microarray-ontol-digest Friday, March 2 2001 Volume 01 : Number 005 ---------------------------------------------------------------------- Date: Fri, 16 Feb 2001 07:55:02 -0800 (PST) From: Mike Cherry Subject: [microarray-ontol] RE: Gene attributes that don't fit into process, (fwd) >From majordom Fri Feb 16 04:10:30 2001 Return-Path: Received: (from majordom@localhost) by alberich.Stanford.EDU (8.8.8/8.8.8) id EAA27086 for gofriends-list; Fri, 16 Feb 2001 04:08:45 -0800 (PST) X-Authentication-Warning: alberich.Stanford.EDU: majordom set sender to owner-gofriends@genome-mail.stanford.edu using -f Received: from mauve.csi.cam.ac.uk (exim@mauve.csi.cam.ac.uk [131.111.8.38]) by alberich.Stanford.EDU (8.8.8/8.8.8) with ESMTP id EAA09189 for ; Fri, 16 Feb 2001 04:08:42 -0800 (PST) Received: from ma11.gen.cam.ac.uk ([131.111.46.169]) by mauve.csi.cam.ac.uk with smtp (Exim 3.16 #1) id 14TiAz-0002tH-00; Fri, 16 Feb 2001 10:31:45 +0000 Received: from ma11 by ma11.gen.cam.ac.uk with local (Exim 1.58 #2) id 14TiAM-0000Ax-00; Fri, 16 Feb 2001 10:31:06 +0000 To: ma11@gen.cam.ac.uk, froth@hms.harvard.edu, R.BRUSKIEWICH@cgiar.org Subject: RE: Gene attributes that don't fit into process, component and fu nction ontologies? Cc: gofriends@geneontology.org X-Sun-Charset: US-ASCII Message-Id: From: Michael Ashburner (Genetics) Date: Fri, 16 Feb 2001 10:31:06 +0000 Sender: owner-gofriends@genome.stanford.edu Precedence: bulk Friends I think that I was a bit brusque when I replied to Fritz's mail ! Richard's mail and that from WinHide show that Fritz has touched a chord. 1. On the question of expression ontologies there is, of course, a working party on this due to report at the MGED meeting in March: see http://www.cbil.upenn.edu/Ontology/MGED_ontology.html 2. I am not quite sure what WinHide is trying to attain. Unless I have completely missed the point (not unknown, I am told) most of his list is satisfied by a well formed GenBank/EMBL-Bank/DDBJ FT statement for a mRNA, e.g. join(AC004277:5175..5676,AC004277:5821..6157, AC004277:6214..6918,AC004277:7020..7153, AC004277:7250..7401) Win, cannot we compute most of what you want from that ? and then represent it in text is you so wish ? >The relative expression of each exon ... I am not sure what you mean here; do you mean expression of each differently spliced protein isoform ? Does it make sense to talk about the expression of an exon independently of the mRNA within which it is contained ? 3. With respect to Richard's email (which I take the liberty of attaching as it was not sent to the list) I do agree that we must extend the domains of cvo's. I also agree that the GO Consortium could evolve into an umbrella group for related cvo's (at the very least for their distribution, but also I would hope for uniformity of syntax, semantics and tools for maintaining and querying). With that in mind I would certainly include the following: anatomy microarray experiments phenotypic variation But I do not think that we should attempt to duplicate work being done by, eg, the Swiss-Prot team on proteins. Best Michael - ----------------------------------------------------------------------------- >From R.BRUSKIEWICH@cgiar.org Fri Feb 16 00:13:58 2001 Envelope-to: ma11@gen.cam.ac.uk Delivery-date: Fri, 16 Feb 2001 00:13:58 +0000 Date: Thu, 15 Feb 2001 15:55:31 -0800 From: "Bruskiewich, Richard" Subject: RE: Gene attributes that don't fit into process, component and fu nction ontologies? To: "'ma11@gen.cam.ac.uk'" , froth@hms.harvard.edu MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Hi Michael and Fritz, I generally agree with you Michael, that we need to keep the current GO project tractable by limiting the controlled vocabularies/ontologies (cvo) to the three current themes. That said, I think we do need to start thinking along the lines Fritz has indicated and chart out a broader map for the future. I'm already doing this within the plant community by developing trait and mutant descriptive ontologies, leveraging the protocols and tools of the GO consortium for cvo's. There are also other efforts in biological ontology for example the microarray groups, even the various XML driven annotation data exchange protocols, all represent cvo's. Our recent Plant & Animal Genome workshop on cvo's was well received by delegates. Based upon my discussions during a recent trip to Japan, our japanese colleagues are also keen to participate. I think many people are recognizing the value of community level protocols for labeling database data to facilitate tractable functional genomic computing and interoperability of heterogeneous databases. The basic question is: can we identify a consortium of consortia dealing with cvo's in various targeted domains and encourage the development of common protocols and tools, leaving content development to each specialist group? Cheers Richard Bruskiewich Bioinformatics Specialist International Rice Research Institute (IRRI) http://www.cgiar.org/irri Tel. +63 (2) 845-0563 Fax +63 (2) 845-0606 Email: r.bruskiewich@cgiar.org Mailing address: MCPO Box 3127, 1271 Makati City, The Philippines Shipping: Suite 1009, 6776 Ayala Ave, Makati City, The Philippines - -- This message is from the GOFriends Mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends@genome.stanford.edu Subscribing send "subscribe" to gofriends-request@genome.stanford.edu Unsubscribing send "unsubscribe" to gofriends-request@genome.stanford.edu Web: http://www.geneontology.org/ ------------------------------ Date: Tue, 20 Feb 2001 16:20:38 GMT From: "Jean-Jack M. Riethoven" Subject: [microarray-ontol] Date: Tue, 20 Feb 2001 16:20:32 -0000 FILES INFO LIST GET END With kind regards, - -- drs. Jean-Jack M. Riethoven EMBL Outstation - Hinxton pow@ebi.ac.uk ICQ#: 3433929 European Bioinformatics Institute Phone: (+44) 1223 494635 Wellcome Trust Genome Campus Fax : (+44) 1223 494468 Hinxton, Cambridge CB10 1SD URL : http://industry.ebi.ac.uk/ UNITED KINGDOM Need to find bioinformatics or molecular biology web sites or resources? Use BioWurld at http://www.ebi.ac.uk/biowurld ------------------------------ Date: Tue, 20 Feb 2001 17:02:03 -0000 From: "Jean-Jack M. Riethoven" Subject: [microarray-ontol] My apologies... - -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 .. for cluttering up the list with abacadabra, and for cluttering again writing this apology. I was trying to help Chris, but lazy lout that I am I sent it to microarray-ontol (should have been ..-request) instead of majordomo. Ah well, it is not everyday that people laugh at me, thinking me a clueless newbie. Ok, back to lurking again. With kind regards, - - -- drs. Jean-Jack M. Riethoven EMBL Outstation - Hinxton pow@ebi.ac.uk ICQ#: 3433929 European Bioinformatics Institute Phone: (+44) 1223 494635 Wellcome Trust Genome Campus Fax : (+44) 1223 494468 Hinxton, Cambridge CB10 1SD URL : http://industry.ebi.ac.uk/ UNITED KINGDOM Need to find bioinformatics or molecular biology web sites or resources? Use BioWurld at http://www.ebi.ac.uk/biowurld - -----BEGIN PGP SIGNATURE----- Version: PGPfreeware 6.5.1 Int. for non-commercial use iQA/AwUBOpKi7dRKgzGsY6sQEQJGHACguYIe/cm+Z4CjiOW0JyIDjJHQZFcAnRBJ gRRzuTHcMly4w7ndBY+OlNtz =/Q4A - -----END PGP SIGNATURE----- ------------------------------ Date: Tue, 20 Feb 2001 12:27:18 -0500 From: Chris Stoeckert Subject: [microarray-ontol] Update on what's happening Dear Group, I just found out that my last two postings did not make it to the list. My email server had changed and so I needed to resubscribe to the list. The following message was sent Jan 25th. Sorry for the delay. I will resend my other mail as well. If you have questions as to whether your mail was ever heard, there is an EBI Microarray Discussion List at http://bfx.kribb.re.kr/microarray/. I will provide a link to this site at the ontologies home page. Cheers, Chris Hello all, First, a warm and heartfelt thank you to Mike Bittner for leading us through the first year. Second, MGED3 is coming up. An official agenda will be posted very soon. The meeting will be held at Stanford from March 29 to the 31st. I have asked that we be given a room at Stanford to hold a workshop meeting on ontologies on March 28th at 3:30. I hope many of you can make it because we only seem to make progress when we get together. Will put together an agenda as we get closer. Third, we had an impromptu mini-ontologies meeting of people attending the MGED steering committee meeting last November. Two developments from that meeting were: 1. I'm drafting a dictionary of MIAME (the minimal requirements document generated by the annotation group). The goal is to provide a definition of the terms listed in the MIAME document as requirements with reference to MAML (the XML document generated by the data exchange group) plus indications of when the terms are appropriate and dependencies on other terms. 2. Species-specific terms will be addressed by Mike Eisen (yeast), Martin Ringwald (mouse), and Thodoros Topotoglou (human). That leaves plants and microbes that I will attempt to cover but would really appreciate any help. Fourth, I will try to update the ontologies home page. I want to add the work going on with the Gene Ontology Consortium that some of you are members of. I see the GO terms as representing a different knowledge domain than microarray experiments but one that we want to be able to map to and we can learn a lot from their approach. I will also post any progress I and the others make on the two developments described above. Will send out a message when this happens. Please send me suggestions for any ontologies, dictionaries, controlled vocabularies, etc. that you use. I'll add them to the list. Chris - -- Chris Stoeckert, Ph.D. Research Associate Professor, Dept. of Genetics Center for Bioinformatics, University of Pennsylvania 418 Guardian Dr., Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111 ------------------------------ Date: Tue, 20 Feb 2001 13:16:11 -0500 From: Chris Stoeckert Subject: [microarray-ontol] reposting Dear group, Here is the other reposting first sent Feb 6th. btw I completely mangled Thodoros Topaloglou name in my last mail. Sorry Thodoros. The official announcement for MGED3 is out. It can be accessed at the MGED home page (http://www.mged.org) or directly at http://www.dnachip.org/mged3/. Here is a tentative agenda for the ontologies working group that will meet on March 28th from 3:30-6:30 PM. Comments and suggested changes are welcome. I will post the agenda on the working group web site within a week or so. 1. Description of an ontology I'd like to quickly get everyone up to speed on what an ontology is so that we are all talking about the same thing. This will include concepts and their definitions, and consideration of is-a and part-of relationships. It will also include the role of controlled vocabularies, schemas, and mappings between knowledge domains (such as between a microarray experiment and an annotated genome). 2. Outline working group goals Our initial mandate was to come up with ontologies for sample description. This remains the major goal. However there are other parts of microarray experiments that can benefit from an ontology in the sense of providing a structure to the MIAME (minimal information about microarray experiment) document that the annotation group has generated. 3. Review progress of the group. Key concepts for sample descriptions have been generated. Several ontologies have been identified for sample descriptions. Working group members have been asked to identify species-specific issues to address. 4. Assign tasks The major goal of this working group meeting is to draw up a list of what we want to accomplish over the next year and identify people willing to take responsibility for the different list items. 5. Plan next working group meeting In order to make any progress, we (or some subset of us) are going to have to meet more frequently so that we don't have to spend much time bringing people up to speed and we can focus on progress reports for assigned tasks. We will look for upcoming meetings that many of us might attend or simply pick a place and time to meet this summer. Chris - -- Chris Stoeckert, Ph.D. Research Associate Professor, Dept. of Genetics Center for Bioinformatics, University of Pennsylvania 418 Guardian Dr., Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111 ------------------------------ Date: Thu, 1 Mar 2001 18:57:02 -0500 From: Chris Stoeckert Subject: [microarray-ontol] update to ontologies home page First of all, this is the last day for registration to MGED3, so please register ! I've added a few new links on the page. http://www.cbil.upenn.edu/Ontology/MGED_ontology.html Notably, links to the MIAME and MAML documents. Also there is a MIAME to MAML link. I've been working up the 6 major MIAME categories in tables providing definitions and constraints with mappings to MAML,this is there as well. Still have two more to go (Measurements and Controls). Comments are welcome - especially as I haven't nailed down a few concepts. I've added two Ontology resources: Arabidopsis Functional Genomics Consortium and the GeneOntology Consortium. Cheers, Chris - -- Chris Stoeckert, Ph.D. Research Associate Professor, Dept. of Genetics Center for Bioinformatics, University of Pennsylvania 418 Guardian Dr., Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111 ------------------------------ End of microarray-ontol-digest V1 #5 ************************************