From: Eric J. <e-...@no...> - 2007-01-16 17:58:30
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Hi Scott, thanks for the follow up. What would the definition of the proposed synonyms be? I'm not sure I get it. It sounds like the name is denormalized for the convenience of Gbrowse, but this then makes changing a name somewhat more complex than it needs to be. Is there a way to write a query with a left outer join to look in the feature table and the synonym table in the same query instead of replicating the name as a synonym (not sure which query this is in Gbrowse)? If that's not an option right now, I'd settle for a 'name' synonym and a 'synonym' synonym. Are those what primary_synonym and is_a synonyms are? I prefer sequecne_similarity_synonym over target_synonym. Thanks again, Eric -----Original Message----- From: Scott Cain [mailto:cai...@gm...] Sent: Tuesday, January 16, 2007 11:33 AM To: Eric Just Cc: gmo...@li... Subject: Re: [GMOD-devel] Loader: Name tag loaded into synonym table Hi Eric, It is a speed issue: when GBrowse wants to look for a name, it is much faster to look in the synonym table rather than look in feature.name and then synonym.name if it fails. I think the different synonym type is a good idea though. In fact, I've been asked if Target names from GFF files could stay out of the synonym table as well, but that would alter the way GBrowse typically works too. So, I would suggest two new synonym types: primary_synonym is_a synonym and target_synonym (or similarity_feature_synonym or something better) is_a synonym Thoughts? Scott On Tue, 2007-01-16 at 08:30 -0600, Eric Just wrote: > Hi Scott, > > It's me again. I've been working with the gmod loader and synonyms > lately. I really like how it loads all the Alias tags into the > synonym table. However, currently the Name tag also gets loaded into > the synonym table with the same type_id as Alias (mapping to a > 'synonym' term). This is a little confusing as the Name also gets > loaded into Feature.Name. In my opinion, Name does not need to go > into the synonym table as this is redundant. I very well may be missing a use case > though. If it does go into synonym, can it have a different type_id > than 'synonym'? I would like to be able to differentiate data from > the Alias tags (for which I like the 'synonym' type_id) from data from > the Name tag (for which I wonder whether it needs a synonym record). > Thanks for looking into this. > > Eric. > > > > > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDE V > _______________________________________________ > Gmod-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-devel -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cai...@gm... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |