Re: [XMLPipeDB-developer] System table subquery
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Re: [XMLPipeDB-developer] System table subquery
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From: Richard B. <rbr...@gm...> - 2011-09-19 01:05:25
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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 <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 <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 <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 <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/ >>>> _______________________________________________ >>>> xmlpipedb-developer mailing list >>>> xml...@li... >>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >>>> >>> >>> >> > |
