Menu
▾
▴
Re: [Gusdev-gusdev] Relation between tables
|
From: <tw...@cs...> - 2004-03-12 13:25:22
|
> (By the way, those reactions are not complete in some of > the XML files.) I expect you know, there are two representations What reactions? How did that permutation happen? Sorry for the typos. It is early still ... but the gist is in the email. Terry On Fri, Mar 12, 2004 at 06:35:16AM -0600, Terry Clark wrote: > Thomas, > > A few months ago I worked out a preliminary set of tables > for *some* KEGG pathway data. > > (By the way, those reactions are not complete in some of > the XML files.) I expect you know, there are two representations > in the XML: one with proteins as nodes; the other with reaction > products as nodes and proteins as edges. > I focused on explicitly representing the latter > (the <reaction> tag part of the XML) but have toyed with > the idea to do a comprehensive KEGG representation in GUS unless > someone else does it first :-) > > I also have a plugin to load the tables. All I am discussing has > been implemented as a site-specific/local extension to GUS. > I put the database files (not the plugin - we can talk > about that later if you are interested) on the web page > > http://flora.uchicago.edu/gus/keggschemadraft/ > > One file you might check first at the URL is > ** kegg-tables.sql *** > > I am not satisfied with some of the design, and there may > be some uninspired things there - caveat emptor. I was > waiting for KEGG to fix some problems in the reaction tags, > and put together this operational db prototype in the meantime. > (For example, check the missing - as of three weeks ago still - > reaction tags in the XML for phenylalanine metabolism.) > > Anyway the files I point to above might be useful to > start with rather than from scratch. > > I also hacked together some table(s) for EnzymeCommission > numbers; there might be something in GUS for that, but at > the time what I did seemed faster for my needs than otherwise. > The OMIM parts there are not related to KEGG but part of > a project I am working on. > > > Terry > > > > > > On Thu, Mar 11, 2004 at 04:58:48PM -0300, Thomas Otto wrote: > > I think I will all the relation in one table... sort of EnzymeRelations... > > > > Thomas > > Thomas Otto wrote: > > > > >Okay, an example: > > >To every enzyme are several reaction associated. i.e. Enzymea, has > > >reaction1, ..., reaction n. > > >(1) I could be to save the name of the reaction in the table > > >EnzymeClassAttribute > > >(2) would be, to save nothing of this in the EnzymeClassAttribute, but > > >in a table (to create) EnzymeReactionRelation. > > > > > >This will mean a lot of new table, because just for the enzymes there > > >are pathways, reaction, compound, substrate, product... > > > > > >But indeed, I also prefer #2, who is less redundend. > > > > > >Thanks, > > >Thomas > > > > > >Angel Pizarro wrote: > > > > > >>In the absence of an example of data a definite schema, definitely #2 > > >>as the data model of choice. You can always implement materialized > > >>view to speed-up/ease queries. > > >> > > >>Cheers > > >>Angel > > >> > > >>Thomas Otto wrote: > > >> > > >>>That's what I was thinking about. So I want to know, which > > >>>representation of datas you prefer. (1 or 2, it is more a general > > >>>question). > > >>> > > >>>Thomas > > >>> > > >>> > > >>>Angel Pizarro wrote: > > >>> > > >>>>OK, I don't see where you are getting EnzymCompoundRelation & > > >>>>CompoundClassAttribute from. Our current version of GUS does not > > >>>>have these tables. The SRes.EnzymeClass table is also looking very > > >>>>wacky to me. Propose a nice structure for this and we can put it in > > >>>>the next release of GUS. > > >>>> > > >>>>Angel > > >>>> > > >>>>Thomas Otto wrote: > > >>>> > > >>>>>Hello, > > >>>>> > > >>>>>I am uploading some kegg data in the GUS system... > > >>>>> > > >>>>>So I looked which tables are existing, and which we are needing > > >>>>>i.e. for compound, reactions. Now I am not sure how is the > > >>>>>convention to relate the data. > > >>>>> > > >>>>>Example: > > >>>>>The Enzymes are related to the compounds. > > >>>>>(1) In EzymeClassAttribute I write the names of the compound > > >>>>>related to each enzyme. In CompoundClassAttribute I write also all > > >>>>>EC-numbers, related to it. > > >>>>>(2) Other possibilty would be to utilize a thrid table > > >>>>>EnzymeCompoundRelation, where I put the primkeys of the relations. > > >>>>> > > >>>>>(1) would be faster, easier to query, but redundend. > > >>>>>(2) Cleaner > > >>>>> > > >>>>>What are you thinking I should use? > > >>>>> > > >>>>>Thanks, > > >>>>>Thomas > > >>>>> > > >>>>> > > >>>>> > > >>>>> > > >>>>>------------------------------------------------------- > > >>>>>This SF.Net email is sponsored by: IBM Linux Tutorials > > >>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of > > >>>>>GenToo technologies. Learn everything from fundamentals to system > > >>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > > >>>>>_______________________________________________ > > >>>>>Gusdev-gusdev mailing list > > >>>>>Gus...@li... > > >>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > >>>> > > >>>> > > >>>> > > >>>> > > >>>> > > >>>> > > >>> > > >> > > >> > > >> > > >>------------------------------------------------------- > > >>This SF.Net email is sponsored by: IBM Linux Tutorials > > >>Free Linux tutorial presented by Daniel Robbins, President and CEO of > > >>GenToo technologies. Learn everything from fundamentals to system > > >>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > > >>_______________________________________________ > > >>Gusdev-gusdev mailing list > > >>Gus...@li... > > >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > >> > > > > > > > > > > > > > > >------------------------------------------------------- > > >This SF.Net email is sponsored by: IBM Linux Tutorials > > >Free Linux tutorial presented by Daniel Robbins, President and CEO of > > >GenToo technologies. Learn everything from fundamentals to system > > >administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > > >_______________________________________________ > > >Gusdev-gusdev mailing list > > >Gus...@li... > > >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by: IBM Linux Tutorials > > Free Linux tutorial presented by Daniel Robbins, President and CEO of > > GenToo technologies. Learn everything from fundamentals to system > > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IBM Linux Tutorials > Free Linux tutorial presented by Daniel Robbins, President and CEO of > GenToo technologies. Learn everything from fundamentals to system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
