > > -- > Dr Christophe Tissier MetaCyc: > http://www.metacyc.org/ > MetaCyc/TAIR Curator AraCyc: > http://www.arabidopsis.org/tools/aracyc/ > Carnegie Institution of Washington tel +1 650 325 > 1521 x267 > Stanford University fax +1 650 > 325 6857 > Stanford, CA94305 > USA > > -- > Dr Christophe Tissier MetaCyc: > http://www.metacyc.org/ > MetaCyc/TAIR Curator AraCyc: > http://www.arabidopsis.org/tools/aracyc/ > Carnegie Institution of Washington tel +1 650 325 > 1521 x267 > Stanford University fax +1 650 > 325 6857 > Stanford, CA94305 > USA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070306/6a4f49ad/attachment.html From suzi at berkeleybop.org Tue Mar 6 19:22:37 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Tue, 6 Mar 2007 19:22:37 -0800 Subject: question concerning annotations based on motif recognition In-Reply-To: <03ECCDB4-5A42-431A-B502-8076C693C626@acoma.stanford.edu> References: <1f70cc570703061650k1864d8f9ue3a418d58bb44548@mail.gmail.com> <03ECCDB4-5A42-431A-B502-8076C693C626@acoma.stanford.edu> Message-ID: From a non-biologist I thought we agreed that common knowledge would use NAS. Or, if this is really well-established by your judgement, then wouldn't this use the same code as we use for interpro? -S On Mar 6, 2007, at 5:58 PM, Tanya Berardini wrote: > Am forwarding this on behalf of Chris, another curator here at > TAIR. We'd appreciate your thoughts. > > Tanya > > > Begin forwarded message: > >> From: "Christophe Tissier" >> Date: March 6, 2007 4:50:02 PM PST >> To: "Tanya Berardini" >> Subject: Fwd: question concerning annotations based on motif >> recognition >> >> hey, did you ever receive this email through the discussion group? >> I never received a single answer! >> >> Chris >> >> ---------- Forwarded message ---------- >> From: Christophe Tissier >> Date: Mar 2, 2007 10:35 AM >> Subject: question concerning annotations based on motif recognition >> To: annotation at genome.stanford.edu >> >> Hi, >> >> should we annotate to motif? For example, I have a paper with ATP- >> and GTP-binding motifs. Often when these results are presented no >> specific method is given as they are often considered common >> knowledge. Should we annotate and if so, to what? I guess RCA >> might fit the bill, it is afterall based on sequence alignments. >> >> Thanks your help >> >> Christophe >> >> -- >> Dr Christophe Tissier MetaCyc: >> http://www.metacyc.org/ >> MetaCyc/TAIR Curator AraCyc: >> http://www.arabidopsis.org/tools/aracyc/ >> Carnegie Institution of Washington tel +1 650 325 >> 1521 x267 >> Stanford University fax +1 >> 650 325 6857 >> Stanford, CA94305 >> USA >> >> -- >> Dr Christophe Tissier MetaCyc: >> http://www.metacyc.org/ >> MetaCyc/TAIR Curator AraCyc: >> http://www.arabidopsis.org/tools/aracyc/ >> Carnegie Institution of Washington tel +1 650 325 >> 1521 x267 >> Stanford University fax +1 >> 650 325 6857 >> Stanford, CA94305 >> USA > From kchris at genome.Stanford.EDU Tue Mar 6 19:42:45 2007 From: kchris at genome.Stanford.EDU (Karen Christie) Date: Tue, 6 Mar 2007 19:42:45 -0800 (PST) Subject: Fwd: question concerning annotations based on motif recognition In-Reply-To: <03ECCDB4-5A42-431A-B502-8076C693C626@acoma.stanford.edu> References: <1f70cc570703061650k1864d8f9ue3a418d58bb44548@mail.gmail.com> <03ECCDB4-5A42-431A-B502-8076C693C626@acoma.stanford.edu> Message-ID: Hi, I would not use RCA for this. This is certainly not similar to the type of analyses that prompted SGD to request the RCA code. The Evidence Code Committee does still need to reconsider what RCA should be for, but I don't think this should be in RCA. If you think this is a sequence similarity method, then we agreed at the GOC to go with the Evidence Code Committee's recommendation to revert the Annotation Camp's decision to use RCA instead of ISS for INterPro based sequence similarity methods that are reviewed by curators. INstead, we agreed to go with the ECC's recommendation that purely ISS based methods should be ISS when curator reviewed or IEA when not. Alternatively, if you feel that there is not enough in the paper to use ISS and you choose to annotate it, then I think you're left with NAS because you are annotating an author statement that is not traceable to a different reference. -Karen On Tue, 6 Mar 2007, Tanya Berardini wrote: > Am forwarding this on behalf of Chris, another curator here at TAIR. We'd > appreciate your thoughts. > > Tanya > > > Begin forwarded message: > >> From: "Christophe Tissier" >> Date: March 6, 2007 4:50:02 PM PST >> To: "Tanya Berardini" >> Subject: Fwd: question concerning annotations based on motif recognition >> >> hey, did you ever receive this email through the discussion group? I never >> received a single answer! >> >> Chris >> >> ---------- Forwarded message ---------- >> From: Christophe Tissier >> Date: Mar 2, 2007 10:35 AM >> Subject: question concerning annotations based on motif recognition >> To: annotation at genome.stanford.edu >> >> Hi, >> >> should we annotate to motif? For example, I have a paper with ATP- and >> GTP-binding motifs. Often when these results are presented no specific >> method is given as they are often considered common knowledge. Should we >> annotate and if so, to what? I guess RCA might fit the bill, it is afterall >> based on sequence alignments. >> >> Thanks your help >> >> Christophe >> >> -- >> Dr Christophe Tissier MetaCyc: >> http://www.metacyc.org/ >> MetaCyc/TAIR Curator AraCyc: >> http://www.arabidopsis.org/tools/aracyc/ >> Carnegie Institution of Washington tel +1 650 325 1521 x267 >> Stanford University fax +1 650 325 >> 6857 >> Stanford, CA94305 >> USA >> >> -- >> Dr Christophe Tissier MetaCyc: >> http://www.metacyc.org/ >> MetaCyc/TAIR Curator AraCyc: >> http://www.arabidopsis.org/tools/aracyc/ >> Carnegie Institution of Washington tel +1 650 325 1521 x267 >> Stanford University fax +1 650 325 >> 6857 >> Stanford, CA94305 >> USA > From pgaudet at northwestern.edu Wed Mar 7 06:35:47 2007 From: pgaudet at northwestern.edu (Pascale Gaudet) Date: Wed, 07 Mar 2007 09:35:47 -0500 Subject: Fwd: question concerning annotations based on motif recognition In-Reply-To: References: <1f70cc570703061650k1864d8f9ue3a418d58bb44548@mail.gmail.com> <03ECCDB4-5A42-431A-B502-8076C693C626@acoma.stanford.edu> Message-ID: <6.0.1.1.2.20070307092831.0378a5e8@lulu.it.northwestern.edu> I often rerun the analysis myself and if it seems convincing, I either use InterPro/Pfam as the "with", assuming the tool they have used must be comparable; otherwise sometimes do not annotate at all or contact the authors to find out how they have made the assessment. Pascale At 07:42 PM 3/6/2007 -0800, Karen Christie wrote: >Hi, > >I would not use RCA for this. This is certainly not similar to the type of >analyses that prompted SGD to request the RCA code. The Evidence Code >Committee does still need to reconsider what RCA should be for, but I >don't think this should be in RCA. > >If you think this is a sequence similarity method, then we agreed at the >GOC to go with the Evidence Code Committee's recommendation to revert the >Annotation Camp's decision to use RCA instead of ISS for INterPro based >sequence similarity methods that are reviewed by curators. INstead, we >agreed to go with the ECC's recommendation that purely ISS based methods >should be ISS when curator reviewed or IEA when not. > >Alternatively, if you feel that there is not enough in the paper to use >ISS and you choose to annotate it, then I think you're left with NAS >because you are annotating an author statement that is not traceable to a >different reference. > >-Karen > > > >On Tue, 6 Mar 2007, Tanya Berardini wrote: > >>Am forwarding this on behalf of Chris, another curator here at >>TAIR. We'd appreciate your thoughts. >> >>Tanya >> >> >>Begin forwarded message: >> >>>From: "Christophe Tissier" >>>Date: March 6, 2007 4:50:02 PM PST >>>To: "Tanya Berardini" >>>Subject: Fwd: question concerning annotations based on motif recognition >>>hey, did you ever receive this email through the discussion group? I >>>never received a single answer! >>>Chris >>>---------- Forwarded message ---------- >>>From: Christophe Tissier >>>Date: Mar 2, 2007 10:35 AM >>>Subject: question concerning annotations based on motif recognition >>>To: annotation at genome.stanford.edu >>>Hi, >>>should we annotate to motif? For example, I have a paper with ATP- and >>>GTP-binding motifs. Often when these results are presented no specific >>>method is given as they are often considered common knowledge. Should we >>>annotate and if so, to what? I guess RCA might fit the bill, it is >>>afterall based on sequence alignments. >>>Thanks your help >>>Christophe >>>-- Dr Christophe Tissier MetaCyc: >>>http://www.metacyc.org/ >>>MetaCyc/TAIR Curator AraCyc: >>>http://www.arabidopsis.org/tools/aracyc/ >>>Carnegie Institution of Washington tel +1 650 325 1521 x267 >>>Stanford University fax +1 650 325 6857 >>>Stanford, CA94305 >>>USA >>>-- Dr Christophe Tissier MetaCyc: >>>http://www.metacyc.org/ >>>MetaCyc/TAIR Curator AraCyc: >>>http://www.arabidopsis.org/tools/aracyc/ >>>Carnegie Institution of Washington tel +1 650 325 1521 x267 >>>Stanford University fax +1 650 325 6857 >>>Stanford, CA94305 >>>USA From val at sanger.ac.uk Wed Mar 7 06:51:07 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 07 Mar 2007 14:51:07 +0000 Subject: Fwd: question concerning annotations based on motif recognition In-Reply-To: <6.0.1.1.2.20070307092831.0378a5e8@lulu.it.northwestern.edu> References: <1f70cc570703061650k1864d8f9ue3a418d58bb44548@mail.gmail.com> <03ECCDB4-5A42-431A-B502-8076C693C626@acoma.stanford.edu> <6.0.1.1.2.20070307092831.0378a5e8@lulu.it.northwestern.edu> Message-ID: <45EED15B.4040103@sanger.ac.uk> I agree that this would be converted to an ISS. You should be able to follow the same logic as the author and annotate using an ortholog or protein family identifier in the 'with' field. If I wasn't convinced I'd contact the author for clarification. Val Pascale Gaudet wrote: > I often rerun the analysis myself and if it seems convincing, I either > use InterPro/Pfam as the "with", assuming the tool they have used must > be comparable; otherwise sometimes do not annotate at all or contact > the authors to find out how they have made the assessment. > > > Pascale > > > At 07:42 PM 3/6/2007 -0800, Karen Christie wrote: > >> Hi, >> >> I would not use RCA for this. This is certainly not similar to the >> type of analyses that prompted SGD to request the RCA code. The >> Evidence Code Committee does still need to reconsider what RCA should >> be for, but I don't think this should be in RCA. >> >> If you think this is a sequence similarity method, then we agreed at >> the GOC to go with the Evidence Code Committee's recommendation to >> revert the Annotation Camp's decision to use RCA instead of ISS for >> INterPro based sequence similarity methods that are reviewed by >> curators. INstead, we agreed to go with the ECC's recommendation that >> purely ISS based methods should be ISS when curator reviewed or IEA >> when not. >> >> Alternatively, if you feel that there is not enough in the paper to >> use ISS and you choose to annotate it, then I think you're left with >> NAS because you are annotating an author statement that is not >> traceable to a different reference. >> >> -Karen >> >> >> >> On Tue, 6 Mar 2007, Tanya Berardini wrote: >> >>> Am forwarding this on behalf of Chris, another curator here at >>> TAIR. We'd appreciate your thoughts. >>> >>> Tanya >>> >>> >>> Begin forwarded message: >>> >>>> From: "Christophe Tissier" >>>> Date: March 6, 2007 4:50:02 PM PST >>>> To: "Tanya Berardini" >>>> Subject: Fwd: question concerning annotations based on motif >>>> recognition >>>> hey, did you ever receive this email through the discussion group? >>>> I never received a single answer! >>>> Chris >>>> ---------- Forwarded message ---------- >>>> From: Christophe Tissier >>>> Date: Mar 2, 2007 10:35 AM >>>> Subject: question concerning annotations based on motif recognition >>>> To: annotation at genome.stanford.edu >>>> Hi, >>>> should we annotate to motif? For example, I have a paper with ATP- >>>> and GTP-binding motifs. Often when these results are presented no >>>> specific method is given as they are often considered common >>>> knowledge. Should we annotate and if so, to what? I guess RCA might >>>> fit the bill, it is afterall based on sequence alignments. >>>> Thanks your help >>>> Christophe >>>> -- Dr Christophe Tissier MetaCyc: >>>> http://www.metacyc.org/ >>>> MetaCyc/TAIR Curator AraCyc: >>>> http://www.arabidopsis.org/tools/aracyc/ >>>> Carnegie Institution of Washington tel +1 650 325 >>>> 1521 x267 >>>> Stanford University fax +1 650 >>>> 325 6857 >>>> Stanford, CA94305 >>>> USA >>>> -- Dr Christophe Tissier MetaCyc: >>>> http://www.metacyc.org/ >>>> MetaCyc/TAIR Curator AraCyc: >>>> http://www.arabidopsis.org/tools/aracyc/ >>>> Carnegie Institution of Washington tel +1 650 325 >>>> 1521 x267 >>>> Stanford University fax +1 650 >>>> 325 6857 >>>> Stanford, CA94305 >>>> USA >>> > > > -- --------------------------------------------------------------------------- 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 From kchris at genome.Stanford.EDU Wed Mar 7 18:26:10 2007 From: kchris at genome.Stanford.EDU (Karen Christie) Date: Wed, 7 Mar 2007 18:26:10 -0800 (PST) Subject: Fwd: question concerning annotations based on motif recognition In-Reply-To: <6.0.1.1.2.20070307092831.0378a5e8@lulu.it.northwestern.edu> References: <1f70cc570703061650k1864d8f9ue3a418d58bb44548@mail.gmail.com> <03ECCDB4-5A42-431A-B502-8076C693C626@acoma.stanford.edu> <6.0.1.1.2.20070307092831.0378a5e8@lulu.it.northwestern.edu> Message-ID: When you rerun the analysis, what do you use as the reference? -Karen On Wed, 7 Mar 2007, Pascale Gaudet wrote: > I often rerun the analysis myself and if it seems convincing, I either use > InterPro/Pfam as the "with", assuming the tool they have used must be > comparable; otherwise sometimes do not annotate at all or contact the authors > to find out how they have made the assessment. > > > Pascale > > > At 07:42 PM 3/6/2007 -0800, Karen Christie wrote: >> Hi, >> >> I would not use RCA for this. This is certainly not similar to the type of >> analyses that prompted SGD to request the RCA code. The Evidence Code >> Committee does still need to reconsider what RCA should be for, but I don't >> think this should be in RCA. >> >> If you think this is a sequence similarity method, then we agreed at the >> GOC to go with the Evidence Code Committee's recommendation to revert the >> Annotation Camp's decision to use RCA instead of ISS for INterPro based >> sequence similarity methods that are reviewed by curators. INstead, we >> agreed to go with the ECC's recommendation that purely ISS based methods >> should be ISS when curator reviewed or IEA when not. >> >> Alternatively, if you feel that there is not enough in the paper to use ISS >> and you choose to annotate it, then I think you're left with NAS because >> you are annotating an author statement that is not traceable to a different >> reference. >> >> -Karen >> >> >> >> On Tue, 6 Mar 2007, Tanya Berardini wrote: >> >>> Am forwarding this on behalf of Chris, another curator here at TAIR. We'd >>> appreciate your thoughts. >>> >>> Tanya >>> >>> >>> Begin forwarded message: >>> >>>> From: "Christophe Tissier" >>>> Date: March 6, 2007 4:50:02 PM PST >>>> To: "Tanya Berardini" >>>> Subject: Fwd: question concerning annotations based on motif recognition >>>> hey, did you ever receive this email through the discussion group? I >>>> never received a single answer! >>>> Chris >>>> ---------- Forwarded message ---------- >>>> From: Christophe Tissier >>>> Date: Mar 2, 2007 10:35 AM >>>> Subject: question concerning annotations based on motif recognition >>>> To: annotation at genome.stanford.edu >>>> Hi, >>>> should we annotate to motif? For example, I have a paper with ATP- and >>>> GTP-binding motifs. Often when these results are presented no specific >>>> method is given as they are often considered common knowledge. Should we >>>> annotate and if so, to what? I guess RCA might fit the bill, it is >>>> afterall based on sequence alignments. >>>> Thanks your help >>>> Christophe >>>> -- Dr Christophe Tissier MetaCyc: >>>> http://www.metacyc.org/ >>>> MetaCyc/TAIR Curator AraCyc: >>>> http://www.arabidopsis.org/tools/aracyc/ >>>> Carnegie Institution of Washington tel +1 650 325 1521 >>>> x267 >>>> Stanford University fax +1 650 325 >>>> 6857 >>>> Stanford, CA94305 >>>> USA >>>> -- Dr Christophe Tissier MetaCyc: >>>> http://www.metacyc.org/ >>>> MetaCyc/TAIR Curator AraCyc: >>>> http://www.arabidopsis.org/tools/aracyc/ >>>> Carnegie Institution of Washington tel +1 650 325 1521 >>>> x267 >>>> Stanford University fax +1 650 325 >>>> 6857 >>>> Stanford, CA94305 >>>> USA > > From pgaudet at northwestern.edu Thu Mar 8 04:52:21 2007 From: pgaudet at northwestern.edu (Pascale Gaudet) Date: Thu, 08 Mar 2007 07:52:21 -0500 Subject: Fwd: question concerning annotations based on motif recognition In-Reply-To: References: <1f70cc570703061650k1864d8f9ue3a418d58bb44548@mail.gmail.com> <03ECCDB4-5A42-431A-B502-8076C693C626@acoma.stanford.edu> <6.0.1.1.2.20070307092831.0378a5e8@lulu.it.northwestern.edu> Message-ID: <6.0.1.1.2.20070308071627.037adcf0@lulu.it.northwestern.edu> If the result is the same, I usually use the published reference. For example, if the authors say "this protein has 7 transmembrane domains" I annotate to component = integral to membrane with CBS:TMHMM citing the paper, same for domains (actin binding domain, calcium binding domain). If however the authors state that a protein has a certain domain or is transmembrane without giving a method, and I cannot confirm the statement with a tool I know, then I don't make the annotation and instead, I put the information in the gene description. Pascale At 06:26 PM 3/7/2007 -0800, Karen Christie wrote: >When you rerun the analysis, what do you use as the reference? > >-Karen > > >On Wed, 7 Mar 2007, Pascale Gaudet wrote: > >>I often rerun the analysis myself and if it seems convincing, I either >>use InterPro/Pfam as the "with", assuming the tool they have used must be >>comparable; otherwise sometimes do not annotate at all or contact the >>authors to find out how they have made the assessment. >> >> >>Pascale >> >> >>At 07:42 PM 3/6/2007 -0800, Karen Christie wrote: >>>Hi, >>>I would not use RCA for this. This is certainly not similar to the type >>>of analyses that prompted SGD to request the RCA code. The Evidence Code >>>Committee does still need to reconsider what RCA should be for, but I >>>don't think this should be in RCA. >>>If you think this is a sequence similarity method, then we agreed at the >>>GOC to go with the Evidence Code Committee's recommendation to revert >>>the Annotation Camp's decision to use RCA instead of ISS for INterPro >>>based sequence similarity methods that are reviewed by curators. >>>INstead, we agreed to go with the ECC's recommendation that purely ISS >>>based methods should be ISS when curator reviewed or IEA when not. >>>Alternatively, if you feel that there is not enough in the paper to use >>>ISS and you choose to annotate it, then I think you're left with NAS >>>because you are annotating an author statement that is not traceable to >>>a different reference. >>>-Karen >>> >>>On Tue, 6 Mar 2007, Tanya Berardini wrote: >>> >>>>Am forwarding this on behalf of Chris, another curator here at >>>>TAIR. We'd appreciate your thoughts. >>>>Tanya >>>> >>>>Begin forwarded message: >>>> >>>>>From: "Christophe Tissier" >>>>>Date: March 6, 2007 4:50:02 PM PST >>>>>To: "Tanya Berardini" >>>>>Subject: Fwd: question concerning annotations based on motif recognition >>>>>hey, did you ever receive this email through the discussion group? I >>>>>never received a single answer! >>>>>Chris >>>>>---------- Forwarded message ---------- >>>>>From: Christophe Tissier >>>>>Date: Mar 2, 2007 10:35 AM >>>>>Subject: question concerning annotations based on motif recognition >>>>>To: annotation at genome.stanford.edu >>>>>Hi, >>>>>should we annotate to motif? For example, I have a paper with ATP- and >>>>>GTP-binding motifs. Often when these results are presented no specific >>>>>method is given as they are often considered common knowledge. Should >>>>>we annotate and if so, to what? I guess RCA might fit the bill, it is >>>>>afterall based on sequence alignments. >>>>>Thanks your help >>>>>Christophe >>>>>-- Dr Christophe Tissier MetaCyc: >>>>>http://www.metacyc.org/ >>>>>MetaCyc/TAIR Curator AraCyc: >>>>>http://www.arabidopsis.org/tools/aracyc/ >>>>>Carnegie Institution of Washington tel +1 650 325 1521 >>>>>x267 >>>>>Stanford University fax +1 650 >>>>>325 6857 >>>>>Stanford, CA94305 >>>>>USA >>>>>-- Dr Christophe Tissier MetaCyc: >>>>>http://www.metacyc.org/ >>>>>MetaCyc/TAIR Curator AraCyc: >>>>>http://www.arabidopsis.org/tools/aracyc/ >>>>>Carnegie Institution of Washington tel +1 650 325 1521 >>>>>x267 >>>>>Stanford University fax +1 650 >>>>>325 6857 >>>>>Stanford, CA94305 >>>>>USA >> From lhannick at tigr.org Thu Mar 8 08:26:06 2007 From: lhannick at tigr.org (Hannick, Linda) Date: Thu, 8 Mar 2007 11:26:06 -0500 Subject: Fwd: question concerning annotations based on motif recognition In-Reply-To: References: <1f70cc570703061650k1864d8f9ue3a418d58bb44548@mail.gmail.com> <03ECCDB4-5A42-431A-B502-8076C693C626@acoma.stanford.edu> <6.0.1.1.2.20070307092831.0378a5e8@lulu.it.northwestern.edu> Message-ID: Could one use a reference to the method, such as this paper: Sigrist C.J.A., Cerutti L., Hulo N., Gattiker A., Falquet L., Pagni M., Bairoch A., Bucher P. "PROSITE: a documented database using patterns and profiles as motif descriptors." Brief Bioinform. 3:265-274(2002). PMID:12230035 For the 'With' column, a Prosite search identified the motifs so the Prosite accession (Prosite:PS00017) should be entered. The Interpro accession (Interpro:IPR001687) is based on the Prosite motif, but it seems to me that the Prosite accession is the most relevant, as it is the direct result. - Linda -----Original Message----- From: owner-annotation at genome.stanford.edu [mailto:owner-annotation at genome.stanford.edu] On Behalf Of Karen Christie Sent: Wednesday, March 07, 2007 9:26 PM To: Pascale Gaudet Cc: Karen Christie; Tanya Berardini; annotation at genome.stanford.edu; Christophe Tissier Subject: Re: Fwd: question concerning annotations based on motif recognition When you rerun the analysis, what do you use as the reference? -Karen On Wed, 7 Mar 2007, Pascale Gaudet wrote: > I often rerun the analysis myself and if it seems convincing, I either use > InterPro/Pfam as the "with", assuming the tool they have used must be > comparable; otherwise sometimes do not annotate at all or contact the authors > to find out how they have made the assessment. > > > Pascale > > > At 07:42 PM 3/6/2007 -0800, Karen Christie wrote: >> Hi, >> >> I would not use RCA for this. This is certainly not similar to the type of >> analyses that prompted SGD to request the RCA code. The Evidence Code >> Committee does still need to reconsider what RCA should be for, but I don't >> think this should be in RCA. >> >> If you think this is a sequence similarity method, then we agreed at the >> GOC to go with the Evidence Code Committee's recommendation to revert the >> Annotation Camp's decision to use RCA instead of ISS for INterPro based >> sequence similarity methods that are reviewed by curators. INstead, we >> agreed to go with the ECC's recommendation that purely ISS based methods >> should be ISS when curator reviewed or IEA when not. >> >> Alternatively, if you feel that there is not enough in the paper to use ISS >> and you choose to annotate it, then I think you're left with NAS because >> you are annotating an author statement that is not traceable to a different >> reference. >> >> -Karen >> >> >> >> On Tue, 6 Mar 2007, Tanya Berardini wrote: >> >>> Am forwarding this on behalf of Chris, another curator here at TAIR. We'd >>> appreciate your thoughts. >>> >>> Tanya >>> >>> >>> Begin forwarded message: >>> >>>> From: "Christophe Tissier" >>>> Date: March 6, 2007 4:50:02 PM PST >>>> To: "Tanya Berardini" >>>> Subject: Fwd: question concerning annotations based on motif recognition >>>> hey, did you ever receive this email through the discussion group? I >>>> never received a single answer! >>>> Chris >>>> ---------- Forwarded message ---------- >>>> From: Christophe Tissier >>>> Date: Mar 2, 2007 10:35 AM >>>> Subject: question concerning annotations based on motif recognition >>>> To: annotation at genome.stanford.edu >>>> Hi, >>>> should we annotate to motif? For example, I have a paper with ATP- and >>>> GTP-binding motifs. Often when these results are presented no specific >>>> method is given as they are often considered common knowledge. Should we >>>> annotate and if so, to what? I guess RCA might fit the bill, it is >>>> afterall based on sequence alignments. >>>> Thanks your help >>>> Christophe >>>> -- Dr Christophe Tissier MetaCyc: >>>> http://www.metacyc.org/ >>>> MetaCyc/TAIR Curator AraCyc: >>>> http://www.arabidopsis.org/tools/aracyc/ >>>> Carnegie Institution of Washington tel +1 650 325 1521 >>>> x267 >>>> Stanford University fax +1 650 325 >>>> 6857 >>>> Stanford, CA94305 >>>> USA >>>> -- Dr Christophe Tissier MetaCyc: >>>> http://www.metacyc.org/ >>>> MetaCyc/TAIR Curator AraCyc: >>>> http://www.arabidopsis.org/tools/aracyc/ >>>> Carnegie Institution of Washington tel +1 650 325 1521 >>>> x267 >>>> Stanford University fax +1 650 325 >>>> 6857 >>>> Stanford, CA94305 >>>> USA > > From pgaudet at northwestern.edu Thu Mar 8 08:35:05 2007 From: pgaudet at northwestern.edu (Pascale Gaudet) Date: Thu, 08 Mar 2007 11:35:05 -0500 Subject: Fwd: question concerning annotations based on motif recognition In-Reply-To: References: <1f70cc570703061650k1864d8f9ue3a418d58bb44548@mail.gmail.com> <03ECCDB4-5A42-431A-B502-8076C693C626@acoma.stanford.edu> <6.0.1.1.2.20070307092831.0378a5e8@lulu.it.northwestern.edu> Message-ID: <6.0.1.1.2.20070308113231.037af2c8@lulu.it.northwestern.edu> I dont think so. This paper is the method itself, it's not where the annotation comes from. The annotation comes from a researcher or a curator applying this method, which is why you need an additional reference describing that. Pascale At 11:26 AM 3/8/2007 -0500, Hannick, Linda wrote: >Could one use a reference to the method, such as this paper: > > Sigrist C.J.A., Cerutti L., Hulo N., Gattiker A., Falquet L., Pagni >M., Bairoch A., Bucher P. "PROSITE: a documented database using patterns >and profiles as motif descriptors." Brief Bioinform. 3:265-274(2002). > PMID:12230035 > >For the 'With' column, a Prosite search identified the motifs so the >Prosite accession (Prosite:PS00017) should be entered. The Interpro >accession (Interpro:IPR001687) is based on the Prosite motif, but it >seems to me that the Prosite accession is the most relevant, as it is >the direct result. > >- Linda > >-----Original Message----- >From: owner-annotation at genome.stanford.edu >[mailto:owner-annotation at genome.stanford.edu] On Behalf Of Karen >Christie >Sent: Wednesday, March 07, 2007 9:26 PM >To: Pascale Gaudet >Cc: Karen Christie; Tanya Berardini; annotation at genome.stanford.edu; >Christophe Tissier >Subject: Re: Fwd: question concerning annotations based on motif >recognition > >When you rerun the analysis, what do you use as the reference? > >-Karen > > >On Wed, 7 Mar 2007, Pascale Gaudet wrote: > > > I often rerun the analysis myself and if it seems convincing, I either >use > > InterPro/Pfam as the "with", assuming the tool they have used must be > > comparable; otherwise sometimes do not annotate at all or contact the >authors > > to find out how they have made the assessment. > > > > > > Pascale > > > > > > At 07:42 PM 3/6/2007 -0800, Karen Christie wrote: > >> Hi, > >> > >> I would not use RCA for this. This is certainly not similar to the >type of > >> analyses that prompted SGD to request the RCA code. The Evidence Code > > >> Committee does still need to reconsider what RCA should be for, but I >don't > >> think this should be in RCA. > >> > >> If you think this is a sequence similarity method, then we agreed at >the > >> GOC to go with the Evidence Code Committee's recommendation to revert >the > >> Annotation Camp's decision to use RCA instead of ISS for INterPro >based > >> sequence similarity methods that are reviewed by curators. INstead, >we > >> agreed to go with the ECC's recommendation that purely ISS based >methods > >> should be ISS when curator reviewed or IEA when not. > >> > >> Alternatively, if you feel that there is not enough in the paper to >use ISS > >> and you choose to annotate it, then I think you're left with NAS >because > >> you are annotating an author statement that is not traceable to a >different > >> reference. > >> > >> -Karen > >> > >> > >> > >> On Tue, 6 Mar 2007, Tanya Berardini wrote: > >> > >>> Am forwarding this on behalf of Chris, another curator here at TAIR. >We'd > >>> appreciate your thoughts. > >>> > >>> Tanya > >>> > >>> > >>> Begin forwarded message: > >>> > >>>> From: "Christophe Tissier" > >>>> Date: March 6, 2007 4:50:02 PM PST > >>>> To: "Tanya Berardini" > >>>> Subject: Fwd: question concerning annotations based on motif >recognition > >>>> hey, did you ever receive this email through the discussion group? >I > >>>> never received a single answer! > >>>> Chris > >>>> ---------- Forwarded message ---------- > >>>> From: Christophe Tissier > >>>> Date: Mar 2, 2007 10:35 AM > >>>> Subject: question concerning annotations based on motif recognition > >>>> To: annotation at genome.stanford.edu > >>>> Hi, > >>>> should we annotate to motif? For example, I have a paper with ATP- >and > >>>> GTP-binding motifs. Often when these results are presented no >specific > >>>> method is given as they are often considered common knowledge. >Should we > >>>> annotate and if so, to what? I guess RCA might fit the bill, it is > >>>> afterall based on sequence alignments. > >>>> Thanks your help > >>>> Christophe > >>>> -- Dr Christophe Tissier MetaCyc: > > >>>> http://www.metacyc.org/ > >>>> MetaCyc/TAIR Curator AraCyc: > >>>> http://www.arabidopsis.org/tools/aracyc/ > >>>> Carnegie Institution of Washington tel +1 650 325 >1521 > >>>> x267 > >>>> Stanford University fax +1 650 >325 > >>>> 6857 > >>>> Stanford, CA94305 > >>>> USA > >>>> -- Dr Christophe Tissier MetaCyc: > > >>>> http://www.metacyc.org/ > >>>> MetaCyc/TAIR Curator AraCyc: > >>>> http://www.arabidopsis.org/tools/aracyc/ > >>>> Carnegie Institution of Washington tel +1 650 325 >1521 > >>>> x267 > >>>> Stanford University fax +1 650 >325 > >>>> 6857 > >>>> Stanford, CA94305 > >>>> USA > > > > From midori at ebi.ac.uk Wed Mar 14 17:00:05 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 15 Mar 2007 00:00:05 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200703150000.l2F006q1084896@mozart.ebi.ac.uk> An HTML attachment was scrubbed... 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Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070322/32a3c180/attachment.pl From midori at ebi.ac.uk Fri Mar 23 17:00:08 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 24 Mar 2007 00:00:08 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200703240000.l2O008L1255022@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070324/d13230dc/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070324/d13230dc/attachment.pl From sart2 at gen.cam.ac.uk Thu Mar 29 06:26:39 2007 From: sart2 at gen.cam.ac.uk (Susan Tweedie) Date: Thu, 29 Mar 2007 14:26:39 +0100 Subject: GO term for innervation Message-ID: <1175174799.19114.39.camel@paul.gen.cam.ac.uk> We are struggling to decide if the GO term 'axonogenesis' is exactly equivalent to 'innervation' (as in the process involving nerve projection and connection with a target - and as used in the mammalian phenotype term 'abnormal innervation' MP:0002184). Axonogenesis has the approriate child terms of 'axon guidance' and 'axon target recogintion' but I'm put off by the word 'towards' in the definition: Generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. If it is the same thing, then I'll make an sf item to add 'innervation' as an exact synonym. Thanks, Susan (and George) From midori at ebi.ac.uk Thu Mar 29 06:36:02 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 29 Mar 2007 14:36:02 +0100 (BST) Subject: GO term for innervation In-Reply-To: <1175174799.19114.39.camel@paul.gen.cam.ac.uk> References: <1175174799.19114.39.camel@paul.gen.cam.ac.uk> Message-ID: I think we could improve the wording of the 'axonogenesis' definition anyway, to make it more consistent with the 'axon' definition in the component ontology (and correct the punctuation error). Suggestion: "Generation of an axon, a long process that extends from the cell body of a neuron and conducts nerve impulses, which usually travel away from the cell body to the terminals and varicosities and towards target cells." But I don't know whether 'innervation' is exactly the same; I'll go with whatever the innervation experts say. midori On Thu, 29 Mar 2007, Susan Tweedie wrote: > We are struggling to decide if the GO term 'axonogenesis' is exactly > equivalent to 'innervation' (as in the process involving nerve > projection and connection with a target - and as used in the mammalian > phenotype term 'abnormal innervation' MP:0002184). Axonogenesis has the > approriate child terms of 'axon guidance' and 'axon target recogintion' > but I'm put off by the word 'towards' in the definition: > > Generation of a long process of a neuron, that carries efferent > (outgoing) action potentials from the cell body towards target cells. > > If it is the same thing, then I'll make an sf item to add 'innervation' > as an exact synonym. > > > Thanks, > > Susan (and George) > From dph at informatics.jax.org Thu Mar 29 07:23:35 2007 From: dph at informatics.jax.org (David Hill) Date: Thu, 29 Mar 2007 10:23:35 -0400 Subject: GO term for innervation In-Reply-To: <1175174799.19114.39.camel@paul.gen.cam.ac.uk> References: <1175174799.19114.39.camel@paul.gen.cam.ac.uk> Message-ID: <460BCBE7.9030203@informatics.jax.org> Susan, I would like comments from others but I do not think they are exact synonyms. I think innervation is composed of both axonogenesis and synaptogenesis. Axonogenesis is the growth of the axon to the correct target and synaptogenesis is the formation of a functional synapse at the correct site. David Susan Tweedie wrote: > We are struggling to decide if the GO term 'axonogenesis' is exactly > equivalent to 'innervation' (as in the process involving nerve > projection and connection with a target - and as used in the mammalian > phenotype term 'abnormal innervation' MP:0002184). Axonogenesis has the > approriate child terms of 'axon guidance' and 'axon target recogintion' > but I'm put off by the word 'towards' in the definition: > > Generation of a long process of a neuron, that carries efferent > (outgoing) action potentials from the cell body towards target cells. > > If it is the same thing, then I'll make an sf item to add 'innervation' > as an exact synonym. > > > Thanks, > > Susan (and George) > > From sart2 at gen.cam.ac.uk Thu Mar 29 07:48:29 2007 From: sart2 at gen.cam.ac.uk (Susan Tweedie) Date: Thu, 29 Mar 2007 15:48:29 +0100 Subject: GO term for innervation In-Reply-To: <460BCBE7.9030203@informatics.jax.org> References: <1175174799.19114.39.camel@paul.gen.cam.ac.uk> <460BCBE7.9030203@informatics.jax.org> Message-ID: <1175179709.19114.53.camel@paul.gen.cam.ac.uk> David, Thanks. Yes - I agree that synaptogenesis would be part of it - I hadn't noticed that term. I also feel that a definition of innervation should refer to whole nerves rather than just the axons (though axonogenesis is still clearly part of the process). I'm not sure if it merits a new term but I think it is something that biologists may expect to find if they searched GO. I'd be interested to hear any other thoughts. Susan On Thu, 2007-03-29 at 10:23 -0400, David Hill wrote: > Susan, > > I would like comments from others but I do not think they are exact > synonyms. I think innervation is composed of both axonogenesis and > synaptogenesis. Axonogenesis is the growth of the axon to the correct > target and synaptogenesis is the formation of a functional synapse at > the correct site. > > > David > > Susan Tweedie wrote: > > We are struggling to decide if the GO term 'axonogenesis' is exactly > > equivalent to 'innervation' (as in the process involving nerve > > projection and connection with a target - and as used in the mammalian > > phenotype term 'abnormal innervation' MP:0002184). Axonogenesis has the > > approriate child terms of 'axon guidance' and 'axon target recogintion' > > but I'm put off by the word 'towards' in the definition: > > > > Generation of a long process of a neuron, that carries efferent > > (outgoing) action potentials from the cell body towards target cells. > > > > If it is the same thing, then I'll make an sf item to add 'innervation' > > as an exact synonym. > > > > > > Thanks, > > > > Susan (and George) > > > > > > From sart2 at gen.cam.ac.uk Thu Mar 29 07:50:42 2007 From: sart2 at gen.cam.ac.uk (Susan Tweedie) Date: Thu, 29 Mar 2007 15:50:42 +0100 Subject: GO term for innervation In-Reply-To: References: <1175174799.19114.39.camel@paul.gen.cam.ac.uk> Message-ID: <1175179842.19114.56.camel@paul.gen.cam.ac.uk> Thanks, Midori. That would be good. Shall I add it to source forge? Susan On Thu, 2007-03-29 at 14:36 +0100, Midori Harris wrote: > I think we could improve the wording of the 'axonogenesis' definition > anyway, to make it more consistent with the 'axon' definition in the > component ontology (and correct the punctuation error). > > Suggestion: > > "Generation of an axon, a long process that extends from the cell body of > a neuron and conducts nerve impulses, which usually travel away from the > cell body to the terminals and varicosities and towards target cells." > > But I don't know whether 'innervation' is exactly the same; I'll go with > whatever the innervation experts say. > > midori > > On Thu, 29 Mar 2007, Susan Tweedie wrote: > > > We are struggling to decide if the GO term 'axonogenesis' is exactly > > equivalent to 'innervation' (as in the process involving nerve > > projection and connection with a target - and as used in the mammalian > > phenotype term 'abnormal innervation' MP:0002184). Axonogenesis has the > > approriate child terms of 'axon guidance' and 'axon target recogintion' > > but I'm put off by the word 'towards' in the definition: > > > > Generation of a long process of a neuron, that carries efferent > > (outgoing) action potentials from the cell body towards target cells. > > > > If it is the same thing, then I'll make an sf item to add 'innervation' > > as an exact synonym. > > > > > > Thanks, > > > > Susan (and George) > > From midori at ebi.ac.uk Thu Mar 29 07:53:53 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 29 Mar 2007 15:53:53 +0100 (BST) Subject: GO term for innervation In-Reply-To: <1175179842.19114.56.camel@paul.gen.cam.ac.uk> References: <1175174799.19114.39.camel@paul.gen.cam.ac.uk> <1175179842.19114.56.camel@paul.gen.cam.ac.uk> Message-ID: Sure; thanks! m On Thu, 29 Mar 2007, Susan Tweedie wrote: > Thanks, Midori. That would be good. Shall I add it to source forge? > > Susan > > On Thu, 2007-03-29 at 14:36 +0100, Midori Harris wrote: >> I think we could improve the wording of the 'axonogenesis' definition >> anyway, to make it more consistent with the 'axon' definition in the >> component ontology (and correct the punctuation error). >> >> Suggestion: >> >> "Generation of an axon, a long process that extends from the cell body of >> a neuron and conducts nerve impulses, which usually travel away from the >> cell body to the terminals and varicosities and towards target cells." >> >> But I don't know whether 'innervation' is exactly the same; I'll go with >> whatever the innervation experts say. >> >> midori >> >> On Thu, 29 Mar 2007, Susan Tweedie wrote: >> >>> We are struggling to decide if the GO term 'axonogenesis' is exactly >>> equivalent to 'innervation' (as in the process involving nerve >>> projection and connection with a target - and as used in the mammalian >>> phenotype term 'abnormal innervation' MP:0002184). Axonogenesis has the >>> approriate child terms of 'axon guidance' and 'axon target recogintion' >>> but I'm put off by the word 'towards' in the definition: >>> >>> Generation of a long process of a neuron, that carries efferent >>> (outgoing) action potentials from the cell body towards target cells. >>> >>> If it is the same thing, then I'll make an sf item to add 'innervation' >>> as an exact synonym. >>> >>> >>> Thanks, >>> >>> Susan (and George) >>> > From dhowe at cs.uoregon.edu Thu Mar 29 09:18:38 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Thu, 29 Mar 2007 09:18:38 -0700 Subject: GO term for innervation In-Reply-To: <460BCBE7.9030203@informatics.jax.org> References: <1175174799.19114.39.camel@paul.gen.cam.ac.uk> <460BCBE7.9030203@informatics.jax.org> Message-ID: <460BE6DE.6000608@cs.uoregon.edu> I concur with David here 100%. -Doug David Hill wrote: > Susan, > > I would like comments from others but I do not think they are exact > synonyms. I think innervation is composed of both axonogenesis and > synaptogenesis. Axonogenesis is the growth of the axon to the correct > target and synaptogenesis is the formation of a functional synapse at > the correct site. > > > David > > Susan Tweedie wrote: >> We are struggling to decide if the GO term 'axonogenesis' is exactly >> equivalent to 'innervation' (as in the process involving nerve >> projection and connection with a target - and as used in the mammalian >> phenotype term 'abnormal innervation' MP:0002184). Axonogenesis has the >> approriate child terms of 'axon guidance' and 'axon target recogintion' >> but I'm put off by the word 'towards' in the definition: >> Generation of a long process of a neuron, that carries efferent >> (outgoing) action potentials from the cell body towards target cells. >> >> If it is the same thing, then I'll make an sf item to add 'innervation' >> as an exact synonym. >> >> >> Thanks, >> >> Susan (and George) >> >> > > From midori at ebi.ac.uk Thu Mar 29 22:00:05 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 30 Mar 2007 05:00:05 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200703300500.l2U50591086447@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070330/54c47f35/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070330/54c47f35/attachment.pl From midori at ebi.ac.uk Fri Mar 30 22:00:05 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 31 Mar 2007 05:00:05 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200703310500.l2V506N1138298@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070331/5164f6db/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070331/5164f6db/attachment.pl