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Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 16 18:43:45 2008 UTC (11 years, 2 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, rast_2008_0924, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_release_2008_09_29
Changes since 1.56: +2 -2 lines
Diff to previous 1.56 , to selected 1.1
Changed some field names to use hyphens instead of underscores. We use hyphens everywhere else.

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 9 21:02:10 2008 UTC (11 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.55: +17 -17 lines
Diff to previous 1.55 , to selected 1.1
Changes for v24 database.

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 12 06:03:28 2008 UTC (11 years, 4 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_08_07
Changes since 1.54: +246 -78 lines
Diff to previous 1.54 , to selected 1.1
Converted to work with the new diagrammer.

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 7 23:16:47 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806, rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21
Changes since 1.53: +10 -0 lines
Diff to previous 1.53 , to selected 1.1
Added a table for keywords.

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 29 20:55:25 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.52: +1 -1 lines
Diff to previous 1.52 , to selected 1.1
Fixed a typo.

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 23 16:32:34 2008 UTC (11 years, 8 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.51: +114 -103 lines
Diff to previous 1.51 , to selected 1.1
Cleaned up the documentation.

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 5 05:46:03 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.50: +6 -0 lines
Diff to previous 1.50 , to selected 1.1
Added comments about the general purpose of the database.

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 16 19:59:33 2007 UTC (12 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.49: +86 -152 lines
Diff to previous 1.49 , to selected 1.1
Updated to use a more PPO-friendly database structure.

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 11 06:37:38 2007 UTC (12 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.48: +101 -0 lines
Diff to previous 1.48 , to selected 1.1
Added new tables for drug target docking results.

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 10 06:13:54 2007 UTC (12 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.47: +14 -0 lines
Diff to previous 1.47 , to selected 1.1
Added new fields for SEED Viewer support.

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 22 20:24:53 2007 UTC (12 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.46: +0 -155 lines
Diff to previous 1.46 , to selected 1.1
Removed old drug target support.

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 29 20:32:06 2006 UTC (13 years ago) by parrello
Branch: MAIN
Changes since 1.45: +3 -3 lines
Diff to previous 1.45 , to selected 1.1
Fixed some comments.

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 3 00:44:01 2006 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.44: +30 -26 lines
Diff to previous 1.44 , to selected 1.1
Removed obsolete data generation tags, added special attribute attribute, and added drug target tables.

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 21 06:43:10 2006 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.43: +1 -1 lines
Diff to previous 1.43 , to selected 1.1
Changed the notes on subsystem classifications to reflect the fact that the heirarchy levels are colon-delimited instead of space-delimited.

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 16 22:56:48 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.42: +3 -3 lines
Diff to previous 1.42 , to selected 1.1
Changed "function" to "tag" in drug topic table.

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 14 18:12:48 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.41: +5 -1 lines
Diff to previous 1.41 , to selected 1.1
Changed the subsystem classification implementation so that we can reconstruct the correct hierarchy.

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 13 21:46:45 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.40: +160 -2 lines
Diff to previous 1.40 , to selected 1.1
Updated to allow for more flexible feature-searching.

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 27 12:58:18 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.39: +16 -0 lines
Diff to previous 1.39 , to selected 1.1
Put a better index on HasRoleInSubsystem.

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 27 12:34:46 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.38: +5 -0 lines
Diff to previous 1.38 , to selected 1.1
Added a relationship between features and subsystems.

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 27 11:07:32 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.37: +2 -2 lines
Diff to previous 1.37 , to selected 1.1
Fixed poor indexing choice on HasFeature.

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 24 17:14:16 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.36: +16 -1 lines
Diff to previous 1.36 , to selected 1.1
Moved NMPDR group into the Genome record. This insures that all of the information required to generate a popup menu of genomes is available without access to secondary tables.

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 19 00:11:12 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.35: +3 -0 lines
Diff to previous 1.35 , to selected 1.1
Changed to include a copy of the functional assignment in the feature table.

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 13 04:27:57 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.34: +0 -22 lines
Diff to previous 1.34 , to selected 1.1
Removed the BBH relation.

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 2 23:51:19 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.33: +1 -1 lines
Diff to previous 1.33 , to selected 1.1
Fixed a duplicate table name.

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 30 05:39:59 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.32: +1 -1 lines
Diff to previous 1.32 , to selected 1.1
Fixed a bad column type.

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 30 01:41:34 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.31: +1 -1 lines
Diff to previous 1.31 , to selected 1.1
Converted function name to a text field.

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 30 01:18:54 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.30: +19 -0 lines
Diff to previous 1.30 , to selected 1.1
Added support for protein families.

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 9 21:16:47 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.29: +2 -3 lines
Diff to previous 1.29 , to selected 1.1
Converted the PCH keys to integers.

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 30 18:31:34 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.28: +1 -1 lines
Diff to previous 1.28 , to selected 1.1
Converted the coupling ID from a hash-string to an ID-string and fixed some call signatures.

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 26 19:13:16 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.27: +3 -0 lines
Diff to previous 1.27 , to selected 1.1
Added support for subsystem classifications.

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 07:34:46 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.26: +8 -0 lines
Diff to previous 1.26 , to selected 1.1
Added support for mapped synonym IDs.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 6 05:07:42 2006 UTC (13 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.25: +8 -0 lines
Diff to previous 1.25 , to selected 1.1
Added a new index to the Annotations table to speed retrieval of recent annotations.

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 27 02:02:47 2006 UTC (13 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.24: +1 -1 lines
Diff to previous 1.24 , to selected 1.1
Changed key size for features.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 13 06:01:23 2006 UTC (13 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.23: +23 -6 lines
Diff to previous 1.23 , to selected 1.1
Updated to reduce key size.

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 19 03:36:29 2006 UTC (13 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.22: +6 -23 lines
Diff to previous 1.22 , to selected 1.1
Backed up to keep database changes for version 7 out of version 6.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 19 03:34:15 2006 UTC (13 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.21: +4 -6 lines
Diff to previous 1.21 , to selected 1.1
Added support for the new "hash-string" key type that creates a key from a digest of symbolic information.

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 26 12:35:21 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.20: +19 -0 lines
Diff to previous 1.20 , to selected 1.1
Added a relationship between Feature and Genome.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 28 22:51:26 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.19: +4 -4 lines
Diff to previous 1.19 , to selected 1.1
Fixed documentation for the variant-code field, which is no longer numeric.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 2 21:47:45 2005 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.18: +19 -6 lines
Diff to previous 1.18 , to selected 1.1
Added a "label" field to the Compound entity to contain the label to be used in displayable_reaction.
Fixed the spelling of "stoichiometry".
Fixed an error in the index definition for IsAComponentOf.
Added a discriminator field to IsAComponentOf that prevents duplicate reaction elements from being collapsed by SELECT DISTINCT.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 20 09:33:25 2005 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.17: +11 -3 lines
Diff to previous 1.17 , to selected 1.1
Removed the RoleName table, and added an optional "EC" field to the Role entity, along with an alternate index to allow retrieving roles by EC number.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 17 05:32:49 2005 UTC (14 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.16: +7 -0 lines
Diff to previous 1.16 , to selected 1.1
Added an index for the CAS IDs.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 15 07:10:46 2005 UTC (14 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.15: +1 -1 lines
Diff to previous 1.15 , to selected 1.1
Changed stoichiometry from numeric to string to account for "N"s.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 03:14:27 2005 UTC (14 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.14: +198 -8 lines
Diff to previous 1.14 , to selected 1.1
Added support for Reactions, Compounds, Role abbreviations, feature clustering on spreadsheets, and  spreadsheet column subsets.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 12:10:08 2005 UTC (14 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.13: +1 -1 lines
Diff to previous 1.13 , to selected 1.1
Fixed field length for feature aliases.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 13 04:04:25 2005 UTC (14 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.12: +1 -1 lines
Diff to previous 1.12 , to selected 1.1
Expanded the key length for subsystem spreadsheet cells.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 13 03:50:59 2005 UTC (14 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.11: +3 -0 lines
Diff to previous 1.11 , to selected 1.1
Added "complete" field.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 11 17:09:19 2005 UTC (14 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.10: +1 -1 lines
Diff to previous 1.10 , to selected 1.1
Fixed an error in the documentation.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 15 18:43:49 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.9: +0 -4 lines
Diff to previous 1.9 , to selected 1.1
Rolled back "complete" field of the genome.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 14 23:59:03 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.8: +5 -5 lines
Diff to previous 1.8 , to selected 1.1
Added a field indicating which genomes are complete.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 22 21:31:47 2005 UTC (14 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.7: +219 -204 lines
Diff to previous 1.7 , to selected 1.1
Added an index for Feature aliases.
Added a field to support checking for Genome completeness and commented it out.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 16 19:10:04 2005 UTC (14 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.6: +0 -9 lines
Diff to previous 1.6 , to selected 1.1
Removed paralogs and percent-match fields from the UsesAsEvidence relationship.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 9 19:06:55 2005 UTC (14 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.5: +99 -15 lines
Diff to previous 1.5 , to selected 1.1
*** empty log message ***

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 7 02:05:34 2005 UTC (14 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.4: +1 -1 lines
Diff to previous 1.4 , to selected 1.1
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Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 26 22:26:09 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.3: +1 -1 lines
Diff to previous 1.3 , to selected 1.1
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Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 26 21:39:34 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.2: +13 -8 lines
Diff to previous 1.2 , to selected 1.1
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Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 25 03:02:07 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.1: +0 -5 lines
Diff to previous 1.1
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Revision 1.1 - (view) (download) (as text) (annotate) - [selected]
Tue Jan 25 01:00:20 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
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