From midori at ebi.ac.uk Tue Oct 2 22:00:04 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 3 Oct 2007 05:00:04 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200710030500.l93504f1353603@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20071003/116af572/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20071003/116af572/attachment.pl From midori at ebi.ac.uk Wed Oct 3 22:00:05 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 4 Oct 2007 05:00:05 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200710040500.l9450671397166@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20071004/5fcce475/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20071004/5fcce475/attachment.pl From dhowe at cs.uoregon.edu Fri Oct 5 13:30:09 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Fri, 05 Oct 2007 13:30:09 -0700 Subject: [annotation] annotation of ion channel subunits Message-ID: <47069ED1.4020605@cs.uoregon.edu> For the Ref. Genomes we are annotating the gene p2rx3, a subunit of an ATP activated cation channel. A paper I have shows that adding this gene to hek293 cells results in the generation of an inward current in the presence of ATP. We know (not from this paper) that p2x receptors are a complex of subunits. Should this be annotated as 'contributes_to' ATP-gated cation channel activity by IDA because it is thought to be part of an ion channel complex, or is it not 'contributes_to' because you get the current by introduction of just the single gene product (even if it is forming a homomeric channel complex)?? Introduction of both zebrafish p2rx3 and rat p2rx5 produces a channel with novel properties....what can be done with that? 'protein heterooligomerization' with the rat p2rx5 by IGI? -Doug From aji at ebi.ac.uk Mon Oct 8 12:39:20 2007 From: aji at ebi.ac.uk (Amelia Ireland) Date: Mon, 8 Oct 2007 20:39:20 +0100 (BST) Subject: [annotation] GO Help query on microRNAs In-Reply-To: Message-ID: Hello, Would someone be able to answer this query about microRNAs, please? Thanks, Amelia. >contactName: Martha Bulyk >contactEmail: mlbulyk at receptor.med.harvard.edu >contactText: How many mammalian microRNAs are in Gene Ontology, and >how many have annotation terms assigned to them? Is there an ongoing >effort to capture microRNA functions as part of GO? > >Thank you, >Martha > -- Amelia Ireland GO Editorial Office, European Bioinformatics Institute, UK. Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp From van_slyke at uoneuro.uoregon.edu Mon Oct 8 17:02:35 2007 From: van_slyke at uoneuro.uoregon.edu (Ceri Van Slyke) Date: Mon, 08 Oct 2007 17:02:35 -0700 Subject: [annotation] GO Help query on microRNAs In-Reply-To: References: Message-ID: <200710090001.l9901Uhq028419@smtp.uoregon.edu> Hi, I have done most of the curation for zebrafish microRNA genes (mirn) at ZFIN. We endeavor to capture GO from the literature for all genes including the microRNA genes. There are 4 GO terms that can be specifically associated with the mirn genes themselves, miRNA-mediated gene silencing (GO:0035195) and micro-ribonucleoprotein complex (GO:0035068), miRNA-mediated gene silencing, negative regulation of translation (GO:0035278) and miRNA-mediated gene silencing, mRNA cleavage (GO:0035279). There are other functions that can be curated but they are not exclusively microRNA functions and tend to be biological processes. We have 68 microRNA genes annotated with miRNA-mediated gene silencing (GO:0035195). Most authors working with zebrafish seem only to state that a particular sequence is a microRNA and so it must be involved in miRNA-mediated gene silencing (GO:0035195). This means most of our annotations have the evidence code NAS. There are a few instances of authors saying this zebrafish microRNA is like that mouse microRNA but the mouse microRNA does not have any GO so we can't really use the ISS evidence code and comply with the reference genome guidelines. Hope this helps, Ceri At 12:39 PM 10/8/2007, you wrote: >Hello, > >Would someone be able to answer this query about microRNAs, please? > >Thanks, >Amelia. > > >contactName: Martha Bulyk > >contactEmail: mlbulyk at receptor.med.harvard.edu > >contactText: How many mammalian microRNAs are in Gene Ontology, and > >how many have annotation terms assigned to them? Is there an ongoing > >effort to capture microRNA functions as part of GO? > > > >Thank you, > >Martha > > > >-- >Amelia Ireland >GO Editorial Office, >European Bioinformatics Institute, UK. >Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp From midori at ebi.ac.uk Mon Oct 8 22:00:04 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 9 Oct 2007 05:00:04 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200710090500.l99505C1088403@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20071009/60c03846/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20071009/60c03846/attachment.pl From dph at informatics.jax.org Tue Oct 9 04:53:14 2007 From: dph at informatics.jax.org (David Hill) Date: Tue, 09 Oct 2007 07:53:14 -0400 Subject: [annotation] annotation of ion channel subunits In-Reply-To: <47069ED1.4020605@cs.uoregon.edu> References: <47069ED1.4020605@cs.uoregon.edu> Message-ID: <470B6BAA.1030500@informatics.jax.org> Hi Doug, I have not been annotating in this way. I only annotate for the data presented in the paper. If we can't tell it has the contributes_to tag from the experiment, we don't use the tag. This is particularly common for mutants where a function is eliminated when you knock out any of the key subunits. David Doug howe wrote: > For the Ref. Genomes we are annotating the gene p2rx3, a subunit of an > ATP activated cation channel. > A paper I have shows that adding this gene to hek293 cells results in > the generation of an inward current in the presence of ATP. > > We know (not from this paper) that p2x receptors are a complex of > subunits. Should this be annotated as 'contributes_to' ATP-gated > cation channel activity by IDA because it is thought to be part of an > ion channel complex, or is it not 'contributes_to' because you get the > current by introduction of just the single gene product (even if it is > forming a homomeric channel complex)?? > > Introduction of both zebrafish p2rx3 and rat p2rx5 produces a channel > with novel properties....what can be done with that? 'protein > heterooligomerization' with the rat p2rx5 by IGI? > > > -Doug From dhowe at cs.uoregon.edu Tue Oct 9 08:02:11 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Tue, 09 Oct 2007 08:02:11 -0700 Subject: [annotation] annotation of ion channel subunits In-Reply-To: <470B6BAA.1030500@informatics.jax.org> References: <47069ED1.4020605@cs.uoregon.edu> <470B6BAA.1030500@informatics.jax.org> Message-ID: <470B97F3.5010402@cs.uoregon.edu> So in one paper if one experiment was done with a single ion channel subunit and another was done with two ion channel subunits, producing different types of currents, would you have one contributes_to and one without contributes_to? -Doug David Hill wrote: > Hi Doug, > > I have not been annotating in this way. I only annotate for the data > presented in the paper. If we can't tell it has the contributes_to tag > from the experiment, we don't use the tag. This is particularly common > for mutants where a function is eliminated when you knock out any of > the key subunits. > > David > > > Doug howe wrote: >> For the Ref. Genomes we are annotating the gene p2rx3, a subunit of >> an ATP activated cation channel. >> A paper I have shows that adding this gene to hek293 cells results in >> the generation of an inward current in the presence of ATP. >> >> We know (not from this paper) that p2x receptors are a complex of >> subunits. Should this be annotated as 'contributes_to' ATP-gated >> cation channel activity by IDA because it is thought to be part of an >> ion channel complex, or is it not 'contributes_to' because you get >> the current by introduction of just the single gene product (even if >> it is forming a homomeric channel complex)?? >> >> Introduction of both zebrafish p2rx3 and rat p2rx5 produces a channel >> with novel properties....what can be done with that? 'protein >> heterooligomerization' with the rat p2rx5 by IGI? >> >> >> -Doug > > From aji at ebi.ac.uk Tue Oct 9 14:47:20 2007 From: aji at ebi.ac.uk (Amelia Ireland) Date: Tue, 9 Oct 2007 22:47:20 +0100 (BST) Subject: [annotation] Re: GO Help query on microRNAs (fwd) Message-ID: Hi annotators, This query came from GO help - does anyone know how many mammalian microRNAs have (biological process) annotations?? > Does this mean that there are very few mammalian microRNAs with > Biological Process annotation? Do you happen to have numbers on that? Thanks, Amelia. -- Amelia Ireland GO Editorial Office, European Bioinformatics Institute, UK. Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp ---------- Forwarded message ---------- Date: Mon, 8 Oct 2007 19:58:47 -0400 (EDT) From: mlbulyk at receptor.med.harvard.edu To: aji at ebi.ac.uk Subject: Re: GO Help query on microRNAs (fwd) Thank you for your reply, Amelia (& Ceri). Does this mean that there are very few mammalian microRNAs with Biological Process annotation? Do you happen to have numbers on that? Thank you very much, Martha -- Martha Bulyk Assistant Professor of Medicine, Pathology, and Health Sciences & Technology (HST) Brigham & Women's Hospital and Harvard Medical School > Dear Martha, > > In answer to your question about mammalian microRNA annotation, one of > the ZFIN [zebrafish] annotation team responded as follows: > > > I have done most of the curation for zebrafish microRNA genes (mirn) > at ZFIN. We endeavor to capture GO from the literature for all > genes including the microRNA genes. > > There are 4 GO terms that can be specifically associated with the > mirn genes themselves, miRNA-mediated gene silencing (GO:0035195) and > micro-ribonucleoprotein complex (GO:0035068), miRNA-mediated gene > silencing, negative regulation of translation (GO:0035278) and > miRNA-mediated gene silencing, mRNA cleavage (GO:0035279). There > are other functions that can be curated but they are not exclusively > microRNA functions and tend to be biological processes. > We have 68 microRNA genes annotated with miRNA-mediated gene > silencing (GO:0035195). > > Most authors working with zebrafish seem only to state that a > particular sequence is a microRNA and so it must be involved in > miRNA-mediated gene silencing (GO:0035195). This means most of our > annotations have the evidence code NAS. There are a few instances of > authors saying this zebrafish microRNA is like that mouse microRNA > but the mouse microRNA does not have any GO so we can't really use > the ISS evidence code and comply with the reference genome guidelines. > > Hope this helps, > Ceri Van Slyke > ZFIN > > -- > > I hope that this response is of use to you. If you have any further > questions, please do not hesitate to contact the GO helpdesk again. > > Kind regards, > Amelia Ireland. > > -- > Amelia Ireland, GO Helpdesk > GO Editorial Office, > European Bioinformatics Institute, UK. > Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp > > > From aji at ebi.ac.uk Tue Oct 9 16:09:16 2007 From: aji at ebi.ac.uk (Amelia Ireland) Date: Wed, 10 Oct 2007 00:09:16 +0100 (BST) Subject: [annotation] Re: GO Help query on microRNAs (fwd) In-Reply-To: <200710092248.l99MmCjJ001932@smtp.uoregon.edu> Message-ID: Back in Gotham City, Ceri Van Slyke wrote: >>This query came from GO help - does anyone know how many mammalian >>microRNAs have (biological process) annotations?? Is anyone annotating microRNAs or is it all genes and proteins? Speak now or forever hold your peace... Thanks, Amelia.> -- Amelia Ireland GO Editorial Office, European Bioinformatics Institute, UK. Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp From rama at genome.Stanford.EDU Tue Oct 9 16:57:45 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Tue, 9 Oct 2007 16:57:45 -0700 Subject: [annotation] Re: GO Help query on microRNAs (fwd) In-Reply-To: References: Message-ID: Can this # be retrieved using GOOSE from the db? rama On Oct 9, 2007, at 4:09 PM, Amelia Ireland wrote: > Back in Gotham City, Ceri Van Slyke wrote: >>> This query came from GO help - does anyone know how many mammalian >>> microRNAs have (biological process) annotations?? > > Is anyone annotating microRNAs or is it all genes and proteins? > Speak now > or forever hold your peace... > > Thanks, > Amelia.> > > -- > Amelia Ireland > GO Editorial Office, > European Bioinformatics Institute, UK. > Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp From midori at ebi.ac.uk Tue Oct 9 22:00:05 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 10 Oct 2007 05:00:05 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200710100500.l9A505K1131039@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20071010/881f75fa/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20071010/881f75fa/attachment.pl From cherry at stanford.edu Tue Oct 9 22:31:10 2007 From: cherry at stanford.edu (Mike Cherry) Date: Tue, 9 Oct 2007 22:31:10 -0700 Subject: [annotation] Re: GO Help query on microRNAs (fwd) In-Reply-To: References: Message-ID: The only DB_Object_Types listed in the gene association files are the following. Thats all that could be found via GOOSE. complex gene protein protein_structure transcript On Oct 9, 2007, at 4:57 PM, Rama Balakrishnan wrote: > Can this # be retrieved using GOOSE from the db? > > rama > > On Oct 9, 2007, at 4:09 PM, Amelia Ireland wrote: > >> Back in Gotham City, Ceri Van Slyke wrote: >>>> This query came from GO help - does anyone know how many mammalian >>>> microRNAs have (biological process) annotations?? >> >> Is anyone annotating microRNAs or is it all genes and proteins? >> Speak now >> or forever hold your peace... >> >> Thanks, >> Amelia.> >> >> -- >> Amelia Ireland >> GO Editorial Office, >> European Bioinformatics Institute, UK. >> Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp From dph at informatics.jax.org Wed Oct 10 05:07:04 2007 From: dph at informatics.jax.org (David Hill) Date: Wed, 10 Oct 2007 08:07:04 -0400 Subject: [annotation] Re: GO Help query on microRNAs (fwd) In-Reply-To: References: Message-ID: <470CC068.90409@informatics.jax.org> We have only annotated one mouse micro-RNA so far. However, our policy is to annotate these when there is experimental literature supporting the annotation. We consider them to be just like any other functional RNA gene product. David Amelia Ireland wrote: > Hi annotators, > > This query came from GO help - does anyone know how many mammalian > microRNAs have (biological process) annotations?? > > >> Does this mean that there are very few mammalian microRNAs with >> Biological Process annotation? Do you happen to have numbers on that? >> > > Thanks, > Amelia. > > From edimmer at ebi.ac.uk Wed Oct 10 05:10:54 2007 From: edimmer at ebi.ac.uk (E Dimmer) Date: Wed, 10 Oct 2007 13:10:54 +0100 Subject: [annotation] Re: GO Help query on microRNAs (fwd) In-Reply-To: <470CC068.90409@informatics.jax.org> References: <470CC068.90409@informatics.jax.org> Message-ID: <470CC14E.7060709@ebi.ac.uk> As GOA only annotates to proteins I'm afraid we don't annotate or integrate annotations to functional RNAs. Emily David Hill wrote: > We have only annotated one mouse micro-RNA so far. However, our policy > is to annotate these when there is experimental literature supporting > the annotation. We consider them to be just like any other functional > RNA gene product. > > David > > Amelia Ireland wrote: >> Hi annotators, >> >> This query came from GO help - does anyone know how many mammalian >> microRNAs have (biological process) annotations?? >> >> >>> Does this mean that there are very few mammalian microRNAs with >>> Biological Process annotation? Do you happen to have numbers on that? >>> >> >> Thanks, >> Amelia. >> >> > -- ************************************ Emily Dimmer 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 ************************************ From aji at ebi.ac.uk Wed Oct 10 09:10:38 2007 From: aji at ebi.ac.uk (Amelia Ireland) Date: Wed, 10 Oct 2007 17:10:38 +0100 (BST) Subject: [annotation] Re: GO Help query on microRNAs (fwd) In-Reply-To: <470CC14E.7060709@ebi.ac.uk> Message-ID: Thank you all for the information on microRNA annotation (or the lack thereof). I've written a suitable reply to the person whose GO help query this came from. Thanks! Amelia. -- Amelia Ireland GO Editorial Office, European Bioinformatics Institute, UK. Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp From val at sanger.ac.uk Thu Oct 11 08:13:54 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 11 Oct 2007 16:13:54 +0100 Subject: [annotation] protein carrier heads up Message-ID: <470E3DB2.4060300@sanger.ac.uk> The old term "protein carrier activity" had a definition whcih made it a transmembrane transporter "Catalysis of the transfer of proteins from one side of a membrane to the other" which made it a transmembrane transporter so it was renamed "protein transmembrane transporter activity" Quite a few of us have used the old term to annotate karyopherins (which was incorrect as the nucler membrane (i.e lipid bilayer) is not penetrated during transport through the nuclear pore). These need moving to protein transporter activity; GOid=GO:0008565; -- 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 midori at ebi.ac.uk Thu Oct 11 22:00:05 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 12 Oct 2007 05:00:05 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200710120500.l9C506Y1240938@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20071012/5a21c956/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20071012/5a21c956/attachment.pl From midori at ebi.ac.uk Wed Oct 17 22:00:05 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 18 Oct 2007 05:00:05 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200710180500.l9I505u1514185@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20071018/55125031/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20071018/55125031/attachment.pl From midori at ebi.ac.uk Fri Oct 19 22:00:06 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 20 Oct 2007 05:00:06 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200710200500.l9K506A1060566@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20071020/bf52d936/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20071020/bf52d936/attachment.pl