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[Gusdev-gusdev] kegg
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From: Thomas O. <ot...@fi...> - 2004-03-12 15:45:14
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ftp://ftp.genome.ad.jp/pub/ ftp://ftp.genome.ad.jp/pub/kegg/tarfiles from the secound directory I download and parsed the tar files. This suppose to be the files, like the kegg-engine are using them. Thomas Terry Clark wrote: >Thomas, >Could you send a pointer to the KEGG FTP URL you are >accessing and the names (or type of) files that >you are using? I would appreciate this to see how >others are using KEGG. > >OMIM is orthogonal; I just described it and the >parts of KEGG I addressed to explain the material >on my web site. > >Terry > > >On Fri, Mar 12, 2004 at 11:08:29AM -0300, Thomas Otto wrote: > > >>Terry, >> >>first, I parse the information from the files of the ftp-server. I do >>not use the xml stuff. >> >>True, there is a lot of stuff in kegg, but I want to represent it in >>GUS, so... >> >>... I think a link to OMIM makes sense, also to Motif/prosite. For me it >>is important to have all the relations without redundend. >> >>Give me some time, I will see, which parts might help me, >> >>cheers, >>Thomas >> >> >>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 > > > |
