From val at sanger.ac.uk Thu Feb 1 01:41:36 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 01 Feb 2007 09:41:36 +0000 Subject: use of Uniprot accession Vs GenBank Accession in With column In-Reply-To: <45C0E5FB.1090905@cornell.edu> References: <45BFAD24.9020706@cornell.edu> <45BFBD35.4000805@cornell.edu> <45C07856.1040807@ebi.ac.uk> <45C07AD9.2090504@sanger.ac.uk> <45C0C519.7000907@ebi.ac.uk> <31147383-06F3-423B-A9E3-27FD01CBA30E@genome.stanford.edu> <45C0E5FB.1090905@cornell.edu> Message-ID: <45C1B5D0.1060307@sanger.ac.uk> Hi Pankaj, From my understanding, what we are discussing here, is an accession number to put in the 'with' column, when an an author or curator has made an inference based on a similarity at the protein level. Bearing this in mind, all of what you say below, which may be true, is not relevant to the discussion of whether this identifier is appropriate for this field in this instance. The proteins are identical, and from the same species. You are not annotating an original experiment, you are annotating an inference based on sequence similarity which is unaffected by any differences in the underlying DNA sequence or expression pattern. If you are annotating an IGI, the entity in the with column will be to an entry within your own database, and you can use your own identifiers to capture the exact locus information to make sure that the entitity that you annotate derives from the DNA sequence of the locus. Does that make sense? A question though, if people were to use the PID what would be database of database:ID ? does that have name space? Val Pankaj Jaiswal wrote: > I agree. Also if you talk to a geneticist and/or an evolutionary > biologists who care about the polymorphism (at nucleotide and protein > levels), this is a significant problem. So far what I have heard from > them is that they expect to find (in case of the example given by > Emily) two protein entries because there are two different gene loci > that encode it. Another reason being both the genes will have > different gene full names and symbols e.g. SEC61G1 and SEC61G2. > > Therefore even though the sequences were 100% identical SEC61G1 and > SEC61G2 are different. This would allow to provide a distinct > expression profile, localization, or interaction data if any. > > Also lets say someone only did the real experiments with SEC61G1 and > not with the SEC61G2, then if by chance I have to generate a GO > annotation based on ISS to the Arabidopsis gene, the idea would be to > use the protein_accession_number of the SEC61G1 and not the SEC61G2, > because only SEC61G1 was characterized using real lab experiments. > > It would be wrong to put both the arabidopsis gene products (SEC61G1 > and SEC61G2) with one single Uniprot entry. However, the GB/EMBL/DDBJ > will most likely maintain separate protein accessions encoded by these > two genes. > > -Pankaj > > > > Gavin Sherlock wrote: > >> Interesting dilemma. >> >> Clearly the result is based on a protein, but what if there are two >> genes, A and B, whose DNA sequences may differ, but whose protein >> products have identical sequences. What if one of them is expressed >> under some circumstances, allowing its product to interact with >> protein X, and the other is never expressed under circumstances that >> would allow its product to interact with protein X. In this case, >> when annotating protein X, knowing the gene whose product it >> interacts with would be important. Of course, I have no examples of >> this, and no reason to expect that they might exist, but it is a >> formal possibility, and there are certainly examples in the >> literature where synonymous changes can affect function. >> >> Cheers, >> Gavin >> >> On Jan 31, 2007, at 8:34 AM, Emily Dimmer wrote: >> >>> Hi, >>> >>> Yes this is true, there is only one UniProtKB record when two >>> proteins are from the same species and 100% identical. >>> I thought this discussion was started what type of accessions should >>> be used in the 'with' column for IPI-evidenced annotations ... if >>> the proteins are identical and the experiment e.g. a protein binding >>> assay, is done with the protein, how much is this a problem? >>> Surely its more correct and more meaningful to the user to use a >>> protein identifier. >>> >>> For an example of two genes encoding the same protein sequence see >>> Q9SW34 (S61G1_ARATH) >>> (http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinId=S61G1_ARATH&pager.offset=null) >>> >>> You can see the two gene name lines here: >>> >>> GN Name=SEC61G1; OrderedLocusNames=At4g24920; ORFNames=F13M23.60; >>> GN and >>> GN Name=SEC61G2; OrderedLocusNames=At5g50460; ORFNames=MBA10.1; >>> >>> Emily >>> >>> Doug Howe wrote: >>> >>>> I seem to recall that identical proteins generated from distinct >>>> genes are represented by a single UniProt record. If that is still >>>> true, isn't that a case where an EMBL accession would be better in >>>> the with field? >>>> -Doug >>>> >>>> On Wed, 31 Jan 2007, Valerie Wood wrote: >>>> >>>>> Emily Dimmer wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> Just a quick note, GenBank Accessions are exactly the same as >>>>>> EMBL accessions. All EMBL accessions are cross-referenced in >>>>>> UniProt. Therefore if you *did* want to find a UniProtKB >>>>>> accession, you should be able just to enter the GenBank >>>>>> accession into the UniProt website (or search via SRS etc...) and >>>>>> it will bring up the quivalent UniProt entry (I do realize that >>>>>> for some groups there is an issue of a UniProtKB accession not >>>>>> yet existing for an equivalent GenBank accession). >>>>>> >>>>> >>>>> In the cases where there is no Uniprot ID, it may be a problem to >>>>> refer to the Genbank/EMBL accession number as this will often be a >>>>> cosmid or contig and contain multiple CDS- in these cases you >>>>> can't refer to the gene/protein uniquely with an EMBL ID. >>>>> >>>>> Presumably though, for the cases where there is no Swiss-Prot >>>>> /Trembl ID then the likelihood that you would be using this as a >>>>> dbxref in the with column for an ISS is very small (I have never >>>>> come across one). Can't we all agree to track down the Uniprot ID >>>>> (which is relatively straightforward), or in cases why there isn't >>>>> one, contact Uniprot to work out why? >>>>> >>>>> Val >>>>> >>>>>> Cheers, >>>>>> Emily >>>>>> >>>>>> Midori Harris wrote: >>>>>> >>>>>>> Actually, GB or GenBank would also be acceptable, because >>>>>>> they're listed as synonyms in GO.xrf_abbs (tthe filtering script >>>>>>> allows anything in the 'aabbreviation' or 'synonym' fields). >>>>>>> >>>>>>> m >>>>>>> >>>>>>> On Tue, 30 Jan 2007, Karen Christie wrote: >>>>>>> >>>>>>>> Note that the abbreviation selected by GO for the IDs for >>>>>>>> GenBank, DDBJ, and EMBL is EMBL, so that's the namespace that >>>>>>>> needs to be used in the gene_association files for GO. >>>>>>>> >>>>>>>> -Karen >>>>>>>> >>>>>>>> >>>>>>>> On Tue, 30 Jan 2007, Pankaj Jaiswal wrote: >>>>>>>> >>>>>>>>> Got it. We will use the GB one. >>>>>>>>> >>>>>>>>> BTW GenBank ID is different than the GenBank Accession. >>>>>>>>> GenBank ID is the ID exclusive for the GenBank database entry. >>>>>>>>> One GB accession can have mappings to several GenBank IDs. >>>>>>>>> >>>>>>>>> Pankaj >>>>>>>>> >>>>>>>>> Karen Christie wrote: >>>>>>>>> >>>>>>>>>> Hi Pankaj, >>>>>>>>>> >>>>>>>>>> GenBank IDs are already allowed in the with column. The main >>>>>>>>>> requirement is that the abbreviation (or namespace) for the >>>>>>>>>> source of the ID be included in the GO.xrf_abbs file. There >>>>>>>>>> is already an entry for IDs coming from GenBank/DDBJ/EMBL, so >>>>>>>>>> these IDs are already permissable. >>>>>>>>>> >>>>>>>>>> -Karen >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> abbreviation: EMBL >>>>>>>>>> database: International Nucleotide Sequence Database >>>>>>>>>> Collaboration, comprising EMBL-EBI International Nucleotide >>>>>>>>>> Sequence Data Library (EMBL-Bank), DNA DataBank of Japan >>>>>>>>>> (DDBJ), and NCBI GenBank >>>>>>>>>> object: Sequence accession number >>>>>>>>>> example_id: EMBL:AA816246 >>>>>>>>>> example_id: DDBJ:AA816246 >>>>>>>>>> example_id: GB:AA816246 >>>>>>>>>> synonym: DDBJ >>>>>>>>>> synonym: GB >>>>>>>>>> synonym: GenBank >>>>>>>>>> generic_url: http://www.ebi.ac.uk/embl/ >>>>>>>>>> generic_url: http://www.ddbj.nig.ac.jp/ >>>>>>>>>> generic_url: http://www.ncbi.nlm.nih.gov/Genbank/ >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Tue, 30 Jan 2007, Pankaj Jaiswal wrote: >>>>>>>>>> >>>>>>>>>>> Hi Everyone, >>>>>>>>>>> >>>>>>>>>>> I know it is an accepted SOP to include either the Uniprot >>>>>>>>>>> accession number or the individual database's own >>>>>>>>>>> gene/protein ID in the WITH column of the association tables. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> However while doing it it seems that it is too much of the >>>>>>>>>>> work to find out what is the Uniprot entry, because often >>>>>>>>>>> the DDBJ and GenBank do not Xref each other using the >>>>>>>>>>> Uniprot accession. However the best alternative is to use >>>>>>>>>>> the GenBank's Accession number. Which I see that almost all >>>>>>>>>>> the databases including Uniprot, DDBJ, EMBL, PIR etc. use it >>>>>>>>>>> to cross refer. It is also the most suitable ID used to find >>>>>>>>>>> the particular nucleotide/protein accession that we are >>>>>>>>>>> looking for using the same query, no matter which db is >>>>>>>>>>> queried. >>>>>>>>>>> >>>>>>>>>>> I hope you would consider my request by adopting the >>>>>>>>>>> GenBank's accession number, unless there is a better option. >>>>>>>>>>> >>>>>>>>>>> Thanks >>>>>>>>>>> Pankaj >>>>>>>>>>> --Pankaj Jaiswal >>>>>>>>>>> G-15, Bradfield Hall >>>>>>>>>>> Dept. of Plant Breeding and Genetics >>>>>>>>>>> Cornell University >>>>>>>>>>> Ithaca, NY-14853, USA >>>>>>>>>>> >>>>>>>>>>> Ph. +1-607-255-3103 / 4199 >>>>>>>>>>> fax: +1-607-255-6683 >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> --Pankaj Jaiswal >>>>>>>>> G-15, Bradfield Hall >>>>>>>>> Dept. of Plant Breeding and Genetics >>>>>>>>> Cornell University >>>>>>>>> Ithaca, NY-14853, USA >>>>>>>>> >>>>>>>>> Ph. +1-607-255-3103 / 4199 >>>>>>>>> fax: +1-607-255-6683 >>>>>>>>> >>>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> ----------------------------------------------------------------------------- >>>>> >>>>> 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 >>>>> >>> >>> >>> --************************************ >>> 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 >>> ************************************ >> >> >> > -- --------------------------------------------------------------------------- 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 val at sanger.ac.uk Thu Feb 1 09:28:58 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 01 Feb 2007 17:28:58 +0000 Subject: Some thoughts on publications that use GO Message-ID: <45C2235A.1000309@sanger.ac.uk> Here is an example I am reading of biologists using GO for datamining of candidate genes (combined with expression data) To identify meiosis-specific RNA-binding proteins that may associate with these ncRNAs, we searched the /S. pombe/ genome database for uncharacterized genes that both harbor RNA-binding motifs and show enhanced expression during meiosis (http://www.genedb.org/genedb/pombe/index.jsp ) (13 ). We screened 275 genes in the genome database AmiGO (http://www.genedb.org/amigo/perl/go.cgi ) using ?RNA binding? as a query word. In addition, we selected genes that display more enhanced expression in meiotic prophase I than in other meiotic phases based on the cDNA microarray data (13 ). This selection yielded three candidate genes, SPBC29A10.02, SPCC1682.08c, and SPAC4G9.05. nice example GO not cited Spo5/Mug12, a putative meiosis-specific RNA-binding protein, is essential for meiotic progression and forms Mei2 dot-like nuclear foci. Eukaryot Cell. 2006 Aug;5(8):1301-13. PMID: 16896214 -- --------------------------------------------------------------------------- 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 val at sanger.ac.uk Thu Feb 1 09:40:59 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 01 Feb 2007 17:40:59 +0000 Subject: Some thoughts on publications that use GO/readable Message-ID: <45C2262B.1040501@sanger.ac.uk> Here is an example I am reading of biologists using GO for datamining of candidate genes (combined with expression data) To identify meiosis-specific RNA-binding proteins that may associate with these ncRNAs, we searched the /S. pombe/ genome database for uncharacterized genes that both harbor RNA-binding motifs and show enhanced expression during meiosis . We screened 275 genes in the genome database AmiGO http://www.genedb.org/amigo/perl/go.cgi using ?RNA binding? as a query word. In addition, we selected genes that display more enhanced expression in meiotic prophase I than in other meiotic phases based on the cDNA microarray data. This selection yielded three candidate genes, SPBC29A10.02, SPCC1682.08c, and SPAC4G9.05. nice example GO not cited Spo5/Mug12, a putative meiosis-specific RNA-binding protein, is essential for meiotic progression and forms Mei2 dot-like nuclear foci. Eukaryot Cell. 2006 Aug;5(8):1301-13. PMID: 16896214 -- --------------------------------------------------------------------------- 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 Thu Feb 1 13:51:12 2007 From: camon at ebi.ac.uk (camon at ebi.ac.uk) Date: Thu, 1 Feb 2007 21:51:12 -0000 (GMT) Subject: Some thoughts on publications that use GO/readable In-Reply-To: <45C2262B.1040501@sanger.ac.uk> References: <45C2262B.1040501@sanger.ac.uk> Message-ID: <33756.212.139.237.203.1170366672.squirrel@webmail.ebi.ac.uk> Hi When reporting on GOA for EBI reviews and for grants we are often requested to give an indication of its usage via google scholar etc... Rarely do papers cite GOA directly either...but if they cite a GOC paper or the phrase'gene ontology' and cite 'human' in title/abstract we usually know the data has come from our goa-human file.. So I guess my question is do we recommend that users cite GOC papers are individual database/mod source of the data.. I think the latter is hard to enforce and we will need a combination of techniques to guess-tim-ate how well used we are in the literature... Evelyn > Here is an example I am reading of biologists using GO for datamining of > candidate genes (combined with expression data) > > To identify meiosis-specific RNA-binding proteins that may associate > with these ncRNAs, we searched the /S. pombe/ genome database for > uncharacterized genes that both harbor RNA-binding motifs and show > enhanced expression during meiosis . We screened 275 genes in the genome > database AmiGO http://www.genedb.org/amigo/perl/go.cgi using ?RNA > binding? as a query word. In addition, we selected genes that display > more enhanced expression in meiotic prophase I than in other meiotic > phases based on the cDNA microarray data. This selection yielded three > candidate genes, SPBC29A10.02, SPCC1682.08c, and SPAC4G9.05. > > nice example > > > GO not cited > > > > Spo5/Mug12, a putative meiosis-specific RNA-binding protein, is > essential for meiotic progression and forms Mei2 dot-like nuclear foci. > Eukaryot Cell. 2006 Aug;5(8):1301-13. > PMID: 16896214 > > > > -- > --------------------------------------------------------------------------- > 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 rama at genome.Stanford.EDU Fri Feb 2 09:44:14 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Fri, 2 Feb 2007 09:44:14 -0800 Subject: AmiGO on New servers-please test Message-ID: Hi All, AmiGO has been installed on the new servers here at Stanford. URL- http://amigo.geneontology.org/cgi-bin/amigo/go.cgi Please test and send comments by Wednesday, Feb 7th, 5:00 PM PST. What is different in the new servers? What should you look for? Production and the new servers should function identically in terms of searching, display, data, etc., except for speed. There are few minor interface level cosmetic changes that you will notice on the new servers that you will not see on the production servers (see below). Please compare your searches against www.godatabase.org and report all oddities/bugs. Please report bugs only. If you have suggestions to improve AmiGO, please post them on the SF tracker. https://sourceforge.net/tracker/?group_id=36855&atid=494390 1) '?' icon for help (check the Advanced Search or BLAST pages) 2) the GO Help desk link on the bottom now goes to the 'Contact GO form' 3) In the header, Gene Ontology on the top left corner is now clickable and goes to the GOC home page 4) if you type in a gene name/symbol that doesn't have annotations (try TRIM100), you will see a message that says- "If you are interested in annotating this gene product, please contact GO Help Desk". Happy testing, Rama and the AmiGO crew From jclark at ebi.ac.uk Tue Feb 6 02:24:03 2007 From: jclark at ebi.ac.uk (J Clark) Date: Tue, 06 Feb 2007 10:24:03 +0000 Subject: Alert: Proposal to obsolete GO:0009781: photosynthetic water oxidation that does not impact existing annotation Message-ID: <45C85743.1070007@ebi.ac.uk> The proposal has been made to obsolete GO:0009781: photosynthetic water oxidation. There exist today no annotations to this term as follows (data from AmiGO). The term is used in no mappings. The term is not found in the generic GO slim set. The reasons for this proposal are that this term represents a function. Following obsoletion a new equivalent term will be instantiated in the function ontology. UNLESS OBJECTIONS ARE RECEIVED BY 13th February WE WILL ASSUME THAT YOU AGREE TO THIS CHANGE. From ma11 at gen.cam.ac.uk Fri Feb 9 04:27:36 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner (Genetics)) Date: Fri, 9 Feb 2007 12:27:36 +0000 (GMT) Subject: Database Registrary Message-ID: Dear Rolf, Amos, and Jim, This is a proposal that will (a) save us all work, (b) be a benefit to the community, and generally be the best thing since sliced bread. The Collaborators, SwissProt and the GO (and doubtless others) use db_xrefs in their databases. They all abbreviate the databases referred to, and normally use a syntax like 'DB:id' for an object to be referred to: e.g., "ASAP:ABE-0000006". The three files that I know of are: http://www.ncbi.nlm.nih.gov/projects/collab/db_xref.html (and its homologs at EBI and DDBJ) http://expasy.org/cgi-bin/lists?dbxref.txt http://www.geneontology.org/cgi-bin/xrefs.cgi But, of course, we do not necessarily use the _same_ acronym for the _same_ database. Urged by some community comments we (GO) think that this would be an easy thing to standardise on. Question to you: Can we agree to standardise on a set of acronyms for databases that are referred to in db_xref lines, or their analogs ? If so, I will make a spreadsheet of 4 columns (database and the three sets of acronyms I know of) with a suggested agreed term. If we can get that far, we would need to establish a central site (the GO would be happy to host this). It would include the sum of the information we each need, plus a domain (NCBI, SwissProt, GO) specific subset, so maintaining your own pages will be trivial. I look forward to your reply and, in anticipation of this tremendous leap forward, I am, Michael Ashburner From dbarrell at ebi.ac.uk Fri Feb 9 07:31:20 2007 From: dbarrell at ebi.ac.uk (Daniel Barrell) Date: Fri, 09 Feb 2007 15:31:20 +0000 Subject: gp2protein.unigene Message-ID: <45CC93C8.8050609@ebi.ac.uk> Hi, Just to let you know that I've changed this file from a Human cluster ID mapping file to one containing multiple species. I hope this doesn't affect the way anyone uses it but you should be aware that there are no longer just Hs.* identifiers anymore. Cheers Dan -- Daniel Barrell EMBL - The EBI Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Phone: +44 (0)1223 492551 Email: dbarrell at ebi.ac.uk From ma11 at gen.cam.ac.uk Fri Feb 9 14:29:19 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner (Genetics)) Date: Fri, 9 Feb 2007 22:29:19 +0000 Subject: Databas Registrary Message-ID: Quite a fast and positive response. I will follow up next week. Michael >From ostell at ncbi.nlm.nih.gov Fri Feb 09 14:07:13 2007 Envelope-to: ma11 at gen.cam.ac.uk Delivery-date: Fri, 09 Feb 2007 14:07:13 +0000 X-Cam-SpamDetails: scanned, SpamAssassin-3.1.7 (score=0) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable Subject: RE: Database Registrary Date: Fri, 9 Feb 2007 09:06:59 -0500 X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Database Registrary Thread-Index: AcdMRbQEtYOkCFuRQPOslXusE1yscAADWj1Q From: "Ostell, Jim \(NIH/NLM/NCBI\) [E]" To: "Michael Ashburner \(Genetics\)" , , Cc: , "Mizrachi, Ilene \(NIH/NLM/NCBI\) [E]" X-OriginalArrivalTime: 09 Feb 2007 14:06:59.0990 (UTC) FILETIME=[90DF5360:01C74C53] X-Status: $$$$ X-UID: 0000013392 Hi Michael, We agree that it makes sense to use the same acronymn for the same database and id type. We have not knowingly invented one that differed from other common usage, but it is certainly possible that we have inadvertently done it. For the dbxrefs we use, we are happy to work to reconcile the acronym to a common usage.=20 Ilene Mizrachi, cc'd above, is the keeper of the GenBank dbxref list and can be the point of contact on this for us. Jim >From parkinson at ebi.ac.uk Fri Feb 09 12:37:20 2007 Envelope-to: ma11 at gen.cam.ac.uk Delivery-date: Fri, 09 Feb 2007 12:37:20 +0000 X-Cam-SpamDetails: scanned, SpamAssassin-3.1.7 (score=0) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Date: Fri, 9 Feb 2007 12:37:05 -0000 (GMT) Subject: Re: Database Registrary From: "Helen Parkinson" To: "Michael Ashburner (Genetics)" User-Agent: SquirrelMail/1.4.6-1 MIME-Version: 1.0 X-Priority: 3 (Normal) Importance: Normal Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by maui.ebi.ac.uk id l19Cb5n05423 X-Status: $$$$ X-UID: 0000013369 Michael good idea. ArrayExpress also needs this and we'd be willing to come into line with the GO community here's our current list of db annotation sources which is probably wider scope - we have ontologies, institutional dbs etc in here, I was hoping some of these end up in obi - have you decided on your scope here? We als= o include URI for all these and I can also generate that if it's helpful cheers Helen >From deustp01 at med.nyu.edu Fri Feb 09 13:43:10 2007 Envelope-to: ma11 at gen.cam.ac.uk Delivery-date: Fri, 09 Feb 2007 13:43:10 +0000 X-Cam-SpamDetails: scanned, SpamAssassin-3.1.7 (score=0) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Date: Fri, 09 Feb 2007 08:38:18 -0500 From: Peter D'Eustachio Subject: Re: Database Registrary To: Alan Ruttenberg Cc: "Michael Ashburner (Genetics)" MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.3028 Content-transfer-encoding: 7bit X-Priority: 3 X-MSMail-priority: Normal X-Status: $$$$ X-UID: 0000013385 Alan, This sounds to me like it has considerable overlap with the BioPax discussion last spring at CSHL of the need for a registry of namespaces. Does BioPax want to jump in here as well, certainly as a user and perhaps as a contributor? (This message is meant for the BioPax developers discussion, and in my absent-mindedness, I forget which e-mail address to post it to to get it there.) Peter >From rolf.apweiler at gmail.com Fri Feb 09 13:42:20 2007 Envelope-to: ma11 at gen.cam.ac.uk Delivery-date: Fri, 09 Feb 2007 13:42:20 +0000 X-Cam-SpamDetails: scanned, SpamAssassin-3.1.7 (score=0) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=beta; h=received:message-id:date:reply-to:organization:user-agent:x-accept-language:mime-version:to:cc:subject:references:in-reply-to:content-type:content-transfer-encoding:from; b=XflGOwsomy/LaQrLMDxclu8H8TmDL+I5lmoqu3PJOPfKRcmy0aagk0l5lR8TixhYhRgIGa1uUPRk8Kc5pcmXtwcGnDfD0SEl//oLJJrAuTZW183K5WcjfRF07uByifqE60+plZAdWY6BxN7RW5vOV+xCsEGfeDngvecZEgV8Dtc= Date: Fri, 09 Feb 2007 13:41:38 +0000 User-Agent: Mozilla Thunderbird 1.0.6 (Windows/20050716) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "Michael Ashburner (Genetics)" CC: ab at isb-sib.ch, ostell at ncbi.nlm.nih.gov, go at genome.stanford.edu Subject: Re: Database Registrary Content-Transfer-Encoding: 7bit From: apweiler X-Status: $$$$ X-UID: 0000013384 Hi Michael, Sounds like a good idea. Rolf From cherry at stanford.edu Sat Feb 10 08:05:33 2007 From: cherry at stanford.edu (Mike Cherry) Date: Sat, 10 Feb 2007 08:05:33 -0800 Subject: annotation table at GO site updated Message-ID: <94370DFC-9752-46AD-B9AB-64E20995E174@stanford.edu> The new version of the Current Annotations has been live for a few days. The big changes include the projects being sorted by species and a reduction in the number of statistics reported. The new page also links our visitors to the CVSWEB for file download. All this was designed by Amelia and the AmiGO Working Group. http://www.geneontology.org/GO.current.annotations.shtml The stats are updated once a day, at the moment, just after the Anonymous CVS repository is updated. -Mike From ma11 at gen.cam.ac.uk Sat Feb 10 16:24:34 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner (Genetics)) Date: Sun, 11 Feb 2007 00:24:34 +0000 Subject: annotation table at GO site updated Message-ID: Looks good. Great job Amelia. M From midori at ebi.ac.uk Fri Feb 16 01:55:06 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 16 Feb 2007 09:55:06 +0000 (GMT) Subject: Feb. 14 managers' minutes Message-ID: Hi, The minutes from yesterday's GO Managers conference call are now on the internal wiki: http://gocwiki.geneontology.org/index.php/Managers_14Feb07 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, contact the GO PIs . Midori From camon at ebi.ac.uk Mon Feb 19 08:36:49 2007 From: camon at ebi.ac.uk (Evelyn Camon) Date: Mon, 19 Feb 2007 16:36:49 +0000 Subject: Good GO usage paper: epilepsy. Message-ID: <45D9D221.2090800@ebi.ac.uk> I know there are loads but I thought this was a goog GO usage paper... which btw does not cite a GOC paper directly... Potential new antiepileptogenic targets indicated by microarray analysis in a rat model for temporal lobe epilepsy. PMID: 17065450 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 jane at ebi.ac.uk Mon Feb 19 08:45:36 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Mon, 19 Feb 2007 16:45:36 +0000 Subject: Good GO usage paper: epilepsy. In-Reply-To: <45D9D221.2090800@ebi.ac.uk> References: <45D9D221.2090800@ebi.ac.uk> Message-ID: <38A2A556-CD1F-4501-930D-A1A784B50606@ebi.ac.uk> It's a bit remiss not to cite GOC, considering this is a line from the abstract: "We used GENMAPP and Gene Ontology to identify global biological trends in gene expression data." They cite GenMAPP (MAPPFinder) instead... jane On 19 Feb 2007, at 16:36, Evelyn Camon wrote: > I know there are loads but I thought this was a goog GO usage paper... > > which btw does not cite a GOC paper directly... > > Potential new antiepileptogenic targets indicated by microarray > analysis in a rat model for temporal lobe epilepsy. > PMID: 17065450 > > 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 camon at ebi.ac.uk Tue Feb 20 03:31:07 2007 From: camon at ebi.ac.uk (Evelyn Camon) Date: Tue, 20 Feb 2007 11:31:07 +0000 Subject: Won For All' Michael Ashburner Message-ID: <45DADBFB.3070302@ebi.ac.uk> Hi, Sorry for the spam...nice to have a light hearted GOC mail for a change :-))) I was just looking up our GOA book chapter in Amazon and thought I would compare our sales rating to Michaels book just for fun (which of course is much better :-))) Anyway I noticed that the perfect partner to Michaels book is listed as: 'The God Delusion' by Richard Dawkins any way it made me giggle... Evelyn http://www.amazon.co.uk/Won-All-M-Ashburner/dp/0879698020/sr=1-1/qid=1171970587/ref=sr_1_1/026-3332777-4545211?ie=UTF8&s=books -- 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 camon at ebi.ac.uk Wed Feb 21 05:27:34 2007 From: camon at ebi.ac.uk (Evelyn Camon) Date: Wed, 21 Feb 2007 13:27:34 +0000 Subject: Highlighting abstracts with GO terms: CiteXplore Message-ID: <45DC48C6.9000507@ebi.ac.uk> Hi, I may have mailed about this before but I wanted to make you aware of the citation browser at the EBI. We are routinely using this instead of Pubmed now. QuickGO now links to CiteXplore(developed by Mark Rijnbeek) rather than Pubmed. Having browsed for papers you can highlight the titles and abstract for GO terms (linked to QuickGO) or protein/gene names linked to UniProtKB. In fact it can be a very quick way of finding a UniProtKB accession. This tool also allows you to browse your history of queries and indicateds the taxonomic species covered by your queried papers which I hope in the future can be updated from our curation. The nice part about this service is I feel that we can adapt it to our needs. So feel free to comment to me about it and Ill forward these to Mark. I attach a figure of the GO term highlighting which only aims for exact GO term matches in the text. 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: CiteXplore.jpg Type: image/jpeg Size: 135359 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20070221/990e851f/attachment.jpg -------------- next part -------------- A non-text attachment was scrubbed... Name: CiteXplore2.jpg Type: image/jpeg Size: 39353 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20070221/990e851f/attachment-0001.jpg From sart2 at gen.cam.ac.uk Thu Feb 22 09:17:43 2007 From: sart2 at gen.cam.ac.uk (Susan Tweedie) Date: Thu, 22 Feb 2007 17:17:43 +0000 Subject: proof Feb newsletter please Message-ID: <1172164663.22797.105.camel@paul.gen.cam.ac.uk> Hi all, Thanks for all your input to the Feb newsletter. A pdf of our latest version is attached. It would be great if you could have a look and let us know if there are any mistakes before we send it out. Thanks, Susan (for the newsletter team) -------------- next part -------------- A non-text attachment was scrubbed... Name: GOnewsletter_Feb07_proof.pdf Type: application/octet-stream Size: 262577 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20070222/ce6a9eae/attachment.obj From midori at ebi.ac.uk Thu Feb 22 09:48:07 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 22 Feb 2007 17:48:07 +0000 (GMT) Subject: proof Feb newsletter please In-Reply-To: <1172164663.22797.105.camel@paul.gen.cam.ac.uk> References: <1172164663.22797.105.camel@paul.gen.cam.ac.uk> Message-ID: Another excellent newsletter! Many thanks to the team. Just some picky little things: - In the RSC blurb, first sentence: the abbreviation 'RSC' should be in parentheses, not square brackets. - In 'Gene of the quarter': -- The gene name 'MSH2' should be italicized, at least for S. cerevisiae, and maybe for some or all of the other species as well. -- The last sentence of the first paragraph is missing a period (aka full stop). - In '3 new genomes': -- There's an 'and' that's in italics by mistake. -- Change 'tickbourne' to 'tick-borne'. midori On Thu, 22 Feb 2007, Susan Tweedie wrote: > Hi all, > > Thanks for all your input to the Feb newsletter. A pdf of our latest > version is attached. It would be great if you could have a look and let > us know if there are any mistakes before we send it out. > > Thanks, > > Susan (for the newsletter team) > > > > > > From donghui at stanford.edu Thu Feb 22 09:59:03 2007 From: donghui at stanford.edu (Donghui Li) Date: Thu, 22 Feb 2007 09:59:03 -0800 Subject: proof Feb newsletter please In-Reply-To: References: <1172164663.22797.105.camel@paul.gen.cam.ac.uk> Message-ID: <45DDD9E7.5080600@stanford.edu> To add to Midori's lis: Gene of the quarter should be Gene of the Quarter. Donghui Midori Harris wrote: > Another excellent newsletter! Many thanks to the team. > > Just some picky little things: > > - In the RSC blurb, first sentence: the abbreviation 'RSC' should be > in parentheses, not square brackets. > > - In 'Gene of the quarter': > -- The gene name 'MSH2' should be italicized, at least for S. > cerevisiae, and maybe for some or all of the other species as well. > -- The last sentence of the first paragraph is missing a period (aka > full stop). > > - In '3 new genomes': > -- There's an 'and' that's in italics by mistake. > -- Change 'tickbourne' to 'tick-borne'. > > midori > > On Thu, 22 Feb 2007, Susan Tweedie wrote: > >> Hi all, >> >> Thanks for all your input to the Feb newsletter. A pdf of our latest >> version is attached. It would be great if you could have a look and let >> us know if there are any mistakes before we send it out. >> >> Thanks, >> >> Susan (for the newsletter team) >> >> >> >> >> >> -- 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 mlgwinn at tigr.org Thu Feb 22 10:21:08 2007 From: mlgwinn at tigr.org (Gwinn, Michelle L.) Date: Thu, 22 Feb 2007 13:21:08 -0500 Subject: proof Feb newsletter please References: <1172164663.22797.105.camel@paul.gen.cam.ac.uk> Message-ID: Hi, Newsletter looks great - one little nit-pick - could you put a blank line between the Euk class announcement and the web address - otherwise it looks like the web site is for just euk and it actually desribes all the classes. If there's room you could also add "For more info on either class visit...." , but if not just the space will do. Thanks, Michelle -----Original Message----- From: owner-go at genome.stanford.edu on behalf of Susan Tweedie Sent: Thu 2/22/2007 12:17 PM To: GO Subject: proof Feb newsletter please Hi all, Thanks for all your input to the Feb newsletter. A pdf of our latest version is attached. It would be great if you could have a look and let us know if there are any mistakes before we send it out. Thanks, Susan (for the newsletter team) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20070222/358e0588/attachment.html From kpilcher at northwestern.edu Thu Feb 22 10:34:13 2007 From: kpilcher at northwestern.edu (Karen Pilcher) Date: Thu, 22 Feb 2007 12:34:13 -0600 Subject: proof Feb newsletter please In-Reply-To: <1172164663.22797.105.camel@paul.gen.cam.ac.uk> References: <1172164663.22797.105.camel@paul.gen.cam.ac.uk> Message-ID: <6.0.0.22.2.20070222123050.05037448@merle.it.northwestern.edu> Hi Susan, - Similar to Donghui's comment, the titles are not consistent: some are sentence case and some are title case. - RSC: Replace 'From' with 'Beginning in' or 'Starting in' ('From' makes me think it will end at some point) - Is there any way to fix the justification in the 3 New genomes section? The line 'downloaded from' looks a bit wacky. Thanks, Karen At 11:17 AM 2/22/2007, Susan Tweedie wrote: >Hi all, > >Thanks for all your input to the Feb newsletter. A pdf of our latest >version is attached. It would be great if you could have a look and let >us know if there are any mistakes before we send it out. > >Thanks, > >Susan (for the newsletter team) > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20070222/bb8f2222/attachment.html From rama at genome.Stanford.EDU Thu Feb 22 10:42:24 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Thu, 22 Feb 2007 10:42:24 -0800 Subject: proof Feb newsletter please In-Reply-To: <6.0.0.22.2.20070222123050.05037448@merle.it.northwestern.edu> References: <1172164663.22797.105.camel@paul.gen.cam.ac.uk> <6.0.0.22.2.20070222123050.05037448@merle.it.northwestern.edu> Message-ID: <3D13A5DB-99C0-4F07-9BE2-0A4C3AFD1788@genome.stanford.edu> Hi newsletter team, Another good newsletter. Great job in putting this together. I have one question- In the gene of the quarter section, I see the following URL http://www.spatial.maine.edu/~mdolan/,... this is in Mary Dolan's space and I was wondering if it can be changed/moved to a general location? Thanks, Rama On Feb 22, 2007, at 10:34 AM, Karen Pilcher wrote: > > Hi Susan, > > - Similar to Donghui's comment, the titles are not consistent: some > are sentence case and some are title case. > > - RSC: Replace 'From' with 'Beginning in' or 'Starting in' ('From' > makes me think it will end at some point) > > - Is there any way to fix the justification in the 3 New genomes > section? The line 'downloaded from' looks a bit wacky. > > Thanks, > > Karen > > > > At 11:17 AM 2/22/2007, Susan Tweedie wrote: >> Hi all, >> >> Thanks for all your input to the Feb newsletter. A pdf of our latest >> version is attached. It would be great if you could have a look >> and let >> us know if there are any mistakes before we send it out. >> >> Thanks, >> >> Susan (for the newsletter team) >> >> >> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20070222/51f277e3/attachment.html From rama at genome.Stanford.EDU Thu Feb 22 10:43:09 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Thu, 22 Feb 2007 10:43:09 -0800 Subject: proof Feb newsletter please In-Reply-To: <6.0.0.22.2.20070222123050.05037448@merle.it.northwestern.edu> References: <1172164663.22797.105.camel@paul.gen.cam.ac.uk> <6.0.0.22.2.20070222123050.05037448@merle.it.northwestern.edu> Message-ID: <58BDAD5E-B3C7-42B1-97C1-6B8093EAE9CF@genome.stanford.edu> Ho, sorry, one more thing. Is there room to squeeze a line about the AmiGO new servers? Thanks, Rama On Feb 22, 2007, at 10:34 AM, Karen Pilcher wrote: > > Hi Susan, > > - Similar to Donghui's comment, the titles are not consistent: some > are sentence case and some are title case. > > - RSC: Replace 'From' with 'Beginning in' or 'Starting in' ('From' > makes me think it will end at some point) > > - Is there any way to fix the justification in the 3 New genomes > section? The line 'downloaded from' looks a bit wacky. > > Thanks, > > Karen > > > > At 11:17 AM 2/22/2007, Susan Tweedie wrote: >> Hi all, >> >> Thanks for all your input to the Feb newsletter. A pdf of our latest >> version is attached. It would be great if you could have a look >> and let >> us know if there are any mistakes before we send it out. >> >> Thanks, >> >> Susan (for the newsletter team) >> >> >> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20070222/b65e67da/attachment.html From tberardi at acoma.Stanford.EDU Thu Feb 22 11:21:28 2007 From: tberardi at acoma.Stanford.EDU (Tanya Berardini) Date: Thu, 22 Feb 2007 11:21:28 -0800 Subject: proof Feb newsletter please In-Reply-To: <1172164663.22797.105.camel@paul.gen.cam.ac.uk> References: <1172164663.22797.105.camel@paul.gen.cam.ac.uk> Message-ID: <45DDED38.1090703@acoma.stanford.edu> Hi all, Great newsletter! Just a couple of things about the Upcoming Meetings section. 1. Swap the order so that the earlier one comes first. 2. Change the URL of the biocurator meeting to: http://biocurator.org/Mtg2007 The other URL may change when we migrate servers and the one above will be stable. Thanks! Tanya Susan Tweedie wrote: > Hi all, > > Thanks for all your input to the Feb newsletter. A pdf of our latest > version is attached. It would be great if you could have a look and let > us know if there are any mistakes before we send it out. > > Thanks, > > Susan (for the newsletter team) > > > > -- ------------------------------------------------------------------------------------------ Tanya Berardini, Ph.D. tberardi at acoma.stanford.edu The Arabidopsis Information Resource FAX: (650) 325-6857 Carnegie Institution of Washington Tel: (650) 325-1521 ext. 325 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 ------------------------------------------------------------------------------------------ From Mary_Dolan at umit.maine.edu Thu Feb 22 12:06:10 2007 From: Mary_Dolan at umit.maine.edu (Mary Dolan) Date: Thu, 22 Feb 2007 15:06:10 -0500 Subject: proof Feb newsletter please In-Reply-To: <3D13A5DB-99C0-4F07-9BE2-0A4C3AFD1788@genome.stanford.edu> References: <3D13A5DB-99C0-4F07-9BE2-0A4C3AFD1788@genome.stanford.edu> Message-ID: Rama Balakrishnan on Thursday, February 22, 2007 at 1:42 PM -0500 wrote: >In the gene of the quarter section, I see the following URL http://www.spatial.maine.edu/~mdolan/RefGenomeGraphs/609309.html > >this is in Mary Dolan's space and I was wondering if it can be changed/moved to a general location? Hi, Rama etal. If there is a place to move things to, I could do that. 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 Thu Feb 22 12:10:13 2007 From: eurie at genome.Stanford.EDU (Eurie Hong) Date: Thu, 22 Feb 2007 12:10:13 -0800 Subject: proof Feb newsletter please In-Reply-To: References: <3D13A5DB-99C0-4F07-9BE2-0A4C3AFD1788@genome.stanford.edu> Message-ID: <9A6FF712-15F8-4A3A-B25E-508A782A6609@genome.stanford.edu> What about the images/ directory on the geneontology.org website? On Feb 22, 2007, at 12:06 PM, Mary Dolan wrote: > Rama Balakrishnan on Thursday, February > 22, 2007 at 1:42 PM -0500 wrote: >> In the gene of the quarter section, I see the following URL > http://www.spatial.maine.edu/~mdolan/RefGenomeGraphs/609309.html >> >> this is in Mary Dolan's space and I was wondering if it can be >> changed/moved to a general location? > > Hi, Rama etal. > If there is a place to move things to, I could do that. > 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 Feb 22 13:09:46 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Thu, 22 Feb 2007 13:09:46 -0800 Subject: Fwd: More inspiration for the WWW HCLSIG demo References: <45DDDE8D.50805@science.uva.nl> Message-ID: <5C98CC31-7C58-4E0E-90AB-502372D7FBD9@berkeleybop.org> some action from our friend Barend Mons that has been noticed. Begin forwarded message: > Resent-From: public-semweb-lifesci at w3.org > From: "M. Scott Marshall" > Date: February 22, 2007 10:18:53 AM PST > To: W3C HCLSIG hcls > Subject: More inspiration for the WWW HCLSIG demo > > > Checkout the demo (i.e. animation) on: > http://www.wikiprofessional.info/ > > > From val at sanger.ac.uk Thu Feb 22 13:32:36 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 22 Feb 2007 21:32:36 UT Subject: Fwd: More inspiration for the WWW HCLSIG demo Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20070222/2207e51d/attachment.pl From pj37 at cornell.edu Thu Feb 22 17:35:16 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 22 Feb 2007 20:35:16 -0500 Subject: Chromosome is an organelle ? Message-ID: <45DE44D4.4030300@cornell.edu> In this graph we see that 'chromosome' is an 'organelle'. I think majority of the researchers would consider it simply ISA cell_part (or ISA intracellular_part). If not it is something like for instance 'plastid chromosome' is a part of 'plastid' where both 'plastid chromosome' and 'plastid' are ISA 'organelle'. Or in lay person's knowledge 'an organ is PARTOF and organ' considering organelle in cell/unicellular organisms is synonymous with organs in multicellular organisms. I am not sure if this is a correct relationship in GO. Pankaj From suzi at berkeleybop.org Thu Feb 22 19:28:39 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Thu, 22 Feb 2007 19:28:39 -0800 Subject: GOC meeting minutes Message-ID: In record time (the longest perhaps) we have a draft version of the minutes from our GOC meeting at Jesus College ready for everyone to critique and revise (additions, amplifications, corrections, etc). The bad news is that there 80 actions items! The good news is that I know at least some of the items are already completed (Yeah!) Take care everyone, it was great to see all of you. Next fall in Princeton (with all action items completed) -S -------------- next part -------------- A non-text attachment was scrubbed... Name: Jan_8_2006_goc_minutes.doc Type: application/octet-stream Size: 249856 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20070222/97b3eb89/attachment.obj -------------- next part -------------- From suzi at berkeleybop.org Thu Feb 22 19:30:29 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Thu, 22 Feb 2007 19:30:29 -0800 Subject: goc minutes redux Message-ID: <66FA6284-773A-4788-A8A6-62A2FCAD11C0@berkeleybop.org> Here without the overhead of the Berkeley track changes -------------- next part -------------- A non-text attachment was scrubbed... Name: Jan_8_2006_goc_minutes.doc Type: application/octet-stream Size: 120320 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20070222/c2052d23/attachment.obj -------------- next part -------------- From ma11 at gen.cam.ac.uk Fri Feb 23 01:09:21 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner) Date: Fri, 23 Feb 2007 09:09:21 +0000 Subject: proof Feb newsletter please In-Reply-To: References: <1172164663.22797.105.camel@paul.gen.cam.ac.uk> Message-ID: Looks great ! Apart from what others have picked up: 1. URLs which link out might be colored, eg in blue. 2. It is not clear why the online version of this is "Expanded" - does it have more content ? If not, "View online ... Well done all. Michael From ma11 at gen.cam.ac.uk Fri Feb 23 02:02:46 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner) Date: Fri, 23 Feb 2007 10:02:46 +0000 Subject: GOC meeting minutes In-Reply-To: References: Message-ID: <3EA2726A-FEAD-4F2C-97DC-63F6D92A5D0B@gen.cam.ac.uk> These look fine EXCEPT for a distressing inconsistency in the use of the period key ".". I have attempted to correct these EGREGIOUS errors :=). Well done to all minute takers. Attached has periods added where called for, and a few other format/ presentation edits. Michael -------------- next part -------------- A non-text attachment was scrubbed... Name: MA-Jan_8_2006minutes.doc Type: application/applefile Size: 382 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20070223/4ad2abae/attachment.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: MA-Jan_8_2006minutes.doc Type: application/octet-stream Size: 152576 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20070223/4ad2abae/attachment.obj From trudy at vbi.vt.edu Fri Feb 23 02:08:13 2007 From: trudy at vbi.vt.edu (Trudy Torto-Alalibo) Date: Fri, 23 Feb 2007 05:08:13 -0500 (EST) Subject: proof Feb newsletter please In-Reply-To: <1172164663.22797.105.camel@paul.gen.cam.ac.uk> References: <1172164663.22797.105.camel@paul.gen.cam.ac.uk> Message-ID: <53000.204.111.138.194.1172225293.squirrel@webmail.vbi.vt.edu> Hi Susan and others, Thanks so much for including PAMGO's upcoming workshop announcement in the newsletter. I wondered though, if it is a mistake that it was labeled GO and PAMGO as was done for the workshop at PAG which was a joint venture. I am just worried that it might be misleading to participants who might think they may meet and talk to people from the "broader" GO consortium. Best, Trudy On Thu, February 22, 2007 12:17 pm, Susan Tweedie wrote: > Hi all, > > > Thanks for all your input to the Feb newsletter. A pdf of our latest > version is attached. It would be great if you could have a look and let us > know if there are any mistakes before we send it out. > > Thanks, > > > Susan (for the newsletter team) > > > > > > > Trudy Torto-Alalibo, Ph.D Senior Research Associate-PAMGO Coordinator Virginia Bioinformatics Institute, Virginia Tech Bioinformatics 1 Washington Street Blacksburg, VA 24061-0447 Tel: 540-231-3572 Fax:540-231-2606 From midori at ebi.ac.uk Fri Feb 23 03:25:38 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 23 Feb 2007 11:25:38 +0000 (GMT) Subject: GOC meeting minutes Message-ID: Thanks for all of this! In the attached, I've added a participant list, and fixed a number of typos (starting with Michael's draft). There are also a couple of new "notes". midori -------------- next part -------------- A non-text attachment was scrubbed... Name: mh-MA-Jan_8_2006minutes.doc Type: application/octet-stream Size: 121856 bytes Desc: Url : http://fafner.stanford.edu/pipermail/go/attachments/20070223/4e410894/attachment.obj -------------- next part -------------- On 23 Feb 2007, at 10:05 am, Midori Harris wrote: > > > ---------- Forwarded message ---------- > Date: Fri, 23 Feb 2007 10:02:46 +0000 > From: Michael Ashburner > To: Suzanna Lewis > Cc: Michael Ashburner , GO LIST > > Subject: Re: GOC meeting minutes > > These look fine EXCEPT for a distressing inconsistency in the use > of the periodkey ".". > I have attempted to correct these EGREGIOUS errors :=). > Well done to all minute takers. > > Attached has periods added where called for, and a few otherformat/ > presentation edits. > > Michael > Midori Harris 20 Perowne Street Cambridge CB1 2AY 01223 700527 07960 017949 midori.harris at ntlworld.com From dhowe at cs.uoregon.edu Fri Feb 23 08:06:20 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Fri, 23 Feb 2007 08:06:20 -0800 Subject: Meeting Announcement - Second International Biocuration Meeting Message-ID: <45DF10FC.9000301@cs.uoregon.edu> *Meeting Announcement* 2nd International Biocuration Meeting October 25-28, 2007 Dolce Hayes Mansion, San Jose, California, USA Purpose: The goal of this meeting is to provide a forum for curators and developers of biological databases to discuss their work, promote collaboration, and foster a sense of community in this important and rapidly growing area of research. Registration, lodging, and abstract submission are now open. The abstract submission deadline is July 1, 2007. For more information, please see the meeting web site at: http://biocurator.org/Mtg2007/ The meeting organizers would like to thank the Genetics Society of America, the National Science Foundation, the Klaus Tschira Foundation, and Bioneer for their support. The First Biocuration Meeting was a great success. We look forward to your participation in the second meeting! Organizing Committee: Maria Costanzo -Saccharomyces and Candida Genome Databases, Stanford University, USA Petra Fey -dictyBase, Northwestern University, USA Takashi Gojobori -Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Japan Win Hide -South African National Bioinformatics Institute, University of the Western Cape, South Africa David Hill -Mouse Genome Informatics, USA Doug Howe -Zebrafish Information Network, University of Oregon, USA Renate Kania -Scientific Databases and Visualization, EML Research gGmbH, Germany Sue Rhee The Arabidopsis Information Resource, Carnegie Institution, USA Mary Schaeffer -USDA ARS , MaizeGDB and University of Missouri, USA Susan St. Pierre -Flybase, Harvard, USA Simon Twigger -Rat Genome Database, Medical College of Wisconsin at Milwaukee, USA Owen White -The Institute for Genomic Research, USA From eurie at genome.Stanford.EDU Fri Feb 23 10:11:47 2007 From: eurie at genome.Stanford.EDU (Eurie Hong) Date: Fri, 23 Feb 2007 10:11:47 -0800 Subject: Proposed Meetings for GO Message-ID: The idea of identifying meetings to target for GO attendance was brought up at the last consortium meeting. We've made a wiki page so that folks can add meetings they feel should have GO attendance: http://gocwiki.geneontology.org/index.php/Calendar#Proposed_Meetings Please put your suggestion for a meeting (including dates, location, URL) and a few sentences about who the target audience would be and why it would be good to have a GO person attend. There are a couple of meetings already listed if you need examples. Putting a meeting up on the wiki doesn't necessarily mean you'd have to attend. Meetings that already have GO attendance are listed on the Google calendar. Jen, Jane, Eurie PS. Does this mean we can cross of action items #39 - 41 from the last GOC meeting ?! =) From jane at ebi.ac.uk Fri Feb 23 11:08:18 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Fri, 23 Feb 2007 19:08:18 +0000 (GMT) Subject: GOC meeting minutes In-Reply-To: References: Message-ID: A couple of corrections: Action item 7 should say 'Jen' not 'Jane'. Action item 30 should say 'AWG' not 'AMG' Good work! Jane On Fri, 23 Feb 2007, Midori Harris wrote: > > Thanks for all of this! > > In the attached, I've added a participant list, and fixed a number oftypos > (starting with Michael's draft). There are also a couple of new"notes". > > midori 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 suzi at berkeleybop.org Fri Feb 23 11:20:53 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Fri, 23 Feb 2007 11:20:53 -0800 Subject: GOC meeting minutes In-Reply-To: References: Message-ID: <562C7170-513E-4C73-9849-6E75DFFDAAB5@berkeleybop.org> Here is a revised version with edits from Michael, Midori, Jane and Rex Karen C, would you please confirm that we have the right Karen everywhere? Please check for truthfulness, as this our only record of what our decisions were. -S -------------- next part -------------- A non-text attachment was scrubbed... Name: Jan_8_2007minutes-v2.doc Type: application/octet-stream Size: 107520 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20070223/1e3bee1f/attachment.obj -------------- next part -------------- On Feb 23, 2007, at 11:08 AM, Jane Lomax wrote: > A couple of corrections: > > Action item 7 should say 'Jen' not 'Jane'. > Action item 30 should say 'AWG' not 'AMG' > > Good work! > > Jane > > > On Fri, 23 Feb 2007, Midori Harris wrote: > >> >> Thanks for all of this! >> >> In the attached, I've added a participant list, and fixed a number >> oftypos (starting with Michael's draft). There are also a couple >> of new"notes". >> >> midori > > 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 suzi at berkeleybop.org Fri Feb 23 11:41:13 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Fri, 23 Feb 2007 11:41:13 -0800 Subject: GOC meeting minutes v3 In-Reply-To: <2E812441-8679-4056-B378-9F742E5D74F3@stanford.edu> References: <8035F1A3-8954-4689-8B5E-C617CCD70F9B@stanford.edu> <2E812441-8679-4056-B378-9F742E5D74F3@stanford.edu> Message-ID: <8F860E54-A3C4-41A8-95AE-0F958BB880A4@berkeleybop.org> Now with another change from Mike -------------- next part -------------- A non-text attachment was scrubbed... Name: Jan_8_2007minutes-v3.doc Type: application/octet-stream Size: 107520 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20070223/20dea505/attachment.obj -------------- next part -------------- From suzi at berkeleybop.org Fri Feb 23 13:19:33 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Fri, 23 Feb 2007 13:19:33 -0800 Subject: Proposed Meetings for GO In-Reply-To: References: Message-ID: I added one! (more to come) On Feb 23, 2007, at 10:11 AM, Eurie Hong wrote: > The idea of identifying meetings to target for GO attendance was > brought up at the last consortium meeting. We've made a wiki page > so that folks can add meetings they feel should have GO attendance: > > http://gocwiki.geneontology.org/index.php/Calendar#Proposed_Meetings > > Please put your suggestion for a meeting (including dates, > location, URL) and a few sentences about who the target audience > would be and why it would be good to have a GO person attend. > There are a couple of meetings already listed if you need examples. > > Putting a meeting up on the wiki doesn't necessarily mean you'd > have to attend. Meetings that already have GO attendance are > listed on the Google calendar. > > Jen, Jane, Eurie > > PS. Does this mean we can cross of action items #39 - 41 from the > last GOC meeting ?! =) > From pj37 at cornell.edu Sat Feb 24 09:04:44 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Sat, 24 Feb 2007 12:04:44 -0500 Subject: Cellular component inconsistencies Message-ID: <45E0702C.7010408@cornell.edu> Hi Everyone, Sorry to bother again. You all have done an excellent job of making the GO IS_A complete, but I am finding few inconsistencies at the very top of the tree in cellular_component section of the ontology (above link). ----GO:0005575 : cellular_component -------is_a--GO:0005623 : cell ---------part_of--GO:0044464 : cell part If we compare the definitions one would infer that cell part = cellular component Also cell is not a subtype (ISA) of cellular_component. May be someone can tell about the history why the term 'cell' is there. Either the 'cell GO:0005623' should be the very top of the term replacing cellular_component or it must become obsolete. However, if the term 'cell' was introduced to capture the annotations to the pathogen cell (unicellular pathogen organisms) present inside the host cell (pathology aspect), then the most appropriate term is 'pathogen cell'/something better and not just the 'cell'. Just to let you know I have often found it hard to explain this situation to both the biology majors when I teach or to the researchers. Its an absolute awkward situation and hopefully can to be corrected. To our understanding the best tree can look like this # all : all --is_a GO:0005575 : cellular_component *** (synonym: cell part) -------------is_a GO:NEW : Pathogen cell/something better -------------is_a GO:0031975 : envelope -------------is_a GO:0031012 : extracellular matrix -------------is_a GO:0044420 : extracellular matrix -------------is_a GO:0005576 : extracellular region -------------is_a GO:0044421 : extracellular region -------------is_a GO:0031974 : membrane-enclosed lumen -------------is_a GO:0043226 : organelle -------------is_a GO:0044422 : organelle part -------------is_a GO:0043234 : protein complex -------------is_a GO:0045202 : synapse -------------is_a GO:0044456 : synapse part -------------is_a GO:0019012 : virion -------------is_a GO:0044423 : virion part * GO:0005623 : cell-->make it obsolete *** the GO:0044464 : cell part can merge into GO:0005575 : cellular_component Best Pankaj From jblake at informatics.jax.org Sun Feb 25 21:24:25 2007 From: jblake at informatics.jax.org (Judith Blake) Date: Mon, 26 Feb 2007 00:24:25 -0500 Subject: GOC meeting minutes Message-ID: <45E26F09.9080904@informatics.jax.org> I added a little more structure based on the agenda, corrected a minor typo or two. Action Item 16...this Action Item is canceled/overwritten as noted on day 3 with note beneath Item 73..." proposal to remove word activity has been postponed..." I added this condition to the action item Action Item 29. this action item was pretty much cancelled later on in the meeting. I added comment on this - see action items 81 and 82 What productive discussions we had...wow. Judy -------------- next part -------------- A non-text attachment was scrubbed... Name: Jan_8_2007minutes-v3_jb.doc Type: application/msword Size: 132608 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20070226/7a93b905/attachment.doc From midori at ebi.ac.uk Mon Feb 26 04:20:31 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Mon, 26 Feb 2007 12:20:31 +0000 (GMT) Subject: Cellular component inconsistencies In-Reply-To: <45E0702C.7010408@cornell.edu> References: <45E0702C.7010408@cornell.edu> Message-ID: We discussed cellular component vs. cell part at the January GOC meeting, and concluded that they are different. One of the meeting action items is to rephrase the cellular component definition to make the distinction clearer. m On Sat, 24 Feb 2007, Pankaj Jaiswal wrote: > > > > Hi Everyone, > > Sorry to bother again. You all have done an excellent job of making the GO > IS_A complete, but I am finding few inconsistencies at the very top of the > tree in cellular_component section of the ontology (above link). > > ----GO:0005575 : cellular_component > -------is_a--GO:0005623 : cell > ---------part_of--GO:0044464 : cell part > > If we compare the definitions one would infer that > cell part = cellular component > > Also cell is not a subtype (ISA) of cellular_component. May be someone can > tell about the history why the term 'cell' is there. Either the 'cell > GO:0005623' should be the very top of the term replacing cellular_component > or it must become obsolete. However, if the term 'cell' was introduced to > capture the annotations to the pathogen cell (unicellular pathogen organisms) > present inside the host cell (pathology aspect), then the most appropriate > term is 'pathogen cell'/something better and not just the 'cell'. > > Just to let you know I have often found it hard to explain this situation to > both the biology majors when I teach or to the researchers. Its an absolute > awkward situation and hopefully can to be corrected. > > To our understanding the best tree can look like this > > # all : all > --is_a GO:0005575 : cellular_component *** (synonym: cell part) > -------------is_a GO:NEW : Pathogen cell/something better > -------------is_a GO:0031975 : envelope > -------------is_a GO:0031012 : extracellular matrix > -------------is_a GO:0044420 : extracellular matrix > -------------is_a GO:0005576 : extracellular region > -------------is_a GO:0044421 : extracellular region > -------------is_a GO:0031974 : membrane-enclosed lumen > -------------is_a GO:0043226 : organelle > -------------is_a GO:0044422 : organelle part > -------------is_a GO:0043234 : protein complex > -------------is_a GO:0045202 : synapse > -------------is_a GO:0044456 : synapse part > -------------is_a GO:0019012 : virion > -------------is_a GO:0044423 : virion part > > > * GO:0005623 : cell-->make it obsolete > *** the GO:0044464 : cell part can merge into GO:0005575 : cellular_component > > Best > Pankaj > From jane at ebi.ac.uk Mon Feb 26 09:10:32 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Mon, 26 Feb 2007 17:10:32 +0000 (GMT) Subject: Chromosome is an organelle ? In-Reply-To: <45DE44D4.4030300@cornell.edu> References: <45DE44D4.4030300@cornell.edu> Message-ID: Hi Pankaj - the definition of organelle is 'Organized structure of distinctive morphology and function' and we've included things like ribosomes and the cytoskeleton, so I can't see, on that basis, why we wouldn't include chromosomes? I don't think an organelle being part of another organelle causes logical problems, and it doesn't cause problems with the graph...we had a lot of discussion about this when we created the organelle terms in the first place: http://sourceforge.net/tracker/index.php?func=detail&aid=1021113&group_id=36855&atid=440764 It seems like organelle is one of those concepts that means different things to different people, so we'll never be completely in line with what's used in the community, but I don't think that should worry us too much. Jane On Thu, 22 Feb 2007, Pankaj Jaiswal wrote: > > > > In this graph we see that 'chromosome' is an 'organelle'. I think majority of > the researchers would consider it simply ISA cell_part (or ISA > intracellular_part). If not it is something like for instance 'plastid > chromosome' is a part of 'plastid' where both 'plastid chromosome' and > 'plastid' are ISA 'organelle'. Or in lay person's knowledge 'an organ is > PARTOF and organ' considering organelle in cell/unicellular organisms is > synonymous with organs in multicellular organisms. > > I am not sure if this is a correct relationship in GO. > > Pankaj > > 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 jclark at ebi.ac.uk Mon Feb 26 09:34:09 2007 From: jclark at ebi.ac.uk (J Clark) Date: Mon, 26 Feb 2007 17:34:09 +0000 Subject: transporter substrates Message-ID: <45E31A11.605@ebi.ac.uk> Hi, As you may know there is a working group tackling the problems in the transporter activity section of the function ontology just now (Jennifer Clark, Val Wood, Michelle Gwinn, Ian Paulsen). We have come across a question in which we would appreciate input from everyone. Question ======== The transporter activity node has children grouping the transporter functions according to substrate. These substrates are listed below. Are any of the substrates below ever transported in any way other than simply from one side of a membrane to the other? Please note that this is the function ontology so we are only asking about types of transport where the transport happens as a function of a gene product or complex, for example sodium ion transport through a channel. We are not interested in broader processes, for example sugar transport in the vascular tissue of a plant. If no one can think of any examples: ================================ The terms covering substrates in which no one thinks of an example will be moved from being is_a transporter activity to be is_a transmembrane transporter activity on 12th March. Thank you very much for taking the time to think about this. Best wishes, Jennifer On behalf of the Transporter Working Group. Substrates ========== low-affinity zinc ion L-ornithine S-adenosylmethionine sulfur amino acid S-methylmethionine adenine nucleotide spermine sulfite glycerophosphodiester guanine nucleotide beta-alanine amine acetylcholine amino acid-polyamine high-affinity basic amino acid high-affinity arginine L-histidine high-affinity lysine high-affinity tryptophan L-tyrosine L-valine creatine dicarboxylic acid L-glutamate high-affinity glutamate inorganic phosphate lipid long-chain fatty acid peroxisomal fatty acyl CoA neurotransmitter dopamine norepinephrine nucleoside nucleotide-sugar nucleotide-sulfate organic acid oxygen purine purine ribonucleotide ATP pyrimidine fructose galactose glucose hydrogen:glucose constitutive hydrogen:glucose high-affinity hydrogen:glucose low-affinity hydrogen:glucose insulin-responsive hydrogen:glucose transepithelial hydrogen:glucose maltose myo-inositol taurine water copper ion iron ion manganese ion zinc ion eye pigment precursor proton-dependent oligopeptide chromaffin granule amine synaptic vesicle amine CMP-sialic acid GDP-fucose GDP-mannose UDP-galactose UDP-glucose UDP-glucuronic acid UDP-N-acetylglucosamine UDP-N-acetylgalactosamine UDP-xylose intracellular nucleocytoplasmic phospholipid monocarboxylic acid cation tetracycline monoamine anion organic anion sucrose folic acid ammonium acetyl-CoA sodium-dependent multivitamin phosphatidylcholine phosphatidylinositol protein triose-phosphate low affinity phosphate delta-pH-dependent nucleoside , against a concentration gradient sphingosine chlorophyll catabolite auxin influx auxin efflux ion monovalent inorganic cation hydrogen ion potassium ion silver ion sodium ion di-, tri-valent inorganic cation aluminum ion calcium ion cadmium ion cobalt ion high affinity copper ion low affinity iron ion ferric iron ferrous iron lead ion magnesium ion mercury ion molybdate ion nickel ion vanadium ion organic cation inorganic anion antimonite arsenite bicarbonate chlorate chloride chromate cyanate iodide nitrate nitrite phosphate silicate sulfate thiosulfate tellurite hexose phosphate phosphoglycerate phosphoenolpyruvate acetate allantoate bile acid canalicular bile acid bilirubin gluconate lactate mevalonate oxaloacetate prostaglandin uronic acid hexuronate glucuronate sialic acid citrate fumarate alpha-ketoglutarate malate succinate tricarboxylic acid urate carbohydrate monosaccharide pentose L-arabinose D-xylose hexose fucose alpha-glucoside glucose-6-phosphate rhamnose disaccharide lactose melibiose oligosaccharide raffinose polysaccharide beta-glucan capsular-polysaccharide teichoic acid hexuronide glucuronoside pyrimidine nucleotide sugar polyol arabitol glycerol glycerol-3-phosphate propanediol amino acid acidic amino acid aromatic amino acid basic amino acid neutral amino acid L-amino acid L-alanine L-arginine L-asparagine L-aspartate L-cystine L-gamma-aminobutyric acid L-glutamine glycine L-isoleucine L-lysine L-leucine L-methionine L-phenylalanine L-proline L-serine L-threonine L-tryptophan peptide oligopeptide betaine methylammonium polyamine urea nucleobase allantoin adenine guanine cytosine uracil purine nucleoside cytidine uridine pyrimidine nucleoside nucleotide purine nucleotide ADP pyrimidine nucleotide DNA-protein complex choline lipopolysaccharide serotonin biopterin biotin carnitine acyl carnitine coenzyme A L-ascorbic acid FAD 5-formyltetrahydrofolate heme pantothenate thiamin cobalamin drug multidrug amiloride aminotriazole benomyl cycloheximide fluconazole fatty acid fatty acyl aminophospholipid sterol channel or pore class sodium-dependent phosphate peptide-acetyl-CoA cationic amino acid high affinity oligopeptide siderophore-iron sodium-independent organic anion thyroid hormone methotrexate multidrug endosomal polyspecific organic cation nucleoside , down a concentration gradient high affinity ammonium primary active low affinity ammonium P-P-bond-hydrolysis-driven decarboxylation-driven active methyl transfer-driven active oxidoreduction-driven active light-driven active putrescine cadaverine formate nitrite efflux transmembrane arabinose efflux transmembrane shikimate sugar efflux bicyclomycin sulfathiazole nalidixic acid organomercurial carbonyl cyanide m-chlorophenylhydrazone galacturonate 3-hydroxyphenyl propanoate propionate xanthosine tartrate C4-dicarboxylate arginine targeting efflux transmembrane threonine efflux transmembrane acriflavin alkane L-idonate p-aminobenzoyl-glutamate N-acetylgalactosamine N-acetylglucosamine beta-glucoside trehalose mannitol sorbitol galactitol mannose D-ribose methylgalactoside allose iron chelate phosphonate organophosphate ester spermidine fatty acyl CoA ferric-enterobactin ferric triacetylfusarinine C ferric-hydroxamate L-diaminopimelate short-chain fatty acid peptidoglycan peptide peptidoglycan lipid-linked peptidoglycan quaternary ammonium group branched-chain aliphatic amino acid formate efflux transmembrane L-lysine efflux transmembrane nicotinamide mononucleotide alcohol nucleobase, nucleoside, nucleotide and nucleic acid glycolipid cholesterol cellobiose sorbose galactosamine oxalate toxin ferric-vibriobactin ion passive active large uncharged polar molecule sodium ion potassium ion cation anion active large uncharged polar molecule transmembrane nitric oxide deoxynucleotide inorganic diphosphate vitamin B6 pyridoxal pyridoxal phosphate pyridoxamine pyridoxine riboflavin aldarate D-galactarate D-glucarate aldonate D-glucuronate D-galactonate amide molybdenum ion 3-phenylpropionic acid antibiotic chloramphenicol polymyxin fosmidomycin arabinose arabinose polymer xanthine xenobiotic acridine colicin group A colicin alkylphosphonate benzoate 3-hydroxyphenylpropionic acid siderophore ferrichrome enterobactin chrysobactin achromobactin dipeptide tripeptide D-amino acid D-alanine D-serine glucoside salicin arbutin lipoprotein dextrin maltodextrin alkanesulfonate homoserine lactone sodium-dependent organic anion odorant azole MAPK MAPK phosphatase cation efflux transmembrane sphingolipid boron metal ion transition metal ion carboxylic acid 3'-phosphoadenosine 5'-phosphosulfate high affinity phosphate D-methionine pyruvate nucleic acid RNA tRNA DNA sugar vitamin cofactor coenzyme ectoine glucosylglycerol mannosylglycerate NAD ammonia lysophospholipid iron-nicotianamine copper chelate copper-nicotianamine From ma11 at gen.cam.ac.uk Mon Feb 26 14:57:49 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner (Genetics)) Date: Mon, 26 Feb 2007 22:57:49 +0000 Subject: transporter substrates Message-ID: This is not really my field, but not as far as I know. Are you in touch with the Transport Classification Database (http://www.tcdb.org/) (and also, perhaps TransportDB (http://www.membranetransport.org/) ). Michael From hjd at informatics.jax.org Mon Feb 26 18:39:26 2007 From: hjd at informatics.jax.org (Harold J. Drabkin) Date: Mon, 26 Feb 2007 21:39:26 -0500 (EST) Subject: Chromosome is an organelle ? In-Reply-To: Message-ID: I agree Jane; After all, a mitochondrial ribosome is an organelle just like a cytosolic ribosme, and the mito rib is found within another organelle (mito). The nucleolus is recognized as an organized structure found in the nucleus; one can actually isolate chromosomes, so I would think that they ARE indeed organelles wtihin another (nucleus). On Mon, 26 Feb 2007, Jane Lomax wrote: > Hi Pankaj - the definition of organelle is 'Organized structure of > distinctive morphology and function' and we've included things like > ribosomes and the cytoskeleton, so I can't see, on that basis, why we > wouldn't include chromosomes? > > I don't think an organelle being part of another organelle causes logical > problems, and it doesn't cause problems with the graph...we had a lot of > discussion about this when we created the organelle terms in the first place: > > http://sourceforge.net/tracker/index.php?func=detail&aid=1021113&group_id=36855&atid=440764 > > It seems like organelle is one of those concepts that means different things to > different people, so we'll never be completely in line with what's used in the > community, but I don't think that should worry us too much. > > Jane > > On Thu, 22 Feb 2007, Pankaj Jaiswal wrote: > > > > > > > > > In this graph we see that 'chromosome' is an 'organelle'. I think majority of > > the researchers would consider it simply ISA cell_part (or ISA > > intracellular_part). If not it is something like for instance 'plastid > > chromosome' is a part of 'plastid' where both 'plastid chromosome' and > > 'plastid' are ISA 'organelle'. Or in lay person's knowledge 'an organ is > > PARTOF and organ' considering organelle in cell/unicellular organisms is > > synonymous with organs in multicellular organisms. > > > > I am not sure if this is a correct relationship in GO. > > > > Pankaj > > > > > > 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 kchris at genome.Stanford.EDU Mon Feb 26 22:32:03 2007 From: kchris at genome.Stanford.EDU (Karen Christie) Date: Mon, 26 Feb 2007 22:32:03 -0800 (PST) Subject: GOC meeting minutes In-Reply-To: <562C7170-513E-4C73-9849-6E75DFFDAAB5@berkeleybop.org> References: <562C7170-513E-4C73-9849-6E75DFFDAAB5@berkeleybop.org> Message-ID: Hi Suzi, I will check whether it is the correct Karen, but I'm on vacation (parents visiting) through Wednesday, so probaby won't have a chance to get to this until the end of this week. Just wanted to let you know I'm not ignoring this thread about the meeting minutes. thanks, -Karen On Fri, 23 Feb 2007, Suzanna Lewis wrote: > Here is a revised version with edits from Michael, Midori, Jane and Rex > > Karen C, would you please confirm that we have the right Karen everywhere? > > Please check for truthfulness, as this our only record of what our decisions > were. > > -S > From jclark at ebi.ac.uk Tue Feb 27 01:46:08 2007 From: jclark at ebi.ac.uk (J Clark) Date: Tue, 27 Feb 2007 09:46:08 +0000 Subject: transporter substrates In-Reply-To: References: Message-ID: <45E3FDE0.3050803@ebi.ac.uk> Hi Michael, Thanks I will send the question there too. Jen Michael Ashburner (Genetics) wrote: > This is not really my field, but not as far as I know. > Are you in touch with the Transport Classification Database (http://www.tcdb.org/) > (and also, perhaps TransportDB (http://www.membranetransport.org/) ). > Michael -- Gene Ontology Consortium EMBL-European Bioinformatics Institute From val at sanger.ac.uk Tue Feb 27 02:29:12 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Tue, 27 Feb 2007 10:29:12 +0000 Subject: transporter substrates In-Reply-To: <45E3FDE0.3050803@ebi.ac.uk> References: <45E3FDE0.3050803@ebi.ac.uk> Message-ID: <45E407F8.7090200@sanger.ac.uk> Ian Paulsen who is helping with this is PI of TransportDB (http://www.membranetransport.org/) However, this question may not easily be answered by the membrane transporter databases, because the question is "which of these terms has been used to annotate gene products which are NOT membrane transporters". Jen, can you simplify the list be removing anything which has a 'membrane transporter' parent (passive transporter activity/active transporter activity) parent and therefore can only refer to a membrane tansporter? For example 'thyroid hormone transporter activity' is a child of porter activity. Also remove anything with 'high-affinity' or low-affinity' 'proton dependent' 'active' passive' 'efflux' 'uptake' in the term names. Can we perhaps move all "ion" transporters under transmembrane also, I'm not sure about this one? The terms I see from a quick glance which are not transmembrane transporter (or have multiple usage) are: intracellular transporter activity nucleocytoplasmic transporter activity (used for karyopherins etc) sterol transporter activity (used for intracellular trafficking of sterol) so this would apply to the parent 'lipid transporters' heme transporter activity (used for heme binding serum proteins like hemopexin) so this would apply to the parent cofactor transporters It will be easier to check the rest if all the above are removed from the list. When we have the reduced list it might be useful to send it to the annotation list which incldes curators (i.e Uniprot) who aren't on the main list. Cheers Val J Clark wrote: > Hi Michael, > > Thanks I will send the question there too. > > Jen > > Michael Ashburner (Genetics) wrote: > >> This is not really my field, but not as far as I know. >> Are you in touch with the Transport Classification Database >> (http://www.tcdb.org/) >> (and also, perhaps TransportDB (http://www.membranetransport.org/) ). >> Michael > > -- --------------------------------------------------------------------------- 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 jane at ebi.ac.uk Tue Feb 27 03:34:36 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Tue, 27 Feb 2007 11:34:36 +0000 Subject: Alert: Proposal to obsolete GO:0043460: response to long exposure to lithium ion and GO:0043459: response to short exposure to lithium ion that impacts existing annotation Message-ID: The proposal has been made to obsolete GO:0043460: response to long exposure to lithium ion and GO:0043459: response to short exposure to lithium ion. There exist today annotations to this term as follows (data from AmiGO): * RGD: 1 objects The reasons for this proposal are that these terms are deemed to be beyond the scope of GO. The SourceForge discussion is to be found on https://sourceforge.net/ tracker/?func=detail&atid=440764&aid=1242391&group_id=36855. UNLESS OBJECTIONS ARE RECEIVED BY 13th March IT WILL BE ASSUMED THAT YOU AGREE TO THIS CHANGE. thanks, Jane From jclark at ebi.ac.uk Tue Feb 27 03:58:51 2007 From: jclark at ebi.ac.uk (J Clark) Date: Tue, 27 Feb 2007 11:58:51 +0000 Subject: transporter substrates In-Reply-To: <45E407F8.7090200@sanger.ac.uk> References: <45E3FDE0.3050803@ebi.ac.uk> <45E407F8.7090200@sanger.ac.uk> Message-ID: <45E41CFB.4090703@ebi.ac.uk> Hi, Val and I have made up a shorter list (below). We would also appreciate information on any examples of the following groups of substrates: nucleobase nucleotide nucleoside amino acid carbohydrate drug, antibiotic and xenobiotic substrate ion that are transported as the function of a gene product or complex, but not just across a membrane. Thanks, Jen GO:0015551 3-hydroxyphenyl propanoate transporter activity GO:0015123 acetate transporter activity GO:0005277 acetylcholine transporter activity GO:0042911 acridine transporter activity GO:0015665 alcohol transporter activity GO:0042959 alkanesulfonate transporter activity GO:0042917 alkylphosphonate transporter activity GO:0015124 allantoate transporter activity GO:0015139 alpha-ketoglutarate transporter activity GO:0042887 amide transporter activity GO:0005275 amine transporter activity GO:0051739 ammonia transporter activity GO:0008519 ammonium transporter activity GO:0015104 antimonite transporter activity GO:0015167 arabitol transporter activity GO:0015105 arsenite transporter activity GO:0010328 auxin influx transporter activity GO:0042925 benzoate transporter activity GO:0015199 betaine transporter activity GO:0015106 bicarbonate transporter activity GO:0015125 bile acid transporter activity GO:0015127 bilirubin transporter activity GO:0046715 boron transporter activity GO:0015556 C4-dicarboxylate transporter activity GO:0015490 cadaverine transporter activity GO:0015434 cadmium-transporting ATPase activity GO:0015126 canalicular bile acid transporter activity GO:0046943 carboxylic acid transporter activity GO:0015107 chlorate transporter activity GO:0015108 chloride transporter activity GO:0010290 chlorophyll catabolite transporter activity GO:0015220 choline transporter activity GO:0005429 chromaffin granule amine transporter activity GO:0015109 chromate transporter activity GO:0042933 chrysobactin transporter activity GO:0015137 citrate transporter activity GO:0015235 cobalamin transporter activity GO:0051981 copper chelate transporter activity GO:0051982 copper-nicotianamine transporter activity GO:0015110 cyanate transporter activity GO:0005310 dicarboxylic acid transporter activity GO:0042936 dipeptide transporter activity GO:0051471 ectoine transporter activity GO:0042931 enterobactin transporter activity GO:0015091 ferric iron transporter activity GO:0015621 ferric triacetylfusarinine C transporter activity GO:0015620 ferric-enterobactin transporter activity GO:0015622 ferric-hydroxamate transporter activity GO:0019535 ferric-vibriobactin transporter activity GO:0042929 ferrichrome transporter activity GO:0015093 ferrous iron transporter activity GO:0015499 formate transporter activity GO:0015138 fumarate transporter activity GO:0015577 galactitol transporter activity GO:0015550 galacturonate transporter activity GO:0015128 gluconate transporter activity GO:0015135 glucuronate transporter activity GO:0015168 glycerol transporter activity GO:0015169 glycerol-3-phosphate transporter activity GO:0001406 glycerophosphodiester transporter activity GO:0015134 hexuronate transporter activity GO:0030504 inorganic diphosphate transporter activity GO:0015111 iodide transporter activity GO:0015603 iron chelate transporter activity GO:0051980 iron-nicotianamine transporter activity GO:0015229 L-ascorbic acid transporter activity GO:0015568 L-idonate transporter activity GO:0015129 lactate transporter activity GO:0042971 lactone transporter activity GO:0022815 large uncharged polar molecule transporter activity GO:0015140 malate transporter activity GO:0015575 mannitol transporter activity GO:0015200 methylammonium transporter activity GO:0015130 mevalonate transporter activity GO:0008504 monoamine transporter activity GO:0008028 monocarboxylic acid transporter activity GO:0005365 myo-inositol transporter activity GO:0003957 NAD(P)+ transhydrogenase (B-specific) activity GO:0005326 neurotransmitter transporter activity GO:0015112 nitrate transporter activity GO:0030184 nitric oxide transporter activity GO:0015113 nitrite transporter activity GO:0005333 norepinephrine transporter activity GO:0043563 odorant transporter activity GO:0015198 oligopeptide transporter activity GO:0005342 organic acid transporter activity GO:0015605 organophosphate ester transporter activity GO:0019531 oxalate transporter activity GO:0015131 oxaloacetate transporter activity GO:0015197 peptide transporter activity GO:0015640 peptidoglycan peptide transporter activity GO:0015647 peptidoglycan transporter activity GO:0015114 phosphate transporter activity GO:0015121 phosphoenolpyruvate transporter activity GO:0015120 phosphoglycerate transporter activity GO:0015604 phosphonate transporter activity GO:0015203 polyamine transporter activity GO:0015166 polyol transporter activity GO:0015170 propanediol transporter activity GO:0015132 prostaglandin transporter activity GO:0015489 putrescine transporter activity GO:0031926 pyridoxal phosphate transporter activity GO:0031925 pyridoxal transporter activity GO:0031927 pyridoxamine transporter activity GO:0031928 pyridoxine transporter activity GO:0050833 pyruvate transporter activity GO:0015651 quaternary ammonium group transporter activity GO:0032217 riboflavin transporter activity GO:0015222 serotonin transporter activity GO:0015530 shikimate transporter activity GO:0042927 siderophore transporter activity GO:0015343 siderophore-iron transporter activity GO:0015115 silicate transporter activity GO:0015321 sodium-dependent phosphate transporter activity GO:0015576 sorbitol transporter activity GO:0015606 spermidine transporter activity GO:0000297 spermine transporter activity GO:0010175 sphingosine transporter activity GO:0015141 succinate transporter activity GO:0015116 sulfate transporter activity GO:0000319 sulfite transporter activity GO:0005430 synaptic vesicle amine transporter activity GO:0015554 tartrate transporter activity GO:0005368 taurine transporter activity GO:0015118 tellurite transporter activity GO:0015234 thiamin transporter activity GO:0015117 thiosulfate transporter activity GO:0019534 toxin transporter activity GO:0015142 tricarboxylic acid transporter activity GO:0042937 tripeptide transporter activity GO:0015143 urate transporter activity GO:0015133 uronic acid transporter activity GO:0031924 vitamin B6 transporter activity GO:0051183 vitamin transporter activity GO:0005372 water transporter activity Valerie Wood wrote: > > Ian Paulsen who is helping with this is PI of TransportDB > (http://www.membranetransport.org/) > > However, this question may not easily be answered by the membrane > transporter databases, because the question is "which of these terms has > been used to annotate gene products which are NOT membrane transporters". > > Jen, can you simplify the list be removing anything which has a > 'membrane transporter' parent (passive transporter activity/active > transporter activity) parent and therefore can only refer to a membrane > tansporter? For example 'thyroid hormone transporter activity' is a > child of porter activity. > > Also remove anything with 'high-affinity' or low-affinity' 'proton > dependent' 'active' passive' 'efflux' 'uptake' in the term names. Can we > perhaps move all "ion" transporters under transmembrane also, I'm not > sure about this one? > > The terms I see from a quick glance which are not transmembrane > transporter (or have multiple usage) are: > > intracellular transporter activity > nucleocytoplasmic transporter activity (used for karyopherins etc) > sterol transporter activity (used for intracellular trafficking of > sterol) so this would apply to the parent 'lipid transporters' > heme transporter activity (used for heme binding serum proteins like > hemopexin) so this would apply to the parent cofactor transporters > > It will be easier to check the rest if all the above are removed from > the list. > > When we have the reduced list it might be useful to send it to the > annotation list which incldes curators (i.e Uniprot) who aren't on the > main list. > > Cheers > > Val > > > > > > J Clark wrote: > >> Hi Michael, >> >> Thanks I will send the question there too. >> >> Jen >> >> Michael Ashburner (Genetics) wrote: >> >>> This is not really my field, but not as far as I know. >>> Are you in touch with the Transport Classification Database >>> (http://www.tcdb.org/) >>> (and also, perhaps TransportDB (http://www.membranetransport.org/) ). >>> Michael >> >> >> > > -- Gene Ontology Consortium EMBL-European Bioinformatics Institute From val at sanger.ac.uk Tue Feb 27 07:01:27 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Tue, 27 Feb 2007 15:01:27 +0000 Subject: GOC meeting minutes v3 query AI 49 In-Reply-To: <8F860E54-A3C4-41A8-95AE-0F958BB880A4@berkeleybop.org> References: <8035F1A3-8954-4689-8B5E-C617CCD70F9B@stanford.edu> <2E812441-8679-4056-B378-9F742E5D74F3@stanford.edu> <8F860E54-A3C4-41A8-95AE-0F958BB880A4@berkeleybop.org> Message-ID: <45E447C7.6040007@sanger.ac.uk> Re. Action item 49, This wasn't quite clear to me, but I might have misunderstood. I'm not sure about the wording: 'Pipes mean intersection (or complex), commas mean union (or a collection of possibilities) I came away with the impression that for IPI the new comma separator will mean multiple independent binary interactions (from the same Pubmed ID), and the existing pipe separator will refer to a complex where the specific interactor cannot be distinguished. I'm not sure this is analogus to union and intersect. Isn't the complex a collection of possibilities? (i.e. we don't know the specific interactor). Also, I thought MGI used IPI for binary interactions but action item 50 says "MGI change all pipes to commas" wich also makes me think that something isn't quite correct. We also discussed this syntax for genetic interactions. I have used pipe for multiple deletions (in a single strain), is this correct, or will this change to comma? I don't remember the outcome. Val Suzanna Lewis wrote: > Now with another change from Mike > > > > -- --------------------------------------------------------------------------- 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 jane at ebi.ac.uk Tue Feb 27 07:33:01 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Tue, 27 Feb 2007 15:33:01 +0000 Subject: Requirements for GO tools In-Reply-To: References: Message-ID: <81326AFD-C946-4648-98E4-8F6897799B0A@ebi.ac.uk> Oh yes - that's not very clear is it, I meant how often they update the GO files within their tool, not how often the tool is improved. I'll make that clearer... Jane On 27 Feb 2007, at 13:39, Michael Ashburner (Genetics) wrote: > Looks good Jane and colleagues. The one thing I take exception to > on the wiki > is: > > 'Update frequency minimum, monthly?' > > For a database, yes, but for a tool ? (When was NCBI Blast last > updated ?). > I think that this is covered by the next point: > 'Actively maintained ...' > > Michael > >> Envelope-to: ma11 at gen.cam.ac.uk >> Delivery-date: Tue, 27 Feb 2007 11:58:07 +0000 >> X-Cam-SpamDetails: scanned, SpamAssassin-3.1.7 (score=0) >> X-Cam-AntiVirus: No virus found >> X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ >> X-Authentication-Warning: fafner.Stanford.EDU: majordom set sender to > owner-go-managers at genome-mail.stanford.edu using -f >> Mime-Version: 1.0 (Apple Message framework v752.3) >> Content-Transfer-Encoding: 7bit >> To: GO Managers List >> From: Jane Lomax >> Subject: Requirements for GO tools >> Date: Tue, 27 Feb 2007 11:57:22 +0000 >> >> Hi - Eurie, Jen and I have been looking at the tools listed on the >> website. We've come up with a draft list of requirements for the >> tools to meet, which is on the wiki: >> >> http://gocwiki.geneontology.org/index.php/Tools_standards >> >> In order that they're listed on the website, the tools will have to >> meet all of the essential requirements stated, and the desirable >> requirements could be used in addition to give a score to the tool >> (possibly in addition to some user rankings - we haven't worked out >> the details of this yet). The set of questions on the wiki was put >> together by Amelia, and is an extension of what we already ask the >> developers to encompass these extra requirements. >> >> The idea is that we'd send an initial email out to all the tools >> developers (this is easy because they're all subscribed to GO >> friends) with these questions, and any tools for which we haven't >> received a response in a certain time period we'll remove from the >> website (this is a good way to get rid of all of the tools that are >> no longer being developed/deprecated tools). We'd warn them that any >> tools that don't meet the essential requirements would also be >> removed from the website (harsh!) at some fixed point in the future >> to give them a chance to modify their tools. And if by the date given >> the tools hadn't been modified, we remove them. >> >> So how does that sound? How about the requirements - too strict/ >> slack? Have we missed anything? >> >> We should add this to the agenda for the meeting tomorrow. >> >> thanks, >> >> Jane and Eurie From camon at ebi.ac.uk Tue Feb 27 07:45:07 2007 From: camon at ebi.ac.uk (Evelyn Camon) Date: Tue, 27 Feb 2007 15:45:07 +0000 Subject: Requirements for GO tools References: <81326AFD-C946-4648-98E4-8F6897799B0A@ebi.ac.uk> Message-ID: <45E45203.9080506@ebi.ac.uk> Hi Jane, Should we ask if they have asked a GO Consortium member to review the tool or would we at least like to advise that they do that???? It would be nice to hear from these tool developers before reading mis-information in publications.... cheers, Evelyn Jane Lomax wrote: > Oh yes - that's not very clear is it, I meant how often they update the > GO files within their tool, not how often the tool is improved. I'll > make that clearer... > > Jane > > > On 27 Feb 2007, at 13:39, Michael Ashburner (Genetics) wrote: > >> Looks good Jane and colleagues. The one thing I take exception to on >> the wiki >> is: >> >> 'Update frequency minimum, monthly?' >> >> For a database, yes, but for a tool ? (When was NCBI Blast last >> updated ?). >> I think that this is covered by the next point: >> 'Actively maintained ...' >> >> Michael >> >>> Envelope-to: ma11 at gen.cam.ac.uk >>> Delivery-date: Tue, 27 Feb 2007 11:58:07 +0000 >>> X-Cam-SpamDetails: scanned, SpamAssassin-3.1.7 (score=0) >>> X-Cam-AntiVirus: No virus found >>> X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ >>> X-Authentication-Warning: fafner.Stanford.EDU: majordom set sender to >> >> owner-go-managers at genome-mail.stanford.edu using -f >> >>> Mime-Version: 1.0 (Apple Message framework v752.3) >>> Content-Transfer-Encoding: 7bit >>> To: GO Managers List >>> From: Jane Lomax >>> Subject: Requirements for GO tools >>> Date: Tue, 27 Feb 2007 11:57:22 +0000 >>> >>> Hi - Eurie, Jen and I have been looking at the tools listed on the >>> website. We've come up with a draft list of requirements for the >>> tools to meet, which is on the wiki: >>> >>> http://gocwiki.geneontology.org/index.php/Tools_standards >>> >>> In order that they're listed on the website, the tools will have to >>> meet all of the essential requirements stated, and the desirable >>> requirements could be used in addition to give a score to the tool >>> (possibly in addition to some user rankings - we haven't worked out >>> the details of this yet). The set of questions on the wiki was put >>> together by Amelia, and is an extension of what we already ask the >>> developers to encompass these extra requirements. >>> >>> The idea is that we'd send an initial email out to all the tools >>> developers (this is easy because they're all subscribed to GO >>> friends) with these questions, and any tools for which we haven't >>> received a response in a certain time period we'll remove from the >>> website (this is a good way to get rid of all of the tools that are >>> no longer being developed/deprecated tools). We'd warn them that any >>> tools that don't meet the essential requirements would also be >>> removed from the website (harsh!) at some fixed point in the future >>> to give them a chance to modify their tools. And if by the date given >>> the tools hadn't been modified, we remove them. >>> >>> So how does that sound? How about the requirements - too strict/ >>> slack? Have we missed anything? >>> >>> We should add this to the agenda for the meeting tomorrow. >>> >>> thanks, >>> >>> Jane and Eurie >> -- 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 cjm at fruitfly.org Tue Feb 27 07:54:57 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Tue, 27 Feb 2007 07:54:57 -0800 Subject: Chromosome is an organelle ? In-Reply-To: References: Message-ID: <0579A87F-8AF8-462B-955E-E5C694B58CDF@fruitfly.org> Organized structure of distinctive morphology and function. According to this definition, these are all organelles: My lungs A tRNA molecule A plasma membrane The gloss of the definition goes on to say: Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. Extensional definitions (ie consisting of a list of entities the definition covers, or entities excluded) aren't good practice. Why is plasma membrane excluded? It just is? The definition includes the word "distinctive" which doesn't seem good. Distinctive to who? The FMA has this genus-differentia definition: Cell component which consists of macromolecules aggregated into discrete structures in the protoplasm. Which is perhaps too human specific, and would presumably exclude mt ribosome, but may be a good start. In the gloss they have: Examples: endoplasmic reticulum, ribosome, cytoskeleton, nuclear envelope, nucleus, mitochondrion. Note the genus of the definition, Cell component, is defined according to what I think is the intuitive definition, contrary to GO's somewhat upside down situation: Cell part which has a definable shape, bounded predominantly by bonafide boundaries and is countable. On Feb 26, 2007, at 6:39 PM, Harold J. Drabkin wrote: > I agree Jane; > After all, a mitochondrial ribosome is an organelle just like a > cytosolic > ribosme, and the mito rib is found within another organelle (mito). > The nucleolus is recognized as an organized structure found in the > nucleus; > one can actually isolate chromosomes, so I would think that they ARE > indeed organelles wtihin another (nucleus). > > On Mon, 26 Feb 2007, Jane Lomax wrote: > >> Hi Pankaj - the definition of organelle is 'Organized structure of >> distinctive morphology and function' and we've included things like >> ribosomes and the cytoskeleton, so I can't see, on that basis, why we >> wouldn't include chromosomes? >> >> I don't think an organelle being part of another organelle causes >> logical >> problems, and it doesn't cause problems with the graph...we had a >> lot of >> discussion about this when we created the organelle terms in the >> first place: >> >> http://sourceforge.net/tracker/index.php? >> func=detail&aid=1021113&group_id=36855&atid=440764 >> >> It seems like organelle is one of those concepts that means >> different things to >> different people, so we'll never be completely in line with what's >> used in the >> community, but I don't think that should worry us too much. >> >> Jane >> >> On Thu, 22 Feb 2007, Pankaj Jaiswal wrote: >> >>> >>> >> 0005694&search_constraint=terms&query=GO: >>> 0005694&view=details&show_associations=list> >>> >>> In this graph we see that 'chromosome' is an 'organelle'. I think >>> majority of >>> the researchers would consider it simply ISA cell_part (or ISA >>> intracellular_part). If not it is something like for instance >>> 'plastid >>> chromosome' is a part of 'plastid' where both 'plastid >>> chromosome' and >>> 'plastid' are ISA 'organelle'. Or in lay person's knowledge 'an >>> organ is >>> PARTOF and organ' considering organelle in cell/unicellular >>> organisms is >>> synonymous with organs in multicellular organisms. >>> >>> I am not sure if this is a correct relationship in GO. >>> >>> Pankaj >>> >>> >> >> 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 cjm at fruitfly.org Tue Feb 27 08:02:23 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Tue, 27 Feb 2007 08:02:23 -0800 Subject: Cellular component inconsistencies In-Reply-To: References: <45E0702C.7010408@cornell.edu> Message-ID: <8B972AB4-C1B3-4D61-B22A-00133C19C9B5@fruitfly.org> Do we have a proposed definition yet? Everyone in the room at the meeting was against any kind of change to the upper nodes of the ontology as we are all used to it, but Pankaj provides evidence the current structure is unintuitive to biologists not familiar with the GO. Perhaps we should do some informal survey amongst our colleagues and see if people find "cell is_a cell component" inutitive, with and without the new definition. On Feb 26, 2007, at 4:20 AM, Midori Harris wrote: > We discussed cellular component vs. cell part at the January GOC > meeting, and concluded that they are different. One of the meeting > action items is to rephrase the cellular component definition to > make the distinction clearer. > > m > > On Sat, 24 Feb 2007, Pankaj Jaiswal wrote: > >> >> > 0044464&search_constraint=terms&query=GO: >> 0005623&view=details&show_associations=list> >> >> Hi Everyone, >> >> Sorry to bother again. You all have done an excellent job of >> making the GO IS_A complete, but I am finding few inconsistencies >> at the very top of the tree in cellular_component section of the >> ontology (above link). >> >> ----GO:0005575 : cellular_component >> -------is_a--GO:0005623 : cell >> ---------part_of--GO:0044464 : cell part >> >> If we compare the definitions one would infer that >> cell part = cellular component >> >> Also cell is not a subtype (ISA) of cellular_component. May be >> someone can tell about the history why the term 'cell' is there. >> Either the 'cell GO:0005623' should be the very top of the term >> replacing cellular_component or it must become obsolete. However, >> if the term 'cell' was introduced to capture the annotations to >> the pathogen cell (unicellular pathogen organisms) present inside >> the host cell (pathology aspect), then the most appropriate term >> is 'pathogen cell'/something better and not just the 'cell'. >> >> Just to let you know I have often found it hard to explain this >> situation to both the biology majors when I teach or to the >> researchers. Its an absolute awkward situation and hopefully can >> to be corrected. >> >> To our understanding the best tree can look like this >> >> # all : all >> --is_a GO:0005575 : cellular_component *** (synonym: cell part) >> -------------is_a GO:NEW : Pathogen cell/something better >> -------------is_a GO:0031975 : envelope >> -------------is_a GO:0031012 : extracellular matrix >> -------------is_a GO:0044420 : extracellular matrix >> -------------is_a GO:0005576 : extracellular region >> -------------is_a GO:0044421 : extracellular region >> -------------is_a GO:0031974 : membrane-enclosed lumen >> -------------is_a GO:0043226 : organelle >> -------------is_a GO:0044422 : organelle part >> -------------is_a GO:0043234 : protein complex >> -------------is_a GO:0045202 : synapse >> -------------is_a GO:0044456 : synapse part >> -------------is_a GO:0019012 : virion >> -------------is_a GO:0044423 : virion part >> >> >> * GO:0005623 : cell-->make it obsolete >> *** the GO:0044464 : cell part can merge into GO:0005575 : >> cellular_component >> >> Best >> Pankaj >> > From pj37 at cornell.edu Tue Feb 27 08:19:10 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 27 Feb 2007 11:19:10 -0500 Subject: Chromosome is an organelle ? In-Reply-To: References: Message-ID: <45E459FE.3090102@cornell.edu> A few more evidences. If we are on to having this relationship, can I request for human Y and X chromosome be added as a child of ISA chromosome or ISA nuclear chromosome, or rather the 10 different chromosomes in the nucleus of the O. sativa species be treated as separate subtypes of nuclear chromosome. They are all different entities and have reasonably different euchromatin content, genes and size. Also by other text book definitions the organelle should be visible to the microscope. So I am not sure to what stage of chromosome we are referring as an organelle. BTW these are just the points raised by some of the researchers while discussing the GO_CC section. Pankaj Harold J. Drabkin wrote: > I agree Jane; > After all, a mitochondrial ribosome is an organelle just like a cytosolic > ribosme, and the mito rib is found within another organelle (mito). > The nucleolus is recognized as an organized structure found in the > nucleus; > one can actually isolate chromosomes, so I would think that they ARE > indeed organelles wtihin another (nucleus). > > On Mon, 26 Feb 2007, Jane Lomax wrote: > >> Hi Pankaj - the definition of organelle is 'Organized structure of >> distinctive morphology and function' and we've included things like >> ribosomes and the cytoskeleton, so I can't see, on that basis, why we >> wouldn't include chromosomes? >> >> I don't think an organelle being part of another organelle causes logical >> problems, and it doesn't cause problems with the graph...we had a lot of >> discussion about this when we created the organelle terms in the first place: >> >> http://sourceforge.net/tracker/index.php?func=detail&aid=1021113&group_id=36855&atid=440764 >> >> It seems like organelle is one of those concepts that means different things to >> different people, so we'll never be completely in line with what's used in the >> community, but I don't think that should worry us too much. >> >> Jane >> >> On Thu, 22 Feb 2007, Pankaj Jaiswal wrote: >> >>> >>> >>> In this graph we see that 'chromosome' is an 'organelle'. I think majority of >>> the researchers would consider it simply ISA cell_part (or ISA >>> intracellular_part). If not it is something like for instance 'plastid >>> chromosome' is a part of 'plastid' where both 'plastid chromosome' and >>> 'plastid' are ISA 'organelle'. Or in lay person's knowledge 'an organ is >>> PARTOF and organ' considering organelle in cell/unicellular organisms is >>> synonymous with organs in multicellular organisms. >>> >>> I am not sure if this is a correct relationship in GO. >>> >>> Pankaj >>> >>> >> 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 >> > > -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From jane at ebi.ac.uk Tue Feb 27 08:22:05 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Tue, 27 Feb 2007 16:22:05 +0000 Subject: Chromosome is an organelle ? In-Reply-To: <0579A87F-8AF8-462B-955E-E5C694B58CDF@fruitfly.org> References: <0579A87F-8AF8-462B-955E-E5C694B58CDF@fruitfly.org> Message-ID: <54DA3AF5-8B7E-4B86-A083-A45434836443@ebi.ac.uk> Well, yes, I see that the definition could use some improvement ;) The difficulty is differentiating organelle from protein complex (the FMA def as it stands would encompass GO protein complexes). And to make matters more difficult, we also include extracellular organelles in GO. Organelles always have a specialized function, but then so do many protein complexes. I think the real distinction between organelles and protein complexes is size - organelles are typically visible under a light microscope, protein complexes usually not. But I bet there are exceptions to this in both categories! I don't know why plasma membrane is excluded - it's just that all of the sources we checked excluded plasma membrane, so we thought we better had too. There is no definitive definition of what an organelle is - this is the problem. Jane On 27 Feb 2007, at 15:54, Chris Mungall wrote: > > Organized structure of distinctive morphology and function. > > According to this definition, these are all organelles: > > My lungs > A tRNA molecule > A plasma membrane > > The gloss of the definition goes on to say: > > Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, > ribosomes and the cytoskeleton. Excludes the plasma membrane. > > Extensional definitions (ie consisting of a list of entities the > definition covers, or entities excluded) aren't good practice. Why > is plasma membrane excluded? It just is? > > The definition includes the word "distinctive" which doesn't seem > good. Distinctive to who? > > The FMA has this genus-differentia definition: > > Cell component which consists of macromolecules aggregated into > discrete structures in the protoplasm. > > Which is perhaps too human specific, and would presumably exclude > mt ribosome, but may be a good start. > > In the gloss they have: > Examples: endoplasmic reticulum, ribosome, cytoskeleton, nuclear > envelope, nucleus, mitochondrion. > > Note the genus of the definition, Cell component, is defined > according to what I think is the intuitive definition, contrary to > GO's somewhat upside down situation: > > Cell part which has a definable shape, bounded predominantly by > bonafide boundaries and is countable. > > > On Feb 26, 2007, at 6:39 PM, Harold J. Drabkin wrote: > >> I agree Jane; >> After all, a mitochondrial ribosome is an organelle just like a >> cytosolic >> ribosme, and the mito rib is found within another organelle (mito). >> The nucleolus is recognized as an organized structure found in the >> nucleus; >> one can actually isolate chromosomes, so I would think that they ARE >> indeed organelles wtihin another (nucleus). >> >> On Mon, 26 Feb 2007, Jane Lomax wrote: >> >>> Hi Pankaj - the definition of organelle is 'Organized structure of >>> distinctive morphology and function' and we've included things like >>> ribosomes and the cytoskeleton, so I can't see, on that basis, >>> why we >>> wouldn't include chromosomes? >>> >>> I don't think an organelle being part of another organelle causes >>> logical >>> problems, and it doesn't cause problems with the graph...we had a >>> lot of >>> discussion about this when we created the organelle terms in the >>> first place: >>> >>> http://sourceforge.net/tracker/index.php? >>> func=detail&aid=1021113&group_id=36855&atid=440764 >>> >>> It seems like organelle is one of those concepts that means >>> different things to >>> different people, so we'll never be completely in line with >>> what's used in the >>> community, but I don't think that should worry us too much. >>> >>> Jane >>> >>> On Thu, 22 Feb 2007, Pankaj Jaiswal wrote: >>> >>>> >>>> >>> 0005694&search_constraint=terms&query=GO: >>>> 0005694&view=details&show_associations=list> >>>> >>>> In this graph we see that 'chromosome' is an 'organelle'. I >>>> think majority of >>>> the researchers would consider it simply ISA cell_part (or ISA >>>> intracellular_part). If not it is something like for instance >>>> 'plastid >>>> chromosome' is a part of 'plastid' where both 'plastid >>>> chromosome' and >>>> 'plastid' are ISA 'organelle'. Or in lay person's knowledge 'an >>>> organ is >>>> PARTOF and organ' considering organelle in cell/unicellular >>>> organisms is >>>> synonymous with organs in multicellular organisms. >>>> >>>> I am not sure if this is a correct relationship in GO. >>>> >>>> Pankaj >>>> >>>> >>> >>> 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 kpilcher at northwestern.edu Tue Feb 27 08:38:56 2007 From: kpilcher at northwestern.edu (Karen Pilcher) Date: Tue, 27 Feb 2007 10:38:56 -0600 Subject: Chromosome is an organelle ? In-Reply-To: <54DA3AF5-8B7E-4B86-A083-A45434836443@ebi.ac.uk> References: <0579A87F-8AF8-462B-955E-E5C694B58CDF@fruitfly.org> <54DA3AF5-8B7E-4B86-A083-A45434836443@ebi.ac.uk> Message-ID: <6.0.0.22.2.20070227103257.04f2e410@merle.it.northwestern.edu> Are there any "organelles" made up strictly of protein components? (I can't think of any off the top of my head.) If not, the definition could specifically exclude specialized cell components that are made up solely of proteins, thus distinguishing 'organelle' from 'protein complex.' Karen At 10:22 AM 2/27/2007, Jane Lomax wrote: >Well, yes, I see that the definition could use some improvement ;) > >The difficulty is differentiating organelle from protein complex (the >FMA def as it stands would encompass GO protein complexes). And to >make matters more difficult, we also include extracellular organelles >in GO. > >Organelles always have a specialized function, but then so do many >protein complexes. I think the real distinction between organelles >and protein complexes is size - organelles are typically visible >under a light microscope, protein complexes usually not. But I bet >there are exceptions to this in both categories! > >I don't know why plasma membrane is excluded - it's just that all of >the sources we checked excluded plasma membrane, so we thought we >better had too. > >There is no definitive definition of what an organelle is - this is >the problem. > >Jane > > > >On 27 Feb 2007, at 15:54, Chris Mungall wrote: > >> >>Organized structure of distinctive morphology and function. >> >>According to this definition, these are all organelles: >> >>My lungs >>A tRNA molecule >>A plasma membrane >> >>The gloss of the definition goes on to say: >> >> Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, >>ribosomes and the cytoskeleton. Excludes the plasma membrane. >> >>Extensional definitions (ie consisting of a list of entities the >>definition covers, or entities excluded) aren't good practice. Why >>is plasma membrane excluded? It just is? >> >>The definition includes the word "distinctive" which doesn't seem >>good. Distinctive to who? >> >>The FMA has this genus-differentia definition: >> >>Cell component which consists of macromolecules aggregated into >>discrete structures in the protoplasm. >> >>Which is perhaps too human specific, and would presumably exclude >>mt ribosome, but may be a good start. >> >>In the gloss they have: >>Examples: endoplasmic reticulum, ribosome, cytoskeleton, nuclear >>envelope, nucleus, mitochondrion. >> >>Note the genus of the definition, Cell component, is defined >>according to what I think is the intuitive definition, contrary to >>GO's somewhat upside down situation: >> >>Cell part which has a definable shape, bounded predominantly by >>bonafide boundaries and is countable. >> >> >>On Feb 26, 2007, at 6:39 PM, Harold J. Drabkin wrote: >> >>>I agree Jane; >>>After all, a mitochondrial ribosome is an organelle just like a >>>cytosolic >>>ribosme, and the mito rib is found within another organelle (mito). >>>The nucleolus is recognized as an organized structure found in the >>>nucleus; >>>one can actually isolate chromosomes, so I would think that they ARE >>>indeed organelles wtihin another (nucleus). >>> >>>On Mon, 26 Feb 2007, Jane Lomax wrote: >>> >>>>Hi Pankaj - the definition of organelle is 'Organized structure of >>>>distinctive morphology and function' and we've included things like >>>>ribosomes and the cytoskeleton, so I can't see, on that basis, >>>>why we >>>>wouldn't include chromosomes? >>>> >>>>I don't think an organelle being part of another organelle causes >>>>logical >>>>problems, and it doesn't cause problems with the graph...we had a >>>>lot of >>>>discussion about this when we created the organelle terms in the >>>>first place: >>>> >>>>http://sourceforge.net/tracker/index.php? >>>>func=detail&aid=1021113&group_id=36855&atid=440764 >>>> >>>>It seems like organelle is one of those concepts that means >>>>different things to >>>>different people, so we'll never be completely in line with >>>>what's used in the >>>>community, but I don't think that should worry us too much. >>>> >>>>Jane >>>> >>>>On Thu, 22 Feb 2007, Pankaj Jaiswal wrote: >>>> >>>>> >>>>>>>>>0005694&search_constraint=terms&query=GO: >>>>>0005694&view=details&show_associations=list> >>>>> >>>>>In this graph we see that 'chromosome' is an 'organelle'. I >>>>>think majority of >>>>>the researchers would consider it simply ISA cell_part (or ISA >>>>>intracellular_part). If not it is something like for instance >>>>>'plastid >>>>>chromosome' is a part of 'plastid' where both 'plastid >>>>>chromosome' and >>>>>'plastid' are ISA 'organelle'. Or in lay person's knowledge 'an >>>>>organ is >>>>>PARTOF and organ' considering organelle in cell/unicellular >>>>>organisms is >>>>>synonymous with organs in multicellular organisms. >>>>> >>>>>I am not sure if this is a correct relationship in GO. >>>>> >>>>>Pankaj >>>>> >>>> >>>>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 >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20070227/82782cd0/attachment.html From midori at ebi.ac.uk Tue Feb 27 08:44:01 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 27 Feb 2007 16:44:01 +0000 (GMT) Subject: Chromosome is an organelle ? In-Reply-To: <6.0.0.22.2.20070227103257.04f2e410@merle.it.northwestern.edu> References: <0579A87F-8AF8-462B-955E-E5C694B58CDF@fruitfly.org> <54DA3AF5-8B7E-4B86-A083-A45434836443@ebi.ac.uk> <6.0.0.22.2.20070227103257.04f2e410@merle.it.northwestern.edu> Message-ID: Lots, I'm afraid ... just looking quickly, there's centriole, cytoskeleton, gas vesicle, polyhedral organelle ... probably also podosome, stereocilium bundle ... m On Tue, 27 Feb 2007, Karen Pilcher wrote: > > Are there any "organelles" made up strictly of protein components? (I can't > think of any off the top of my head.) If not, the definition could > specifically exclude specialized cell components that are made up solely of > proteins, thus distinguishing 'organelle' from 'protein complex.' > > Karen > > > At 10:22 AM 2/27/2007, Jane Lomax wrote: >> Well, yes, I see that the definition could use some improvement ;) >> >> The difficulty is differentiating organelle from protein complex (the >> FMA def as it stands would encompass GO protein complexes). And to >> make matters more difficult, we also include extracellular organelles >> in GO. >> >> Organelles always have a specialized function, but then so do many >> protein complexes. I think the real distinction between organelles >> and protein complexes is size - organelles are typically visible >> under a light microscope, protein complexes usually not. But I bet >> there are exceptions to this in both categories! >> >> I don't know why plasma membrane is excluded - it's just that all of >> the sources we checked excluded plasma membrane, so we thought we >> better had too. >> >> There is no definitive definition of what an organelle is - this is >> the problem. >> >> Jane >> >> >> >> On 27 Feb 2007, at 15:54, Chris Mungall wrote: >> >>> >>> Organized structure of distinctive morphology and function. >>> >>> According to this definition, these are all organelles: >>> >>> My lungs >>> A tRNA molecule >>> A plasma membrane >>> >>> The gloss of the definition goes on to say: >>> >>> Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, >>> ribosomes and the cytoskeleton. Excludes the plasma membrane. >>> >>> E