Menu
▾
▴
gusdev-gusdev
|
From: Jason H. <jha...@pr...> - 2004-03-09 00:13:03
|
Hi all, I am working with Laurie Kramer to port the GUS platform to PostgreSQL. Most things work, or are pretty trivial to get working (more on that later). The only real issue I have run into is PostgreSQL uses array as a reserved word (it's a datatype), and you can't make a table called array. This is as of PostgreSQL 7.4 (and is a keyword according to SQL99). PostgreSQL 7.3 doesn't reserve this word, but is a bit gimpy on sub-selects, if necessary we can downgrade, but this will be an issue in the future, as 7.3 departs and 7.4 takes over for it. Cheers, Jason Jason A. Hackney Graduate Student Princeton University |
|
From: Chris S. <sto...@pc...> - 2004-03-09 13:16:09
|
Hi Jason, Great to hear of your progress. Sounds like we will need to change the table name for Array in RAD. Any suggestions? "Array_" "ArrayP" (for ArraryPostgreSQL) Chris On Mar 8, 2004, at 7:04 PM, Jason Hackney wrote: > Hi all, > > I am working with Laurie Kramer to port the GUS platform to > PostgreSQL. Most things work, or are pretty trivial to get working > (more on that later). The only real issue I have run into is > PostgreSQL uses array as a reserved word (it's a datatype), and you > can't make a table called array. This is as of PostgreSQL 7.4 (and is > a keyword according to SQL99). PostgreSQL 7.3 doesn't reserve this > word, but is a bit gimpy on sub-selects, if necessary we can > downgrade, but this will be an issue in the future, as 7.3 departs and > 7.4 takes over for it. > > Cheers, > Jason > > Jason A. Hackney > Graduate Student > Princeton University > > > > ------------------------------------------------------- > 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 > |
|
From: Steve F. <sfi...@pc...> - 2004-03-09 15:18:54
|
I think we need to find a name that is appropriate across all platforms, and is self-explanatory. we just need to find a prefix which captures the full generality of the Array as we are using it. how about: MicroArray BioArray ExpressionArray HybridizationArray steve Chris Stoeckert wrote: > Hi Jason, > Great to hear of your progress. Sounds like we will need to change the > table name for Array in RAD. > > Any suggestions? "Array_" "ArrayP" (for ArraryPostgreSQL) > > Chris > > On Mar 8, 2004, at 7:04 PM, Jason Hackney wrote: > >> Hi all, >> >> I am working with Laurie Kramer to port the GUS platform to >> PostgreSQL. Most things work, or are pretty trivial to get working >> (more on that later). The only real issue I have run into is >> PostgreSQL uses array as a reserved word (it's a datatype), and you >> can't make a table called array. This is as of PostgreSQL 7.4 (and is >> a keyword according to SQL99). PostgreSQL 7.3 doesn't reserve this >> word, but is a bit gimpy on sub-selects, if necessary we can >> downgrade, but this will be an issue in the future, as 7.3 departs >> and 7.4 takes over for it. >> >> Cheers, >> Jason >> >> Jason A. Hackney >> Graduate Student >> Princeton University >> >> >> >> ------------------------------------------------------- >> 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 |
|
From: Angel P. <an...@pc...> - 2004-03-09 15:22:07
|
Actually, The Array table is an "ArrayDesign" object in MAGE. Why not just name it that? Angel Steve Fischer wrote: > I think we need to find a name that is appropriate across all > platforms, and is self-explanatory. > we just need to find a prefix which captures the full generality of > the Array as we are using it. > > how about: > MicroArray > BioArray > ExpressionArray > HybridizationArray > > steve > > Chris Stoeckert wrote: > >> Hi Jason, >> Great to hear of your progress. Sounds like we will need to change >> the table name for Array in RAD. >> >> Any suggestions? "Array_" "ArrayP" (for ArraryPostgreSQL) >> >> Chris >> >> On Mar 8, 2004, at 7:04 PM, Jason Hackney wrote: >> >>> Hi all, >>> >>> I am working with Laurie Kramer to port the GUS platform to >>> PostgreSQL. Most things work, or are pretty trivial to get working >>> (more on that later). The only real issue I have run into is >>> PostgreSQL uses array as a reserved word (it's a datatype), and you >>> can't make a table called array. This is as of PostgreSQL 7.4 (and >>> is a keyword according to SQL99). PostgreSQL 7.3 doesn't reserve >>> this word, but is a bit gimpy on sub-selects, if necessary we can >>> downgrade, but this will be an issue in the future, as 7.3 departs >>> and 7.4 takes over for it. >>> >>> Cheers, >>> Jason >>> >>> Jason A. Hackney >>> Graduate Student >>> Princeton University >>> >>> >>> >>> ------------------------------------------------------- >>> 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 > > |
|
From: Steve F. <sfi...@pc...> - 2004-03-09 15:28:48
|
that sounds good to me. steve Angel Pizarro wrote: > Actually, The Array table is an "ArrayDesign" object in MAGE. Why not > just name it that? > > Angel > Steve Fischer wrote: > >> I think we need to find a name that is appropriate across all >> platforms, and is self-explanatory. we just need to find a prefix >> which captures the full generality of the Array as we are using it. >> >> how about: >> MicroArray >> BioArray >> ExpressionArray >> HybridizationArray >> >> steve >> >> Chris Stoeckert wrote: >> >>> Hi Jason, >>> Great to hear of your progress. Sounds like we will need to change >>> the table name for Array in RAD. >>> >>> Any suggestions? "Array_" "ArrayP" (for ArraryPostgreSQL) >>> >>> Chris >>> >>> On Mar 8, 2004, at 7:04 PM, Jason Hackney wrote: >>> >>>> Hi all, >>>> >>>> I am working with Laurie Kramer to port the GUS platform to >>>> PostgreSQL. Most things work, or are pretty trivial to get working >>>> (more on that later). The only real issue I have run into is >>>> PostgreSQL uses array as a reserved word (it's a datatype), and you >>>> can't make a table called array. This is as of PostgreSQL 7.4 (and >>>> is a keyword according to SQL99). PostgreSQL 7.3 doesn't reserve >>>> this word, but is a bit gimpy on sub-selects, if necessary we can >>>> downgrade, but this will be an issue in the future, as 7.3 departs >>>> and 7.4 takes over for it. >>>> >>>> Cheers, >>>> Jason >>>> >>>> Jason A. Hackney >>>> Graduate Student >>>> Princeton University >>>> >>>> >>>> >>>> ------------------------------------------------------- >>>> 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 |
|
From: Jason H. <jha...@pr...> - 2004-03-09 15:28:04
|
Hi Chris, Well, I wouldn't be so fast to do that just yet. As of this morning, I have rebuilt Pg 7.3, and reinstalled GUS. Everything builds fine, including the array and associated tables, as far as I can tell. I can register plugins using ga. That's about it, so far. What I think would be useful would be some examples of Perl modules built using Oracle, just so I can make sure that everything is kosher. Anyone want to volunteer a couple of modules they have built, so I can compare and contrast? So far, so good, though. Cheers, Jason On Mar 9, 2004, at 8:06 AM, Chris Stoeckert wrote: > Hi Jason, > Great to hear of your progress. Sounds like we will need to change the > table name for Array in RAD. > > Any suggestions? "Array_" "ArrayP" (for ArraryPostgreSQL) > > Chris > > On Mar 8, 2004, at 7:04 PM, Jason Hackney wrote: > >> Hi all, >> >> I am working with Laurie Kramer to port the GUS platform to >> PostgreSQL. Most things work, or are pretty trivial to get working >> (more on that later). The only real issue I have run into is >> PostgreSQL uses array as a reserved word (it's a datatype), and you >> can't make a table called array. This is as of PostgreSQL 7.4 (and is >> a keyword according to SQL99). PostgreSQL 7.3 doesn't reserve this >> word, but is a bit gimpy on sub-selects, if necessary we can >> downgrade, but this will be an issue in the future, as 7.3 departs >> and 7.4 takes over for it. >> >> Cheers, >> Jason >> >> Jason A. Hackney >> Graduate Student >> Princeton University >> >> >> >> ------------------------------------------------------- >> 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 >> |
|
From: Steve F. <sfi...@pc...> - 2004-03-09 15:48:38
|
Jason- Here is a quote from a mail i sent on Feb 13: ---------------------------------------------------------------------------------- Porting the Object Layer I just did a quick look in the object layer code (Perl). (we can defer for now on the java object layer since its not in wide use). Only two files seem to use oracle system tables, both in $PROJECT_HOME/GUS/ObjRelP/lib/perl: DbiTable.pm and DbiDatabase.pm. There are about 10 separate sql queries that use the oracle system tables (listed below). A quick fix would be to supply an Oracle.pm and a PostgreSQL.pm which have methods that provide the correct sql for those queries. IF postgres has parallel tables, then this should be trivial. if not...? here are the tables used: all_sequences all_cons_columns all_constraints all_tab_columns all_views ---------------------------------------------------------------------------------- I know that Laurie was working on porting the queries found in the object layer, and seems to have succeeded. I suggested that we factor those queries out of the DbiTable.pm and DbiDatabase.pm files, and place them into an Oracle.pm and PostgreSQL.pm. How did you guys integrate the PostgreSQL specific queries into the object layer? If you haven't done a clean refactoring we can work together on that... steve Jason Hackney wrote: > Hi Chris, > > Well, I wouldn't be so fast to do that just yet. As of this morning, I > have rebuilt Pg 7.3, and reinstalled GUS. Everything builds fine, > including the array and associated tables, as far as I can tell. I can > register plugins using ga. That's about it, so far. What I think would > be useful would be some examples of Perl modules built using Oracle, > just so I can make sure that everything is kosher. Anyone want to > volunteer a couple of modules they have built, so I can compare and > contrast? So far, so good, though. > > Cheers, > Jason > > On Mar 9, 2004, at 8:06 AM, Chris Stoeckert wrote: > >> Hi Jason, >> Great to hear of your progress. Sounds like we will need to change >> the table name for Array in RAD. >> >> Any suggestions? "Array_" "ArrayP" (for ArraryPostgreSQL) >> >> Chris >> >> On Mar 8, 2004, at 7:04 PM, Jason Hackney wrote: >> >>> Hi all, >>> >>> I am working with Laurie Kramer to port the GUS platform to >>> PostgreSQL. Most things work, or are pretty trivial to get working >>> (more on that later). The only real issue I have run into is >>> PostgreSQL uses array as a reserved word (it's a datatype), and you >>> can't make a table called array. This is as of PostgreSQL 7.4 (and >>> is a keyword according to SQL99). PostgreSQL 7.3 doesn't reserve >>> this word, but is a bit gimpy on sub-selects, if necessary we can >>> downgrade, but this will be an issue in the future, as 7.3 departs >>> and 7.4 takes over for it. >>> >>> Cheers, >>> Jason >>> >>> Jason A. Hackney >>> Graduate Student >>> Princeton University >>> >>> >>> >>> ------------------------------------------------------- >>> 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 |
|
From: Jason H. <jha...@pr...> - 2004-03-09 16:09:29
|
Steve- On Mar 9, 2004, at 10:39 AM, Steve Fischer wrote: > Jason- > > Here is a quote from a mail i sent on Feb 13: > <snip> > I know that Laurie was working on porting the queries found in the > object layer, and seems to have succeeded. > > I suggested that we factor those queries out of the DbiTable.pm and > DbiDatabase.pm files, and place them into an Oracle.pm and > PostgreSQL.pm. > > How did you guys integrate the PostgreSQL specific queries into the > object layer? I generally really just plunked them into an 'elsif' where there is an 'if' that asks for getDSN =~/oracle/ Pretty messy. There is one strangely nested if if elsif. That's about it. > If you haven't done a clean refactoring we can work together on that... > I was getting ready to clean some things up. There are changes in DbiTable and DbiDatabase, like you said, there is also a one-line change in DbiRow.pm. I would be happy to help in the code refactoring in any way that I can. I have diffs associated with all of the changes I have made, if you want those. Two of the queries that Laurie wrote don't work, so I rewrote those. Jason > steve > > Jason Hackney wrote: > >> Hi Chris, >> >> Well, I wouldn't be so fast to do that just yet. As of this morning, >> I have rebuilt Pg 7.3, and reinstalled GUS. Everything builds fine, >> including the array and associated tables, as far as I can tell. I >> can register plugins using ga. That's about it, so far. What I think >> would be useful would be some examples of Perl modules built using >> Oracle, just so I can make sure that everything is kosher. Anyone >> want to volunteer a couple of modules they have built, so I can >> compare and contrast? So far, so good, though. >> >> Cheers, >> Jason >> >> On Mar 9, 2004, at 8:06 AM, Chris Stoeckert wrote: >> >>> Hi Jason, >>> Great to hear of your progress. Sounds like we will need to change >>> the table name for Array in RAD. >>> >>> Any suggestions? "Array_" "ArrayP" (for ArraryPostgreSQL) >>> >>> Chris >>> >>> On Mar 8, 2004, at 7:04 PM, Jason Hackney wrote: >>> >>>> Hi all, >>>> >>>> I am working with Laurie Kramer to port the GUS platform to >>>> PostgreSQL. Most things work, or are pretty trivial to get working >>>> (more on that later). The only real issue I have run into is >>>> PostgreSQL uses array as a reserved word (it's a datatype), and you >>>> can't make a table called array. This is as of PostgreSQL 7.4 (and >>>> is a keyword according to SQL99). PostgreSQL 7.3 doesn't reserve >>>> this word, but is a bit gimpy on sub-selects, if necessary we can >>>> downgrade, but this will be an issue in the future, as 7.3 departs >>>> and 7.4 takes over for it. >>>> >>>> Cheers, >>>> Jason >>>> >>>> Jason A. Hackney >>>> Graduate Student >>>> Princeton University >>>> >>>> >>>> >>>> ------------------------------------------------------- >>>> 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 > |
|
From: Jason H. <jha...@pr...> - 2004-03-09 23:17:00
|
Hi Steve, > I suggested that we factor those queries out of the DbiTable.pm and > DbiDatabase.pm files, and place them into an Oracle.pm and > PostgreSQL.pm. > > How did you guys integrate the PostgreSQL specific queries into the > object layer? > > If you haven't done a clean refactoring we can work together on that... > > steve > It looks like I have a rough first pass refactoring for Oracle and PostgreSQL. It still relies on checking the dsn to decide whether to use the Oracle of PostgreSQL specific sql outputter I wrote. I implemented it as a method for DbiDatabase called getDbSpecSql. This method creates a new instance of an GUS::ObjRelP::Oracle or ::PostgreSQL class. These classes have methods for giving the correct sql statements. This could be done for DbiTable, as well, I just don't have it that way right now. So far it seems to build GUS for PostgreSQL. How many people are using Sybase? I ask because some of the places that call for db specific sql ask whether you are using Sybase and others don't. However, I haven't written anything for Sybase, since I don't really see too much of that stuff around. What is the consensus on the case sensitivity for fetchrow_hashref? If it is enough to merely make sure that it is called with either 'NAME_lc' or 'NAME_uc' that would be great by me. Anybody have any thoughts on this? Jason |
|
From: Steve F. <sfi...@pc...> - 2004-03-10 14:03:59
|
sounds good. in the code i am working on now (WDK), I call the method getDbPlatform(). for fetchrow, yes, we'll just use NAME_uc. steve Jason Hackney wrote: > Hi Steve, > >> I suggested that we factor those queries out of the DbiTable.pm and >> DbiDatabase.pm files, and place them into an Oracle.pm and >> PostgreSQL.pm. >> >> How did you guys integrate the PostgreSQL specific queries into the >> object layer? >> >> If you haven't done a clean refactoring we can work together on that... >> >> steve >> > > It looks like I have a rough first pass refactoring for Oracle and > PostgreSQL. It still relies on checking the dsn to decide whether to > use the Oracle of PostgreSQL specific sql outputter I wrote. I > implemented it as a method for DbiDatabase called getDbSpecSql. This > method creates a new instance of an GUS::ObjRelP::Oracle or > ::PostgreSQL class. These classes have methods for giving the correct > sql statements. This could be done for DbiTable, as well, I just don't > have it that way right now. > > So far it seems to build GUS for PostgreSQL. How many people are using > Sybase? I ask because some of the places that call for db specific sql > ask whether you are using Sybase and others don't. However, I haven't > written anything for Sybase, since I don't really see too much of that > stuff around. > > What is the consensus on the case sensitivity for fetchrow_hashref? If > it is enough to merely make sure that it is called with either > 'NAME_lc' or 'NAME_uc' that would be great by me. Anybody have any > thoughts on this? > > Jason |
|
From: Jason H. <jha...@pr...> - 2004-03-10 14:34:19
|
Cool. I'll change it to getDbPlatform in DbiDatabase. I included a setDbPlatform that takes one argument that is used to determine which Db specific class to call. So, what about the Sybase specific stuff? It's really cluttering things in it's present form, and I have no idea how I would make a Sybase.pm. I am making a DefaultDb.pm that has some information about what each of the queries does, and gives some default action when the database engine isn't recognized. So far, all it does is cough up an error message and return undefined, rather than an sql statement. Jason On Mar 10, 2004, at 8:54 AM, Steve Fischer wrote: > sounds good. in the code i am working on now (WDK), I call the method > getDbPlatform(). > > for fetchrow, yes, we'll just use NAME_uc. > > steve > Jason Hackney wrote: > >> Hi Steve, >> >>> I suggested that we factor those queries out of the DbiTable.pm and >>> DbiDatabase.pm files, and place them into an Oracle.pm and >>> PostgreSQL.pm. >>> >>> How did you guys integrate the PostgreSQL specific queries into the >>> object layer? >>> >>> If you haven't done a clean refactoring we can work together on >>> that... >>> >>> steve >>> >> >> It looks like I have a rough first pass refactoring for Oracle and >> PostgreSQL. It still relies on checking the dsn to decide whether to >> use the Oracle of PostgreSQL specific sql outputter I wrote. I >> implemented it as a method for DbiDatabase called getDbSpecSql. This >> method creates a new instance of an GUS::ObjRelP::Oracle or >> ::PostgreSQL class. These classes have methods for giving the correct >> sql statements. This could be done for DbiTable, as well, I just >> don't have it that way right now. >> >> So far it seems to build GUS for PostgreSQL. How many people are >> using Sybase? I ask because some of the places that call for db >> specific sql ask whether you are using Sybase and others don't. >> However, I haven't written anything for Sybase, since I don't really >> see too much of that stuff around. >> >> What is the consensus on the case sensitivity for fetchrow_hashref? >> If it is enough to merely make sure that it is called with either >> 'NAME_lc' or 'NAME_uc' that would be great by me. Anybody have any >> thoughts on this? >> >> Jason > |
|
From: Thomas O. <ot...@fi...> - 2004-03-11 18:03:34
|
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 |
|
From: Steve F. <sfi...@pc...> - 2004-03-11 19:20:53
|
thomas- I don't know the answer to this. I will ask around. steve 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 |
|
From: Angel P. <an...@pc...> - 2004-03-11 19:38:57
|
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 |
|
From: Thomas O. <ot...@fi...> - 2004-03-11 19:42:51
|
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 > > > |
|
From: Angel P. <an...@pc...> - 2004-03-11 19:46:21
|
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 >> >> >> >> > |
|
From: Thomas O. <ot...@fi...> - 2004-03-11 19:54:52
|
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 > |
|
From: Thomas O. <ot...@fi...> - 2004-03-11 20:09:22
|
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 > |
|
From: Steve F. <sfi...@pc...> - 2004-03-11 20:18:24
|
Thomas- when you have a first draft of your ideas, send us the table or tables, including the attributes and data types. that way we will be able to give you the best advice. steve 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 |
|
From: Thomas O. <ot...@fi...> - 2004-03-11 23:18:48
|
Okay, first an overview of the table and after that the sql code
Following table I need (* - to implement)
EnzymeClass
EnzymeClassAttribute
Pathway - I do not know if the dots::pathway does what I want :-)
compound *
reaction *
Motif/Prosite
Disease *
Classment for Functions and Proteins *
Relations:
1. CompoundRelations * - will hold the relation to reaction, enzyme,
2. EnzymeRelations * - will hold the relation of the enzyms to reaction,
Motif, Diesease
ECpathway - would be obsolete
The namespace should be sres.
Maybe I could put 1 and 2 together, but... anyhow, all data are related.
(All information comes from kegg)
Here the tables:
the question of the two following table is, if it would be better to do
a table compoundattribute...
CREATE TABLE SRes.compound (
compound_id number(12)
NOT NULL,
ENTRY VARCHAR2(90)
NOT NULL,
NAME VARCHAR2(90)
NOT NULL,
FORMULA VARCHAR2(90)
NULL,
DBLINKS
VARCHAR2(120) NULL,
MODIFICATION_DATE
DATE NOT NULL,
USER_READ NUMBER(1)
...
CREATE TABLE SRes.reaction (
reaction_id number(5)
NOT NULL,
ENTRY VARCHAR2(90)
NOT NULL,
NAME VARCHAR2(90) NULL,
DEFINITION
VARCHAR2(90) NULL,
EQUATION
VARCHAR2(120) NULL,
COMMENTS
VARCHAR2(120) NULL,
MODIFICATION_DATE
DATE NOT NULL,
USER_READ NUMBER(1)
...
Motif and Disease not sure, I think I will put the Attributes like in
the EnzymeClassattribute - table
EnzymeRelations and CompoundRelations will be the same.
CREATE TABLE SRes.EnzymeRelations (
Enzyme_Relations_id
number(12) NOT NULL,
enzyme_class_id number(12) NOT NULL,
foreign_id number(12) NOT NULL,
TYPE Varchar2(20) NOT NULL,
MODIFICATION_DATE
DATE NOT NULL,
So that's my idea.
Thomas
Steve Fischer wrote:
> Thomas-
>
> when you have a first draft of your ideas, send us the table or
> tables, including the attributes and data types. that way we will be
> able to give you the best advice.
>
> steve
>
> 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
>
|
|
From: <tw...@cs...> - 2004-03-12 12:46:21
|
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 |
|
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 |
|
From: <tw...@cs...> - 2004-03-12 14:48:30
|
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 > >> > >> > > > > > > > |
|
From: Thomas O. <ot...@fi...> - 2004-03-12 15:45:14
|
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 > > > |
|
From: Angel P. <an...@pc...> - 2004-03-12 16:31:44
|
Thomas and Terry, I think that both OMIM and KEGG are good candidates for integration into GUS. Here is my advise on how to proceed and get you guys running as quick as possible: 1) Create new schema spaces OMIM and KEGG. Enter this data into Core.DatabaseInfo. 2) Make the tables as GUS compliant and enter the Core.TableInfo information 3) Update the timestamp of $PROJETC_HOME/GUS/Model/schema/VERSION by: %> touch $PROJETC_HOME/GUS/Model/schema/VERSION 4) rebuild the objects by: %> build GUS/Model install -append This should create new objects for these schema spaces for use in plugins Document your schema and send it to the gusdev list once you have the bugs worked and and THEN we can look to see if existing GUS tables already fill that role or if these are new tables that should be folded into GUS propoer or if these new tables actually do a better job that the current GUS tables that holds this data. I think this is a good model for further GUS development, and we can release these types of development efforts as "contributed" modules of code. The contributed modules can be upgraded to "official" after they pass a review process and provide data migration scripts. Any comments? Angel Thomas Otto wrote: > 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 >> >> >> > > > > > ------------------------------------------------------- > 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 |
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X