From jclark at ebi.ac.uk Wed May 9 03:36:58 2007 From: jclark at ebi.ac.uk (J Clark) Date: Wed, 09 May 2007 11:36:58 +0100 Subject: [transport] exchanger activity Message-ID: <4641A44A.1020708@ebi.ac.uk> Hi, Do you know of any reason why 'anion exchanger activity' shouldn't be an exact synonym of 'anion:anion antiporter activity'? Thanks, Jen -- Gene Ontology Consortium EMBL-European Bioinformatics Institute From jclark at ebi.ac.uk Wed May 9 07:34:20 2007 From: jclark at ebi.ac.uk (J Clark) Date: Wed, 09 May 2007 15:34:20 +0100 Subject: [transport] Transporter activity overhaul Message-ID: <4641DBEC.1000804@ebi.ac.uk> Hi, I'm sure many of you will know that we have been doing a lot of work on the transporter activity section of the function ontology. Well it's been going on for quite a while now and we have revamped a lot of the top level terms, though the work is by no means over. Anyway, two of the four people on the working group are away on holiday for the next couple of weeks so I thought this might be a good time for you all to have a quick look at what we've done if you're interested. The file can be downloaded from: http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/transport.obo and you can vew it by loading it into OBO-Edit. You can see the part we've changed by using the term search facility and searching on 'ancestor' 'name' 'equals' 'transporter activity'. I have attached a couple of pictures of how to set up the search in case that's useful. If any of you can see anything that's still glaringly wrong and easy to fix could you possibly send me a list? As far I can see it's mostly the more granular terms that need moved around or redefined and the more difficult undefined terms that still need fixed. Also there are questions over chaperone activities, things to do with drug, xenobiotic and so on, and a stricter application of standard definitions to the graph. We have plans to get on to these, but it would be nice to have some feedback on what we've done at this half way point. If you would like to know what we have done then the notes are here: http://wiki.geneontology.org/index.php?title=Transporters In general the changes that you will notice are that 'permease' 'porter' and 'carrier' no longer appear in term names and that the structure and definitions are along the lines shown here: http://wiki.geneontology.org/index.php/Docs Hope you like it. Thanks, Jen (on behalf of the transporter activity working group Jennifer Clark, Michelle Gwinn-Giglio, Val Wood and IanPaulsen.) -- Gene Ontology Consortium EMBL-European Bioinformatics Institute -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 20.png Type: image/png Size: 20197 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/transport/attachments/20070509/b172fc69/attachment.png -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 21.png Type: image/png Size: 19650 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/transport/attachments/20070509/b172fc69/attachment-0001.png From midori at ebi.ac.uk Fri May 11 04:40:04 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 11 May 2007 12:40:04 +0100 (BST) Subject: [transport] Re: Transporter activity overhaul In-Reply-To: <4641DBEC.1000804@ebi.ac.uk> References: <4641DBEC.1000804@ebi.ac.uk> Message-ID: Hi, It's great to see how much this group has done in just a few weeks. I'm nowhere near expert level myself, but the upper level organization looks fine as far as I can tell. I've taken the liberty of fixing a couple of typos, and I have some comments, mostly pretty small. Looks like a missing relationship: substrate-specific transmembrane transporter activity GO:0022891 is_a substrate-specific transporter activity GO:0022892 For these term names, make singular and correct case, and shouldn't they have 'activity' at the end? transmembrane electron transfer carriers GO:0022865 Transmembrane 1-Electron Transfer Carriers GO:0022866 transmembrane 2-Electron Transfer Carriers GO:0022867 The def of large uncharged polar molecule transporter activity GO:0022815 should be worded more like the others. The def wording for cation transmembrane transporter activity GO:0008324 should be more like that of anion transmembrane transporter activity GO:0008509. Amine transporter activity GO:0005275 is under transmembrane transporter activity, but its def doesn't have the across-a-membrane bit, nor do those of at least some of the children. The def of mobile ion carrier activity GO:0022809 doesn't seem to emphasize the activity quite enough. Maybe something like "Enables the movement of an ion by enclosing the ion and traveling across the membrane; does not form a fully open pore in the membrane."? I guess this is historical, but it seems odd that the def of voltage-gated ion channel activity GO:0005244 has an explanation of what an ion is, when the parent terms don't. In a similar vein, cation channel activity GO:0005261 has a "reaction" whereas most other defs don't. That said, I know it would be a huge task to get all of the definitions fully consistently worded, and as long as the glaring problems are fixed, it's probably not a high priority. Cheers, and thanks again for all the effort, midori On Wed, 9 May 2007, J Clark wrote: > Hi, > > I'm sure many of you will know that we have been doing a lot of work on the > transporter activity section of the function ontology. Well it's been going > on for quite a while now and we have revamped a lot of the top level terms, > though the work is by no means over. > > Anyway, two of the four people on the working group are away on holiday for > the next couple of weeks so I thought this might be a good time for you all > to have a quick look at what we've done if you're interested. The file can be > downloaded from: > > http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/transport.obo > > and you can vew it by loading it into OBO-Edit. > > You can see the part we've changed by using the term search facility and > searching on 'ancestor' 'name' 'equals' 'transporter activity'. > I have attached a couple of pictures of how to set up the search in case > that's useful. > > If any of you can see anything that's still glaringly wrong and easy to fix > could you possibly send me a list? As far I can see it's mostly the more > granular terms that need moved around or redefined and the more difficult > undefined terms that still need fixed. Also there are questions over > chaperone activities, things to do with drug, xenobiotic and so on, and a > stricter application of standard definitions to the graph. We have plans to > get on to these, but it would be nice to have some feedback on what we've > done at this half way point. > > If you would like to know what we have done then the notes are here: > http://wiki.geneontology.org/index.php?title=Transporters > > In general the changes that you will notice are that 'permease' 'porter' and > 'carrier' no longer appear in term names and that the structure and > definitions are along the lines shown here: > > http://wiki.geneontology.org/index.php/Docs > > Hope you like it. > > Thanks, > > Jen > > (on behalf of the transporter activity working group > Jennifer Clark, Michelle Gwinn-Giglio, Val Wood and IanPaulsen.) > > >