From suzi at berkeleybop.org Sun Jul 1 16:38:35 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Sun, 1 Jul 2007 16:38:35 -0700 Subject: [go] another immune related query GO and CL In-Reply-To: References: <35521.217.43.59.130.1182522231.squirrel@webmail.ebi.ac.uk> Message-ID: <3268AF5F-A9F6-4402-BAA7-34F5EEF2F9A8@berkeleybop.org> I quite like this Chris. Do we need to be concerned at all about what this relationship is? -S On Jun 25, 2007, at 11:35 AM, Chris Mungall wrote: > > I sketched out the proposal for col 16 here: > http://gocwiki.geneontology.org/index.php/Annotation_Cross_products > > I need some help filling out the use cases > > Once I get sample files from Mary and Dan (and anyone else who is > interested in an early test) I can link to these > > On Jun 22, 2007, at 7:23 AM, camon at ebi.ac.uk wrote: > >> Hi, >> >> GOA can now annotate cell types as comments in our annotation tool >> and as >> I understand it MGI also capture this information. At the moment >> in GOA we >> Cell type curation is not compulsary. >> >> For the immune gene GO annotation effort which may or may not get >> underway >> soon...curating cell types as well seems to me to be critical.. >> >> so for example... >> >> chicken IL-10 is secreted from say.e.g macrophages BUT >> causes 'negative regulation of interferon gamma biosynthesis' in >> chicken >> splenocytes.. >> >> its particularly the latter use I am interested in.. >> >> So I guess I would like to see a column that might allow the cell >> type >> ontology Id??? (oh oh I hear you all shriek) >> >> maybe its something unique that could be done for WT immune GO grant >> releases but I thought others may/may not also like to use it and >> exchange >> it in a standardized way?? >> >> Cell type ontology can of course be uploaded into OBO-edit but can >> also be >> queried easily by curators in the EBI Ontology Lookup Service(OLS) >> http://www.ebi.ac.uk/ontology-lookup/ >> >> any thoughts on this... >> >> Evelyn >> >> >> >> >> > > From suzi at berkeleybop.org Sun Jul 1 16:41:44 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Sun, 1 Jul 2007 16:41:44 -0700 Subject: [go] recombination and toxin in GO In-Reply-To: References: Message-ID: <688FDABB-B182-4B3A-9446-2B0798A1803E@berkeleybop.org> Hi Jane, Busy as we all are, lets not forget this one. Perhaps a combined GO & SO content meeting for viruses. Talk about a plan for this in September? -S On Jun 26, 2007, at 11:21 AM, Jane Lomax wrote: > Michael - the problem we have with incorporating Ariane's phage > terms into GO is that they don't intergrate at all well with the > existing viral terms, which were added for the purposes of > annotating a eukaryotic virus (herpes simplex I think). > > What we need to do is reorganise the current tree to incorporate a > generic set of viral terms, and the more specific terms (like > these) can be added at the leaves as we need them. To do this we > really need a meeting with > input from experts from different viral communities, which is > doable, but we need someone to drive this from the GO end and we're > a bit strapped for time at the moment...there was a suggestion that > Michelle might be able to take this up, but I think she may be > quite busy at the moment too...? > > Jane > > > On Tue, 26 Jun 2007, Michael Ashburner wrote: > >> Ariane >> >> This looks like very productive work ! >> >> I am not clear as to the long-term objective, at least wrt to the >> relationship >> between this and the GO. I can see that most (if not all) of the >> terms under the >> 'phage function' and 'phage process' nodes could well be - and >> should be - incorporated into >> the GO. The same goes for the terms under the 3 'recombination' >> nodes. >> >> The 'phage component' terms would be harder. I wonder if what you >> could aim for is >> essentially a 'phage anatomy' ontology, analagous to those for >> cellular organisms ? >> >> Chris M: Could you have a look at this work ? The obo file is at: >> http://aclame.ulb.ac.be/Classification/PhiGO/PhiGO_live.obo >> >> There is a way using OBO-EDIT 1.2 where you can build an ontology >> for use within a domain (e.g. phage) >> by picking and choosing from several other ontologies. I am not >> sure exactly how this is done but >> I am sure Chris can advise. >> >> Best wishes - Michael >> > > Dr Jane Lomax > GO Editorial Office > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > Cambridgeshire, UK > CB10 1SD > > p: +44 1223 492516 > f: +44 1223 494468 > From jane at ebi.ac.uk Mon Jul 2 03:47:57 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Mon, 2 Jul 2007 11:47:57 +0100 (BST) Subject: [go] recombination and toxin in GO In-Reply-To: <688FDABB-B182-4B3A-9446-2B0798A1803E@berkeleybop.org> References: <688FDABB-B182-4B3A-9446-2B0798A1803E@berkeleybop.org> Message-ID: Hi Suzi - yes, I totally agree, I think it's really important we get these terms in, especially as we're likely to have more viral annotation in the future. Unfortauntely I won't be at the September meeting (baby is due the same week!) but I'm happy to be volunteered to help out with this if necessary. Lets put it on the agenda. cheers, Jane On Sun, 1 Jul 2007, Suzanna Lewis wrote: > Hi Jane, > > Busy as we all are, lets not forget this one. Perhaps a combined GO & SO > content meeting for viruses. > > Talk about a plan for this in September? > > -S > > On Jun 26, 2007, at 11:21 AM, Jane Lomax wrote: > >> Michael - the problem we have with incorporating Ariane's phage terms into >> GO is that they don't intergrate at all well with the existing viral terms, >> which were added for the purposes of annotating a eukaryotic virus (herpes >> simplex I think). >> >> What we need to do is reorganise the current tree to incorporate a generic >> set of viral terms, and the more specific terms (like these) can be added >> at the leaves as we need them. To do this we really need a meeting with >> input from experts from different viral communities, which is doable, but >> we need someone to drive this from the GO end and we're a bit strapped for >> time at the moment...there was a suggestion that Michelle might be able to >> take this up, but I think she may be quite busy at the moment too...? >> >> Jane >> >> >> On Tue, 26 Jun 2007, Michael Ashburner wrote: >> >>> Ariane >>> >>> This looks like very productive work ! >>> >>> I am not clear as to the long-term objective, at least wrt to the >>> relationship >>> between this and the GO. I can see that most (if not all) of the terms >>> under the >>> 'phage function' and 'phage process' nodes could well be - and should be - >>> incorporated into >>> the GO. The same goes for the terms under the 3 'recombination' nodes. >>> >>> The 'phage component' terms would be harder. I wonder if what you could >>> aim for is >>> essentially a 'phage anatomy' ontology, analagous to those for cellular >>> organisms ? >>> >>> Chris M: Could you have a look at this work ? The obo file is at: >>> http://aclame.ulb.ac.be/Classification/PhiGO/PhiGO_live.obo >>> >>> There is a way using OBO-EDIT 1.2 where you can build an ontology for use >>> within a domain (e.g. phage) >>> by picking and choosing from several other ontologies. I am not sure >>> exactly how this is done but >>> I am sure Chris can advise. >>> >>> Best wishes - Michael >>> >> >> Dr Jane Lomax >> GO Editorial Office >> EMBL-EBI >> Wellcome Trust Genome Campus >> Hinxton >> Cambridgeshire, UK >> CB10 1SD >> >> p: +44 1223 492516 >> f: +44 1223 494468 >> > Dr Jane Lomax GO Editorial Office EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridgeshire, UK CB10 1SD p: +44 1223 492516 f: +44 1223 494468 From jdeegan at ebi.ac.uk Mon Jul 2 12:58:02 2007 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Mon, 02 Jul 2007 20:58:02 +0100 Subject: [go] ontology freeze Message-ID: <468958CA.8080600@ebi.ac.uk> Hi, I'd like to request a freeze on gene_ontology_edit.obo file commits starting from 11am BST tomorrow please. I'm going to be merging in the changes to the transporter activity node in the function ontology that we have been making over the last few months. Please could you make sure that you have committed all of your changes before 11am BST tomorrow (Tuesday) so that I can check the live file out at that time and merge in the transport changes before committing back to the live repository. I will write to the list again when I have finished the commit so that the freeze can be lifted. Thanks for your help in this. Best wishes, Jennifer -- Jennifer Deegan nee Clark EMBL-European Bioinformatics Institute Gene Ontology Consortium From jdeegan at ebi.ac.uk Tue Jul 3 05:26:43 2007 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Tue, 03 Jul 2007 13:26:43 +0100 Subject: [go] transporter activity Message-ID: <468A4083.3090405@ebi.ac.uk> Hi, I have now committed back the transporter activity changes to the live repository. The ontology editing freeze is lifted and everyone can go back to editing the file. Please make sure that you check out a new copy of the ontology file before beginning your edits. The commit this morning involved a very complex file merge (more than 5000 edits were merged into the live file) and it is just possible that small errors may have crept in. If you see any problems at all with the file please would it be possible for you to get in touch with me as soon as possible so that I can make repairs? Thanks for your help in this. I hope you like the improvements that we have made. Best wishes, Jennifer -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From jdeegan at ebi.ac.uk Tue Jul 3 06:51:55 2007 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Tue, 03 Jul 2007 14:51:55 +0100 Subject: [go] annotation outreach Message-ID: <468A547B.8050401@ebi.ac.uk> Hi, I'm about to compile the annotation outreach report for June. If you made any progress on outreach to new groups that might be interested in starting GO annotation please would it be possible to write and let me know? Thanks, Jennifer -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From midori at ebi.ac.uk Wed Jul 4 06:54:38 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Wed, 4 Jul 2007 14:54:38 +0100 (BST) Subject: [go] Ontology development - June highlights Message-ID: Dear GO, The most recent monthly report on ontology content, for June 2007, is now available at: http://gocwiki.geneontology.org/index.php/June2007_ontology_report Some highlights from June: * Reorganization of the transporter terms in the molecular function ontology has been completed, and will be live by the time you read this (http://wiki.geneontology.org/index.php?title=Transporters). * The content meeting on cardiovascular physiology was a success, with about 100 new terms added during the meeting and more work going on to follow up (http://gocwiki.geneontology.org/index.php/Cardiovascular_physiology/development). * The content meeting on muscle development has been scheduled for July 25-26 , in collaboration with Giorgio Valle, Erika Feltrin, and several muscle experts at the University of Padua (http://wiki.geneontology.org/index.php/Muscle_Development). * Work on process terms for rRNA processing is almost complete (http://gocwiki.geneontology.org/index.php/RNA_processing). * All terms in the cellular component ontology have definitions. For July, cross-products with the Cell Ontology and ChEBI are still in our sights. As usual, details of small- and medium-scale changes are available in the SourceForge Curator Requests tracker. Please contact us if you want to help out with ontology work in a particular area, or if you have any comments or questions about what's going on. Midori & David on behalf of GO's ontology developers From midori at ebi.ac.uk Fri Jul 6 09:17:44 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 6 Jul 2007 17:17:44 +0100 (BST) Subject: [go] recombination and toxin in GO In-Reply-To: <661293.66681.qm@web26705.mail.ukl.yahoo.com> References: <661293.66681.qm@web26705.mail.ukl.yahoo.com> Message-ID: Dear Ariane, Thanks for your message; don't worry about hurrying to look at the SourceForge link -- we have plenty to do in the meantime. As you've seen from other responses to your initial email, this areas is important to both GO and SO, so we do want to work with you to expand and improve what GO has -- but several of the most suitable people need to figure out when they'll be available. I'm sure I won't be the only one working on this part of GO, or in collaboration with you. In particular, I think there are one or two people in GO whose opinions on "DNA breakage reunion reaction" would be more informed than mine. I've cc'd the GO list with the aim of getting their input, and to help ensure that communication doesn't become fragmented. I would also like to have comments from you and from GO curators/annotators before I act on your suggestions and my responses (as I've put in email and in the SourceForge entry). Midori On Fri, 6 Jul 2007, Ariane Pourbaix wrote: > Dear Midori, > I'll try to get to that link one of these coming days. I'm presently on > vacation and have only limited access to the net. I'd like to have your > opinion on our choice (George Chaconas and I !) of the term "DNA > breakage reunion reaction"? I'm not absolutely sure opf the coherence of > my list. I have for instance the terms integrase, resolvase and > transposase for the ser- nd tyr-based enzymes but I do not have > integrase for the DDE enzyme (the retroviral integrases). That's easy to > correct though. Rega rds. Ariane. > > > > > Midori Harris a ?crit : Dear Ariane, > > Thank you for your comments on these areas of GO. I'm going to leave aside > the question about 'toxin' for the moment, because I think that will > involve a longer discussion, and we can address some of the other comments > in the meantime. In particular, your suggestions will allow us to improve > the integrase terms at once. > > I have created an entry in our SourceForge tracker for your specific > comments, and will post my responses there as well as below. > >> >> >> Accession >> GO:0008907 integrase activity >> Ontology >> molecular function >> Synonyms >> None >> Definition >> Catalysis of the integration of lambdoid phage DNA during >> establishment, probably by forming a transient DNA-protein link. >> [source: ISBN:0198506732] >> My comment >> This type of integration concerns far more genetic entities than >> lambdoid phage genomes. See my definition phi:0000132. Site-specific DNA >> integration: The process by which a segment of DNA is incorporated into >> another by a site-specific recombination event. > > I agree -- this definition is much too specific. I'll try to rehprase it > so it doesn't restrict itself to lambdoid phage DNA (I'll put details in > the SourceForge item). > >> >> Accession >> GO:0008979 prophage integrase activity >> Ontology >> molecular function >> Synonyms >> None >> Definition >> None >> My comment: this term does not make any sense since the phage has the >> same integrase activity. This term should be made obsolete especially >> because it tends to be used for all integrases in bacterial genomes, >> many of which are not prophage-associated! > > This term is also only used for 5 annotations, which could be transferred > to the parent term (once the latter's definition has been sorted out). An > alternative to making GO:0008979 obsolete may beto merge it into its > parent, which has the advantage that it can be done immediately (we give a > 2-week notice period for obsoletes). Do you have a preference? > >> >> Accession >> GO:0009037 tyrosine-based site-specific recombinase activity >> Ontology >> molecular function >> Synonyms >> None >> Definition >> Catalysis of the formation of new phosphodiester bonds between a >> pair of short, unique DNA target sequences; occurs through a >> phosphotyrosyl intermediate in which the target sequence is first >> cleaved by the nucleophilic attack by a tyrosine in the active site. >> [source: GOC:elh, PMID:11090626] >> >> My comment: this defitnition is almost correct but should be seen in the >> context of a parent term such as "DNA breakage reunion activity". I >> presently have children for the term, to cover recombination leading to >> integration, excision or resolution. However a better solution may be to >> associate this activity with the processes integration, excision or >> resolution? > > Could you suggest a definition for a new term for "DNA breakage reunion > activity"? > > At present, we do not have any relationships between terms from different > ontologies, so we cannot yet capture any connections between recombinase > terms and the process terms for integration, excision, etc. As Jane may > have told you, we are planning to add links between biological process and > molecular function (once some tools are in place, and we've established > what the relationship type will be), and your knowledge of the bacterial > processes and the enzymes involved will be very helpful when we're ready > to add the links. > >> >> Accession >> GO:0004803 transposase activity >> Ontology >> molecular function >> Synonyms >> None >> Definition > >> Catalysis of the transposition of transposable elements or >> transposons. Transposases are involved in site-specific DNA >> recombination required for transposition in bacteria and other >> organisms. [source: ISBN:0198506732] >> >> My comment: most transposases are DDE enzymes and hence are not >> site-specific recombinases (they rather use specific sites on the >> transposable element and random target sites!). So my definition, >> phi:0000153, DDE transposase activity (again under "DNA breakage reunion >> reaction/activity"): Catalysis of the transpositional recombination of a >> discrete DNA segment. DDE transposase have a related amino-acid motif >> (the DDE motif), which forms the active site of the transposase and is >> responsible for coordinating the cleavage and joining steps of >> transposition. Breakage of the DNA occurs at the end of the element >> (usually a hydrolysis) and is followed by breakage and integration at >> the target site (a transesterification reaction). > > Protein family membership per se is not used as a criterion for creating > GO terms or determining their parentage, but because the DDE motif is > involved in catalysis, we can phrase a definition that uses the DDE > information. > >> >> >> Accession >> GO:0045090 retroviral genome replication >> Ontology >> biological process >> Synonyms >> None >> Definition >> Any process involved in the replication of a retroviral genome. >> Retroviruses use RNA as their nucleic acid and reverse transcriptase to >> copy their genome into the DNA of the host cells chromosomes. [source: >> GOC:go_curators, ISBN:0198506732, http://cancerweb.ncl.ac.uk/] >> >> My comment: this definition does not appear correct as the cDNA is not >> copied into the genome but copied and then integrated in the host genome >> to be transcribed/replicated. As it is now the retroviral integrase has >> no place to go! > > I agree, this definition needs considerable improvement -- in addition to > the problem you've noticed, it also doesn't say what the beginning and end > are. > > The definition of the parent, 'viral genome replication', is also not > ideal. I'll make some specific suggestions in the SourceForge entry. > > Thanks again for your thoughts! > > Midori > > ============================ > Midori A. Harris, Ph.D. > GO Editor > EMBL - EBI > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD UK > > Tel: +44 (0) 1223 494667 > Fax: +44 (0) 1223 494468 > Email: midori at ebi.ac.uk > > > > --------------------------------- > Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail From ma11 at gen.cam.ac.uk Mon Jul 9 00:34:17 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner (Genetics)) Date: Mon, 9 Jul 2007 08:34:17 +0100 (BST) Subject: [go] Ontology development - June highlights Message-ID: Great progress ! Michael From midori at ebi.ac.uk Mon Jul 9 02:58:55 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Mon, 9 Jul 2007 10:58:55 +0100 (BST) Subject: [go] Alert: Proposal to obsolete GO:0030489 (process ontology) that impacts existing annotation Message-ID: Hello, The proposal has been made to obsolete processing of 27S pre-rRNA ; GO:0030489 There exist today annotations to this term as follows (none are IEA): GeneDB_Spombe 3 FB 2 SGD 19 This term is not used in any GO slim set maintained within the OBO flat file, nor is it used in any external mappings. The reason for this proposal is that the term is not defined, and does not correspond to the production of a single specific mature rRNA product (it corresponds to maturation of both the LSU and 5.8S rRNAs). Suggested terms to use to replace annotations: maturation of LSU-rRNA ; GO:0000470 maturation of 5.8S rRNA ; GO:0000460 Additional discussion can be found in three SourceForge items, and on the internal wiki. Wiki link: http://gocwiki.geneontology.org/index.php/RNA_processing Links to SourceForge entries: https://sourceforge.net/tracker/?func=detail&aid=780275&group_id=36855&atid=440764 https://sourceforge.net/tracker/?func=detail&aid=1067017&group_id=36855&atid=440764 https://sourceforge.net/tracker/?func=detail&aid=1566692&group_id=36855&atid=440764 The two-week comment period ends on Monday, July 23, 2007. Midori on behalf of the RNA processing working group (Karen Christie, Harold Drabkin & Ceri Van Slyke) From ma11 at gen.cam.ac.uk Tue Jul 10 02:15:24 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner) Date: Tue, 10 Jul 2007 10:15:24 +0100 Subject: [go] recombination and toxin in GO In-Reply-To: <962963.99958.qm@web26713.mail.ukl.yahoo.com> References: <962963.99958.qm@web26713.mail.ukl.yahoo.com> Message-ID: <89AE0930-7DEE-48D3-B731-6130052D876E@gen.cam.ac.uk> Ariane Thanks, I understand that. I think the thing to to do is let Karen and the GO office work on these terms and then we will see just how much of PhiGO will be covered. Best - Michael On 6 Jul 2007, at 15:37, Ariane Pourbaix wrote: > Dear Michael, > The reason for assembling that list of phage and recombination > terms is essentially that we need a robust and structured system to > annotate the protein families in our ACLAME database. We hope that > people using ACLAME will then be 'tempted' to use the same > ontology. After the meeting we had last September in Hinxton I knew > just enough to try following the GO schema of processes, components > and functions. I looked at the virus related terms that are in GO > and found things like 'capsomer', so I felt comfortable introducing > the other components of the phage capsid? > I thought it would be good to have as many of these terms in GO as > possible. If some don' fit we'll just keep them in PhiGO. One point > that isn't completely clear to me yet is whether we'll better keep > PhiGO as it is, even if most of it gets integrated in GO. > As Jane mentioned, I think it would be interesting to build a list > of generic terms for viruses. This I suppose should also be done > for mobile genetic elements (not easy either). > In my suggestions for some reorganisation of the terms related to > recombination, I'm afraid some may provoke some discussion if not > disagreement? in any case I thin it is urgent to get something done > there because the confusion between the different types of > integrases, transposases etc. is increasing in recent annotations. > Clear and correct definitions are obviously required. I'm not sure > mine are perfect tough, but they are not wrong! > I'm sure we'll progress on this? though on my side it may a bit > slow since I'm away from the lab and with interrupted internet > connection until the end of august! > I hope this clarifies things a least a little! Best regards. Ariane. > > > Michael Ashburner a ?crit : > Ariane > > This looks like very productive work ! > > I am not clear as to the long-term objective, at least wrt to the > relationship > between this and the GO. I can see that most (if not all) of the > terms under the > 'phage function' and 'phage process' nodes could well be - and > should be - incorporated into > the GO. The same goes for the terms under the 3 'recombination' nodes. > > The 'phage component' terms would be harder. I wonder if what you > could aim for is > essentially a 'phage anatomy' ontology, analagous to those for > cellular organisms ? > > Chris M: Could you have a look at this work ? The obo file is at: > http://aclame.ulb.ac.be/Classification/PhiGO/PhiGO_live.obo > > There is a way using OBO-EDIT 1.2 where you can build an ontology > for use within a domain (e.g. phage) > by picking and choosing from several other ontologies. I am not > sure exactly how this is done but > I am sure Chris can advise. > > Best wishes - Michael > > > Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers > Yahoo! Mail -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20070710/3c27422c/attachment.html From ma11 at gen.cam.ac.uk Tue Jul 10 09:49:35 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner (Genetics)) Date: Tue, 10 Jul 2007 17:49:35 +0100 (BST) Subject: [go] Forward email re Paramecium Message-ID: ------------- Begin Forwarded Message ------------- Envelope-to: ma11 at gen.cam.ac.uk Delivery-date: Tue, 10 Jul 2007 17:48:45 +0100 Mime-Version: 1.0 (Apple Message framework v752.3) Cc: Michael Ashburner , Chris Mungall , Suzanna Lewis Content-Transfer-Encoding: 7bit From: Michael Ashburner Subject: Date: Tue, 10 Jul 2007 17:48:55 +0100 To: sperling at cgm.cnrs-gif.fr Linda I was passed some email between you and Chris. I am not sure that I understand all of the issues but : >>>>>> For the moment, we only have a rudimentary paramecium anatomy >>>>>> ontology. GO does not have everything we need for the >>>>>> entities. But we do use PATO for quality/value. >>>>>> I think the bits of single-celled organisms should be in the CC part of the GO. If GO does not have what you need you should either put a request thru on the GO sourceforge tracker, or contact Midori Harris (midori at ebi.ac.uk) directly. (Preferably the former). Let me know if I can help. Best Michael ------------- End Forwarded Message ------------- Envelope-to: ma11 at gen.cam.ac.uk Delivery-date: Mon, 02 Jul 2007 04:44:18 +0100 X-Cam-SpamDetails: scanned, SpamAssassin-3.2.0 (score=0) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Mime-Version: 1.0 (Apple Message framework v752.3) Content-Transfer-Encoding: quoted-printable From: Suzanna Lewis Subject: Fwd: [Bbop-ncbo] Re: PheNote Date: Sun, 1 Jul 2007 20:44:03 -0700 To: Michael Ashburner X-Virus-Scanned: by amavisd-new at fruitfly.org X-Keywords: Thoughts? Where do we draw the line on "anatomy" vs. CC. This also applies to the FMA Begin forwarded message: > From: Chris Mungall > Date: July 1, 2007 8:28:24 PM PDT > To: Suzanna Lewis > Cc: Linda Sperling , bbop- > ncbo at berkeleybop.org > Subject: Re: [Bbop-ncbo] Re: PheNote > > > On Jul 1, 2007, at 6:43 PM, Suzanna Lewis wrote: > >> Knowing just what I've learned from reading these e-mails it seems >> to me that putting "trichocyst and its subparts be in a Paramecium >> anatomy ontology, the term trichocyst itself cross-referenced to >> "secretory granule"" from the GO-CC is the way to go here. > > GO:0055039 trichocyst [DEF: "A crystalline exocytotic organelle > composed of small, acidic proteins existing primarily as disulphide- > linked dimers. The trichocyst is an organelle that releases long > filamentous proteins that capture predators in "nets" to slow them > down when the cell is disturbed. The protein is nontoxic and shaped > like a long, striated, fibrous shaft."] > > (currently no annotations in the GO DB) > > However, GO doesn't have the various subparts of trichocyst (which > paramecium_anatomy does have) > >> There are precedents. For bacteria there is the beginnings of work >> on an "anatomy" for colony morphology. >> >> Likewise for the fungi, there is an anatomy. > > FAO does only have 68 terms, 10 are already in CL, and a couple are > already in CC. I'm really not sure what the criteria for deciding > when a subcellular entity is too taxon-specific to go in GO. It > seems a little inconsistent; eg GO has "hyphal tip" and "hyphal > growth", but no "hypha" (and hypha is in FAO). I'll check.. > >> >> -S >> >> On Jun 26, 2007, at 1:06 AM, Linda Sperling wrote: >> >>> Hi Chris, >>> >>> We could work towards having the Entity terms we need added to GO >>> CC. But, Paramecium is not just a big cell, it is a complex >>> organism. Are you suggesting that we do not need an anatomy >>> ontology at all? Or just that terms should be cross-referenced in >>> GO? >>> >>> Is the objective of GO to include all specific terms for all >>> organisms? >>> >>> For example, a "trichocyst" is a very architecturally complex >>> secretory granule with a genetically determined shape, whose >>> content is a metastable protein crystalline array that changes >>> conformation upon secretion, releasing energy stored during >>> biogenesis by protein processing. And "trichocyst" only exists >>> in Paramecium (and maybe a few other ciliates that are not >>> studied very much). Do you really want to include trichocyst with >>> all of its subparts in GO? Or should trichocyst and its subparts >>> be in a Paramecium anatomy ontology, the term trichocyst itself >>> cross-referenced to "secretory granule" ? >>> >>> Linda >>> >>> >>> On Jun 25, 2007, at 10:05 PM, Chris Mungall wrote: >>> >>>> >>>> On Jun 25, 2007, at 8:07 AM, mark gibson wrote: >>>> >>>>> hey linda - sorry for the delayed reply but i was away on vacation >>>>> well this is great to hear - yes phenote is ready to use and >>>>> some groups are already using it. that is standalone phenote >>>>> (webby phenote is a different matter but i assume standalone is >>>>> good by you and its what i would recommend) >>>>> >>>>> >>>>> >>>>> >>>>> On Jun 18, 2007, at 5:52 AM, Linda Sperling wrote: >>>>> >>>>>> Hi Mark, >>>>>> >>>>>> Now that Apollo/JDBC is working for us, we are thinking about >>>>>> the next step! Which is improving our description of >>>>>> phenotypes, and trying to make an anatomy ontology for >>>>>> paramecium (Barry Smith has already spontaneously contacted me >>>>>> to encourage us to use CARO). >>>>> >>>>> yes i believe using caro is the way to go - and it will make >>>>> cross species comparisons easier >>>> >>>> In the case of paramecium, a unicellular organism, I don't think >>>> we have to worry about CARO so much. Instead we have to think in >>>> terms of the GO cellular component ontology (and trust that GO >>>> is CARO compliant) >>>> >>>> Let's see. Everything I know about Paramecium anatomy I learned >>>> in the last 90 seconds on: >>>> http://en.wikipedia.org/wiki/Paramecium >>>> >>>> GO certainly has terms like pellice, trichocyst, macronucleus, >>>> cilium. It doesn't have cell mouth and anal pore - but perhaps >>>> these are functional names for existing terms - or perhaps GO-CC >>>> needs extended. I'd be happy to help work with you and the >>>> editors to help make sure GO meets the needs of interesting >>>> protists. >>>> >>>>>> So my question is: can we use PheNote? >>>>> yes >>>> >>>> ++ >>>> >>>>>> Is it ready for users like us or is there still a lot of >>>>>> development work to be done? >>>>> >>>>> its ready - im still constantly adding stuff to it but its >>>>> ready to use >>>>> >>>>>> What do we need? >>>>> >>>>> you can webstart it from .... >>>>> you will then want to configure it for paramecium - i am >>>>> currently working on a gui for configuration but its not quite >>>>> ready yet - nicole has written up some great docs on >>>>> configuring phenote through the xml config file ... >>>>> >>>>>> For the moment, we only have a rudimentary paramecium anatomy >>>>>> ontology. GO does not have everything we need for the >>>>>> entities. But we do use PATO for quality/value. >>>>> >>>>> well phenote use may probably move these ontologies along >>>>> hopefully >>>>> >>>>> cheers - mark >>>>> >>>>>> >>>>>> Incidentally, the weather here since the beginning of May has >>>>>> been awful, you were really lucky last year! >>>>>> >>>>>> best, >>>>>> Linda >>>>>> >>>>>> >>>>>> >>>>>> Linda Sperling >>>>>> Centre de G?n?tique Mol?culaire >>>>>> CNRS >>>>>> Avenue de la Terrasse >>>>>> 91198 Gif-sur-Yvette CEDEX >>>>>> FRANCE >>>>>> >>>>>> sperling at cgm.cnrs-gif.fr >>>>>> +33 (0)1 69 82 32 09 (telephone) >>>>>> +33 (0)1 69 82 31 50 (fax) >>>>>> http://paramecium.cgm.cnrs-gif.fr/ >>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Bbop-ncbo mailing list >>>>> Bbop-ncbo at fruitfly.org >>>>> http://mail.fruitfly.org/mailman/listinfo/bbop-ncbo >>>>> >>>> >>> >>> Linda Sperling >>> Centre de G?n?tique Mol?culaire >>> CNRS >>> Avenue de la Terrasse >>> 91198 Gif-sur-Yvette CEDEX >>> FRANCE >>> >>> sperling at cgm.cnrs-gif.fr >>> +33 (0)1 69 82 32 09 (telephone) >>> +33 (0)1 69 82 31 50 (fax) >>> http://paramecium.cgm.cnrs-gif.fr/ >>> >>> >>> _______________________________________________ >>> Bbop-ncbo mailing list >>> Bbop-ncbo at fruitfly.org >>> http://mail.fruitfly.org/mailman/listinfo/bbop-ncbo >> >> > > From ma11 at gen.cam.ac.uk Tue Jul 10 10:10:05 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner (Genetics)) Date: Tue, 10 Jul 2007 18:10:05 +0100 (BST) Subject: [go] paper on GO in PNAS Message-ID: Lerman & Shakhnovich, PNAS July 3 page 11334-39 From midori at ebi.ac.uk Tue Jul 10 10:40:15 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 10 Jul 2007 18:40:15 +0100 (BST) Subject: hypha (Re: [go] Forward email re Paramecium) In-Reply-To: References: Message-ID: >> FAO does only have 68 terms, 10 are already in CL, and a couple are >> already in CC. I'm really not sure what the criteria for deciding >> when a subcellular entity is too taxon-specific to go in GO. It >> seems a little inconsistent; eg GO has "hyphal tip" and "hyphal >> growth", but no "hypha" (and hypha is in FAO). I'll check.. If I recall correctly, at least some types of hypha are made of more than one cell, and some are types of cell. I know that doesn't address the question of how taxon-specific to GO ... we've never explicitly said anything was too specific, but neither have we really had a discussion. m From ma11 at gen.cam.ac.uk Wed Jul 11 23:44:49 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner (Genetics)) Date: Thu, 12 Jul 2007 07:44:49 +0100 Subject: [go] Jones et al BMC paper Message-ID: I have just seen, but not yet read, this paper: BMC Genomics. 2007 Jul 9;8(1):222 [Epub ahead of print] Click here to read Quantitative assessment of relationship between sequence similarity and function similarity. Joshi T, Xu D. http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=Abstract&db=PubMed&list_uids=17620139 Michael From camon at ebi.ac.uk Wed Jul 18 07:26:04 2007 From: camon at ebi.ac.uk (camon at ebi.ac.uk) Date: Wed, 18 Jul 2007 15:26:04 +0100 (BST) Subject: [go] Surveying GO community outreach Message-ID: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> Hi guys, I think I have queried a few people on this before but I was wondering if each group would mind indicating to me (approximately) the percentage of GO annotations contributed to your manual GO curation effort by wetlab scientists as a result of Workshops or community outreach iniatives. We are grant writing this end and I think there is a lack of understanding of the ammount of manual GO annotation (especially IDA, IEP, IGI, IMP, IPI) that can be retrieved from dedicated annotation workshops(for wetlab scientists rather than groups specific GO or database funding).. Im thinking 90-99 percent of annotation would generated be using GO/ DB curators..so I'm guestimating up to 9% direct from wetlabs but at least for GOA thats an overestimate but we have only run one workshop.. thanks, Evelyn From dph at informatics.jax.org Wed Jul 18 09:28:24 2007 From: dph at informatics.jax.org (David Hill) Date: Wed, 18 Jul 2007 12:28:24 -0400 Subject: [go] Surveying GO community outreach In-Reply-To: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> References: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> Message-ID: <469E3FA8.4090207@informatics.jax.org> As far as I know, 0%. We do get some input through the MGI help desk and may be a result of their workshops, but the number of annotations is far less that 1% of all of the annotations we make. David camon at ebi.ac.uk wrote: > Hi guys, > > I think I have queried a few people on this before but I was wondering if > each group would mind indicating to me (approximately) the percentage of > GO annotations contributed to your manual GO curation effort by wetlab > scientists as a result of Workshops or community outreach iniatives. > > We are grant writing this end and I think there is a lack of understanding > of the ammount of manual GO annotation (especially IDA, IEP, IGI, IMP, > IPI) that can be retrieved from dedicated annotation workshops(for wetlab > scientists rather than groups specific GO or database funding).. > > Im thinking 90-99 percent of annotation would generated be using GO/ DB > curators..so I'm guestimating up to 9% direct from wetlabs but at least > for GOA thats an overestimate but we have only run one workshop.. > > thanks, > > Evelyn > > From pgaudet at northwestern.edu Wed Jul 18 09:42:39 2007 From: pgaudet at northwestern.edu (Pascale Gaudet) Date: Wed, 18 Jul 2007 12:42:39 -0400 Subject: [go] Surveying GO community outreach In-Reply-To: <469E3FA8.4090207@informatics.jax.org> References: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> <469E3FA8.4090207@informatics.jax.org> Message-ID: <6.0.1.1.2.20070718124149.036c4e20@lulu.it.northwestern.edu> Same for us! At 12:28 PM 7/18/2007 -0400, David Hill wrote: >As far as I know, 0%. We do get some input through the MGI help desk and >may be a result of their workshops, but the number of annotations is far >less that 1% of all of the annotations we make. > >David > >camon at ebi.ac.uk wrote: >>Hi guys, >> >>I think I have queried a few people on this before but I was wondering if >>each group would mind indicating to me (approximately) the percentage of >>GO annotations contributed to your manual GO curation effort by wetlab >>scientists as a result of Workshops or community outreach iniatives. >> >>We are grant writing this end and I think there is a lack of understanding >>of the ammount of manual GO annotation (especially IDA, IEP, IGI, IMP, >>IPI) that can be retrieved from dedicated annotation workshops(for wetlab >>scientists rather than groups specific GO or database funding).. >> >>Im thinking 90-99 percent of annotation would generated be using GO/ DB >>curators..so I'm guestimating up to 9% direct from wetlabs but at least >>for GOA thats an overestimate but we have only run one workshop.. >> >>thanks, >> >>Evelyn >> >> > From dph at informatics.jax.org Wed Jul 18 09:43:51 2007 From: dph at informatics.jax.org (David Hill) Date: Wed, 18 Jul 2007 12:43:51 -0400 Subject: [go] neuroblast division- obsolete Message-ID: <469E4347.1060207@informatics.jax.org> I wanted to give everyone a heads-up that Jen and I finally made changes to the neuroblast division part of the graph. This takes care of an old SF discussion that kept rearing its head every time someone looked closely at the definition of neuroblast division, so it is nice to have it done. The old term was obsoleted and replaced by a new neuroblast division term that was correctly defined. We also added new children for symmetric and asymmetric neuroblast divisions and moved the correctly defined existing terms under the new term. The neuroblast division 'sensu' terms were merged into the new term. All of these new terms should be sufficient for people to update their annotations. A simple move to the new term will maintain correctness in any annotation, but a re-annotation to one of the new children may allow for greater specificity. David From kchris at genome.Stanford.EDU Wed Jul 18 09:48:31 2007 From: kchris at genome.Stanford.EDU (Karen Christie) Date: Wed, 18 Jul 2007 09:48:31 -0700 (PDT) Subject: [go] Surveying GO community outreach In-Reply-To: <469E3FA8.4090207@informatics.jax.org> References: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> <469E3FA8.4090207@informatics.jax.org> Message-ID: Pretty much the same for SGD. We occasionally get comments from users (mostly Val Wood) that a particular annotation looks fishy. Sometimes, the user will suggest a new term. However, most of these comments are just that a given annotation looks incorrect. So most of the time, even when we've had community input that the annotations for a given gene should be looked at, an SGD curator is still the source of the annotation. -Karen On Wed, 18 Jul 2007, David Hill wrote: > As far as I know, 0%. We do get some input through the MGI help desk and may > be a result of their workshops, but the number of annotations is far less > that 1% of all of the annotations we make. > > David > > camon at ebi.ac.uk wrote: >> Hi guys, >> >> I think I have queried a few people on this before but I was wondering if >> each group would mind indicating to me (approximately) the percentage of >> GO annotations contributed to your manual GO curation effort by wetlab >> scientists as a result of Workshops or community outreach iniatives. >> >> We are grant writing this end and I think there is a lack of understanding >> of the ammount of manual GO annotation (especially IDA, IEP, IGI, IMP, >> IPI) that can be retrieved from dedicated annotation workshops(for wetlab >> scientists rather than groups specific GO or database funding).. >> >> Im thinking 90-99 percent of annotation would generated be using GO/ DB >> curators..so I'm guestimating up to 9% direct from wetlabs but at least >> for GOA thats an overestimate but we have only run one workshop.. >> >> thanks, >> >> Evelyn >> >> > > From vpetri at mcw.edu Wed Jul 18 10:07:57 2007 From: vpetri at mcw.edu (Petri, Victoria) Date: Wed, 18 Jul 2007 12:07:57 -0500 Subject: [go] Surveying GO community outreach In-Reply-To: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> References: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> Message-ID: <1448A38A42714048B9C53E473E13CCF0010A5F80@davis.hmgc.mcw.edu> Probably close to %; if there is any input that is usually coming from another GO curator, else it may be a comment on the annotation itself not a suggestion/contribution to manual annotations. Victoria Victoria Petri, Ph.D. Research Scientist Rat Genome Database (http://rgd.mcw.edu) Bioinformatics Program Human and Molecular Genetics Center Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI 53226 (414) 456-7507 Fax (414) 456-6595 vpetri at mcw.edu vpetri at mail.brc.mcw.edu -----Original Message----- From: owner-go at genome.stanford.edu [mailto:owner-go at genome.stanford.edu] On Behalf Of camon at ebi.ac.uk Sent: Wednesday, July 18, 2007 9:26 AM To: go at genome.stanford.edu Subject: [go] Surveying GO community outreach Hi guys, I think I have queried a few people on this before but I was wondering if each group would mind indicating to me (approximately) the percentage of GO annotations contributed to your manual GO curation effort by wetlab scientists as a result of Workshops or community outreach iniatives. We are grant writing this end and I think there is a lack of understanding of the ammount of manual GO annotation (especially IDA, IEP, IGI, IMP, IPI) that can be retrieved from dedicated annotation workshops(for wetlab scientists rather than groups specific GO or database funding).. Im thinking 90-99 percent of annotation would generated be using GO/ DB curators..so I'm guestimating up to 9% direct from wetlabs but at least for GOA thats an overestimate but we have only run one workshop.. thanks, Evelyn From ranjana at caltech.edu Wed Jul 18 10:44:11 2007 From: ranjana at caltech.edu (Ranjana Kishore) Date: Wed, 18 Jul 2007 10:44:11 -0700 Subject: [go] Surveying GO community outreach In-Reply-To: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> References: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> Message-ID: <469E516B.7040604@caltech.edu> Same answer here, as of now 0%, though we have a plan to make public a form where users can submit annotations. Cheers Ranjana WormBase camon at ebi.ac.uk wrote: > Hi guys, > > I think I have queried a few people on this before but I was wondering if > each group would mind indicating to me (approximately) the percentage of > GO annotations contributed to your manual GO curation effort by wetlab > scientists as a result of Workshops or community outreach iniatives. > > We are grant writing this end and I think there is a lack of understanding > of the ammount of manual GO annotation (especially IDA, IEP, IGI, IMP, > IPI) that can be retrieved from dedicated annotation workshops(for wetlab > scientists rather than groups specific GO or database funding).. > > Im thinking 90-99 percent of annotation would generated be using GO/ DB > curators..so I'm guestimating up to 9% direct from wetlabs but at least > for GOA thats an overestimate but we have only run one workshop.. > > thanks, > > Evelyn > > From donghui at stanford.edu Wed Jul 18 10:51:41 2007 From: donghui at stanford.edu (Donghui Li) Date: Wed, 18 Jul 2007 10:51:41 -0700 Subject: [go] Surveying GO community outreach In-Reply-To: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> References: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> Message-ID: <43039CA0-991B-4B3A-95E0-618B1219887D@stanford.edu> We have worked very hard to get TAIR users to submit their annotations to us. Our main effort include a) regular community submissions and b) working with the National Science Foundation and the PIs of the NSF 2010 projects to get GO annotations based on the data from their 2010 projects. We have just received a large number of submissions from these 2010 projects PIs - with the help of and some pressure from the NSF (and the PIs of course). I am in the process of extracting/processing these submissions. My estimate is that these submissions could generate several hundred GO annotations eventually. We also receive regular user submissions but on a smaller scale (1 to 5 annotations per submission, or more, varies). In total I estimate several percent (What do you think Tanya?) of the GO annotation at TAIR is from users as a result of community outreach activities (the total number of GO annotations at TAIR is around 100,000). Donghui On Jul 18, 2007, at 7:26 AM, camon at ebi.ac.uk wrote: > Hi guys, > > I think I have queried a few people on this before but I was > wondering if > each group would mind indicating to me (approximately) the > percentage of > GO annotations contributed to your manual GO curation effort by wetlab > scientists as a result of Workshops or community outreach iniatives. > > We are grant writing this end and I think there is a lack of > understanding > of the ammount of manual GO annotation (especially IDA, IEP, IGI, IMP, > IPI) that can be retrieved from dedicated annotation workshops(for > wetlab > scientists rather than groups specific GO or database funding).. > > Im thinking 90-99 percent of annotation would generated be using > GO/ DB > curators..so I'm guestimating up to 9% direct from wetlabs but at > least > for GOA thats an overestimate but we have only run one workshop.. > > thanks, > > Evelyn > ------------------------------------------- Donghui Li, PhD TAIR Curator Carnegie Institution Department of Plant Biology 260 Panama Street Stanford, CA 94305 U.S.A donghui at stanford.edu Tel (650) 325 1521 ext 356 Fax (650) 325 6857 http://www.arabidopsis.org http://www.geneontology.org ------------------------------------------- From sherlock at genome.Stanford.EDU Wed Jul 18 11:18:05 2007 From: sherlock at genome.Stanford.EDU (Gavin Sherlock) Date: Wed, 18 Jul 2007 11:18:05 -0700 Subject: [go] Surveying GO community outreach In-Reply-To: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> References: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> Message-ID: I would say that the answer for CGD is also ~0%. All of our non-IEA annotations were done by CGD curators. There was a community effort to provide IEA annotations, which actually form the lion's share of our total number of GO annotations available from CGD, though these are now all filtered out of our file on the GO site, as they are more than a year old. I don't believe any GO annotations with experimental evidence have been contributed by wet-lab scientists, Cheers, Gavin On Jul 18, 2007, at 7:26 AM, camon at ebi.ac.uk wrote: > Hi guys, > > I think I have queried a few people on this before but I was > wondering if > each group would mind indicating to me (approximately) the > percentage of > GO annotations contributed to your manual GO curation effort by wetlab > scientists as a result of Workshops or community outreach iniatives. > > We are grant writing this end and I think there is a lack of > understanding > of the ammount of manual GO annotation (especially IDA, IEP, IGI, IMP, > IPI) that can be retrieved from dedicated annotation workshops(for > wetlab > scientists rather than groups specific GO or database funding).. > > Im thinking 90-99 percent of annotation would generated be using > GO/ DB > curators..so I'm guestimating up to 9% direct from wetlabs but at > least > for GOA thats an overestimate but we have only run one workshop.. > > thanks, > > Evelyn From cherry at stanford.edu Wed Jul 18 18:26:30 2007 From: cherry at stanford.edu (Mike Cherry) Date: Wed, 18 Jul 2007 18:26:30 -0700 Subject: [go] Registration for Princeton GOC meetings Message-ID: The registration form for the GOC meetings at Princeton University this September is now open. Please register by August 1, 2007. Sorry for the short notice. We need to determine the how many will be attending to reserve appropriate meeting rooms. The web form can be found at: http://www.geneontology.org/cgi-bin/princeton-registration.pl There are three meeting that will be held at Princeton. 18th Consortium Meeting, September 23-24 3rd GOC Scientific Advisory Board Meeting, September 25 Reference Genome Working Group Meeting, September 26-27 -Mike P.S. if you have a problem with the form please report it to go- admin at genome.stanford.edu From sart2 at gen.cam.ac.uk Thu Jul 19 02:27:59 2007 From: sart2 at gen.cam.ac.uk (Susan Tweedie) Date: Thu, 19 Jul 2007 10:27:59 +0100 Subject: [go] Surveying GO community outreach In-Reply-To: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> References: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> Message-ID: <1184837279.18209.121.camel@paul.gen.cam.ac.uk> Hi FlyBase are 0% too. We get occasional suggestions from users about corrections/addtions to GO data but no direct submission of annotations. Susan On Wed, 2007-07-18 at 15:26 +0100, camon at ebi.ac.uk wrote: > Hi guys, > > I think I have queried a few people on this before but I was wondering if > each group would mind indicating to me (approximately) the percentage of > GO annotations contributed to your manual GO curation effort by wetlab > scientists as a result of Workshops or community outreach iniatives. > > We are grant writing this end and I think there is a lack of understanding > of the ammount of manual GO annotation (especially IDA, IEP, IGI, IMP, > IPI) that can be retrieved from dedicated annotation workshops(for wetlab > scientists rather than groups specific GO or database funding).. > > Im thinking 90-99 percent of annotation would generated be using GO/ DB > curators..so I'm guestimating up to 9% direct from wetlabs but at least > for GOA thats an overestimate but we have only run one workshop.. > > thanks, > > Evelyn > -- --------------------------------- Susan Tweedie FlyBase GO curator Department of Genetics University of Cambridge Downing Street Cambridge CB2 3EH UK email: s.tweedie at gen.cam.ac.uk phone: +44 [0]1223 333963 fax:+ 44 [0]1223 333992 From dph at informatics.jax.org Thu Jul 19 04:37:35 2007 From: dph at informatics.jax.org (David Hill) Date: Thu, 19 Jul 2007 07:37:35 -0400 Subject: [go] Surveying GO community outreach In-Reply-To: <1184837279.18209.121.camel@paul.gen.cam.ac.uk> References: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> <1184837279.18209.121.camel@paul.gen.cam.ac.uk> Message-ID: <469F4CFF.1060500@informatics.jax.org> I should also clarify. We never get direct submissions either. Instead we get suggestions through our help desk. We have recently added a link on our textual descriptions inviting people to suggest papers for review, but it is too new to judge its success. David Susan Tweedie wrote: > Hi > > FlyBase are 0% too. We get occasional suggestions from users about > corrections/addtions to GO data but no direct submission of annotations. > > Susan > > On Wed, 2007-07-18 at 15:26 +0100, camon at ebi.ac.uk wrote: > >> Hi guys, >> >> I think I have queried a few people on this before but I was wondering if >> each group would mind indicating to me (approximately) the percentage of >> GO annotations contributed to your manual GO curation effort by wetlab >> scientists as a result of Workshops or community outreach iniatives. >> >> We are grant writing this end and I think there is a lack of understanding >> of the ammount of manual GO annotation (especially IDA, IEP, IGI, IMP, >> IPI) that can be retrieved from dedicated annotation workshops(for wetlab >> scientists rather than groups specific GO or database funding).. >> >> Im thinking 90-99 percent of annotation would generated be using GO/ DB >> curators..so I'm guestimating up to 9% direct from wetlabs but at least >> for GOA thats an overestimate but we have only run one workshop.. >> >> thanks, >> >> Evelyn >> >> From camon at ebi.ac.uk Thu Jul 19 04:52:44 2007 From: camon at ebi.ac.uk (camon at ebi.ac.uk) Date: Thu, 19 Jul 2007 12:52:44 +0100 (BST) Subject: [go] Surveying GO community outreach In-Reply-To: <469F4CFF.1060500@informatics.jax.org> References: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> <1184837279.18209.121.camel@paul.gen.cam.ac.uk> <469F4CFF.1060500@informatics.jax.org> Message-ID: <48494.217.43.58.122.1184845964.squirrel@webmail.ebi.ac.uk> Hi everyone, Thanks for the comments. I understand that Ruth and Jen already had collected some information so sorry for duplicate mail shot. To put everyone in the picture we(UCD, EBI, UCL and MGI) are re-submitting a grant to cover immune gene GO annotation of human, mouse, cattle and pig species. There is a considerable amount of community outreach in our grant and a series of workshops are expected. We are hoping that by inviting 20-30 immune experts to curate or review particular immune genes or processes might prove fruitful. We think the key is that the immunology community feels some ownership/responsibility for the GO data in their field. Fingers crossed.. Evelyn > I should also clarify. We never get direct submissions either. Instead > we get suggestions through our help desk. We have recently added a link > on our textual descriptions inviting people to suggest papers for > review, but it is too new to judge its success. > > David > > Susan Tweedie wrote: >> Hi >> >> FlyBase are 0% too. We get occasional suggestions from users about >> corrections/addtions to GO data but no direct submission of annotations. >> >> Susan >> >> On Wed, 2007-07-18 at 15:26 +0100, camon at ebi.ac.uk wrote: >> >>> Hi guys, >>> >>> I think I have queried a few people on this before but I was wondering >>> if >>> each group would mind indicating to me (approximately) the percentage >>> of >>> GO annotations contributed to your manual GO curation effort by wetlab >>> scientists as a result of Workshops or community outreach iniatives. >>> >>> We are grant writing this end and I think there is a lack of >>> understanding >>> of the ammount of manual GO annotation (especially IDA, IEP, IGI, IMP, >>> IPI) that can be retrieved from dedicated annotation workshops(for >>> wetlab >>> scientists rather than groups specific GO or database funding).. >>> >>> Im thinking 90-99 percent of annotation would generated be using GO/ DB >>> curators..so I'm guestimating up to 9% direct from wetlabs but at least >>> for GOA thats an overestimate but we have only run one workshop.. >>> >>> thanks, >>> >>> Evelyn >>> >>> > > From pfey at northwestern.edu Thu Jul 19 15:10:33 2007 From: pfey at northwestern.edu (Petra Fey) Date: Thu, 19 Jul 2007 17:10:33 -0500 Subject: [go] Call for Aug newsletter contributions Message-ID: <1A556392-DFE8-4C68-855C-91049FD4B271@northwestern.edu> Hi All, we are starting to work on the August edition of the GO newsletter. If you have any contributions, or any suggestions for contributions, please send them to me. Thanks, Petra and the GO newsletter working group From cherry at stanford.edu Mon Jul 23 10:08:24 2007 From: cherry at stanford.edu (Mike Cherry) Date: Mon, 23 Jul 2007 10:08:24 -0700 Subject: [go] Paper of potential interest to you Message-ID: Manual curation is not sufficient for annotation of genomic databases William A. Baumgartner, Jr, K. Bretonnel Cohen, Lynne M. Fox, George Acquaah-Mensah, and Lawrence Hunter Bioinformatics 2007 23: i41-i48. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/ i41?etoc From gail at genome.Stanford.EDU Mon Jul 23 11:33:46 2007 From: gail at genome.Stanford.EDU (Gail Binkley) Date: Mon, 23 Jul 2007 11:33:46 -0700 (PDT) Subject: [go] GO wiki changes to fight spam Message-ID: Several changes have recently been made to the GO public wiki (http://wiki.geneontology.org/) and GOC wiki (http://gocwiki.geneontology.org) to prevent and identify spam. These changes include: 1. All wiki passwords must now be at least 6 characters in length. 2. A regular expression of known spam words is now used to reject dubious edits. 3. A cronjob is run nightly to report recent changes and users of unknown origin. Please contact go-admin at genome.stanford.edu if any of these wiki changes cause unintended problems. Thanks, Gail Binkley Stanford From cjm at fruitfly.org Wed Jul 25 13:44:15 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Wed, 25 Jul 2007 13:44:15 -0700 Subject: [go] GO Managers Meeting (18 July) minutes available Message-ID: http://gocwiki.geneontology.org/index.php/Managers_18July07 From cjm at fruitfly.org Wed Jul 25 14:27:55 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Wed, 25 Jul 2007 14:27:55 -0700 Subject: [go] The seven deadly sins of bioinformatics Message-ID: <0FF50944-13EC-4271-B0BD-71B5A33AE9B0@fruitfly.org> Carole Goble's talk at ISMB/Bosc this year: http://www.slideshare.net/dullhunk/the-seven-deadly-sins-of- bioinformatics/ Fair amount in there about ontologies/obo (I wasn't at ISMB but the slides are amusing and easy to follow when read online) From hitz at genome.Stanford.EDU Wed Jul 25 14:57:49 2007 From: hitz at genome.Stanford.EDU (Benjamin Hitz) Date: Wed, 25 Jul 2007 14:57:49 -0700 Subject: [go] The seven deadly sins of bioinformatics In-Reply-To: <0FF50944-13EC-4271-B0BD-71B5A33AE9B0@fruitfly.org> References: <0FF50944-13EC-4271-B0BD-71B5A33AE9B0@fruitfly.org> Message-ID: <2950FE47-E61D-4A0A-BDDC-6311EAFD06F9@genome.stanford.edu> On Jul 25, 2007, at 2:27 PM, Chris Mungall wrote: > Carole Goble's talk at ISMB/Bosc this year: > > http://www.slideshare.net/dullhunk/the-seven-deadly-sins-of- > bioinformatics/ > > Fair amount in there about ontologies/obo > Wow, giant 94 slide strawman. Although there are bits of truth in there. Ben -- Ben Hitz Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium Stanford University ** hitz at genome.stanford.edu From jblake at informatics.jax.org Fri Jul 27 10:37:18 2007 From: jblake at informatics.jax.org (Judith Blake) Date: Fri, 27 Jul 2007 13:37:18 -0400 Subject: [go] [Fwd: An amazing technology. Imagine the applications in brain imaging. [and e-journal publishing]] Message-ID: <46AA2D4E.6080408@informatics.jax.org> Check this out. The future for digital images... Judy "This is worth as much time as it takes! An amazing technology. Imagine the applications in brain imaging." http://www.ted.com/index.php/talks/view/id/129? ________________________________ (Added by BG: Information from TED [Technology, Entertainment, Design] conference website) About this Talk Using photos of oft-snapped subjects (like Notre Dame) scraped from around the Web, Photosynth (based on Seadragon technology) creates breathtaking multidimensional spaces with zoom and navigation features that outstrip all expectation. Its architect, Blaise Aguera y Arcas , shows it off in this standing-ovation demo. Curious about that speck in corner? Dive into a freefall and watch as the speck becomes a gargoyle. With an unpleasant grimace. And an ant-sized chip in its lower left molar. "Perhaps the most amazing demo I've seen this year," wrote Ethan Zuckerman, after TED2007. Indeed, Photosynth might utterly transform the way we manipulate and experience digital images. About Blaise Aguera y Arcas Why you should listen to him: Blaise Aguera y Arcas' background is as multidimensional as the visions he helps create. In the 1990s, he authored patents on both video compression and 3D visualization techniques, and in 2001, he made an influential computational discovery that cast doubt on Gutenberg's role as the father of movable type. He also created Seadragon (acquired by Microsoft in 2006), the visualization technology that gives Photosynth its amazingly smooth digital rendering and zoom capabilities. Photosynth itself is a vastly powerful piece of software capable of taking a wide variety of images, analyzing them for similarities, and grafting them together into an interactive three-dimensional space. This seamless patchwork of images can be viewed via multiple angles and magnifications, allowing us to look around corners or "fly" in for a (much) closer look. Simply put, it could utterly transform the way we experience digital images. "Perhaps the most amazing demo I've seen this year." Ethan Zuckerman, TED attendee and Global Voices blogger From tberardi at acoma.Stanford.EDU Mon Jul 30 10:11:55 2007 From: tberardi at acoma.Stanford.EDU (Tanya Berardini) Date: Mon, 30 Jul 2007 10:11:55 -0700 Subject: [go] Surveying GO community outreach In-Reply-To: <43039CA0-991B-4B3A-95E0-618B1219887D@stanford.edu> References: <44747.217.43.214.159.1184768764.squirrel@webmail.ebi.ac.uk> <43039CA0-991B-4B3A-95E0-618B1219887D@stanford.edu> Message-ID: <46AE1BDB.8060207@acoma.stanford.edu> Donghui Li wrote: > We have worked very hard to get TAIR users to submit their annotations > to us. Our main effort include a) regular community submissions and b) > working with the National Science Foundation and the PIs of the NSF 2010 > projects to get GO annotations based on the data from their 2010 projects. > > We have just received a large number of submissions from these 2010 > projects PIs - with the help of and some pressure from the NSF (and the > PIs of course). I am in the process of extracting/processing these > submissions. My estimate is that these submissions could generate > several hundred GO annotations eventually. > > We also receive regular user submissions but on a smaller scale (1 to 5 > annotations per submission, or more, varies). > > In total I estimate several percent (What do you think Tanya?) of the GO > annotation at TAIR is from users as a result of community outreach > activities (the total number of GO annotations at TAIR is around 100,000). An estimate of 1-2% (1,000 - 2,000 annotations) is probably right. Tanya > Donghui > > On Jul 18, 2007, at 7:26 AM, camon at ebi.ac.uk wrote: > >> Hi guys, >> >> I think I have queried a few people on this before but I was wondering if >> each group would mind indicating to me (approximately) the percentage of >> GO annotations contributed to your manual GO curation effort by wetlab >> scientists as a result of Workshops or community outreach iniatives. >> >> We are grant writing this end and I think there is a lack of >> understanding >> of the ammount of manual GO annotation (especially IDA, IEP, IGI, IMP, >> IPI) that can be retrieved from dedicated annotation workshops(for wetlab >> scientists rather than groups specific GO or database funding).. >> >> Im thinking 90-99 percent of annotation would generated be using GO/ DB >> curators..so I'm guestimating up to 9% direct from wetlabs but at least >> for GOA thats an overestimate but we have only run one workshop.. >> >> thanks, >> >> Evelyn >> > > ------------------------------------------- > Donghui Li, PhD > TAIR Curator > > Carnegie Institution > Department of Plant Biology > 260 Panama Street > Stanford, CA 94305 > U.S.A > > donghui at stanford.edu > Tel (650) 325 1521 ext 356 > Fax (650) 325 6857 > > http://www.arabidopsis.org > http://www.geneontology.org > ------------------------------------------- > > > > -- ------------------------------------------------------------------------------------------ Tanya Berardini, Ph.D. tberardi at acoma.stanford.edu The Arabidopsis Information Resource FAX: (650) 325-6857 Carnegie Institution of Washington Tel: (650) 325-1521 ext. 325 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 ------------------------------------------------------------------------------------------ From jdeegan at ebi.ac.uk Tue Jul 31 07:55:08 2007 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Tue, 31 Jul 2007 15:55:08 +0100 Subject: [go] annotation outreach for July Message-ID: <46AF4D4C.8060000@ebi.ac.uk> Hi, If you did anything during July that encouraged new groups to start annotating to the GO would it be possible to write and let me know? I am making up the July report. If you would like to know more about what goes into these reports, the previous ones are at: http://gocwiki.geneontology.org/index.php/Annotation_Outreach_group_reports Thanks, Jen -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium