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Re: [Gusdev-gusdev] Relation between tables
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From: <tw...@cs...> - 2004-03-12 12:46:21
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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 |
