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 dhowe at cs.uoregon.edu Mon Feb 5 11:00:00 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Mon, 05 Feb 2007 11:00:00 -0800 Subject: tissue vs. organ regeneration Message-ID: <45C77EB0.1030607@cs.uoregon.edu> Can anyone elaborate when to use 'tissue regeneration' vs. 'organ regeneration'? Also, Should 'organ regeneration' be part_of 'wound healing'? Example, fish are used to study regeneration of heart muscle tissue after a small snip is removed....'tissue regeneration' or 'organ regeneration'?? -Doug From dph at informatics.jax.org Mon Feb 5 11:04:15 2007 From: dph at informatics.jax.org (David Hill) Date: Mon, 05 Feb 2007 14:04:15 -0500 Subject: tissue vs. organ regeneration In-Reply-To: <45C77EB0.1030607@cs.uoregon.edu> References: <45C77EB0.1030607@cs.uoregon.edu> Message-ID: <45C77FAF.9030000@informatics.jax.org> My rule of thumb would be to look at the thing being regenerated. If it is defined in your organism's anatomical dictionary as a tissue, then it is tissue regenration, if it is defined as an organ, then it is organ regeneration. Then we need to hope that tissues and organs are defined in the same way across anatomical dictionaries, but that is out of our realm. David Doug howe wrote: > Can anyone elaborate when to use 'tissue regeneration' vs. 'organ > regeneration'? Also, Should 'organ regeneration' be part_of 'wound > healing'? > > Example, fish are used to study regeneration of heart muscle tissue > after a small snip is removed....'tissue regeneration' or 'organ > regeneration'?? > > -Doug From stacia at genome.Stanford.EDU Mon Feb 5 11:06:57 2007 From: stacia at genome.Stanford.EDU (Stacia Engel) Date: Mon, 5 Feb 2007 11:06:57 -0800 Subject: tissue vs. organ regeneration In-Reply-To: <45C77FAF.9030000@informatics.jax.org> References: <45C77EB0.1030607@cs.uoregon.edu> <45C77FAF.9030000@informatics.jax.org> Message-ID: seems to me that regeneration of heart muscle tissue would be tissue generation, whereas regeneration of an *entire* heart would be organ regeneration (if that even occurs!). stacia On Feb 5, 2007, at 11:04 AM, David Hill wrote: > My rule of thumb would be to look at the thing being regenerated. > If it is defined in your organism's anatomical dictionary as a > tissue, then it is tissue regenration, if it is defined as an > organ, then it is organ regeneration. Then we need to hope that > tissues and organs are defined in the same way across anatomical > dictionaries, but that is out of our realm. > > David > > Doug howe wrote: >> Can anyone elaborate when to use 'tissue regeneration' vs. 'organ >> regeneration'? Also, Should 'organ regeneration' be part_of >> 'wound healing'? >> >> Example, fish are used to study regeneration of heart muscle >> tissue after a small snip is removed....'tissue regeneration' or >> 'organ regeneration'?? >> >> -Doug > From midori at ebi.ac.uk Mon Feb 5 16:00:07 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 6 Feb 2007 00:00:07 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200702060000.l16007v1286739@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070206/62c4070d/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070206/62c4070d/attachment.pl From midori at ebi.ac.uk Wed Feb 7 16:00:08 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 8 Feb 2007 00:00:08 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200702080000.l18008C1438942@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070208/8d65f457/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070208/8d65f457/attachment.pl From mhaendel at uoneuro.uoregon.edu Wed Feb 7 16:41:30 2007 From: mhaendel at uoneuro.uoregon.edu (Melissa Haendel) Date: Wed, 07 Feb 2007 16:41:30 -0800 Subject: tissue vs. organ regeneration In-Reply-To: References: <45C77EB0.1030607@cs.uoregon.edu> <45C77FAF.9030000@informatics.jax.org> Message-ID: <45CA71BA.8060001@uoneuro.uoregon.edu> Hi all, Here are the definitions of organ, multi-tissue structure, and tissue from the new CARO (common anatomy reference ontology). These are types that refer to structures at varying levels of granularity, which seems to be at the crux of the question here. Melissa Portion of tissue: Anatomical structure that has as its parts cells of one or more types spatially arranged in a characteristic pattern. Multi-tissue structure: Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. Compound Organ: Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. Stacia Engel wrote: > seems to me that regeneration of heart muscle tissue would be tissue > generation, whereas regeneration of an *entire* heart would be organ > regeneration (if that even occurs!). > > stacia > > On Feb 5, 2007, at 11:04 AM, David Hill wrote: > >> My rule of thumb would be to look at the thing being regenerated. If >> it is defined in your organism's anatomical dictionary as a tissue, >> then it is tissue regenration, if it is defined as an organ, then it >> is organ regeneration. Then we need to hope that tissues and organs >> are defined in the same way across anatomical dictionaries, but that >> is out of our realm. >> >> David >> >> Doug howe wrote: >>> Can anyone elaborate when to use 'tissue regeneration' vs. 'organ >>> regeneration'? Also, Should 'organ regeneration' be part_of 'wound >>> healing'? >>> >>> Example, fish are used to study regeneration of heart muscle tissue >>> after a small snip is removed....'tissue regeneration' or 'organ >>> regeneration'?? >>> >>> -Doug >> -- Melissa Haendel, Ph.D. ZFIN Scientific Curator Zebrafish Information Network 5291 University of Oregon Eugene, OR 97403-5291 Phone: (541) 346-5108 From midori at ebi.ac.uk Mon Feb 12 16:00:09 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 13 Feb 2007 00:00:09 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200702130000.l1D009v1111636@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070213/7b21756c/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070213/7b21756c/attachment.pl From midori at ebi.ac.uk Wed Feb 14 16:00:06 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 15 Feb 2007 00:00:06 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200702150000.l1F00621192195@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070215/e2fc6f20/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070215/e2fc6f20/attachment.pl From midori at ebi.ac.uk Thu Feb 15 16:00:08 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 16 Feb 2007 00:00:08 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200702160000.l1G008m1254340@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070216/37fc1979/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070216/37fc1979/attachment.pl From jane at ebi.ac.uk Mon Feb 19 08:04:25 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Mon, 19 Feb 2007 16:04:25 +0000 Subject: annotation section of wiki Message-ID: <9E4744F8-FED1-4048-A346-C998A18167F9@ebi.ac.uk> The GO FAQ has moved to the wiki where it's easier for everyone to edit (it's currently on the private wiki, but will be moved to the public wiki shortly). However, some sections are a bit out of date, so before we make public, please can you check and update where necessary the section 'annotations': http://gocwiki.geneontology.org/index.php/GO_FAQ#Annotations Let me know when it's done and we can make this public. thanks! Jane From midori at ebi.ac.uk Tue Feb 20 16:00:06 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 21 Feb 2007 00:00:06 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200702210000.l1L006Z1415093@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070221/24752fd5/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070221/24752fd5/attachment.pl From midori at ebi.ac.uk Thu Feb 22 16:00:07 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 23 Feb 2007 00:00:07 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200702230000.l1N007Q1511901@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070223/f85ee9b0/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070223/f85ee9b0/attachment.pl From dhowe at cs.uoregon.edu Fri Feb 23 10:12:33 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Fri, 23 Feb 2007 10:12:33 -0800 Subject: constitutively active mutant mRNA injection = IDA or IMP? Message-ID: <45DF2E91.1090201@cs.uoregon.edu> If a constitutively active mRNA is injected into an embryo, producing some effect, is this IDA or IMP? Seems to be IDA to me...? -Doug From dhowe at cs.uoregon.edu Fri Feb 23 10:22:03 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Fri, 23 Feb 2007 10:22:03 -0800 Subject: constitutively active mutant mRNA injection = IDA or IMP? In-Reply-To: <45DF2E91.1090201@cs.uoregon.edu> References: <45DF2E91.1090201@cs.uoregon.edu> Message-ID: <45DF30CB.2080503@cs.uoregon.edu> I'm still confused by the ev code doc. The IMP evidence doc states that IMP is for: "Overexpression/ectopic expression of wild-type or mutant genes" I thought at the last annotation camp we decided that introduction of an mRNA constituted IDA evidence, while introduction of a dominant negative would be IMP. Along these lines, I've presupposed that introduction of a constitutively active mRNA would also be IDA..? Does the IMP doc still need to be updated, or am I just misinformed? -Doug Doug howe wrote: > If a constitutively active mRNA is injected into an embryo, producing > some effect, is this IDA or IMP? Seems to be IDA to me...? > -Doug > From midori at ebi.ac.uk Fri Feb 23 10:24:02 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 23 Feb 2007 18:24:02 +0000 (GMT) Subject: constitutively active mutant mRNA injection = IDA or IMP? In-Reply-To: <45DF30CB.2080503@cs.uoregon.edu> References: <45DF2E91.1090201@cs.uoregon.edu> <45DF30CB.2080503@cs.uoregon.edu> Message-ID: I'm pretty sure it's just that the doc uphate has yet to be done ... m On Fri, 23 Feb 2007, Doug howe wrote: > I'm still confused by the ev code doc. The IMP evidence doc states that IMP > is for: > "Overexpression/ectopic expression of wild-type or mutant genes" > > I thought at the last annotation camp we decided that introduction of an mRNA > constituted IDA evidence, while introduction of a dominant negative would be > IMP. Along these lines, I've presupposed that introduction of a > constitutively active mRNA would also be IDA..? > > Does the IMP doc still need to be updated, or am I just misinformed? > > -Doug > > > Doug howe wrote: >> If a constitutively active mRNA is injected into an embryo, producing some >> effect, is this IDA or IMP? Seems to be IDA to me...? >> -Doug >> > From kpilcher at northwestern.edu Fri Feb 23 10:24:18 2007 From: kpilcher at northwestern.edu (Karen Pilcher) Date: Fri, 23 Feb 2007 12:24:18 -0600 Subject: constitutively active mutant mRNA injection = IDA or IMP? In-Reply-To: <45DF2E91.1090201@cs.uoregon.edu> References: <45DF2E91.1090201@cs.uoregon.edu> Message-ID: <6.0.0.22.2.20070223122029.05081380@merle.it.northwestern.edu> Hi Doug, I assume that the mRNA encodes a constitutively active gene product? If so, this would be a mutation and therefore an IMP. Karen At 12:12 PM 2/23/2007, Doug howe wrote: >If a constitutively active mRNA is injected into an embryo, producing some >effect, is this IDA or IMP? Seems to be IDA to me...? >-Doug -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070223/ac4cd391/attachment.html From pgaudet at northwestern.edu Fri Feb 23 10:26:43 2007 From: pgaudet at northwestern.edu (Pascale Gaudet) Date: Fri, 23 Feb 2007 13:26:43 -0500 Subject: constitutively active mutant mRNA injection = IDA or IMP? In-Reply-To: <45DF30CB.2080503@cs.uoregon.edu> References: <45DF2E91.1090201@cs.uoregon.edu> <45DF30CB.2080503@cs.uoregon.edu> Message-ID: <6.0.1.1.2.20070223132317.036e8490@lulu.it.northwestern.edu> Doug, What is the experiment exactly? Are the authors trying to see what happens when you overexpress the gene, or did they overexpress to do an assay? For example: 1. overexpress a transcription factor in cell line X and observe the expression of a reporter gene -> function = transcription factor activity, IDA 2. Overexpress a ras protein and see aberrant cytoskeleton arrangement -> process = cytoskeleton organization and biogenesis, IMP. Does that make any sense? That's how I understand it. The fact that they are overexpressing does not immediately tell you what evidence code to use. Pascale At 10:22 AM 2/23/2007 -0800, Doug howe wrote: >I'm still confused by the ev code doc. The IMP evidence doc states that >IMP is for: >"Overexpression/ectopic expression of wild-type or mutant genes" > >I thought at the last annotation camp we decided that introduction of an >mRNA constituted IDA evidence, while introduction of a dominant negative >would be IMP. Along these lines, I've presupposed that introduction of a >constitutively active mRNA would also be IDA..? > >Does the IMP doc still need to be updated, or am I just misinformed? > >-Doug > > >Doug howe wrote: >>If a constitutively active mRNA is injected into an embryo, producing >>some effect, is this IDA or IMP? Seems to be IDA to me...? >>-Doug From nash at genome.Stanford.EDU Fri Feb 23 10:36:45 2007 From: nash at genome.Stanford.EDU (Rob Nash) Date: Fri, 23 Feb 2007 10:36:45 -0800 Subject: constitutively active mutant mRNA injection = IDA or IMP? In-Reply-To: <6.0.0.22.2.20070223122029.05081380@merle.it.northwestern.edu> References: <45DF2E91.1090201@cs.uoregon.edu> <6.0.0.22.2.20070223122029.05081380@merle.it.northwestern.edu> Message-ID: <76583505-5481-474B-A03A-7CBEF34A0FC3@genome.stanford.edu> I agree, as this is a 'mutant' form of the mRNA. Rob On Feb 23, 2007, at 10:24 AM, Karen Pilcher wrote: > > Hi Doug, > > I assume that the mRNA encodes a constitutively active gene > product? If so, this would be a mutation and therefore an IMP. > > Karen > > At 12:12 PM 2/23/2007, Doug howe wrote: >> If a constitutively active mRNA is injected into an embryo, >> producing some effect, is this IDA or IMP? Seems to be IDA to me...? >> -Doug Rob Nash, Ph.D. Senior Scientific Curator Saccharomyces Genome Database Department of Genetics Stanford University Medical Center Stanford, CA 94305-5120 USA phone: (650) 725-8956 fax: (650) 725-1534 email: nash at genome.stanford.edu http://www.yeastgenome.org/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070223/80513b86/attachment.html From dhowe at cs.uoregon.edu Fri Feb 23 10:45:56 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Fri, 23 Feb 2007 10:45:56 -0800 Subject: constitutively active mutant mRNA injection = IDA or IMP? In-Reply-To: <45DF30CB.2080503@cs.uoregon.edu> References: <45DF2E91.1090201@cs.uoregon.edu> <45DF30CB.2080503@cs.uoregon.edu> Message-ID: <45DF3664.1060107@cs.uoregon.edu> Fair enough: 1. Doc still needs updating. Could this task get a higher priority? Myself and our curators rely on this doc to help us make consistent decisions over time..especially when curation policies are updated. 2. Injection of unaltered mRNA would generally be IDA, while injection of any sort of altered mRNA is generally IMP. -Doug Doug howe wrote: > I'm still confused by the ev code doc. The IMP evidence doc states > that IMP is for: > "Overexpression/ectopic expression of wild-type or mutant genes" > > I thought at the last annotation camp we decided that introduction of > an mRNA constituted IDA evidence, while introduction of a dominant > negative would be IMP. Along these lines, I've presupposed that > introduction of a constitutively active mRNA would also be IDA..? > > Does the IMP doc still need to be updated, or am I just misinformed? > > -Doug > > > Doug howe wrote: >> If a constitutively active mRNA is injected into an embryo, producing >> some effect, is this IDA or IMP? Seems to be IDA to me...? >> -Doug >> > From rama at genome.Stanford.EDU Fri Feb 23 11:22:24 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Fri, 23 Feb 2007 11:22:24 -0800 Subject: constitutively active mutant mRNA injection = IDA or IMP? In-Reply-To: <45DF3664.1060107@cs.uoregon.edu> References: <45DF2E91.1090201@cs.uoregon.edu> <45DF30CB.2080503@cs.uoregon.edu> <45DF3664.1060107@cs.uoregon.edu> Message-ID: <00F32999-F1A8-48BB-ABF3-B06A6D38C937@genome.stanford.edu> Doug, Yes, the evidence code committee is working on this. Rama On Feb 23, 2007, at 10:45 AM, Doug howe wrote: > Fair enough: > 1. Doc still needs updating. Could this task get a higher > priority? Myself and our curators rely on this doc to help us make > consistent decisions over time..especially when curation policies > are updated. > 2. Injection of unaltered mRNA would generally be IDA, while > injection of any sort of altered mRNA is generally IMP. > > -Doug > > Doug howe wrote: >> I'm still confused by the ev code doc. The IMP evidence doc >> states that IMP is for: >> "Overexpression/ectopic expression of wild-type or mutant genes" >> >> I thought at the last annotation camp we decided that introduction >> of an mRNA constituted IDA evidence, while introduction of a >> dominant negative would be IMP. Along these lines, I've >> presupposed that introduction of a constitutively active mRNA >> would also be IDA..? >> >> Does the IMP doc still need to be updated, or am I just misinformed? >> >> -Doug >> >> >> Doug howe wrote: >>> If a constitutively active mRNA is injected into an embryo, >>> producing some effect, is this IDA or IMP? Seems to be IDA to >>> me...? >>> -Doug >>> >> From hjd at informatics.jax.org Fri Feb 23 13:03:10 2007 From: hjd at informatics.jax.org (Harold Drabkin) Date: Fri, 23 Feb 2007 16:03:10 -0500 Subject: constitutively active mutant mRNA injection = IDA or IMP? In-Reply-To: <45DF2E91.1090201@cs.uoregon.edu> References: <45DF2E91.1090201@cs.uoregon.edu> Message-ID: <45DF568E.20700@informatics.jax.org> Doug howe wrote: > If a constitutively active mRNA is injected into an embryo, producing > some effect, is this IDA or IMP? Seems to be IDA to me...? > -Doug At mgi it would be an IDA; if the mRNA is not mutant. IF, however, you are getting a comparison between inject 1 with wt vs a mutant mRNA in injection 2, then the observed effect would be used in an IMP I assume that however, you say "c constitutively active" because the NORMAL gene_product is NOT constitutively active? If so, you are annotating the mutant gene product and not the wild type. For example, if you make a mutant that replaces an active site requiring amino acid with one that doesn't work (eg, and arg to ala mutation), and when you do , you no longer get an effect , you apply the process or activity statement as IMP because you are comparing wt to the mutant to get the info. hjd From midori at ebi.ac.uk Mon Feb 26 16:00:06 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 27 Feb 2007 00:00:06 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200702270000.l1R006f1164058@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070227/d34d24fb/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070227/d34d24fb/attachment.pl From jclark at ebi.ac.uk Tue Feb 27 04:03:38 2007 From: jclark at ebi.ac.uk (J Clark) Date: Tue, 27 Feb 2007 12:03:38 +0000 Subject: transporter substrates Message-ID: <45E41E1A.9010509@ebi.ac.uk> Hi, I am part of a working group tackling the problems in the transporter activity section of the GO function ontology just now (The full group includes Val Wood, Michelle Gwinn, Ian Paulsen). Could ask you all for some input from you on a specific question? The transporter activity node has children grouping transporter functions according to substrate (http://tinyurl.com/3brydh). These substrate-specific terms are listed below. We would like to know if any of these substrates are ever transported in any way other than simply from one side of a membrane to the other? 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. We would also be interested to know of any examples of the substrate groups: nucleobase nucleotide nucleoside amino acid carbohydrate drug, antibiotic and xenobiotic ion are transported in this way. We are sending this question to a number of groups, and 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 in our draft file on 12th March, to be implemented in the live GO at a later date. Thank you very much for taking the time to think about this. Best wishes, Jennifer Clark GO Curator On behalf of the Transporter Working Group. Substrate specific terms: 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 From midori at ebi.ac.uk Tue Feb 27 16:00:07 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 28 Feb 2007 00:00:07 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200702280000.l1S007a1214969@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070228/82c65aa3/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070228/82c65aa3/attachment.pl From midori at ebi.ac.uk Wed Feb 28 07:46:40 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Wed, 28 Feb 2007 15:46:40 +0000 (GMT) Subject: HGNC database like In-Reply-To: <20070226104741.J33706@diamond.gene.ucl.ac.uk> References: <20070226104741.J33706@diamond.gene.ucl.ac.uk> Message-ID: Hi Michael, Thanks for telling us about the update to HGNC links. It would make the most sense for us to create two new entries, one for the symbol and one for IDs, so we can use an unambiguous prefix for each case. I propose changing the plain HGNC entry to: abbreviation: HGNC database: HUGO Gene Nomenclature Committee generic_url: http://www.gene.ucl.ac.uk/nomenclature/ and adding these: abbreviation: HGNC_gene database: HUGO Gene Nomenclature Committee object: Gene symbol example_id: HGNC:ABCA1 generic_url: http://www.gene.ucl.ac.uk/nomenclature/ url_syntax: http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?app_sym= url_example: http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?app_sym=ABCA1 abbreviation: HGNC_id database: HUGO Gene Nomenclature Committee object: Identifier example_id: HGNC_id:29 generic_url: http://www.gene.ucl.ac.uk/nomenclature/ url_syntax: http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id= url_example: http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id=HGNC:29 Let me know if this is OK, and I'll update the file behind the abbreviations page. Regards, Midori ============================ Midori A. Harris, Ph.D. GO Editor EMBL - EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 (0) 1223 494667 Fax: +44 (0) 1223 494468 Email: midori at ebi.ac.uk On Wed, 28 Feb 2007, michael wrote: > > > I was looking at your GO Database Abbreviations page > (http://www.geneontology.org/cgi-bin/xrefs.cgi) and notice that the > database link for the HGNC is out of date > > You can now link via HGNC ID or symbol. > > http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id=HGNC:29 > http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?app_sym=ABCA1 > > -- > Michael > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Michael John Lush PhD Tel:44-20-7679-5027 > Nomenclature Bioinformatician Fax:44-20-7387-3496 > HUGO Gene Nomenclature Committee Email: nome at galton.ucl.ac.uk > The Galton Laboratory > University College London, UK > URL: http://www.gene.ucl.ac.uk/nomenclature/ > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > From midori at ebi.ac.uk Wed Feb 28 13:11:14 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Wed, 28 Feb 2007 21:11:14 +0000 (GMT) Subject: HGNC database like In-Reply-To: <6479DEEE-312C-4023-983B-72F0F61C40EB@fruitfly.org> References: <20070226104741.J33706@diamond.gene.ucl.ac.uk> <6479DEEE-312C-4023-983B-72F0F61C40EB@fruitfly.org> Message-ID: So would you use two entries, HGNC as in HGNC:29, and HGNC_gene for ABCA1? m On Wed, 28 Feb 2007, Chris Mungall wrote: > I think we should make the prefix for the IDs HGNC, and add suffixes for > non-ID retrieval (otherwise we should have FlyBase_id, GO_id, etc). There's > no need for an HGNC_id entry. > > On Feb 28, 2007, at 7:46 AM, Midori Harris wrote: > >> Hi Michael, >> >> Thanks for telling us about the update to HGNC links. It would make the >> most sense for us to create two new entries, one for the symbol and one for >> IDs, so we can use an unambiguous prefix for each case. I propose changing >> the plain HGNC entry to: >> >> abbreviation: HGNC >> database: HUGO Gene Nomenclature Committee >> generic_url: http://www.gene.ucl.ac.uk/nomenclature/ >> >> and adding these: >> >> abbreviation: HGNC_gene >> database: HUGO Gene Nomenclature Committee >> object: Gene symbol >> example_id: HGNC:ABCA1 >> generic_url: http://www.gene.ucl.ac.uk/nomenclature/ >> url_syntax: >> http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?app_sym= >> url_example: >> http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?app_sym=ABCA1 >> >> abbreviation: HGNC_id >> database: HUGO Gene Nomenclature Committee >> object: Identifier >> example_id: HGNC_id:29 >> generic_url: http://www.gene.ucl.ac.uk/nomenclature/ >> url_syntax: >> http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id= >> url_example: >> http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id=HGNC:29 >> >> Let me know if this is OK, and I'll update the file behind the >> abbreviations page. >> >> Regards, >> Midori >> >> ============================ >> Midori A. Harris, Ph.D. >> GO Editor >> EMBL - EBI >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD UK >> >> Tel: +44 (0) 1223 494667 >> Fax: +44 (0) 1223 494468 >> Email: midori at ebi.ac.uk >> >> On Wed, 28 Feb 2007, michael wrote: >> >>> >>> >>> I was looking at your GO Database Abbreviations page >>> (http://www.geneontology.org/cgi-bin/xrefs.cgi) and notice that the >>> database link for the HGNC is out of date >>> >>> You can now link via HGNC ID or symbol. >>> >>> http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id=HGNC:29 >>> http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?app_sym=ABCA1 >>> >>> -- >>> Michael >>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>> Michael John Lush PhD Tel:44-20-7679-5027 >>> Nomenclature Bioinformatician Fax:44-20-7387-3496 >>> HUGO Gene Nomenclature Committee Email: nome at galton.ucl.ac.uk >>> The Galton Laboratory >>> University College London, UK >>> URL: http://www.gene.ucl.ac.uk/nomenclature/ >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>> > From cjm at fruitfly.org Wed Feb 28 14:48:08 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Wed, 28 Feb 2007 14:48:08 -0800 Subject: HGNC database like In-Reply-To: References: <20070226104741.J33706@diamond.gene.ucl.ac.uk> <6479DEEE-312C-4023-983B-72F0F61C40EB@fruitfly.org> Message-ID: <74DD2BCC-2D97-4686-9BA2-374CC5D2F38D@fruitfly.org> On Feb 28, 2007, at 1:11 PM, Midori Harris wrote: > So would you use two entries, HGNC as in HGNC:29, and HGNC_gene for > ABCA1? yes, I think so. We designate the first as the primary one through the 'object' field in the metadata; this should presumably be the stable ID, whereas the second one is useful for making links > m > > On Wed, 28 Feb 2007, Chris Mungall wrote: > >> I think we should make the prefix for the IDs HGNC, and add >> suffixes for non-ID retrieval (otherwise we should have >> FlyBase_id, GO_id, etc). There's no need for an HGNC_id entry. >> >> On Feb 28, 2007, at 7:46 AM, Midori Harris wrote: >> >>> Hi Michael, >>> Thanks for telling us about the update to HGNC links. It would >>> make the most sense for us to create two new entries, one for the >>> symbol and one for IDs, so we can use an unambiguous prefix for >>> each case. I propose changing the plain HGNC entry to: >>> >>> abbreviation: HGNC >>> database: HUGO Gene Nomenclature Committee >>> generic_url: http://www.gene.ucl.ac.uk/nomenclature/ >>> and adding these: >>> >>> abbreviation: HGNC_gene >>> database: HUGO Gene Nomenclature Committee >>> object: Gene symbol >>> example_id: HGNC:ABCA1 >>> generic_url: http://www.gene.ucl.ac.uk/nomenclature/ >>> url_syntax: >>> http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?app_sym= >>> url_example: >>> http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php? >>> app_sym=ABCA1 >>> >>> abbreviation: HGNC_id >>> database: HUGO Gene Nomenclature Committee >>> object: Identifier >>> example_id: HGNC_id:29 >>> generic_url: http://www.gene.ucl.ac.uk/nomenclature/ >>> url_syntax: >>> http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id= >>> url_example: >>> http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php? >>> hgnc_id=HGNC:29 >>> Let me know if this is OK, and I'll update the file behind the >>> abbreviations page. >>> Regards, >>> Midori >>> ============================ >>> Midori A. Harris, Ph.D. >>> GO Editor >>> EMBL - EBI >>> Wellcome Trust Genome Campus >>> Hinxton >>> Cambridge CB10 1SD UK >>> Tel: +44 (0) 1223 494667 >>> Fax: +44 (0) 1223 494468 >>> Email: midori at ebi.ac.uk >>> On Wed, 28 Feb 2007, michael wrote: >>>> I was looking at your GO Database Abbreviations page >>>> (http://www.geneontology.org/cgi-bin/xrefs.cgi) and notice that the >>>> database link for the HGNC is out of date >>>> You can now link via HGNC ID or symbol. >>>> http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php? >>>> hgnc_id=HGNC:29 >>>> http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php? >>>> app_sym=ABCA1 >>>> -- >>>> Michael >>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>> ~ >>>> Michael John Lush PhD Tel:44-20-7679-5027 >>>> Nomenclature Bioinformatician Fax:44-20-7387-3496 >>>> HUGO Gene Nomenclature Committee Email: nome at galton.ucl.ac.uk >>>> The Galton Laboratory >>>> University College London, UK >>>> URL: http://www.gene.ucl.ac.uk/nomenclature/ >>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>> ~ >> > From cjm at fruitfly.org Wed Feb 28 10:30:33 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Wed, 28 Feb 2007 10:30:33 -0800 Subject: HGNC database like In-Reply-To: References: <20070226104741.J33706@diamond.gene.ucl.ac.uk> Message-ID: <6479DEEE-312C-4023-983B-72F0F61C40EB@fruitfly.org> I think we should make the prefix for the IDs HGNC, and add suffixes for non-ID retrieval (otherwise we should have FlyBase_id, GO_id, etc). There's no need for an HGNC_id entry. On Feb 28, 2007, at 7:46 AM, Midori Harris wrote: > Hi Michael, > > Thanks for telling us about the update to HGNC links. It would make > the most sense for us to create two new entries, one for the symbol > and one for IDs, so we can use an unambiguous prefix for each case. > I propose changing the plain HGNC entry to: > > abbreviation: HGNC > database: HUGO Gene Nomenclature Committee > generic_url: http://www.gene.ucl.ac.uk/nomenclature/ > > and adding these: > > abbreviation: HGNC_gene > database: HUGO Gene Nomenclature Committee > object: Gene symbol > example_id: HGNC:ABCA1 > generic_url: http://www.gene.ucl.ac.uk/nomenclature/ > url_syntax: > http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?app_sym= > url_example: > http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php? > app_sym=ABCA1 > > abbreviation: HGNC_id > database: HUGO Gene Nomenclature Committee > object: Identifier > example_id: HGNC_id:29 > generic_url: http://www.gene.ucl.ac.uk/nomenclature/ > url_syntax: > http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id= > url_example: > http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php? > hgnc_id=HGNC:29 > > Let me know if this is OK, and I'll update the file behind the > abbreviations page. > > Regards, > Midori > > ============================ > Midori A. Harris, Ph.D. > GO Editor > EMBL - EBI > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD UK > > Tel: +44 (0) 1223 494667 > Fax: +44 (0) 1223 494468 > Email: midori at ebi.ac.uk > > On Wed, 28 Feb 2007, michael wrote: > >> >> >> I was looking at your GO Database Abbreviations page >> (http://www.geneontology.org/cgi-bin/xrefs.cgi) and notice that the >> database link for the HGNC is out of date >> >> You can now link via HGNC ID or symbol. >> >> http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php? >> hgnc_id=HGNC:29 >> http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php? >> app_sym=ABCA1 >> >> -- >> Michael >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> Michael John Lush PhD Tel:44-20-7679-5027 >> Nomenclature Bioinformatician Fax:44-20-7387-3496 >> HUGO Gene Nomenclature Committee Email: nome at galton.ucl.ac.uk >> The Galton Laboratory >> University College London, UK >> URL: http://www.gene.ucl.ac.uk/nomenclature/ >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >