[Bio] Log of /Sprout/SproutDBD.xml

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 16 18:43:45 2008 UTC (11 years, 3 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, 3 months ago) by parrello
Branch: MAIN
Changes since 1.35: +3 -0 lines
Diff to previous 1.35

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

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

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

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

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

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

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

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

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

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

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

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

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, 8 months ago) by parrello
Branch: MAIN
Changes since 1.22: +6 -23 lines
Diff to previous 1.22

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, 8 months ago) by parrello
Branch: MAIN
Changes since 1.21: +4 -6 lines
Diff to previous 1.21

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

*** 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

no message

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

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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

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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) - [select for diffs]
Tue Jan 25 01:00:20 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN

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