From jclark at ebi.ac.uk Tue Jan 2 02:27:41 2007 From: jclark at ebi.ac.uk (J Clark) Date: Tue, 02 Jan 2007 10:27:41 +0000 Subject: is_a complete biological process Message-ID: <459A339D.8020804@ebi.ac.uk> Hi, I have just committed the version of the ontology file with the is_a complete biological process ontology. I hope you all enjoy the new setup. It will take a couple of days for the information to trickle down from gene_ontology_edit.obo to gene_ontology.obo and then on to the GO flat file format. Please do write if you have any comments. Thanks, Jennifer (On behalf of the is_a complete team: David, Jane, Jen, Tanya and Midori.) From midori at ebi.ac.uk Tue Jan 2 06:22:05 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 2 Jan 2007 14:22:05 +0000 (GMT) Subject: Action Items from St Croix In-Reply-To: References: Message-ID: Here's a version with some updates, and a few assignee corrections. m -------------- next part -------------- A non-text attachment was scrubbed... Name: StCroixActionItems_mah.doc Type: application/msword Size: 35328 bytes Desc: Url : http://fafner.stanford.edu/pipermail/go/attachments/20070102/aa3dee6b/attachment.doc From cjm at fruitfly.org Tue Jan 2 09:40:35 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Tue, 2 Jan 2007 17:40:35 +0000 Subject: Specifying gene type in gene association file In-Reply-To: <4EBC6452-AAB5-4B2E-9C48-CC0C7CE54F82@berkeleybop.org> References: <457FD044.7070406@informatics.jax.org> <4EBC6452-AAB5-4B2E-9C48-CC0C7CE54F82@berkeleybop.org> Message-ID: <8BC85E63-5E8D-4C60-A2FE-05769C73B2F1@fruitfly.org> On Dec 18, 2006, at 12:39 PM, Suzanna Lewis wrote: > On Dec 13, 2006, at 5:17 AM, Midori Harris wrote: > >> There's certainly a consensus that the DB_object_type column >> should use SO ids (or terms) from now on. But I think that still >> leaves the other question unaddressed -- the discussion so far >> hasn't explicitly stated that the SO ids in DB_object_type will >> still represent the type of object in the database (as opposed to >> what type of molecule actually has the activity/location/etc.), >> but that's sort of been implied. > > I don't think there is any un-addressed question. The database is > holding (representing) different types of molecules. And using the > SO term in the DB_object_type column specifies the molecular type > that the database is representing. Agreed - anything else would be v confusing. The type of molecule that has the activity/location/etc is usually implicit, and where it isn't we can use the qualifier column > cheers, S > > P.S. my vote is to use the SO-ID and not the string Using the SO ID and not the string will require big changes by everyone consuming these files. Given the small subset of SO we'll be using I'm not sure this is justified. Also remember, we also allow in principle "complex" which is not a SO term. (although so far no one is making assignments at the level of complexes) Anyway, I think we need to hold of judgement on this issue until we solve the fundamental issue of what kinds of entities are represented in SO, and does SO:chromosome represent the same entity as GO:chromosome https://sourceforge.net/tracker/index.php? func=detail&aid=1587313&group_id=36855&atid=440764 I haven't added my comments to this tracker item yet, as my thoughts on the matter are still evolving. From hitz at genome.Stanford.EDU Tue Jan 2 10:08:15 2007 From: hitz at genome.Stanford.EDU (Benjamin Hitz) Date: Tue, 2 Jan 2007 10:08:15 -0800 Subject: [Go-database] AmiGO In-Reply-To: References: <44255ea80611240557x35252b86qe900f9f505c4d1c@mail.gmail.com> Message-ID: > Thiago - Sorry to hear about your problem, but we don't really know how to fix it. Could you please create a bug report here: http://sourceforge.net/tracker/?group_id=36855&atid=908269 Please include all system information. Does the latest go-dev version work with any obo database? I just cannot be sure if you are having a database problem or an amigo problem... If you use mysql queries on the database, does it have what you expect (number of associations, terms, etc.) If your database looks OK, then it might be a problem with some outdated perl module, perhaps CGI::Session. Thanks, Ben >> From: "Thiago Venancio" >> Date: November 24, 2006 5:57:38 AM PST >> To: go-database at fruitfly.org >> Subject: [Go-database] AmiGO >> >> Dear all, >> >> I have been using AmiGO locally about one year with no problems. >> Now we are with a new project, so I have build a new association >> file (with the latest GO file) and loaded a new mysql database >> (with the latest format). >> >> The AmiGO browser loads ok, with no error messages, but we cannot >> browse more than 1 level. For example, one clicks on Biological >> process. Ok. After that on "pigmentation", and the browser returns >> to the initial window, with no error messages in the screen nor in >> the Apache logs. >> >> I have also tested the latest go-dev, but the error persists. >> >> The older database is ok. >> >> Any tips? >> >> Thanks in advance. >> >> Thiago >> -- >> "Science may set limits to knowledge, but should not set limits to >> imagination." >> Bertrand Russell >> >> -------------------------------------- >> Thiago Motta Venancio, MSc >> PhD student in Bioinformatics >> _______________________________________________ >> Go-database mailing list >> Go-database at fruitfly.org >> http://mail.fruitfly.org/mailman/listinfo/go-database > -- Ben Hitz Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium Stanford University ** hitz at genome.stanford.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20070102/ce2ed238/attachment.html From val at sanger.ac.uk Wed Jan 3 05:04:49 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 03 Jan 2007 13:04:49 +0000 Subject: GOC meeting ..... When you arrive Message-ID: <459BA9F1.7060201@sanger.ac.uk> Happy New Year everyone. When you arrive at Jesus College: By taxi Ask the taxi to drop you at the 'pedestrian entrance' (the main entrance on Jesus Lane). By car If you are driving you will need to come to the 'Victoria Avenue' entrance and use the intercom for entry. Proceed to the porters lodge to collect your room key (this should be clearly signposted). The porters will give you directions to the 'Prioress's Room' for registration. There is a wedding at the college on Sunday so be discreet and don't explore until Monday. There are maps here (of Cambridge and Jesus College) if you need them http://conference.jesus.cam.ac.uk/maps/index.htm See you all next week Val and Ev -- --------------------------------------------------------------------------- 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 camon at ebi.ac.uk Wed Jan 3 08:18:37 2007 From: camon at ebi.ac.uk (Evelyn Camon) Date: Wed, 03 Jan 2007 16:18:37 +0000 Subject: GOC meeting posters and abstracts Message-ID: <459BD75D.5050207@ebi.ac.uk> Hi, We have a grand total of 4 posters from EBI, MGI, RGD, HGNC. Van already loaded with poster boards. I need any further abstracts by tomorrow afternoon UK time. thanks very much, Evelyn -- Evelyn Camon GOA Coordinator Senior Scientific Curator European Bioinformatics Institute Tel:01223-494465 Fax:01223-494468 E-mail: camon at ebi.ac.uk URL: http://www.ebi.ac.uk/goa From midori at ebi.ac.uk Wed Jan 3 09:10:18 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Wed, 3 Jan 2007 17:10:18 +0000 (GMT) Subject: draftAGENDA-GOC meeting Jan.2006 In-Reply-To: <45942002.9000800@informatics.jax.org> References: <45942002.9000800@informatics.jax.org> Message-ID: Just one thing from me and David: we'd like to change the order of the ontology development topics, to allow a smoother transition to Chris and software. New order: Cell Ontology links Collaboration with Jonathan Liu and MIT IS_A complete Regulates: a joint ontology development/software perspective -Chris Thanks, m On Thu, 28 Dec 2006, Judith Blake wrote: > Hi all, > > Here is the draft of the Agenda for the GOC meeting Jan 7-10. > As you can see, it is a very full agenda. > We incorporated suggestions from the wiki and from email threads. > > If you see anything egregiously missing or mis-stated, let us know. > > Otherwise...we will see (some of ) you in Cambridge, > > Happy New Year to all. > Judy Michael Suzi Mike > From jane at ebi.ac.uk Wed Jan 3 09:20:47 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Wed, 3 Jan 2007 17:20:47 +0000 Subject: Action Items from St Croix In-Reply-To: References: Message-ID: <65381A04-6BE4-4F19-B72A-C4214BA4E6F5@ebi.ac.uk> Version with mine and Midori's changes (with track changes on)... jane -------------- next part -------------- A non-text attachment was scrubbed... Name: StCroixActionItems_jl.doc Type: application/octet-stream Size: 37888 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20070103/8587ff1a/attachment.obj -------------- next part -------------- On 2 Jan 2007, at 14:22, Midori Harris wrote: > Here's a version with some updates, and a few assignee corrections. > > m > From suzi at berkeleybop.org Wed Jan 3 10:40:24 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Wed, 3 Jan 2007 10:40:24 -0800 Subject: Action Items from St Croix In-Reply-To: <65381A04-6BE4-4F19-B72A-C4214BA4E6F5@ebi.ac.uk> References: <65381A04-6BE4-4F19-B72A-C4214BA4E6F5@ebi.ac.uk> Message-ID: <64569D73-0260-4BC6-9AC1-BE78868A8881@berkeleybop.org> Thanks, Other folk? I'd really like to hear from everyone (even if you have no changes) so that we don't have to do this during the meeting. -S On Jan 3, 2007, at 9:20 AM, Jane Lomax wrote: > Version with mine and Midori's changes (with track changes on)... > > jane > > > > On 2 Jan 2007, at 14:22, Midori Harris wrote: > >> Here's a version with some updates, and a few assignee corrections. >> >> m >> > From rama at genome.Stanford.EDU Wed Jan 3 15:10:28 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Wed, 3 Jan 2007 15:10:28 -0800 Subject: Autogenerating map2slim mapping files? In-Reply-To: <40DF1E01-6C43-44DC-AA05-FC7BCDC91B6D@hmgc.mcw.edu> References: <40DF1E01-6C43-44DC-AA05-FC7BCDC91B6D@hmgc.mcw.edu> Message-ID: <8035FC86-761C-4C1A-80D8-FBF6DDE6D961@genome.stanford.edu> Simon, To avoid having to install the perl modules etc, you can use the web interface available at Princeton University. It uses the map2slim script and you can use any GO slim/ gene_association file or input your GO slim. http://go.princeton.edu/cgi-bin/GOTermMapper Providing (by autogeneration) these mapping files on the GOC ftp site sounds like a good idea. At SGD, we have a web interface to do the mapping and we also provide a mapping file of the annotations on our FTP site, although we don't provide the mapping of the go terms to their go slims. Rama On Jan 3, 2007, at 1:46 PM, Twigger Simon wrote: > Hi there, > > Working with Larry Wall's definitions of Chief Virtues of a > Programmer, I'm exercising my 'Laziness' muscle here. > > Via the GOC we generate daily OBO files and a whole bunch of 'Other > Useful Files' on the GO website so people can access the latest > terms and annotations. What I find Im also in need of quite > frequently are GO Slim versions of the annotations using the > Generic GO Slim along with the mapping of the current GO terms to > their respective GO Slim terms. Certainly it is possible to > download and install the various perl modules and run the map2slim > script, etc. to derive these files from the raw data but is there > any merit to autogenerating these and adding them to the 'other > useful files' so people dont have to install all the perl code to > run this manually? > > Speaking for myself, the mapping file would be spectacular to have > available so I could automatically FTP it over and crank through > current annotations to get the appropriate GO Slim versions. It > might get a bit unwieldy to run all annotation files against all > standard GO Slims on the site but if we could generate one mapping > file for each Maintained GO Slim that would just be four new files > that anyone could then use to convert GO annotations to their > respective Slimmed version. > > Would anyone else find this useful or is it just me being lazy > (remembering that Laziness is a Virtue). :) > > Simon. > > -- > > Simon N. Twigger, Ph.D. > Assistant Professor, Department of Physiology > Medical College of Wisconsin > 8701 Watertown Plank Road, > Milwaukee, WI, USA > tel: 414-456-8802 > fax: 414-456-6595 > AIM/iChat: simontatmcw > > > > -- > This message is from the GOFriends moderated mailing list. A list > of public > announcements and discussion of the Gene Ontology (GO) project. > Problems with the list? E-mail: owner- > gofriends at geneontology.org > Subscribing send "subscribe" to gofriends- > request at geneontology.org > Unsubscribing send "unsubscribe" to gofriends- > request at geneontology.org > Web: http://www.geneontology.org/ From Mary_Dolan at umit.maine.edu Wed Jan 3 16:06:25 2007 From: Mary_Dolan at umit.maine.edu (Mary Dolan) Date: Wed, 03 Jan 2007 19:06:25 -0500 Subject: Autogenerating map2slim mapping files? In-Reply-To: <8035FC86-761C-4C1A-80D8-FBF6DDE6D961@genome.stanford.edu> References: <8035FC86-761C-4C1A-80D8-FBF6DDE6D961@genome.stanford.edu> Message-ID: Rama Balakrishnan on Wednesday, January 03, 2007 at 6:10 PM -0500 wrote: >Simon, >To avoid having to install the perl modules etc, you can use the web >interface available at Princeton University. It uses the map2slim >script and you can use any GO slim/ gene_association file or input >your GO slim. >http://go.princeton.edu/cgi-bin/GOTermMapper > >Providing (by autogeneration) these mapping files on the GOC ftp site >sounds like a good idea. At SGD, we have a web interface to do the >mapping and we also provide a mapping file of the annotations on our >FTP site, although we don't provide the mapping of the go terms to >their go slims. >Rama > > >On Jan 3, 2007, at 1:46 PM, Twigger Simon wrote: >> Hi there, >> >> Working with Larry Wall's definitions of Chief Virtues of a >> Programmer, I'm exercising my 'Laziness' muscle here. >> >> Via the GOC we generate daily OBO files and a whole bunch of 'Other >> Useful Files' on the GO website so people can access the latest >> terms and annotations. What I find Im also in need of quite >> frequently are GO Slim versions of the annotations using the >> Generic GO Slim along with the mapping of the current GO terms to >> their respective GO Slim terms. Certainly it is possible to >> download and install the various perl modules and run the map2slim >> script, etc. to derive these files from the raw data but is there >> any merit to autogenerating these and adding them to the 'other >> useful files' so people dont have to install all the perl code to >> run this manually? >> >> Speaking for myself, the mapping file would be spectacular to have >> available so I could automatically FTP it over and crank through >> current annotations to get the appropriate GO Slim versions. It >> might get a bit unwieldy to run all annotation files against all >> standard GO Slims on the site but if we could generate one mapping >> file for each Maintained GO Slim that would just be four new files >> that anyone could then use to convert GO annotations to their >> respective Slimmed version. >> >> Would anyone else find this useful or is it just me being lazy >> (remembering that Laziness is a Virtue). :) >> >> Simon. > Hi, Simon and Rama. > Because the MGI GO_Slim set ( http://proto.informatics.jax.org/prototypes/GOTools/web-docs/MGI_GO_Slim.html ) is defined using unions and disjunctions of GO terms, (as far as I know) it cannot currently be used with the standard tools (e.g. map2slim script). Therefore, we provide a regularly updated file to map GO_ids to MGI GO_Slim category. http://proto.informatics.jax.org/prototypes/GOTools/web-docs/map2MGIslim.txt Mary Mary E. Dolan, Ph.D. ************************************ Mouse Genome Informatics Consortium, The Jackson Laboratory mdolan at informatics.jax.org (207)288-6439 Research Faculty, NCGIA Department of Spatial Information Science and Engineering, University of Maine Boardman Hall 329 University of Maine Orono, Maine 04469 fax: 207.581.2206 mary_dolan at umit.maine.edu ************************************ From eurie at genome.Stanford.EDU Wed Jan 3 16:21:29 2007 From: eurie at genome.Stanford.EDU (Eurie Hong) Date: Wed, 3 Jan 2007 16:21:29 -0800 Subject: Action Items from St Croix In-Reply-To: <64569D73-0260-4BC6-9AC1-BE78868A8881@berkeleybop.org> References: <65381A04-6BE4-4F19-B72A-C4214BA4E6F5@ebi.ac.uk> <64569D73-0260-4BC6-9AC1-BE78868A8881@berkeleybop.org> Message-ID: <0F8A61A9-DAE1-4527-9A55-2EB655FD00A2@genome.stanford.edu> Hi Suzi, Items #40 and #41 are done. Item 31: No conclusion about how to distinguish large- vs small- scale experiments was reached. People are encouraged to keep thinking about this issue, which clearly needs more discussion. [Eurie Hong] This was discussed at Annotation Camp (see p. 16 of minutes) and the recommendation was to proceed with further discussion with examples among the greater GO group. Sorry, I dropped the ball on this one and didn't add it to the agenda on the wiki in time. Will there still be time to add this to the agenda? Maybe after the evidence code discussions? eurie On Jan 3, 2007, at 10:40 AM, Suzanna Lewis wrote: > Thanks, > > Other folk? I'd really like to hear from everyone (even if you have > no changes) so that we don't have to do this during the meeting. > > -S > > On Jan 3, 2007, at 9:20 AM, Jane Lomax wrote: > >> Version with mine and Midori's changes (with track changes on)... >> >> jane >> >> >> >> On 2 Jan 2007, at 14:22, Midori Harris wrote: >> >>> Here's a version with some updates, and a few assignee corrections. >>> >>> m >>> >> From eurie at genome.Stanford.EDU Wed Jan 3 16:24:38 2007 From: eurie at genome.Stanford.EDU (Eurie Hong) Date: Wed, 3 Jan 2007 16:24:38 -0800 Subject: GO managers minutes 1-3-2007 Message-ID: <4A75C1D8-9034-4548-AFE9-3B1169EF5542@genome.stanford.edu> The minutes from today's GO Managers conference call are now on the internal wiki: http://gocwiki.geneontology.org/index.php/Managers_3Jan07 If you would like a particular issue to be discussed at the next managers' call, please contact the relevant manager(s): Reference Genomes: Rex User Advocacy: Jane and Eurie Content Development: Midori and David Annotation Outreach: Jennifer Software: Chris For general management and budget issues, please contact the GO PIs . Thanks, eurie From jblake at informatics.jax.org Wed Jan 3 21:33:41 2007 From: jblake at informatics.jax.org (Judith Blake) Date: Thu, 04 Jan 2007 00:33:41 -0500 Subject: Action Items from St Croix In-Reply-To: <0F8A61A9-DAE1-4527-9A55-2EB655FD00A2@genome.stanford.edu> References: <65381A04-6BE4-4F19-B72A-C4214BA4E6F5@ebi.ac.uk> <64569D73-0260-4BC6-9AC1-BE78868A8881@berkeleybop.org> <0F8A61A9-DAE1-4527-9A55-2EB655FD00A2@genome.stanford.edu> Message-ID: <459C91B5.3060401@informatics.jax.org> I will add discussion of large vs small experiment distinction to evidence code section of agenda. we will need to prioritize evidence code discussions at the meeting judy Eurie Hong wrote: > Hi Suzi, > > Items #40 and #41 are done. > > Item 31: No conclusion about how to distinguish large- vs small-scale > experiments was reached. People are encouraged to keep thinking about > this issue, which clearly needs more discussion. [Eurie Hong] > > This was discussed at Annotation Camp (see p. 16 of minutes) and the > recommendation was to proceed with further discussion with examples > among the greater GO group. > > Sorry, I dropped the ball on this one and didn't add it to the agenda > on the wiki in time. Will there still be time to add this to the > agenda? Maybe after the evidence code discussions? > > eurie > > > On Jan 3, 2007, at 10:40 AM, Suzanna Lewis wrote: > >> Thanks, >> >> Other folk? I'd really like to hear from everyone (even if you have >> no changes) so that we don't have to do this during the meeting. >> >> -S >> >> On Jan 3, 2007, at 9:20 AM, Jane Lomax wrote: >> >>> Version with mine and Midori's changes (with track changes on)... >>> >>> jane >>> >>> >>> >>> On 2 Jan 2007, at 14:22, Midori Harris wrote: >>> >>>> Here's a version with some updates, and a few assignee corrections. >>>> >>>> m >>>> >>> > From kchris at genome.Stanford.EDU Wed Jan 3 22:01:04 2007 From: kchris at genome.Stanford.EDU (Karen Christie) Date: Wed, 3 Jan 2007 22:01:04 -0800 (PST) Subject: Action Items from St Croix In-Reply-To: <459C91B5.3060401@informatics.jax.org> References: <65381A04-6BE4-4F19-B72A-C4214BA4E6F5@ebi.ac.uk> <64569D73-0260-4BC6-9AC1-BE78868A8881@berkeleybop.org> <0F8A61A9-DAE1-4527-9A55-2EB655FD00A2@genome.stanford.edu> <459C91B5.3060401@informatics.jax.org> Message-ID: I've been part of an "evidence code committee" of annotators for the last couple months. We have come up with our proposal for the new evidence code documentation and more importantly, with a summary of the main points. The summary should help us get through the evidence code issues quickly and efficiently. The evidence code committee has until 9:30 am Pacific on Thursday to let me know if I missed anything and then I'll send it to Mike to include with the meeting agenda and supporting info. -Karen On Thu, 4 Jan 2007, Judith Blake wrote: > I will add discussion of large vs small experiment distinction to evidence > code section of agenda. we will need to prioritize evidence code discussions > at the meeting > > judy > > Eurie Hong wrote: >> Hi Suzi, >> >> Items #40 and #41 are done. >> >> Item 31: No conclusion about how to distinguish large- vs small-scale >> experiments was reached. People are encouraged to keep thinking about this >> issue, which clearly needs more discussion. [Eurie Hong] >> >> This was discussed at Annotation Camp (see p. 16 of minutes) and the >> recommendation was to proceed with further discussion with examples among >> the greater GO group. >> >> Sorry, I dropped the ball on this one and didn't add it to the agenda on >> the wiki in time. Will there still be time to add this to the agenda? >> Maybe after the evidence code discussions? >> >> eurie >> >> >> On Jan 3, 2007, at 10:40 AM, Suzanna Lewis wrote: >> >>> Thanks, >>> >>> Other folk? I'd really like to hear from everyone (even if you have no >>> changes) so that we don't have to do this during the meeting. >>> >>> -S >>> >>> On Jan 3, 2007, at 9:20 AM, Jane Lomax wrote: >>> >>>> Version with mine and Midori's changes (with track changes on)... >>>> >>>> jane >>>> >>>> >>>> >>>> On 2 Jan 2007, at 14:22, Midori Harris wrote: >>>> >>>>> Here's a version with some updates, and a few assignee corrections. >>>>> >>>>> m >>>>> >>>> >> > > From aji at ebi.ac.uk Thu Jan 4 02:31:25 2007 From: aji at ebi.ac.uk (Amelia Ireland) Date: Thu, 4 Jan 2007 10:31:25 +0000 Subject: Action Items from St Croix In-Reply-To: <65381A04-6BE4-4F19-B72A-C4214BA4E6F5@ebi.ac.uk> References: <65381A04-6BE4-4F19-B72A-C4214BA4E6F5@ebi.ac.uk> Message-ID: <1B6F2999-7A5D-435E-9518-6020870BAF82@ebi.ac.uk> On 3 Jan 2007, at 17:20, Jane Lomax wrote: > Version with mine and Midori's changes (with track changes on)... Made some further updates and changes (again, with track changes on). -------------- next part -------------- A non-text attachment was scrubbed... Name: StCroixActionItems_ai.doc Type: application/octet-stream Size: 39936 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20070104/cc19b996/attachment.obj -------------- next part -------------- -- 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 Thu Jan 4 02:32:07 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 4 Jan 2007 10:32:07 +0000 (GMT) Subject: Action Items from St Croix In-Reply-To: <64569D73-0260-4BC6-9AC1-BE78868A8881@berkeleybop.org> References: <65381A04-6BE4-4F19-B72A-C4214BA4E6F5@ebi.ac.uk> <64569D73-0260-4BC6-9AC1-BE78868A8881@berkeleybop.org> Message-ID: I can now confirm that itme #21 WILL be done by the meeting (I'm going to finish it tomorrow). m From r-chisholm at northwestern.edu Thu Jan 4 05:02:24 2007 From: r-chisholm at northwestern.edu (Chisholm, Rex FSM) Date: Thu, 4 Jan 2007 07:02:24 -0600 Subject: Action Items from St Croix In-Reply-To: References: Message-ID: Here are mine.. Rex -----Original Message----- From: owner-go-managers at genome.stanford.edu [mailto:owner-go-managers at genome.stanford.edu] On Behalf Of Suzanna Lewis Sent: Saturday, December 23, 2006 6:25 PM To: GO Managers List Cc: GO LIST Subject: Action Items from St Croix Hello from shaky California, I am on tap for summarizing the status on the action items from our previous meeting at our upcoming meeting. I am extremely grateful to Kimberly and Ranjana for the fantastic job they did on the minutes, and for that fact that we keep these in a central repository. Finding and assembling them was as easy as pie. I need help though because for many of them I just don't know what has happened since. I've guessed in a few places, but these were just guesses so no guarantees. In many cases no particular person was made responsible, so I've somewhat arbitrarily pick someone, but please anyone who has information should get back to me and let me know where things stand at the moment. I tried to organize them into 4 categories according to the following decision tree: 1. unknown status 2. known status 2.a done 2.a.i done and no follow-up required 2.a.ii done and follow-up needed (at upcoming meeting) 2.b not done Would everyone please look this over and get back to me with corrections, and completion status on the unknowns (there are a lot of these). It would be nice to have everything in the known category, even if the are known to be undone. Much appreciated, S -------------- next part -------------- A non-text attachment was scrubbed... Name: StCroixActionItems rex.doc Type: application/msword Size: 191488 bytes Desc: StCroixActionItems rex.doc Url : http://fafner.stanford.edu/pipermail/go/attachments/20070104/ae3c6132/attachment.doc From cjm at fruitfly.org Thu Jan 4 05:02:49 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Thu, 4 Jan 2007 13:02:49 +0000 Subject: Autogenerating map2slim mapping files? In-Reply-To: References: <8035FC86-761C-4C1A-80D8-FBF6DDE6D961@genome.stanford.edu> Message-ID: <61DB9F48-4EC6-4524-98ED-F5B65F30DA2D@fruitfly.org> On Jan 4, 2007, at 12:06 AM, Mary Dolan wrote: > Rama Balakrishnan on Wednesday, January > 03, 2007 at 6:10 PM -0500 wrote: >> Simon, >> To avoid having to install the perl modules etc, you can use the web >> interface available at Princeton University. It uses the map2slim >> script and you can use any GO slim/ gene_association file or input >> your GO slim. >> http://go.princeton.edu/cgi-bin/GOTermMapper >> >> Providing (by autogeneration) these mapping files on the GOC ftp site >> sounds like a good idea. At SGD, we have a web interface to do the >> mapping and we also provide a mapping file of the annotations on our >> FTP site, although we don't provide the mapping of the go terms to >> their go slims. >> Rama >> >> >> On Jan 3, 2007, at 1:46 PM, Twigger Simon wrote: >>> Hi there, >>> >>> Working with Larry Wall's definitions of Chief Virtues of a >>> Programmer, I'm exercising my 'Laziness' muscle here. >>> >>> Via the GOC we generate daily OBO files and a whole bunch of 'Other >>> Useful Files' on the GO website so people can access the latest >>> terms and annotations. What I find Im also in need of quite >>> frequently are GO Slim versions of the annotations using the >>> Generic GO Slim along with the mapping of the current GO terms to >>> their respective GO Slim terms. Certainly it is possible to >>> download and install the various perl modules and run the map2slim >>> script, etc. to derive these files from the raw data but is there >>> any merit to autogenerating these and adding them to the 'other >>> useful files' so people dont have to install all the perl code to >>> run this manually? >>> >>> Speaking for myself, the mapping file would be spectacular to have >>> available so I could automatically FTP it over and crank through >>> current annotations to get the appropriate GO Slim versions. It >>> might get a bit unwieldy to run all annotation files against all >>> standard GO Slims on the site but if we could generate one mapping >>> file for each Maintained GO Slim that would just be four new files >>> that anyone could then use to convert GO annotations to their >>> respective Slimmed version. >>> >>> Would anyone else find this useful or is it just me being lazy >>> (remembering that Laziness is a Virtue). :) >>> >>> Simon. >> > Hi, Simon and Rama. >> > Because the MGI GO_Slim set ( http://proto.informatics.jax.org/ > prototypes/GOTools/web-docs/MGI_GO_Slim.html ) is defined using > unions and disjunctions of GO terms, (as far as I know) it cannot > currently be used with the standard tools (e.g. > map2slim script). Therefore, we provide a regularly updated file to > map GO_ids to MGI GO_Slim category. > http://proto.informatics.jax.org/prototypes/GOTools/web-docs/ > map2MGIslim.txt Simon - can you give more background on why you need the annotation files mapped to the generic slim? This could in principle be pre-computed, but I'm not sure we want to be encouraging use of pre-slimmed annotation files. Mary - this is interesting, I wasn't aware that MGI were using slims that included disjunctions and negations. In fact it is possible to express disjunctions in obo-format. It may be an idea to express your slims in this way to make them maximally interoperable (this way future versions of map2slim and other more advanced tools can make use of these). You can't express negation in obo-format, but that's ok because you only use this for 'other' categories which can be generated automatically For example, for this: ER/Golgi: endoplasmic reticulum OR ER-Golgi intermediate compartment OR Golgi apparatus OR transport vesicle OR Golgi vesicle OR sarcoplasmic reticulum You can specify the following in your obo file: union_of: GO:0005783 !endoplasmic reticulum union_of: GO:0005793 !ER-Golgi intermediate compartment union_of: GO:0005794 !Golgi apparatus union_of: GO:0030133 !transport vesicle union_of: GO:0005798 !Golgi vesicle union_of: GO:0016529 !sarcoplasmic reticulum (Of course, I am fundamentally against 'other' categories in the main ontology, I am absolutely fine with having them at the application level via a slim). > Mary > > Mary E. Dolan, Ph.D. > ************************************ > Mouse Genome Informatics Consortium, The Jackson Laboratory > mdolan at informatics.jax.org > (207)288-6439 > > Research Faculty, NCGIA > Department of Spatial Information Science and Engineering, > University of Maine > Boardman Hall 329 > University of Maine > Orono, Maine 04469 > fax: 207.581.2206 > mary_dolan at umit.maine.edu > ************************************ > > From jane at ebi.ac.uk Thu Jan 4 07:06:54 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Thu, 4 Jan 2007 15:06:54 +0000 (GMT) Subject: Autogenerating map2slim mapping files? In-Reply-To: <61DB9F48-4EC6-4524-98ED-F5B65F30DA2D@fruitfly.org> References: <8035FC86-761C-4C1A-80D8-FBF6DDE6D961@genome.stanford.edu> <61DB9F48-4EC6-4524-98ED-F5B65F30DA2D@fruitfly.org> Message-ID: I think GOA already provide a 'pre-slimmed' annotation file from their website, so there's obviously some demand for it. Is that right Evelyn/Emily? Jane On Thu, 4 Jan 2007, Chris Mungall wrote: > > On Jan 4, 2007, at 12:06 AM, Mary Dolan wrote: > >> Rama Balakrishnan on Wednesday, January 03, 2007 >> at 6:10 PM -0500 wrote: >>> Simon, >>> To avoid having to install the perl modules etc, you can use the web >>> interface available at Princeton University. It uses the map2slim >>> script and you can use any GO slim/ gene_association file or input >>> your GO slim. >>> http://go.princeton.edu/cgi-bin/GOTermMapper >>> >>> Providing (by autogeneration) these mapping files on the GOC ftp site >>> sounds like a good idea. At SGD, we have a web interface to do the >>> mapping and we also provide a mapping file of the annotations on our >>> FTP site, although we don't provide the mapping of the go terms to >>> their go slims. >>> Rama >>> >>> >>> On Jan 3, 2007, at 1:46 PM, Twigger Simon wrote: >>>> Hi there, >>>> >>>> Working with Larry Wall's definitions of Chief Virtues of a >>>> Programmer, I'm exercising my 'Laziness' muscle here. >>>> >>>> Via the GOC we generate daily OBO files and a whole bunch of 'Other >>>> Useful Files' on the GO website so people can access the latest >>>> terms and annotations. What I find Im also in need of quite >>>> frequently are GO Slim versions of the annotations using the >>>> Generic GO Slim along with the mapping of the current GO terms to >>>> their respective GO Slim terms. Certainly it is possible to >>>> download and install the various perl modules and run the map2slim >>>> script, etc. to derive these files from the raw data but is there >>>> any merit to autogenerating these and adding them to the 'other >>>> useful files' so people dont have to install all the perl code to >>>> run this manually? >>>> >>>> Speaking for myself, the mapping file would be spectacular to have >>>> available so I could automatically FTP it over and crank through >>>> current annotations to get the appropriate GO Slim versions. It >>>> might get a bit unwieldy to run all annotation files against all >>>> standard GO Slims on the site but if we could generate one mapping >>>> file for each Maintained GO Slim that would just be four new files >>>> that anyone could then use to convert GO annotations to their >>>> respective Slimmed version. >>>> >>>> Would anyone else find this useful or is it just me being lazy >>>> (remembering that Laziness is a Virtue). :) >>>> >>>> Simon. >>> >> Hi, Simon and Rama. >>> >> Because the MGI GO_Slim set ( >> http://proto.informatics.jax.org/prototypes/GOTools/web-docs/MGI_GO_Slim.html >> ) is defined using unions and disjunctions of GO terms, (as far as I know) >> it cannot currently be used with the standard tools (e.g. >> map2slim script). Therefore, we provide a regularly updated file to map >> GO_ids to MGI GO_Slim category. >> http://proto.informatics.jax.org/prototypes/GOTools/web-docs/map2MGIslim.txt > > Simon - can you give more background on why you need the annotation files > mapped to the generic slim? > > This could in principle be pre-computed, but I'm not sure we want to be > encouraging use of pre-slimmed annotation files. > > Mary - this is interesting, I wasn't aware that MGI were using slims that > included disjunctions and negations. In fact it is possible to express > disjunctions in obo-format. It may be an idea to express your slims in this > way to make them maximally interoperable (this way future versions of > map2slim and other more advanced tools can make use of these). > > You can't express negation in obo-format, but that's ok because you only use > this for 'other' categories which can be generated automatically > > For example, for this: > ER/Golgi: endoplasmic reticulum OR ER-Golgi intermediate compartment OR Golgi > apparatus OR transport vesicle OR Golgi vesicle OR sarcoplasmic reticulum > > You can specify the following in your obo file: > > union_of: GO:0005783 !endoplasmic reticulum > union_of: GO:0005793 !ER-Golgi intermediate compartment > union_of: GO:0005794 !Golgi apparatus > union_of: GO:0030133 !transport vesicle > union_of: GO:0005798 !Golgi vesicle > union_of: GO:0016529 !sarcoplasmic reticulum > > (Of course, I am fundamentally against 'other' categories in the main > ontology, I am absolutely fine with having them at the application level via > a slim). > >> Mary >> >> Mary E. Dolan, Ph.D. >> ************************************ >> Mouse Genome Informatics Consortium, The Jackson Laboratory >> mdolan at informatics.jax.org >> (207)288-6439 >> >> Research Faculty, NCGIA >> Department of Spatial Information Science and Engineering, University of >> Maine >> Boardman Hall 329 >> University of Maine >> Orono, Maine 04469 >> fax: 207.581.2206 >> mary_dolan at umit.maine.edu >> ************************************ >> > -- 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 edimmer at ebi.ac.uk Thu Jan 4 07:16:39 2007 From: edimmer at ebi.ac.uk (Emily Dimmer) Date: Thu, 04 Jan 2007 15:16:39 +0000 Subject: Autogenerating map2slim mapping files? In-Reply-To: References: <8035FC86-761C-4C1A-80D8-FBF6DDE6D961@genome.stanford.edu> <61DB9F48-4EC6-4524-98ED-F5B65F30DA2D@fruitfly.org> Message-ID: <459D1A57.6090500@ebi.ac.uk> Hi, Yes, there is a GO slim available from our GOA ftp site that is supplied alongside a corresponding gene association file, where the annotations provided in the UniProt gene association file are instead mapped to the GO slim terms. At the moment this is a very short slim (with 79 terms), however we are thinking of perhaps changing this to the larger generic GO slim (which uses about 150 GO terms), so that it will probably cover more categories of interest to users. All the files are available from: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/goslim/ I should also say that all annotations which have the qualifier 'NOT' have been stripped out of this 'GO slim gene association file'. Emily Jane Lomax wrote: > I think GOA already provide a 'pre-slimmed' annotation file from their > website, so there's obviously some demand for it. > > Is that right Evelyn/Emily? > > Jane > > > On Thu, 4 Jan 2007, Chris Mungall wrote: > >> >> On Jan 4, 2007, at 12:06 AM, Mary Dolan wrote: >> >>> Rama Balakrishnan on Wednesday, January >>> 03, 2007 at 6:10 PM -0500 wrote: >>> >>>> Simon, >>>> To avoid having to install the perl modules etc, you can use the web >>>> interface available at Princeton University. It uses the map2slim >>>> script and you can use any GO slim/ gene_association file or input >>>> your GO slim. >>>> http://go.princeton.edu/cgi-bin/GOTermMapper >>>> >>>> Providing (by autogeneration) these mapping files on the GOC ftp site >>>> sounds like a good idea. At SGD, we have a web interface to do the >>>> mapping and we also provide a mapping file of the annotations on our >>>> FTP site, although we don't provide the mapping of the go terms to >>>> their go slims. >>>> Rama >>>> >>>> >>>> On Jan 3, 2007, at 1:46 PM, Twigger Simon wrote: >>>> >>>>> Hi there, >>>>> >>>>> Working with Larry Wall's definitions of Chief Virtues of a >>>>> Programmer, I'm exercising my 'Laziness' muscle here. >>>>> >>>>> Via the GOC we generate daily OBO files and a whole bunch of 'Other >>>>> Useful Files' on the GO website so people can access the latest >>>>> terms and annotations. What I find Im also in need of quite >>>>> frequently are GO Slim versions of the annotations using the >>>>> Generic GO Slim along with the mapping of the current GO terms to >>>>> their respective GO Slim terms. Certainly it is possible to >>>>> download and install the various perl modules and run the map2slim >>>>> script, etc. to derive these files from the raw data but is there >>>>> any merit to autogenerating these and adding them to the 'other >>>>> useful files' so people dont have to install all the perl code to >>>>> run this manually? >>>>> >>>>> Speaking for myself, the mapping file would be spectacular to have >>>>> available so I could automatically FTP it over and crank through >>>>> current annotations to get the appropriate GO Slim versions. It >>>>> might get a bit unwieldy to run all annotation files against all >>>>> standard GO Slims on the site but if we could generate one mapping >>>>> file for each Maintained GO Slim that would just be four new files >>>>> that anyone could then use to convert GO annotations to their >>>>> respective Slimmed version. >>>>> >>>>> Would anyone else find this useful or is it just me being lazy >>>>> (remembering that Laziness is a Virtue). :) >>>>> >>>>> Simon. >>>> >>>> >>> Hi, Simon and Rama. >>> >>>> >>> Because the MGI GO_Slim set ( >>> http://proto.informatics.jax.org/prototypes/GOTools/web-docs/MGI_GO_Slim.html >>> ) is defined using unions and disjunctions of GO terms, (as far as I >>> know) it cannot currently be used with the standard tools (e.g. >>> map2slim script). Therefore, we provide a regularly updated file to >>> map GO_ids to MGI GO_Slim category. >>> http://proto.informatics.jax.org/prototypes/GOTools/web-docs/map2MGIslim.txt >>> >> >> >> Simon - can you give more background on why you need the annotation >> files mapped to the generic slim? >> >> This could in principle be pre-computed, but I'm not sure we want to >> be encouraging use of pre-slimmed annotation files. >> >> Mary - this is interesting, I wasn't aware that MGI were using slims >> that included disjunctions and negations. In fact it is possible to >> express disjunctions in obo-format. It may be an idea to express your >> slims in this way to make them maximally interoperable (this way >> future versions of map2slim and other more advanced tools can make >> use of these). >> >> You can't express negation in obo-format, but that's ok because you >> only use this for 'other' categories which can be generated >> automatically >> >> For example, for this: >> ER/Golgi: endoplasmic reticulum OR ER-Golgi intermediate compartment >> OR Golgi apparatus OR transport vesicle OR Golgi vesicle OR >> sarcoplasmic reticulum >> >> You can specify the following in your obo file: >> >> union_of: GO:0005783 !endoplasmic reticulum >> union_of: GO:0005793 !ER-Golgi intermediate compartment >> union_of: GO:0005794 !Golgi apparatus >> union_of: GO:0030133 !transport vesicle >> union_of: GO:0005798 !Golgi vesicle >> union_of: GO:0016529 !sarcoplasmic reticulum >> >> (Of course, I am fundamentally against 'other' categories in the main >> ontology, I am absolutely fine with having them at the application >> level via a slim). >> >>> Mary >>> >>> Mary E. Dolan, Ph.D. >>> ************************************ >>> Mouse Genome Informatics Consortium, The Jackson Laboratory >>> mdolan at informatics.jax.org >>> (207)288-6439 >>> >>> Research Faculty, NCGIA >>> Department of Spatial Information Science and Engineering, >>> University of Maine >>> Boardman Hall 329 >>> University of Maine >>> Orono, Maine 04469 >>> fax: 207.581.2206 >>> mary_dolan at umit.maine.edu >>> ************************************ >>> >> > -- ************************************ Emily Dimmer GOA and IntAct Database Curator 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 Mary_Dolan at umit.maine.edu Thu Jan 4 07:31:41 2007 From: Mary_Dolan at umit.maine.edu (Mary Dolan) Date: Thu, 04 Jan 2007 10:31:41 -0500 Subject: Autogenerating map2slim mapping files? In-Reply-To: <61DB9F48-4EC6-4524-98ED-F5B65F30DA2D@fruitfly.org> References: <61DB9F48-4EC6-4524-98ED-F5B65F30DA2D@fruitfly.org> Message-ID: Chris Mungall on Thursday, January 04, 2007 at 8:02 AM -0500 wrote: >Mary - this is interesting, I wasn't aware that MGI were using slims >that included disjunctions and negations. In fact it is possible to >express disjunctions in obo-format. It may be an idea to express your >slims in this way to make them maximally interoperable (this way >future versions of map2slim and other more advanced tools can make >use of these). > >You can't express negation in obo-format, but that's ok because you >only use this for 'other' categories which can be generated >automatically > >For example, for this: >ER/Golgi: endoplasmic reticulum OR ER-Golgi intermediate compartment >OR Golgi apparatus OR transport vesicle OR Golgi vesicle OR >sarcoplasmic reticulum > >You can specify the following in your obo file: > >union_of: GO:0005783 !endoplasmic reticulum >union_of: GO:0005793 !ER-Golgi intermediate compartment >union_of: GO:0005794 !Golgi apparatus >union_of: GO:0030133 !transport vesicle >union_of: GO:0005798 !Golgi vesicle >union_of: GO:0016529 !sarcoplasmic reticulum > >(Of course, I am fundamentally against 'other' categories in the main >ontology, I am absolutely fine with having them at the application >level via a slim). Hi, Chris. We do something like that to produce an old-format file that can be loaded into OBO-Edit for viewing purposes: http://proto.informatics.jax.org/prototypes/GOTools/web-docs/mgi_go_slim.go (I see that it is time to update since it still includes unknowns.) But I can try recasting it into a form as you describe and see if that works with the standard tools. Mary Mary E. Dolan, Ph.D. ************************************ Mouse Genome Informatics Consortium, The Jackson Laboratory mdolan at informatics.jax.org (207)288-6439 Research Faculty, NCGIA Department of Spatial Information Science and Engineering, University of Maine Boardman Hall 329 University of Maine Orono, Maine 04469 fax: 207.581.2206 mary_dolan at umit.maine.edu ************************************ From simont at hmgc.mcw.edu Thu Jan 4 07:49:35 2007 From: simont at hmgc.mcw.edu (Twigger Simon) Date: Thu, 4 Jan 2007 09:49:35 -0600 Subject: Autogenerating map2slim mapping files? In-Reply-To: <61DB9F48-4EC6-4524-98ED-F5B65F30DA2D@fruitfly.org> References: <8035FC86-761C-4C1A-80D8-FBF6DDE6D961@genome.stanford.edu> <61DB9F48-4EC6-4524-98ED-F5B65F30DA2D@fruitfly.org> Message-ID: Hi Chris, I building some annotation tools and have the full GO annotations already incorporated but for some summary data having the GO Slim terms also available would be really convenient. I could certainly do the map2slim myself but Im building the system using ruby and am trying to avoid tying in a bunch of perl dependencies if possible. From my perspective I dont think we need each gene association file available as a slimmed version, I would be happier with the mapping file that map2slim creates, showing the mapping between each term in the full ontology and its corresponding slim term. I can download this mapping at the same time as I download the ontology and gene_association files and then add in the slimmed data when I load the latest ontology and annotations. Rama - thanks for pointing out your script, I think that will be handy for some of our tools. A web page is not the best for what I need in this instance as I'm trying to do all this automatically in my code where possible. Simon. On Jan 4, 2007, at 7:02 AM, Chris Mungall wrote: > > Simon - can you give more background on why you need the annotation > files mapped to the generic slim? > > This could in principle be pre-computed, but I'm not sure we want > to be encouraging use of pre-slimmed annotation files. > > Mary - this is interesting, I wasn't aware that MGI were using > slims that included disjunctions and negations. In fact it is > possible to express disjunctions in obo-format. It may be an idea > to express your slims in this way to make them maximally > interoperable (this way future versions of map2slim and other more > advanced tools can make use of these). > > You can't express negation in obo-format, but that's ok because you > only use this for 'other' categories which can be generated > automatically > > For example, for this: > ER/Golgi: endoplasmic reticulum OR ER-Golgi intermediate > compartment OR Golgi apparatus OR transport vesicle OR Golgi > vesicle OR sarcoplasmic reticulum > > You can specify the following in your obo file: > > union_of: GO:0005783 !endoplasmic reticulum > union_of: GO:0005793 !ER-Golgi intermediate compartment > union_of: GO:0005794 !Golgi apparatus > union_of: GO:0030133 !transport vesicle > union_of: GO:0005798 !Golgi vesicle > union_of: GO:0016529 !sarcoplasmic reticulum > > (Of course, I am fundamentally against 'other' categories in the > main ontology, I am absolutely fine with having them at the > application level via a slim). > >> Mary >> >> Mary E. Dolan, Ph.D. >> ************************************ >> Mouse Genome Informatics Consortium, The Jackson Laboratory >> mdolan at informatics.jax.org >> (207)288-6439 >> >> Research Faculty, NCGIA >> Department of Spatial Information Science and Engineering, >> University of Maine >> Boardman Hall 329 >> University of Maine >> Orono, Maine 04469 >> fax: 207.581.2206 >> mary_dolan at umit.maine.edu >> ************************************ >> >> > From cjm at fruitfly.org Thu Jan 4 08:01:53 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Thu, 4 Jan 2007 16:01:53 +0000 Subject: Autogenerating map2slim mapping files? In-Reply-To: References: <8035FC86-761C-4C1A-80D8-FBF6DDE6D961@genome.stanford.edu> <61DB9F48-4EC6-4524-98ED-F5B65F30DA2D@fruitfly.org> Message-ID: <05E1DC0D-4479-4116-8773-053F9B26A7B0@fruitfly.org> On Jan 4, 2007, at 3:49 PM, Twigger Simon wrote: > Hi Chris, > > I building some annotation tools and have the full GO annotations > already incorporated but for some summary data having the GO Slim > terms also available would be really convenient. I could certainly > do the map2slim myself but Im building the system using ruby and am > trying to avoid tying in a bunch of perl dependencies if possible. > > From my perspective I dont think we need each gene association file > available as a slimmed version, I would be happier with the mapping > file that map2slim creates, showing the mapping between each term > in the full ontology and its corresponding slim term. I can > download this mapping at the same time as I download the ontology > and gene_association files and then add in the slimmed data when I > load the latest ontology and annotations. ah I see, so you want a file with mappings of GO IDs. OK, that makes lots of sense, I agree it would be very useful to provide each slim file as a 2-column mapping table > Rama - thanks for pointing out your script, I think that will be > handy for some of our tools. A web page is not the best for what I > need in this instance as I'm trying to do all this automatically in > my code where possible. > > Simon. > > > On Jan 4, 2007, at 7:02 AM, Chris Mungall wrote: > > >> >> Simon - can you give more background on why you need the >> annotation files mapped to the generic slim? >> >> This could in principle be pre-computed, but I'm not sure we want >> to be encouraging use of pre-slimmed annotation files. >> >> Mary - this is interesting, I wasn't aware that MGI were using >> slims that included disjunctions and negations. In fact it is >> possible to express disjunctions in obo-format. It may be an idea >> to express your slims in this way to make them maximally >> interoperable (this way future versions of map2slim and other more >> advanced tools can make use of these). >> >> You can't express negation in obo-format, but that's ok because >> you only use this for 'other' categories which can be generated >> automatically >> >> For example, for this: >> ER/Golgi: endoplasmic reticulum OR ER-Golgi intermediate >> compartment OR Golgi apparatus OR transport vesicle OR Golgi >> vesicle OR sarcoplasmic reticulum >> >> You can specify the following in your obo file: >> >> union_of: GO:0005783 !endoplasmic reticulum >> union_of: GO:0005793 !ER-Golgi intermediate compartment >> union_of: GO:0005794 !Golgi apparatus >> union_of: GO:0030133 !transport vesicle >> union_of: GO:0005798 !Golgi vesicle >> union_of: GO:0016529 !sarcoplasmic reticulum >> >> (Of course, I am fundamentally against 'other' categories in the >> main ontology, I am absolutely fine with having them at the >> application level via a slim). >> >>> Mary >>> >>> Mary E. Dolan, Ph.D. >>> ************************************ >>> Mouse Genome Informatics Consortium, The Jackson Laboratory >>> mdolan at informatics.jax.org >>> (207)288-6439 >>> >>> Research Faculty, NCGIA >>> Department of Spatial Information Science and Engineering, >>> University of Maine >>> Boardman Hall 329 >>> University of Maine >>> Orono, Maine 04469 >>> fax: 207.581.2206 >>> mary_dolan at umit.maine.edu >>> ************************************ >>> >>> >> > > From cjm at fruitfly.org Thu Jan 4 08:07:33 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Thu, 4 Jan 2007 16:07:33 +0000 Subject: Autogenerating map2slim mapping files? In-Reply-To: References: <61DB9F48-4EC6-4524-98ED-F5B65F30DA2D@fruitfly.org> Message-ID: <460F7879-AC33-4154-BFE4-FE2F5A4DE456@fruitfly.org> On Jan 4, 2007, at 3:31 PM, Mary Dolan wrote: > Chris Mungall on Thursday, January 04, 2007 at > 8:02 AM -0500 wrote: >> Mary - this is interesting, I wasn't aware that MGI were using slims >> that included disjunctions and negations. In fact it is possible to >> express disjunctions in obo-format. It may be an idea to express your >> slims in this way to make them maximally interoperable (this way >> future versions of map2slim and other more advanced tools can make >> use of these). >> >> You can't express negation in obo-format, but that's ok because you >> only use this for 'other' categories which can be generated >> automatically >> >> For example, for this: >> ER/Golgi: endoplasmic reticulum OR ER-Golgi intermediate compartment >> OR Golgi apparatus OR transport vesicle OR Golgi vesicle OR >> sarcoplasmic reticulum >> >> You can specify the following in your obo file: >> >> union_of: GO:0005783 !endoplasmic reticulum >> union_of: GO:0005793 !ER-Golgi intermediate compartment >> union_of: GO:0005794 !Golgi apparatus >> union_of: GO:0030133 !transport vesicle >> union_of: GO:0005798 !Golgi vesicle >> union_of: GO:0016529 !sarcoplasmic reticulum >> >> (Of course, I am fundamentally against 'other' categories in the main >> ontology, I am absolutely fine with having them at the application >> level via a slim). > > Hi, Chris. > We do something like that to produce an old-format file that can be > loaded into OBO-Edit for viewing purposes: > http://proto.informatics.jax.org/prototypes/GOTools/web-docs/ > mgi_go_slim.go > (I see that it is time to update since it still includes unknowns.) > > But I can try recasting it into a form as you describe and see if > that works with the standard tools. If this slim is only used internally at MGI then this probably isn't a high priority. Actually the simplest thing to do is probably to make it available as a mapping table, as Simon suggests > Mary > > Mary E. Dolan, Ph.D. > ************************************ > Mouse Genome Informatics Consortium, The Jackson Laboratory > mdolan at informatics.jax.org > (207)288-6439 > > Research Faculty, NCGIA > Department of Spatial Information Science and Engineering, > University of Maine > Boardman Hall 329 > University of Maine > Orono, Maine 04469 > fax: 207.581.2206 > mary_dolan at umit.maine.edu > ************************************ > > From Mary_Dolan at umit.maine.edu Thu Jan 4 08:16:27 2007 From: Mary_Dolan at umit.maine.edu (Mary Dolan) Date: Thu, 04 Jan 2007 11:16:27 -0500 Subject: Autogenerating map2slim mapping files? In-Reply-To: <460F7879-AC33-4154-BFE4-FE2F5A4DE456@fruitfly.org> References: <460F7879-AC33-4154-BFE4-FE2F5A4DE456@fruitfly.org> Message-ID: Chris Mungall on Thursday, January 04, 2007 at 11:07 AM -0500 wrote: >If this slim is only used internally at MGI then this probably isn't >a high priority. > >Actually the simplest thing to do is probably to make it available as >a mapping table, as Simon suggests > That mapping is currently available as a 4-column tab-delimited text file with GO_id, GO_term, MGI_GOSlim_category, GO_aspect: http://proto.informatics.jax.org/prototypes/GOTools/web-docs/map2MGIslim.txt I can also post a two-column table. Mary Mary E. Dolan, Ph.D. ************************************ Mouse Genome Informatics Consortium, The Jackson Laboratory mdolan at informatics.jax.org (207)288-6439 Research Faculty, NCGIA Department of Spatial Information Science and Engineering, University of Maine Boardman Hall 329 University of Maine Orono, Maine 04469 fax: 207.581.2206 mary_dolan at umit.maine.edu ************************************ From cjm at fruitfly.org Thu Jan 4 08:33:28 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Thu, 4 Jan 2007 16:33:28 +0000 Subject: Autogenerating map2slim mapping files? In-Reply-To: References: <460F7879-AC33-4154-BFE4-FE2F5A4DE456@fruitfly.org> Message-ID: On Jan 4, 2007, at 4:16 PM, Mary Dolan wrote: > Chris Mungall on Thursday, January 04, 2007 at > 11:07 AM -0500 wrote: >> If this slim is only used internally at MGI then this probably isn't >> a high priority. >> >> Actually the simplest thing to do is probably to make it available as >> a mapping table, as Simon suggests >> > That mapping is currently available as a 4-column tab-delimited > text file with GO_id, GO_term, MGI_GOSlim_category, GO_aspect: > http://proto.informatics.jax.org/prototypes/GOTools/web-docs/ > map2MGIslim.txt > I can also post a two-column table. OK, my brain is only just waking up after the holidays... of course, for slims that effectively create new bins that correspond to disjunctions of GO IDs, a 2-column mapping file isn't sufficient in itself, as it doesn't give the DAG placement of the extra binning terms (but it's still useful though). So, we should probably standardise both: a 2-column ID mapping file for most slims (additional columns giving the names could be optional). This file plus the reference ontology should be sufficient for most applications if the slim doesn't introduce new binning terms. use of obo-format for expressing disjunctions of terms in slims; but this is only a priority if there is demand for this outside MGI > Mary > > Mary E. Dolan, Ph.D. > ************************************ > Mouse Genome Informatics Consortium, The Jackson Laboratory > mdolan at informatics.jax.org > (207)288-6439 > > Research Faculty, NCGIA > Department of Spatial Information Science and Engineering, > University of Maine > Boardman Hall 329 > University of Maine > Orono, Maine 04469 > fax: 207.581.2206 > mary_dolan at umit.maine.edu > ************************************ > > From suzi at berkeleybop.org Thu Jan 4 21:38:07 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Thu, 4 Jan 2007 21:38:07 -0800 Subject: Action Items from St Croix In-Reply-To: References: <65381A04-6BE4-4F19-B72A-C4214BA4E6F5@ebi.ac.uk> <64569D73-0260-4BC6-9AC1-BE78868A8881@berkeleybop.org> Message-ID: <54F4DDCF-6771-49A4-9888-259ED451A5CB@berkeleybop.org> hip, hip hooray! i love moving things to the done list. On Jan 4, 2007, at 2:32 AM, Midori Harris wrote: > I can now confirm that itme #21 WILL be done by the meeting (I'm > going to finish it tomorrow). > > m > > From suzi at berkeleybop.org Thu Jan 4 22:20:41 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Thu, 4 Jan 2007 22:20:41 -0800 Subject: Action Items from St Croix TO PRINT In-Reply-To: <459D187E.2020701@ebi.ac.uk> References: <459D187E.2020701@ebi.ac.uk> Message-ID: <79F3600C-2D09-46F9-AC34-AF7EBAF06563@berkeleybop.org> Hi Ev & Val, Would you please make copies for everyone. I'm sure there are still some mistakes, but we'll sort that when we all talk on Monday. Got up to 20 done! (half of them), although I suppose that does mean that the other half are not done. But most of these are in the works, only a few have stalled. -S -------------- next part -------------- A non-text attachment was scrubbed... Name: StCroixActionItems_v2.doc Type: application/octet-stream Size: 45568 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20070104/2ca654b1/attachment.obj -------------- next part -------------- On Jan 4, 2007, at 7:08 AM, Evelyn Camon wrote: > Hi Judy, > > Jesus College start breakfast at 8am..so I don't think 8.15am is a > fair start time for the meeting.. Liz has added 8.30 would that > work on the monday... > > cheers, > > Evelyn > -- > Evelyn Camon > GOA Coordinator > Senior Scientific Curator > European Bioinformatics Institute > Tel:01223-494465 > Fax:01223-494468 > E-mail: camon at ebi.ac.uk > URL: http://www.ebi.ac.uk/goa > > From suzi at berkeleybop.org Thu Jan 4 22:23:35 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Thu, 4 Jan 2007 22:23:35 -0800 Subject: Action Items from St Croix In-Reply-To: <1B6F2999-7A5D-435E-9518-6020870BAF82@ebi.ac.uk> References: <65381A04-6BE4-4F19-B72A-C4214BA4E6F5@ebi.ac.uk> <1B6F2999-7A5D-435E-9518-6020870BAF82@ebi.ac.uk> Message-ID: <13288B44-3614-4F47-856C-ECB869FF2497@berkeleybop.org> BTW, thanks to everyone who got back to me on this! (and the rest of you know who you are ;-) -S From camon at ebi.ac.uk Fri Jan 5 03:06:56 2007 From: camon at ebi.ac.uk (Evelyn Camon) Date: Fri, 05 Jan 2007 11:06:56 +0000 Subject: Jesus Colllege Message-ID: <459E3150.4010800@ebi.ac.uk> Hi, For those attending the GOC meeting here is the url. http://conference.jesus.cam.ac.uk/ From this link you will find a map of the grounds. http://conference.jesus.cam.ac.uk/maps/College.pdf We believe the porters lodge will give you these maps on arrival but some of you (UK members) have already asked for this info. The meeting will be held in the Upper Hall. cheers, Evelyn and Val -- Evelyn Camon GOA Coordinator Senior Scientific Curator European Bioinformatics Institute Tel:01223-494465 Fax:01223-494468 E-mail: camon at ebi.ac.uk URL: http://www.ebi.ac.uk/goa From midori at ebi.ac.uk Fri Jan 5 08:01:13 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 5 Jan 2007 16:01:13 +0000 (GMT) Subject: actin polymerization (Re: Action Items from St Croix) In-Reply-To: <13288B44-3614-4F47-856C-ECB869FF2497@berkeleybop.org> References: <65381A04-6BE4-4F19-B72A-C4214BA4E6F5@ebi.ac.uk> <1B6F2999-7A5D-435E-9518-6020870BAF82@ebi.ac.uk> <13288B44-3614-4F47-856C-ECB869FF2497@berkeleybop.org> Message-ID: A quick question about this item: action item: make actin polymerization a function term Do we want to replace the process terms (i.e. make them obsolete), or have function terms in addition? The process terms encompass regulation (either way, the regulation terms would stay in the process ontology). thanks, m existing process terms: [Term] id: GO:0008154 name: actin polymerization and/or depolymerization namespace: biological_process def: "Assembly or disassembly of actin filaments by the addition or removal of actin monomers from a filament." [GOC:mah] is_a: GO:0030036 ! actin cytoskeleton organization and biogenesis is_a: GO:0044260 ! cellular macromolecule metabolic process [Term] id: GO:0030041 name: actin filament polymerization namespace: biological_process def: "Assembly of actin filaments by the addition of actin monomers to a filament." [GOC:mah] synonym: "actin polymerizing activity" RELATED [] is_a: GO:0008154 ! actin polymerization and/or depolymerization is_a: GO:0051258 ! protein polymerization [Term] id: GO:0030042 name: actin filament depolymerization namespace: biological_process def: "Disassembly of actin filaments by the removal of actin monomers from a filament." [GOC:mah] synonym: "actin depolymerization" EXACT [] synonym: "actin depolymerizing activity" RELATED [] is_a: GO:0008154 ! actin polymerization and/or depolymerization is_a: GO:0051261 ! protein depolymerization From val at sanger.ac.uk Fri Jan 5 09:22:09 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Fri, 05 Jan 2007 17:22:09 +0000 Subject: actin polymerization (Re: Action Items from St Croix) In-Reply-To: References: <65381A04-6BE4-4F19-B72A-C4214BA4E6F5@ebi.ac.uk> <1B6F2999-7A5D-435E-9518-6020870BAF82@ebi.ac.uk> <13288B44-3614-4F47-856C-ECB869FF2497@berkeleybop.org> Message-ID: <459E8941.4070704@sanger.ac.uk> I would say we need to keep the process terms. I have 11 gene products annotated to "actin filament polymerization" but I would not annotatate them all to the function term 'actin polymerization' (i.e via the child term sequstering of actin monomers....perhaps sequestering is also a function though?). In this case can we also have a function term for actin capping, severing and cross-linking (these were previously vetoed). Is this on SF? Val Midori Harris wrote: > A quick question about this item: > > action item: make actin polymerization a function term > > Do we want to replace the process terms (i.e. make them obsolete), or > have function terms in addition? The process terms encompass > regulation (either way, the regulation terms would stay in the process > ontology). > > thanks, > m > > existing process terms: > > [Term] > id: GO:0008154 > name: actin polymerization and/or depolymerization > namespace: biological_process > def: "Assembly or disassembly of actin filaments by the addition or > removal of actin monomers from a filament." [GOC:mah] > is_a: GO:0030036 ! actin cytoskeleton organization and biogenesis > is_a: GO:0044260 ! cellular macromolecule metabolic process > > [Term] > id: GO:0030041 > name: actin filament polymerization > namespace: biological_process > def: "Assembly of actin filaments by the addition of actin monomers to > a filament." [GOC:mah] > synonym: "actin polymerizing activity" RELATED [] > is_a: GO:0008154 ! actin polymerization and/or depolymerization > is_a: GO:0051258 ! protein polymerization > > [Term] > id: GO:0030042 > name: actin filament depolymerization > namespace: biological_process > def: "Disassembly of actin filaments by the removal of actin monomers > from a filament." [GOC:mah] > synonym: "actin depolymerization" EXACT [] > synonym: "actin depolymerizing activity" RELATED [] > is_a: GO:0008154 ! actin polymerization and/or depolymerization > is_a: GO:0051261 ! protein depolymerization > > -- --------------------------------------------------------------------------- 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 john.richter at aya.yale.edu Fri Jan 5 11:22:23 2007 From: john.richter at aya.yale.edu (John Day-Richter) Date: Fri, 05 Jan 2007 12:22:23 -0700 Subject: OBO-Edit 2.0 Development Roadmap Message-ID: <459EA56F.1050806@aya.yale.edu> In case anyone is interested, I've posted a development roadmap for OBO-Edit 2.0 (OBO-Edit 1.1 is a mutated mouse whisker away from release) on the OBO-Edit developers Wiki: http://wiki.geneontology.org/index.php/OBO-Edit_2.0_Development_Roadmap This is a general overview of big, system-wide moves. This doesn't discuss self-contained feature requests. I'm interested in any comments, corrections, or additions you'd like to make! -John From hjd at informatics.jax.org Fri Jan 5 11:25:41 2007 From: hjd at informatics.jax.org (Harold Drabkin) Date: Fri, 05 Jan 2007 14:25:41 -0500 Subject: OBO-Edit 2.0 Development Roadmap In-Reply-To: <459EA56F.1050806@aya.yale.edu> References: <459EA56F.1050806@aya.yale.edu> Message-ID: <459EA635.10907@informatics.jax.org> John Day-Richter wrote: > In case anyone is interested, I've posted a development roadmap for > OBO-Edit 2.0 (OBO-Edit 1.1 is a mutated mouse whisker away from release) HEY! watch it!..............................^^^^^ > on the OBO-Edit developers Wiki: > > > http://wiki.geneontology.org/index.php/OBO-Edit_2.0_Development_Roadmap > > This is a general overview of big, system-wide moves. This doesn't > discuss self-contained feature requests. > > I'm interested in any comments, corrections, or additions you'd like to > make! > > -John > From aji at ebi.ac.uk Fri Jan 5 15:28:45 2007 From: aji at ebi.ac.uk (Amelia Ireland) Date: Fri, 5 Jan 2007 23:28:45 +0000 (GMT) Subject: GOC Meeting documents and downloads Message-ID: Hello all, The GO consortium meeting page on the wiki has been updated with links to documents pertinent to the upcoming meeting. Please see http://gocwiki.geneontology.org/index.php/GO_Consortium_Meeting The progress reports from each group are available on the GO website at http://www.geneontology.org/meeting/minutes/20070108_Progress-Reports/ if you want to download some reading material for the plane journey! If you have a progress report to submit, please cc it to me and I can put it up on the website before the meeting. Have a safe trip and see you all on Sunday! Amelia. PS: On a green note, to help reduce GO's carbon footprint you might like to offset your carbon dioxide emissions for the trip; try http://carbonfund.org/site/pages/how_help/category/Tag%20Your%20Flight/ (US) , http://www.co2.org/ (UK) or http://www.ecobusinesslinks.com/carbon_offset_wind_credits_carbon_reduction.htm (list) to compensate for your GOC meeting emissions. :) From midori at ebi.ac.uk Mon Jan 8 07:20:09 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Mon, 8 Jan 2007 15:20:09 +0000 (GMT) Subject: GO photos (fwd) Message-ID: type "geneontology" into the 'Pass Phrase' box (leave the 'Search Files' box blank) ---------- Forwarded message ---------- Date: Mon, 8 Jan 2007 13:47:47 +0000 (GMT) From: Tim Rayner To: Midori Harris Subject: GO photos Well, the best of the bunch (I think) are now here: http://www.ebi.ac.uk/systems-srv/mp/file-exchange/ ...use "geneontology" as the pass phrase to find them. Neither is going to win any awards, I'm afraid. The darker exposure looks best on my screen here, but I've put in the lighter exposure as well, in case that reproduces better in certain cases. T From ranjana at its.caltech.edu Mon Jan 8 17:11:20 2007 From: ranjana at its.caltech.edu (Ranjana Kishore) Date: Mon, 08 Jan 2007 17:11:20 -0800 Subject: which ontology file do we work with? Message-ID: <45A2EBB8.4070001@its.caltech.edu> Hello All, Maybe I missed this on the e-mails, but is it now advised that we all work with 'gene_ontology_edit.obo' instead of 'gene_ontology.obo'. This means we (and am sure other groups too?) have to change several of our scripts. This came to my attention when I uploaded the new gene_association file and was alerted to a 1000+ errors being stripped out by the GOC checking script. A quick diff between the script that we downloaded recently (because we run in-house error-checking) and the current one on the ftp site showed that the filter-gene-association.pl script uses the gene_ontology_edit.obo. While this might not be the reason for all of our errors, I am guessing this contributes to most (especially after all the 'is_a complete project for BP) of our stripped errors. Along these lines, maybe it would be a good idea to alert groups when there are changes to the 'filter-gene-association.pl' script that affects gene_association files, and to give groups time to adjust to the new changes. Sorry if all this was decided (though I did not really find one e-mail that talks about this) and I somehow missed it! Cheers Ranjana WormBase From cherry at genome.Stanford.EDU Tue Jan 9 01:17:40 2007 From: cherry at genome.Stanford.EDU (Mike Cherry) Date: Tue, 9 Jan 2007 01:17:40 -0800 (PST) Subject: which ontology file do we work with? In-Reply-To: <45A2EBB8.4070001@its.caltech.edu> References: <45A2EBB8.4070001@its.caltech.edu> Message-ID: Ranjana, The gene_ontology_edit.obo file is the file that should be edited. The two files are different versions of the OBO format. The gene_ontology.obo file is v1.0 and is no long the primary source of the ontologies, that is now the gene_ontology_edit.obo file, v1.2. The gene_ontology.obo file is rebuilt nightly from the gene_ontology_edit.obo file. So if you are just grabbing the current term names and IDs using the gene_ontology.obo should be fine. I believe using the gene_ontology.obo file should not cause the problem you mention. The filtering script does use the v1.2 file. The change to using v1.2 file was well announced and included in the newsletter in September. It appears the ontology changes that are causing the errors happened on December 21, 2006. It seems there are only six GOIDs that changed: 1283 GO:0007582 GO:0008150 17 GO:0007046 GO:0042254 11 GO:0002217 GO:0006952 9 GO:0006445 GO:0006417 5 GO:0016478 GO:0017148 1 GO:0043037 GO:0006412 above first column is number of changes needed, second is secondary GOID and third column is current GOID. -Mike On Mon, 8 Jan 2007, Ranjana Kishore wrote: > Hello All, > Maybe I missed this on the e-mails, but is it now advised that we all work > with 'gene_ontology_edit.obo' instead of 'gene_ontology.obo'. > > This means we (and am sure other groups too?) have to change several of our > scripts. This came to my attention when I uploaded the new gene_association > file and was alerted to a 1000+ errors being stripped out by the GOC checking > script. A quick diff between the script that we downloaded recently (because > we run in-house error-checking) and the current one on the ftp site showed > that the filter-gene-association.pl script uses the gene_ontology_edit.obo. > While this might not be the reason for all of our errors, I am guessing this > contributes to most (especially after all the 'is_a complete project for BP) > of our stripped errors. > > Along these lines, maybe it would be a good idea to alert groups when there > are changes to the 'filter-gene-association.pl' script that affects > gene_association files, and to give groups time to adjust to the new changes. > > Sorry if all this was decided (though I did not really find one e-mail that > talks about this) and I somehow missed it! > > Cheers > Ranjana > WormBase > From midori at ebi.ac.uk Tue Jan 9 08:00:51 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 9 Jan 2007 16:00:51 UT Subject: SourceForge Update Message-ID: <200701091600.l09G0p31366158@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20070109/a03e3897/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20070109/a03e3897/attachment.pl From val at sanger.ac.uk Tue Jan 9 08:24:09 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Tue, 9 Jan 2007 16:24:09 UT Subject: Fwd: Campus Signalling Day - February 2 Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20070109/154a4927/attachment.pl From val at sanger.ac.uk Wed Jan 10 06:24:15 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 10 Jan 2007 14:24:15 +0000 Subject: power book adaptor with US plug, left behind Message-ID: <45A4F70F.7090907@sanger.ac.uk> I now have it with me in Hinxton, but I can pass it to the OBO edit workshop if it belongs back in Cambridge. Also a single US adaptor. Val From midori at ebi.ac.uk Wed Jan 10 08:01:06 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 10 Jan 2007 16:01:06 UT Subject: SourceForge Update Message-ID: <200701101601.l0AG16R1427058@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20070110/38859dd3/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20070110/38859dd3/attachment.pl From jane at ebi.ac.uk Thu Jan 11 02:16:01 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Thu, 11 Jan 2007 10:16:01 +0000 (GMT) Subject: which ontology file do we work with? In-Reply-To: References: <45A2EBB8.4070001@its.caltech.edu> Message-ID: Hi Mike - what's the problem with these terms? Are they now fixed or do we need to do something? thanks! Jane On Tue, 9 Jan 2007, Mike Cherry wrote: > Ranjana, > > The gene_ontology_edit.obo file is the file that should be edited. > The two files are different versions of the OBO format. The > gene_ontology.obo file is v1.0 and is no long the primary source of > the ontologies, that is now the gene_ontology_edit.obo file, v1.2. > The gene_ontology.obo file is rebuilt nightly from the > gene_ontology_edit.obo file. So if you are just grabbing the current > term names and IDs using the gene_ontology.obo should be fine. I > believe using the gene_ontology.obo file should not cause the problem > you mention. > > The filtering script does use the v1.2 file. The change to using v1.2 > file was well announced and included in the newsletter in September. > > It appears the ontology changes that are causing the errors happened on > December 21, 2006. It seems there are only six GOIDs that changed: > > 1283 GO:0007582 GO:0008150 > 17 GO:0007046 GO:0042254 > 11 GO:0002217 GO:0006952 > 9 GO:0006445 GO:0006417 > 5 GO:0016478 GO:0017148 > 1 GO:0043037 GO:0006412 > > above first column is number of changes needed, second is secondary > GOID and third column is current GOID. > > -Mike > > > On Mon, 8 Jan 2007, Ranjana Kishore wrote: > >> Hello All, >> Maybe I missed this on the e-mails, but is it now advised that we all work >> with 'gene_ontology_edit.obo' instead of 'gene_ontology.obo'. >> >> This means we (and am sure other groups too?) have to change several of our >> scripts. This came to my attention when I uploaded the new >> gene_association file and was alerted to a 1000+ errors being stripped out >> by the GOC checking script. A quick diff between the script that we >> downloaded recently (because we run in-house error-checking) and the >> current one on the ftp site showed that the filter-gene-association.pl >> script uses the gene_ontology_edit.obo. While this might not be the reason >> for all of our errors, I am guessing this contributes to most (especially >> after all the 'is_a complete project for BP) of our stripped errors. >> >> Along these lines, maybe it would be a good idea to alert groups when there >> are changes to the 'filter-gene-association.pl' script that affects >> gene_association files, and to give groups time to adjust to the new >> changes. >> >> Sorry if all this was decided (though I did not really find one e-mail that >> talks about this) and I somehow missed it! >> >> Cheers >> Ranjana >> WormBase >> > 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 midori at ebi.ac.uk Thu Jan 11 08:00:34 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 11 Jan 2007 16:00:34 +0000 (GMT) Subject: which ontology file do we work with? In-Reply-To: References: <45A2EBB8.4070001@its.caltech.edu> Message-ID: These are all merges that were done recently -- the gene_ontology_edit.obo file looks OK. m On Thu, 11 Jan 2007, Jane Lomax wrote: > Hi Mike - what's the problem with these terms? Are they now fixed or do we > need to do something? > > thanks! > > Jane > > > > On Tue, 9 Jan 2007, Mike Cherry wrote: > >> Ranjana, >> >> The gene_ontology_edit.obo file is the file that should be edited. >> The two files are different versions of the OBO format. The >> gene_ontology.obo file is v1.0 and is no long the primary source of >> the ontologies, that is now the gene_ontology_edit.obo file, v1.2. >> The gene_ontology.obo file is rebuilt nightly from the >> gene_ontology_edit.obo file. So if you are just grabbing the current >> term names and IDs using the gene_ontology.obo should be fine. I >> believe using the gene_ontology.obo file should not cause the problem >> you mention. >> >> The filtering script does use the v1.2 file. The change to using v1.2 >> file was well announced and included in the newsletter in September. >> >> It appears the ontology changes that are causing the errors happened on >> December 21, 2006. It seems there are only six GOIDs that changed: >> >> 1283 GO:0007582 GO:0008150 >> 17 GO:0007046 GO:0042254 >> 11 GO:0002217 GO:0006952 >> 9 GO:0006445 GO:0006417 >> 5 GO:0016478 GO:0017148 >> 1 GO:0043037 GO:0006412 >> >> above first column is number of changes needed, second is secondary >> GOID and third column is current GOID. >> >> -Mike >> >> >> On Mon, 8 Jan 2007, Ranjana Kishore wrote: >> >>> Hello All, >>> Maybe I missed this on the e-mails, but is it now advised that we all work >>> with 'gene_ontology_edit.obo' instead of 'gene_ontology.obo'. >>> >>> This means we (and am sure other groups too?) have to change several of >>> our scripts. This came to my attention when I uploaded the new >>> gene_association file and was alerted to a 1000+ errors being stripped out >>> by the GOC checking script. A quick diff between the script that we >>> downloaded recently (because we run in-house error-checking) and the >>> current one on the ftp site showed that the filter-gene-association.pl >>> script uses the gene_ontology_edit.obo. While this might not be the reason >>> for all of our errors, I am guessing this contributes to most (especially >>> after all the 'is_a complete project for BP) of our stripped errors. >>> >>> Along these lines, maybe it would be a good idea to alert groups when >>> there are changes to the 'filter-gene-association.pl' script that affects >>> gene_association files, and to give groups time to adjust to the new >>> changes. >>> >>> Sorry if all this was decided (though I did not really find one e-mail >>> that talks about this) and I somehow missed it! >>> >>> Cheers >>> Ranjana >>> WormBase >>> >> > > 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 parkinson at ebi.ac.uk Fri Jan 12 03:26:13 2007 From: parkinson at ebi.ac.uk (Helen Parkinson) Date: Fri, 12 Jan 2007 11:26:13 +0000 Subject: ISMB Ontology and Database track Message-ID: <45A77055.3000807@ebi.ac.uk> Dear Friends, Helen Parkinson and Robert Stevens are chairing the Ontologies and Databases area at ISMB this year. We would like a really good set of papers to review and for inclusion in a very strong session. We therefore encourage you to submit papers. The deadline for paper submission is 2 February 2007. The general call and instructions can be found at http://www.iscb.org/ismbeccb2007/deadlines/. The remit for both database and ontology papers is wide, but direct relevance to biology is a must. Use of the ontology or database, rather than a simple description, is encouraged. Papers about ontological issues in biology, their solution and practical application are welcome. Above all, be interesting. Our apologies if you receive this mail more than once. Robert and Helen -- Helen Parkinson, PhD Curation Coordinator Microarray Informatics Team, EBI EBI 01223 494672 Skype: helen.parkinson.ebi From midori at ebi.ac.uk Tue Jan 16 09:27:24 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 16 Jan 2007 17:27:24 +0000 (GMT) Subject: SF 1635783 distributive segregation (fwd) Message-ID: Hi, Susan has asked for input on this item, especially from those of you who work on yeast or C. elegans. Thanks, m ---------- Forwarded message ---------- Date: Tue, 16 Jan 2007 09:25:03 -0800 From: SourceForge.net To: noreply at sourceforge.net Subject: [ geneontology-Curator requests-1635783 ] ntr: distributive segregation Curator requests item #1635783, was opened at 2007-01-15 11:12 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1635783&group_id=36855 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: New term request Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: susantweedie (stweedie) Assigned to: Nobody/Anonymous (nobody) Summary: ntr: distributive segregation Initial Comment: ntr: distributive segregation This term was requested by R. Scott Hawley, Stowers Institute for Medical Research. My definition is based on that of the parental term GO:0016321 with mimimal elaboration. Scott approved my suggestion but also offered to draft a more expansive version if anyone feels this is appropriate - yeast and C. elegans folk may like to comment...? I include snippets of his email correspondence below. Scott writes, "The term 'distributive segregation' refers to those processes that ensure the segregation of those chromosomes that have NOT undergone meiotic crossingover. (Crossingover is the usual means of ensuring homolog segregation). There are a number of mutants in flies that strongly affect distributive segregation, but the most-specific and well characterized of these is nod. Others include Axs, mtrm, mei-S51, ald (mps1), and alpha-tubulin 67C. Distributive segregation is well documented genetically in yeast and C elegans and there is tantalizing evidence that it may also in human oocytes." I queried whether we should call the term achiasmate segregation and whether it is sex specific. His response was, "Although I might actually prefer the term achiasmate segregation in some ways, distributive segregation has a long history and provenance in the fly worm and yeast communities. Most people who search for this process will look for the terms distributive segregation or distributive pairing. Moreover, it is the specific process referred to as distributive segregation that IS specific to female meiosis. (Distributive segregation, as it is defined in females, does not occur in males and mutants that specifically disrupt distributive segregation in females do not affect male meiosis) Fly males have an alternative process(es) of achiasmate segregation) but these are very different from the events that underlie the segregation of achiasmate chromosomes in females (distributive segregation). The term 'achiasmate meiosis I;GO:0000705' perfectly describes the events in fly male meiosis. So much as I dislike the term, I think the interests if the community are best served by denoting the process as distributive segregation with the synonyms distributive pairing and achiasmate segregation." name: distributive segregation namespace: biological_process def: "The cell cycle process whereby genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during the meiotic cell cycle in a female without crossing-over taking place." [GOC:sart, R. Scott Hawley?] exact_synonym: "achiasmate segregation" narrower_synonym: "distributive pairing" is_a: GO:0016321 ! female meiosis chromosome segregation ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2007-01-16 17:25 Message: Logged In: YES user_id=436423 Originator: NO I think I would find it helpful to have a bit more in the definitions to explain how distributive segregation differs from the process represented by the existing achiasmate meiosis I term (I'm not trying to second-guess a community expert, so I don't doubt that a new term is called for; I just don't know enough of the background to get the distinction without some help). I'll also email the GO list to alert the yeast and worm people. m ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1635783&group_id=36855 From eurie at genome.Stanford.EDU Wed Jan 17 10:22:10 2007 From: eurie at genome.Stanford.EDU (Eurie Hong) Date: Wed, 17 Jan 2007 10:22:10 -0800 Subject: Google calendar on wiki Message-ID: You can now view upcoming meetings being attended by members of the GO Consortium on the wiki: http://gocwiki.geneontology.org/index.php/Calendar This calendar is also linked from the left hand navigation menu. If you would like to add information to the calendar, please contact one of the GO managers (Rex, Jane, Midori, David, Jennifer, Chris, Eurie, Karen E) so they can add your name to access the Google calendars. eurie From lhannick at tigr.org Thu Jan 18 08:19:06 2007 From: lhannick at tigr.org (Hannick, Linda) Date: Thu, 18 Jan 2007 11:19:06 -0500 Subject: Eukaryotic Genome Annotation course at TIGR Message-ID: FYI: Eukaryotic Genome Annotation and Analysis Course TIGR is offering a new three-day course in Eukaryotic Genome Annotation and Analysis. This course will familiarize attendees with TIGR's eukaryotic annotation methods, tools and computational pipeline for annotation, including our manual annotation tool Manatee . In this class you will learn about many of the searches, tools, and processes we use to annotate, analyze and compare eukaryotic genomes, including a session on GO. This course is aimed at researchers, post-doctoral fellows, university faculty, students and others who desire to better understand how genes and other features of genomes are predicted, and how to understand and make better use of the vast amount of information flowing from genome projects. Upcoming Dates for the Course The course is offered on the following dates at TIGR's Rockville, MD, US Campus: March 6-8, 2007 June 26-28, 2007 Sept. 18-20, 2007 Tuition of $595.00 includes all class materials and lunch each day. For more information, see the website: http://www.tigr.org/edutraining/training/eukaryotic_annotation.shtml, or call Anna von Arx at 301-795-7943. Thanks, Linda ~~~~~~~~~~~~~~~~~ Linda I. Hannick, Ph.D. Bioinformatics Analyst The Institute for Genomic Research (TIGR) Rockville, MD 20850 USA ~~~~~~~~~~~~~~~~~~~ 301-795-7857 voice 301-838-0227 fax ~~~~~~~~~~~~~~~~~~~ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20070118/91585d0c/attachment.html From mlgwinn at tigr.org Thu Jan 18 13:54:07 2007 From: mlgwinn at tigr.org (Gwinn, Michelle L.) Date: Thu, 18 Jan 2007 16:54:07 -0500 Subject: Eukaryotic Genome Annotation course at TIGR References: Message-ID: Hello, We'd like to let GO friends know about another TIGR course: Prokaryotic Genome Annotation and Analysis Course Since 2002 TIGR TIGR has offered a three-day course in Prokaryotic Genome Annotation and Analysis. This course will familiarize attendees with TIGR's prokaryotic annotation methods, tools, and computational pipeline for annotation, including our manual annotation tool Manatee (an open source tool which can be found at http://manatee.sourceforge.net) . In this class you will learn about many of the searches, tools, and processes we use to annotate, analyze and compare prokaryotic genomes, including a detailed session on GO. This course is aimed at anyone who desires to know how prokaryotic annotation works. The only prerequisite is a basic knowledge of biology. Computers will be provided for the hands-on portions of the course General outline: Day 1: gene finding, sequence similarity-based searches, evidence evaluation, protein naming guidelines, the Gene Ontology system, Manatee demo Day 2: Hands-on annotation exercises with Manatee, overview of Manatee architecture and underlying database structure, overview of local installatin of Manatee Day 3: A detailed look at the Comprehensive Microbial Resource (CMR) and a tutorial on how to use some of its many genome comparision and analysis tools, and hands-on exercises. Upcoming Dates for the Course in 2007: March 27-29, 2007 June 12-14, 2007 August 21-23, 2007 October 16-18, 2007 Tuition of $595.00 includes all class materials and lunch each day. The course is held on the TIGR campus in Rockville, MD, USA. For more information, see the website: http://www.tigr.org/AnnotationClass, email me, or call Anna von Arx at 301-795-7943. ALSO OF INTEREST: This course is a perfect complement to TIGR's Annotation Engine Service, a FREE service through which TIGR provides gene finding, automatic annotation, all accompanying search data, a MySQL database housing the data, and the manual annotation tool Manatee to anyone who has a prokaryotic DNA sequence they wish to annotate. The sequence need not be completely finished. For more information on this service please go to http://www.tigr.org/AnnotationEngine Thanks for reading, Michelle --------------------------- Michelle Gwinn Giglio, Ph.D. Prokaryotic Annotation Group TIGR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20070118/69c8ddfa/attachment.html From mlgwinn at tigr.org Thu Jan 18 13:54:54 2007 From: mlgwinn at tigr.org (Gwinn, Michelle L.) Date: Thu, 18 Jan 2007 16:54:54 -0500 Subject: Prokaryotic Genome Annotation Course at TIGR References: Message-ID: Sorry forgot to change the subject line on that email when I sent out the notice on the prok class. So sorry for the duplication. -----Original Message----- From: Gwinn, Michelle L. Sent: Thu 1/18/2007 4:54 PM To: Hannick, Linda; Gene Ontology; go-friends at genome.stanford.edu Cc: Gwinn, Michelle L. Subject: RE: Eukaryotic Genome Annotation course at TIGR Hello, We'd like to let GO friends know about another TIGR course: Prokaryotic Genome Annotation and Analysis Course Since 2002 TIGR TIGR has offered a three-day course in Prokaryotic Genome Annotation and Analysis. This course will familiarize attendees with TIGR's prokaryotic annotation methods, tools, and computational pipeline for annotation, including our manual annotation tool Manatee (an open source tool which can be found at http://manatee.sourceforge.net) . In this class you will learn about many of the searches, tools, and processes we use to annotate, analyze and compare prokaryotic genomes, including a detailed session on GO. This course is aimed at anyone who desires to know how prokaryotic annotation works. The only prerequisite is a basic knowledge of biology. Computers will be provided for the hands-on portions of the course General outline: Day 1: gene finding, sequence similarity-based searches, evidence evaluation, protein naming guidelines, the Gene Ontology system, Manatee demo Day 2: Hands-on annotation exercises with Manatee, overview of Manatee architecture and underlying database structure, overview of local installatin of Manatee Day 3: A detailed look at the Comprehensive Microbial Resource (CMR) and a tutorial on how to use some of its many genome comparision and analysis tools, and hands-on exercises. Upcoming Dates for the Course in 2007: March 27-29, 2007 June 12-14, 2007 August 21-23, 2007 October 16-18, 2007 Tuition of $595.00 includes all class materials and lunch each day. The course is held on the TIGR campus in Rockville, MD, USA. For more information, see the website: http://www.tigr.org/AnnotationClass, email me, or call Anna von Arx at 301-795-7943. ALSO OF INTEREST: This course is a perfect complement to TIGR's Annotation Engine Service, a FREE service through which TIGR provides gene finding, automatic annotation, all accompanying search data, a MySQL database housing the data, and the manual annotation tool Manatee to anyone who has a prokaryotic DNA sequence they wish to annotate. The sequence need not be completely finished. For more information on this service please go to http://www.tigr.org/AnnotationEngine Thanks for reading, Michelle --------------------------- Michelle Gwinn Giglio, Ph.D. Prokaryotic Annotation Group TIGR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20070118/2fb3772e/attachment.html From cjm at fruitfly.org Sun Jan 21 21:56:48 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Sun, 21 Jan 2007 21:56:48 -0800 Subject: Some thoughts on publications that use GO Message-ID: <3DE2C2A0-9CBB-4A0C-AF32-D12F492239F4@fruitfly.org> Some semi-connected thoughts on publications that use GO and in particular GO-based enrichment analyses 1. Aside from the papers mentioned in the newsletter, what are people's favourite examples of a paper GO enrichment analysis to discover something interesting and/or of relevance to human health? I see the Allen Brain Atlas paper in Nature did the standard GO enrichment analysis (though they have some curious usages of the term "ontology" - "Certain functional ontologies are over-represented" and "Classical definition of brain regions is based on a combination of overall morphology, cellular cytoarchitecture, ontological development and functional connectivity") The bee paper also included the usual analysis and had some interesting results to do with caste determination Would these be candidates for the newsletter? Or are there just too many papers like this to choose from now? 2. I notice the Sjoblom paper mentioned in the newsletter isn't in our biblio database - we should probably keep these things in sync 3. I imagine curating the biblio database is a large and never ending task. Is there anything we can do to make this easier? Does anyone use social bookmarking systems like deli.cio.us or connotea? The latter is a good idea - it's the Nature people. The idea is you bookmark papers, share your bookmarks, and "tag" the articles with descriptive terms. There are currently 97 articles tagged "GO": http://www.connotea.org/tag/GO as you can see, not all are our GO, but given the user base "GO" is usually fairly univocal Thats a fraction of what we have in our biblio database. In addition the biblio database is curated. Still, I wonder - is there some way to combine these systems in some way... to make the biblio database more "social/web2.0", or to upload our biblio db to connotea.. (this is quite easy but it requires a URL for each ref) any interesting ideas to the Hub Group It's pretty easy to use connotea - details here: http://www.connotea.org/ 4. I was worried by what David said at the meeting about not being able to reproduce the results of the term enrichment analysis in the cancer paper. I like the suggestion of having a Minimum Information About A Term Enrichment Analysis (MIAATEA?? Anyone have other acronym suggestions?). Should we form some kind of ad-hoc WG to come up with some recommendations? I think the folks at the Ontologies for Biomedical Investigations meeting I'm attending next week would be interested in this, so if you have thoughts on this matter, send em in the next week! Cheers Chris From midori at ebi.ac.uk Mon Jan 22 06:13:53 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Mon, 22 Jan 2007 14:13:53 +0000 (GMT) Subject: Some thoughts on publications that use GO In-Reply-To: <3DE2C2A0-9CBB-4A0C-AF32-D12F492239F4@fruitfly.org> References: <3DE2C2A0-9CBB-4A0C-AF32-D12F492239F4@fruitfly.org> Message-ID: Replying to just a few of the points ... > 2. I notice the Sjoblom paper mentioned in the newsletter isn't in our biblio > database - we should probably keep these things in sync Yep; I'll add the Sjoblom paper, and pay attention to future newsletters. > 3. I imagine curating the biblio database is a large and never ending task. > Is there anything we can do to make this easier? I do pretty much all of it; it's not that bad, as quite a bit of it is done by scripts already (thanks, Amelia!). The slow part is determining which of our biblio categories a paper fits into (it does support more than one category per paper); I haven't thought of any way to automate that. > Does anyone use social bookmarking systems like deli.cio.us or connotea? The > latter is a good idea - it's the Nature people. The idea is you bookmark > papers, share your bookmarks, and "tag" the articles with descriptive terms. > > There are currently 97 articles tagged "GO": > http://www.connotea.org/tag/GO > as you can see, not all are our GO, but given the user base "GO" is usually > fairly univocal > > Thats a fraction of what we have in our biblio database. In addition the > biblio database is curated. Still, I wonder - is there some way to combine > these systems in some way... to make the biblio database more > "social/web2.0", or to upload our biblio db to connotea.. (this is quite easy > but it requires a URL for each ref) any interesting ideas to the Hub Group I just do an extremely simplistic PubMed search every week or so; I'm sure it would improve our biblio coverage is if we could come up with a reliable way to find papers that don't turn up in my PubMed search. I also do a full text search at PLoS once in a while, but less frequently and less regularly. Is there an easy way to compare our biblio with the GO-tagged Connotea set? (I'd only be inclined to bother if it's quick and easy, since we already have an order of magnitude more pubs.) The vast majority (1169/1208) of our papers have PubMed IDs, so can be plugged into the PubMed abstract URL. m > > It's pretty easy to use connotea - details here: > http://www.connotea.org/ From jclark at ebi.ac.uk Tue Jan 23 04:43:37 2007 From: jclark at ebi.ac.uk (J Clark) Date: Tue, 23 Jan 2007 12:43:37 +0000 Subject: annotation outreach report Message-ID: <45B602F9.5010304@ebi.ac.uk> Hi, I'm going to write up a report on all the annotation outreach activities of the consortium that took place in December and January. If you have been involved in any activities to encourage new groups to submit annotation to the consortium could write and let me know brief details? I'm going to submit the report the end of January, and it will be on the wiki for all in the consortium to see. Thanks, Jennifer From jane at ebi.ac.uk Tue Jan 23 08:43:23 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Tue, 23 Jan 2007 16:43:23 +0000 (GMT) Subject: Manager meeting minutes 17th Jan Message-ID: The minutes for the Jan 17th managers meeting are now available on the wiki: http://gocwiki.geneontology.org/index.php/Managers_17Jan07 If you would like a topic to be discussed at the next managers meeting, which be on 31st January, please contact the relevant manager(s): Reference Genomes: Rex User Advocacy: Jane and Eurie Content Development: Midori and David Annotation Outreach: Jennifer Software: Chris Or the GO PIs (go-top at genome.stanford.edu) for general management and budget issues. thanks, GO managers From val at sanger.ac.uk Wed Jan 24 05:14:27 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 24 Jan 2007 13:14:27 UT Subject: 'metabolic process' term name changes question Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20070124/74559c19/attachment.pl From val at sanger.ac.uk Wed Jan 24 05:14:35 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 24 Jan 2007 13:14:35 UT Subject: 'metabolic process' term name changes question Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20070124/426e457a/attachment.pl From val at sanger.ac.uk Wed Jan 24 05:14:49 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 24 Jan 2007 13:14:49 UT Subject: 'metabolic process' term name changes question Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20070124/e6b90204/attachment.pl From val at sanger.ac.uk Wed Jan 24 05:14:57 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 24 Jan 2007 13:14:57 UT Subject: 'metabolic process' term name changes question Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20070124/fb7a890e/attachment.pl From jane at ebi.ac.uk Wed Jan 24 05:31:44 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Wed, 24 Jan 2007 13:31:44 +0000 Subject: 'metabolic process' term name changes question In-Reply-To: References: Message-ID: <4CD01476-6C99-4272-BEDC-B7E8BF26A32C@ebi.ac.uk> Hi Val - it's because of the way we redesigned biological process - basically metabolism is the totality of the biosynthetic and catabolic processes in an organism, so each of the child terms would be a part of that whole metabolism...but because metabolism in GO only had is_a children, we figured that what it actually meant was metabolic process. We did the same with development which is now developmental process. Does that make any sort of sense? Sorry about the 'xxx metabolism' synonyms - looks like I did the biosynthesis and catabolism ones, but forgot the metabolism ones - I'll get on to it... Jane On 24 Jan 2007, at 13:14, Valerie Wood wrote: > > > I know that the change from metabolism-> metabolic process was > mentioned at the consortium meeting, but why was this required? I > think I missed the reason, but I also assumed it was only necessary > for the high level nodes like 'cellular metabolic process'. The > new term names aren't as intuitive (or readable) as the old ones. > > Also some don't appear to have the synonyms: > > urea metabolic process doesn't have the synonym urea metabolism > adenosine metabolic process does not have synonym adenosine metabolism > > so they are returning 0 results with the old term names. > > From donghui at stanford.edu Wed Jan 24 11:52:54 2007 From: donghui at stanford.edu (Donghui Li) Date: Wed, 24 Jan 2007 11:52:54 -0800 Subject: Obo-edit ID profile mismatch In-Reply-To: <200608241700.k7OH0NO1419706@mozart.ebi.ac.uk> References: <200608241700.k7OH0NO1419706@mozart.ebi.ac.uk> Message-ID: <45B7B916.3080909@stanford.edu> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20070124/8e771005/attachment.html From kchris at genome.Stanford.EDU Wed Jan 24 11:55:27 2007 From: kchris at genome.Stanford.EDU (Karen Christie) Date: Wed, 24 Jan 2007 11:55:27 -0800 (PST) Subject: Obo-edit ID profile mismatch In-Reply-To: <45B7B916.3080909@stanford.edu> References: <200608241700.k7OH0NO1419706@mozart.ebi.ac.uk> <45B7B916.3080909@stanford.edu> Message-ID: just say No! Basically, just say that you don't want to use the ID profile loaded from the file because you don't want that one. You want to use the one you have set up in your own OBO-Edit, so just say no to this dialog box. -Karen On Wed, 24 Jan 2007, Donghui Li wrote: > Hello everyone, > > I wonder if any of you could help me. I just downloaded the gene_ontology_edit.obo file this > morning. When I tried to open it with obo-edit (ver 1.002), I got the following message: > > ID Profile Mismatch: > The ID generation profile in this file does not match the current ID generation profile. Use > the profile loaded from the file? > > When I chose Yes, and tried to add a new term, the ID assigned (GO:0043685) does not belong > to TAIR. I checked my obo-edit ID Manager PlugIn, it is set as default value > (GO:$sequence(7,0009500,0011000)$). > > I wonder if this has something to do with my obo-edit set-up (it was OK when I did the last > edit) or the ontology file. Should I simply answer No to the ID Profile Mismatch question? > > Thanks! > > Donghui > > midori at ebi.ac.uk wrote: > Here are today's new SourceForge requests: > > Follow the link to see the full description or to add comments to an item. > You can use the monitor option to receive any comments added to an item. > > 1545831 2006-08-24 02:23 mp: DNA unwinding during.../DNA topological change > 1545839 2006-08-24 02:58 mp: DNA unwinding during.../DNA topological change > 1545865 2006-08-24 03:49 NTR: Nucleotide excision repair > > You can also go to the SourceForge GO Curator Requests Tracker > to see the complete list of submissions: > http://sourceforge.net/tracker/?atid=440764&group_id=36855&func=browse > > Signed, > > the sf-digest daemon. > > __________________________________________________________________________________________ > > > -- > Donghui Li, PhD > > The Arabidopsis Information Resource > Carnegie Institution > Department of Plant Biology > 260 Panama Street > Stanford CA 94305 > > donghui at stanford.edu > tel (650)325 1521 ext 356 > fax (650)325 6857 > > From midori at ebi.ac.uk Wed Jan 24 14:19:00 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Wed, 24 Jan 2007 22:19:00 +0000 (GMT) Subject: Obo-edit ID profile mismatch In-Reply-To: References: <200608241700.k7OH0NO1419706@mozart.ebi.ac.uk> <45B7B916.3080909@stanford.edu> Message-ID: Karen's right; you want to say no if this dialog appears. That said, usually we save the gene_ontology_edit.obo file without any ID rules, so the dialog doesn't appear in the first place. Apparently a version got committed with ID rules in it; I've just committed a new revision without them. There's a pulldown menu is the Save As dialog box where you can select what to write out to the file. For GO we normally choose "Don't write ID rules." Gory details are in the User's Guide under "The ID Manager Plugin" and "The OBO Adapter." Midori On Wed, 24 Jan 2007, Karen Christie wrote: > just say No! > > Basically, just say that you don't want to use the ID profile loaded from the > file because you don't want that one. You want to use the one you have set up > in your own OBO-Edit, so just say no to this dialog box. > > -Karen > > > On Wed, 24 Jan 2007, Donghui Li wrote: > >> Hello everyone, >> >> I wonder if any of you could help me. I just downloaded the >> gene_ontology_edit.obo file this >> morning. When I tried to open it with obo-edit (ver 1.002), I got the >> following message: >> >> ID Profile Mismatch: >> The ID generation profile in this file does not match the current ID >> generation profile. Use >> the profile loaded from the file? >> >> When I chose Yes, and tried to add a new term, the ID assigned (GO:0043685) >> does not belong >> to TAIR. I checked my obo-edit ID Manager PlugIn, it is set as default >> value >> (GO:$sequence(7,0009500,0011000)$). >> >> I wonder if this has something to do with my obo-edit set-up (it was OK >> when I did the last >> edit) or the ontology file. Should I simply answer No to the ID Profile >> Mismatch question? >> >> Thanks! >> >> Donghui >> >> midori at ebi.ac.uk wrote: >> Here are today's new SourceForge requests: >> >> Follow the link to see the full description or to add comments to an >> item. >> You can use the monitor option to receive any comments added to an >> item. >> >> 1545831 2006-08-24 02:23 mp: DNA unwinding during.../DNA topological >> change >> 1545839 2006-08-24 02:58 mp: DNA unwinding during.../DNA topological >> change >> 1545865 2006-08-24 03:49 NTR: Nucleotide excision repair >> >> You can also go to the SourceForge GO Curator Requests Tracker >> to see the complete list of submissions: >> http://sourceforge.net/tracker/?atid=440764&group_id=36855&func=browse >> >> Signed, >> >> the sf-digest daemon. >> >> __________________________________________________________________________________________ >> >> >> -- Donghui Li, PhD >> >> The Arabidopsis Information Resource >> Carnegie Institution >> Department of Plant Biology >> 260 Panama Street >> Stanford CA 94305 >> >> donghui at stanford.edu >> tel (650)325 1521 ext 356 >> fax (650)325 6857 >> >> > From donghui at stanford.edu Wed Jan 24 15:47:33 2007 From: donghui at stanford.edu (Donghui Li) Date: Wed, 24 Jan 2007 15:47:33 -0800 Subject: Obo-edit ID profile mismatch In-Reply-To: <45B7EF38.5010501@berkeleybop.org> References: <200608241700.k7OH0NO1419706@mozart.ebi.ac.uk> <45B7B916.3080909@stanford.edu> <45B7EF38.5010501@berkeleybop.org> Message-ID: <45B7F015.1020003@stanford.edu> Thanks everyone. I have fixed the problem following Karen's advice. Additionally, Midori has committed a copy of the ontology file that does not contain the ID profile information. So the dialog box should not pop out again. -Donghui John Day-Richter wrote: > Karen is quite right. You only want to use a profile loaded from a file > if you plan to edit the file, and want to be sure you use the original > author's id profile. > > You should be able to restore your old profile using the ID Manager Plugin. > > -John > > Karen Christie wrote: > >> just say No! >> >> Basically, just say that you don't want to use the ID profile loaded >> from the file because you don't want that one. You want to use the one >> you have set up in your own OBO-Edit, so just say no to this dialog box. >> >> -Karen >> >> >> On Wed, 24 Jan 2007, Donghui Li wrote: >> >> >>> Hello everyone, >>> >>> I wonder if any of you could help me. I just downloaded the >>> gene_ontology_edit.obo file this >>> morning. When I tried to open it with obo-edit (ver 1.002), I got >>> the following message: >>> >>> ID Profile Mismatch: >>> The ID generation profile in this file does not match the current ID >>> generation profile. Use >>> the profile loaded from the file? >>> >>> When I chose Yes, and tried to add a new term, the ID assigned >>> (GO:0043685) does not belong >>> to TAIR. I checked my obo-edit ID Manager PlugIn, it is set as >>> default value >>> (GO:$sequence(7,0009500,0011000)$). >>> >>> I wonder if this has something to do with my obo-edit set-up (it was >>> OK when I did the last >>> edit) or the ontology file. Should I simply answer No to the ID >>> Profile Mismatch question? >>> >>> Thanks! >>> >>> Donghui >>> >>> midori at ebi.ac.uk wrote: >>> Here are today's new SourceForge requests: >>> >>> Follow the link to see the full description or to add comments >>> to an item. >>> You can use the monitor option to receive any comments added to >>> an item. >>> >>> 1545831 2006-08-24 02:23 mp: DNA unwinding during.../DNA >>> topological change >>> 1545839 2006-08-24 02:58 mp: DNA unwinding during.../DNA >>> topological change >>> 1545865 2006-08-24 03:49 NTR: Nucleotide excision repair >>> >>> You can also go to the SourceForge GO Curator Requests Tracker >>> to see the complete list of submissions: >>> >>> http://sourceforge.net/tracker/?atid=440764&group_id=36855&func=browse >>> >>> Signed, >>> >>> the sf-digest daemon. >>> >>> >>> __________________________________________________________________________________________ >>> >>> >>> >>> -- Donghui Li, PhD >>> >>> The Arabidopsis Information Resource >>> Carnegie Institution >>> Department of Plant Biology >>> 260 Panama Street >>> Stanford CA 94305 >>> >>> donghui at stanford.edu >>> tel (650)325 1521 ext 356 >>> fax (650)325 6857 >>> >>> >>> > > -- Donghui Li, PhD The Arabidopsis Information Resource Carnegie Institution Department of Plant Biology 260 Panama Street Stanford CA 94305 donghui at stanford.edu tel (650)325 1521 ext 356 fax (650)325 6857 From donghui at stanford.edu Wed Jan 24 15:50:25 2007 From: donghui at stanford.edu (Donghui Li) Date: Wed, 24 Jan 2007 15:50:25 -0800 Subject: CVS 'conflict' In-Reply-To: References: <200608241700.k7OH0NO1419706@mozart.ebi.ac.uk> <45B7B916.3080909@stanford.edu> Message-ID: <45B7F0C1.4080809@stanford.edu> Midori, Jane, While editing the gene_ontology file this afternoon, I run into the classical problem: someone else (Jane, I think) has also committed changes since I checked out the file. I did a cvs update to merge my edited copy of the file with the repository copy. In the end I managed to check in my copy, but not sure if I have messed up Jane's changes (apologize if that happened). Please could you double check this please. I copied part of the log file here. Please let me know if you want more information on what I did. Thanks! -Donghui RCS file: /share/go/cvs/go/ontology/gene_ontology_edit.obo,v retrieving revision 5.118 retrieving revision 5.120 diff -r5.118 -r5.120 2,4c2,4 < date: 24:01:2007 17:39 < saved-by: jane < auto-generated-by: OBO-Edit 1.100-beta18 --- > date: 24:01:2007 13:53 > saved-by: donghui > auto-generated-by: OBO-Edit 1.002 11,12c11 < namespace-id-rule: * GO:$sequence(7,42001,45000)$ < remark: cvs version: $Revision: 5.118 $ --- > remark: cvs version: $Revision: 5.120 $ 4068c4067 < xref: MetaCyc:(R\,R)-BUTANEDIOL-DEHYDROGENASE-RXN --- > xref: MetaCyc:(R,R)-BUTANEDIOL-DEHYDROGENASE-RXN 11052,11055c11051,11054 < synonym: "PAMP receptor signaling pathway" EXACT [ISBN:0781735149, PMID:15199967, PMID:15728447] < synonym: "pathogen receptor signaling pathway" EXACT [ISBN:0781735149, PMID:15199967, PMID:15728447] < synonym: "pathogen receptor signalling pathway" EXACT [ISBN:0781735149, PMID:15199967, PMID:15728447] < synonym: "PRR signaling pathway" EXACT [ISBN:0781735149, PMID:15199967, PMID:15728447] --- > synonym: "PAMP receptor signaling pathway" EXACT [PMID:15728447, ISBN:0781735149, PMID:15199967] > synonym: "pathogen receptor signaling pathway" EXACT [PMID:15728447, ISBN:0781735149, PMID:15199967] > synonym: "pathogen receptor signalling pathway" EXACT [PMID:15728447, ISBN:0781735149, PMID:15199967] > synonym: "PRR signaling pathway" EXACT [PMID:15728447, ISBN:0781735149, PMID:15199967] 18544c18543 Midori Harris wrote: > Karen's right; you want to say no if this dialog appears. > > That said, usually we save the gene_ontology_edit.obo file without any > ID rules, so the dialog doesn't appear in the first place. Apparently > a version got committed with ID rules in it; I've just committed a new > revision without them. > > There's a pulldown menu is the Save As dialog box where you can select > what to write out to the file. For GO we normally choose "Don't write > ID rules." Gory details are in the User's Guide under "The ID Manager > Plugin" and "The OBO Adapter." > > Midori > > On Wed, 24 Jan 2007, Karen Christie wrote: > >> just say No! >> >> Basically, just say that you don't want to use the ID profile loaded >> from the file because you don't want that one. You want to use the >> one you have set up in your own OBO-Edit, so just say no to this >> dialog box. >> >> -Karen >> >> >> On Wed, 24 Jan 2007, Donghui Li wrote: >> >>> Hello everyone, >>> >>> I wonder if any of you could help me. I just downloaded the >>> gene_ontology_edit.obo file this >>> morning. When I tried to open it with obo-edit (ver 1.002), I got >>> the following message: >>> >>> ID Profile Mismatch: >>> The ID generation profile in this file does not match the current ID >>> generation profile. Use >>> the profile loaded from the file? >>> >>> When I chose Yes, and tried to add a new term, the ID assigned >>> (GO:0043685) does not belong >>> to TAIR. I checked my obo-edit ID Manager PlugIn, it is set as >>> default value >>> (GO:$sequence(7,0009500,0011000)$). >>> >>> I wonder if this has something to do with my obo-edit set-up (it was >>> OK when I did the last >>> edit) or the ontology file. Should I simply answer No to the ID >>> Profile Mismatch question? >>> >>> Thanks! >>> >>> Donghui >>> >>> midori at ebi.ac.uk wrote: >>> Here are today's new SourceForge requests: >>> >>> Follow the link to see the full description or to add comments >>> to an item. >>> You can use the monitor option to receive any comments added >>> to an item. >>> >>> 1545831 2006-08-24 02:23 mp: DNA unwinding during.../DNA >>> topological change >>> 1545839 2006-08-24 02:58 mp: DNA unwinding during.../DNA >>> topological change >>> 1545865 2006-08-24 03:49 NTR: Nucleotide excision repair >>> >>> You can also go to the SourceForge GO Curator Requests Tracker >>> to see the complete list of submissions: >>> >>> http://sourceforge.net/tracker/?atid=440764&group_id=36855&func=browse >>> >>> Signed, >>> >>> the sf-digest daemon. >>> >>> >>> __________________________________________________________________________________________ >>> >>> >>> >>> -- Donghui Li, PhD >>> >>> The Arabidopsis Information Resource >>> Carnegie Institution >>> Department of Plant Biology >>> 260 Panama Street >>> Stanford CA 94305 >>> >>> donghui at stanford.edu >>> tel (650)325 1521 ext 356 >>> fax (650)325 6857 >>> >>> >> -- Donghui Li, PhD The Arabidopsis Information Resource Carnegie Institution Department of Plant Biology 260 Panama Street Stanford CA 94305 donghui at stanford.edu tel (650)325 1521 ext 356 fax (650)325 6857 From midori at ebi.ac.uk Thu Jan 25 02:00:07 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 25 Jan 2007 10:00:07 +0000 (GMT) Subject: CVS 'conflict' In-Reply-To: <45B7F0C1.4080809@stanford.edu> References: <200608241700.k7OH0NO1419706@mozart.ebi.ac.uk> <45B7B916.3080909@stanford.edu> <45B7F0C1.4080809@stanford.edu> Message-ID: Hi Donghui, This looks fine -- I've checked the CVS log, and the numbers of lines added and removed suggest that Jane's edits and yours are OK. Midori On Wed, 24 Jan 2007, Donghui Li wrote: > Midori, Jane, > > While editing the gene_ontology file this afternoon, I run into the classical > problem: someone else (Jane, I think) has also committed changes since I > checked out the file. I did a cvs update to merge my edited copy of the file > with the repository copy. In the end I managed to check in my copy, but not > sure if I have messed up Jane's changes (apologize if that happened). Please > could you double check this please. I copied part of the log file here. > Please let me know if you want more information on what I did. > > Thanks! > > -Donghui > > > > RCS file: /share/go/cvs/go/ontology/gene_ontology_edit.obo,v > retrieving revision 5.118 > retrieving revision 5.120 > diff -r5.118 -r5.120 > 2,4c2,4 > < date: 24:01:2007 17:39 > < saved-by: jane > < auto-generated-by: OBO-Edit 1.100-beta18 > --- >> date: 24:01:2007 13:53 >> saved-by: donghui >> auto-generated-by: OBO-Edit 1.002 > 11,12c11 > < namespace-id-rule: * GO:$sequence(7,42001,45000)$ > < remark: cvs version: $Revision: 5.118 $ > --- >> remark: cvs version: $Revision: 5.120 $ > 4068c4067 > < xref: MetaCyc:(R\,R)-BUTANEDIOL-DEHYDROGENASE-RXN > --- >> xref: MetaCyc:(R,R)-BUTANEDIOL-DEHYDROGENASE-RXN > 11052,11055c11051,11054 > < synonym: "PAMP receptor signaling pathway" EXACT [ISBN:0781735149, > PMID:15199967, PMID:15728447] > < synonym: "pathogen receptor signaling pathway" EXACT [ISBN:0781735149, > PMID:15199967, PMID:15728447] > < synonym: "pathogen receptor signalling pathway" EXACT [ISBN:0781735149, > PMID:15199967, PMID:15728447] > < synonym: "PRR signaling pathway" EXACT [ISBN:0781735149, PMID:15199967, > PMID:15728447] > --- >> synonym: "PAMP receptor sign