Re: [XMLPipeDB-developer] System table subquery
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Re: [XMLPipeDB-developer] System table subquery
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From: Kam D. <kda...@lm...> - 2011-09-19 18:09:38
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Hi, LMU can accept 20 MB attachments now; I don't know how big your file is zipped, but that's an option. You could also use LionShare. Glad to see success! Kam At 06:05 PM 9/18/2011, you wrote: >Tried to post my latest gdb export to the biodb wiki but receiving >log in error (per separate email) > >But, I wanted to let you know I verified that each improper system >table does in fact contain the id and species name (samples of each): > > >Pfam >ID Species Date >PF02866 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >PF07050 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >PF03479 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >PF02317 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >PF03279 |Pseudomonas aeruginosa| 9/14/2011 >PF09922 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >PF04205 |Pseudomonas aeruginosa| 9/14/2011 >PF03379 |Pseudomonas aeruginosa| 9/14/2011 >PF05389 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 > > >RefSeq >ID Species Date >YP_039973 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >YP_040411 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >YP_039521 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >NP_253798 |Pseudomonas aeruginosa| 9/14/2011 >NP_254101 |Pseudomonas aeruginosa| 9/14/2011 >NP_248930 |Pseudomonas aeruginosa| 9/14/2011 >NP_251503 |Pseudomonas aeruginosa| 9/14/2011 >NP_249960 |Pseudomonas aeruginosa| 9/14/2011 >NP_253220 |Pseudomonas aeruginosa| 9/14/2011 >YP_040877 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >NP_253802 |Pseudomonas aeruginosa| 9/14/2011 > > >GeneId >ID Species Date >879140 |Pseudomonas aeruginosa| 9/14/2011 >2859243 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >879337 |Pseudomonas aeruginosa| 9/14/2011 >2860668 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >881899 |Pseudomonas aeruginosa| 9/14/2011 >882312 |Pseudomonas aeruginosa| 9/14/2011 >2860009 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >881520 |Pseudomonas aeruginosa| 9/14/2011 >2861152 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >881596 |Pseudomonas aeruginosa| 9/14/2011 > > >InterPro >ID Species Date >IPR022522 |Pseudomonas aeruginosa| 9/14/2011 >IPR003538 |Pseudomonas aeruginosa| 9/14/2011 >IPR016379 |Pseudomonas aeruginosa| 9/14/2011 >IPR016920 |Pseudomonas aeruginosa| 9/14/2011 >IPR000477 |Pseudomonas aeruginosa| 9/14/2011 >IPR008948 |Pseudomonas aeruginosa| 9/14/2011 >IPR005415 |Pseudomonas aeruginosa| 9/14/2011 >IPR009651 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >IPR007895 |Pseudomonas aeruginosa| 9/14/2011 >IPR008231 |Pseudomonas aeruginosa| 9/14/2011 >IPR004558 |Pseudomonas aeruginosa| 9/14/2011 >IPR011067 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >IPR006358 |Pseudomonas aeruginosa| 9/14/2011 > > >PDB >ID Species Date >2ZWS |Pseudomonas aeruginosa| 9/14/2011 >2F9I |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >2EXV |Pseudomonas aeruginosa| 9/14/2011 >3L34 |Pseudomonas aeruginosa| 9/14/2011 >1EZM |Pseudomonas aeruginosa| 9/14/2011 >2WYB |Pseudomonas aeruginosa| 9/14/2011 >2F1L |Pseudomonas aeruginosa| 9/14/2011 >1D7L |Pseudomonas aeruginosa| 9/14/2011 >1Y12 |Pseudomonas aeruginosa| 9/14/2011 >2IXH |Pseudomonas aeruginosa| 9/14/2011 >1XAG |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >2IXI |Pseudomonas aeruginosa| 9/14/2011 > > >EMBL >ID Species Date >AJ003006 |Pseudomonas aeruginosa| 9/14/2011 >BX571856 |Staphylococcus aureus (strain MRSA252)| 9/14/2011 >AJ633619 |Pseudomonas aeruginosa| 9/14/2011 >AJ633602 |Pseudomonas aeruginosa| 9/14/2011 >U07359 |Pseudomonas aeruginosa| 9/14/2011 >X54201 |Pseudomonas aeruginosa| 9/14/2011 >AY899300 |Pseudomonas aeruginosa| 9/14/2011 >AB085582 |Pseudomonas aeruginosa| 9/14/2011 >AB075926 |Pseudomonas aeruginosa| 9/14/2011 >AF306766 |Pseudomonas aeruginosa| 9/14/2011 >X99471 |Pseudomonas aeruginosa| 9/14/2011 >M21093 |Pseudomonas aeruginosa| 9/14/2011 > > >Richard > >On Wed, Sep 14, 2011 at 6:50 PM, Richard Brous ><<mailto:rbr...@gm...>rbr...@gm...> wrote: >OK, going to commit my changes to UniProtDatabaseProfile: >getSystemTableManager() > >Here is some logging info to confirm result.next() within the while >loop is both id and species name: > >3070712 [Thread-4] >INFO >edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile >- getSystemTableManager(): while loop: ID:: IPR006314 Species:: >Staphylococcus aureus (strain MRSA252) >3070712 [Thread-4] >INFO >edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile >- getSystemTableManager(): while loop: ID:: IPR013840 Species:: >Staphylococcus aureus (strain MRSA252) >3070728 [Thread-4] >INFO >edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile >- getSystemTableManager(): while loop: ID:: IPR015887 Species:: >Pseudomonas aeruginosa >3070728 [Thread-4] >INFO >edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile >- getSystemTableManager(): while loop: ID:: IPR016148 Species:: >Pseudomonas aeruginosa > >Richard > >On Wed, Sep 14, 2011 at 3:20 PM, Richard Brous ><<mailto:rbr...@gm...>rbr...@gm...> wrote: >Solid progress made and I now have a compilable working copy. > >I'm now working through how to plug the results of the query into >the proper slots under the while loop. I had stumbled on an error >where I was supplying the column name instead of the actual data >from the tuple. Solved that and am hoping the current export will be >the last before I commit to sourceforge. > >Richard > > >On Mon, Sep 12, 2011 at 10:59 PM, Richard Brous ><<mailto:rbr...@gm...>rbr...@gm...> wrote: >Spent the weekend reviewing sql and I have achieved some clarity. > >I'm still working through things but not at least I have better >context and can ask intelligent questions. > >The sub query was a big help, I'm not sure how long it would have >taken me to do all the joins using ON to return "hjid | species name" > >Dondi - I'll stop by after theory tomorrow to discuss further. > >Thanks. > >Richard > > >On Thu, Sep 8, 2011 at 5:24 PM, John David N. Dionisio ><<mailto:do...@lm...>do...@lm...> wrote: >Hi Rich, > >As discussed in our meeting, here is a first step toward the new >system table query: > > SELECT entrytype.hjid, organismnametype.value FROM entrytype > INNER JOIN organismtype ON (entrytype.organism = organismtype.hjid) > inner join organismnametype on (organismtype.hjid = > organismnametype.organismtype_name_hjid) INNER JOIN dbreferencetype > ON(dbreferencetype.organismtype_dbreference_hjid = > organismtype.hjid) WHERE dbreferencetype.type = 'NCBI Taxonomy' and > (id = '90371'); > >(substitute the "id = " clause accordingly) > >John David N. Dionisio, PhD >Associate Professor, Computer Science >Associate Director, University Honors Program >Loyola Marymount University > > > > >------------------------------------------------------------------------------ >Why Cloud-Based Security and Archiving Make Sense >Osterman Research conducted this study that outlines how and why cloud >computing security and archiving is rapidly being adopted across the IT >space for its ease of implementation, lower cost, and increased >reliability. Learn more. ><http://www.accelacomm.com/jaw/sfnl/114/51425301/>http://www.accelacomm.com/jaw/sfnl/114/51425301/ >_______________________________________________ >xmlpipedb-developer mailing list ><mailto:xml...@li...>xml...@li... >https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > > > > > |
