| 7e4a9c0 | Tom Hicks | 05 May 2015, 20:40:11 UTC | Add transport/translocation. | 05 May 2015, 20:40:11 UTC |
| f8aeb54 | Tom Hicks | 05 May 2015, 19:02:24 UTC | Cleanups. | 05 May 2015, 19:02:24 UTC |
| 2e64893 | Tom Hicks | 05 May 2015, 17:55:48 UTC | Add positive regulation. | 05 May 2015, 17:55:48 UTC |
| 5982bea | Tom Hicks | 05 May 2015, 09:18:16 UTC | Add Phosphorylation. | 05 May 2015, 09:18:16 UTC |
| 385079c | Tom Hicks | 05 May 2015, 06:30:56 UTC | Redo binding using options. | 05 May 2015, 06:30:56 UTC |
| 96af9bd | Tom Hicks | 05 May 2015, 04:46:46 UTC | Fix: restore null partA site. | 05 May 2015, 04:46:46 UTC |
| 6c440c3 | Tom Hicks | 05 May 2015, 04:28:26 UTC | Push binding participants to B, cause in A. | 05 May 2015, 04:28:26 UTC |
| 4de90a9 | Tom Hicks | 05 May 2015, 04:26:25 UTC | Add cause arguments extractor. | 05 May 2015, 04:26:25 UTC |
| e844abf | Tom Hicks | 04 May 2015, 22:35:51 UTC | Pull section filtering and rules from branch 'master' into frexport. | 04 May 2015, 23:53:35 UTC |
| b787aeb | Tom Hicks | 04 May 2015, 22:31:27 UTC | Manually integrate section filter changes to RunSystem. | 04 May 2015, 22:31:27 UTC |
| 36dbccf | Marco Antonio Valenzuela Escárcega | 04 May 2015, 21:35:43 UTC | added section filtering | 04 May 2015, 21:35:43 UTC |
| a57b60e | enoriega | 04 May 2015, 19:49:34 UTC | Added the nxml file for the PMC3902907 paper | 04 May 2015, 19:49:34 UTC |
| 447a075 | Gus Hahn-Powell | 04 May 2015, 18:49:28 UTC | Working rule generation from kb files. | 04 May 2015, 18:49:28 UTC |
| 4ee0348 | Tom Hicks | 04 May 2015, 17:52:00 UTC | Add JSON for binding arguments, evidence field, and function doc strings. | 04 May 2015, 17:52:00 UTC |
| 499dcb0 | Tom Hicks | 04 May 2015, 06:17:24 UTC | Memoize only root children. Begin content for Binding. | 04 May 2015, 06:17:24 UTC |
| 5134560 | Tom Hicks | 04 May 2015, 03:30:43 UTC | Use better type alias names. Redefine root events. | 04 May 2015, 03:30:43 UTC |
| d18cce1 | Tom Hicks | 04 May 2015, 03:12:48 UTC | Update RunSystem to output text or FRIES JSON. | 04 May 2015, 03:12:48 UTC |
| 4230524 | Tom Hicks | 04 May 2015, 03:11:02 UTC | Change main signature to omit document object. | 04 May 2015, 03:11:02 UTC |
| 248cf2c | Tom Hicks | 04 May 2015, 00:35:38 UTC | FriesDriver: Redo file handling. Rewrite flow more like bionlp. | 04 May 2015, 00:35:38 UTC |
| 096a12b | Tom Hicks | 04 May 2015, 00:21:47 UTC | FriesOutput: Redo file handling. Memoize root mentions. | 04 May 2015, 00:21:47 UTC |
| 9b387df | Tom Hicks | 04 May 2015, 00:20:56 UTC | MentionManager: Redo file handling. Show xRefs in textual output. | 04 May 2015, 00:20:56 UTC |
| ad9e29b | Tom Hicks | 03 May 2015, 13:18:01 UTC | Pull latest RunSystem changes from branch 'master' into frexport. | 03 May 2015, 13:18:01 UTC |
| 90c40b7 | Tom Hicks | 03 May 2015, 13:14:35 UTC | Add neg info field. | 03 May 2015, 13:14:35 UTC |
| 4804c4b | Gus Hahn-Powell | 03 May 2015, 06:41:28 UTC | Merge branch 'master' of github.com:sistanlp/reach | 03 May 2015, 06:41:28 UTC |
| bd8dadc | Marco Antonio Valenzuela Escárcega | 03 May 2015, 05:03:15 UTC | output a single file per paper | 03 May 2015, 05:03:15 UTC |
| 6fc9523 | Tom Hicks | 03 May 2015, 01:06:30 UTC | Add preliminary event filter. | 03 May 2015, 01:06:30 UTC |
| 879313e | Tom Hicks | 03 May 2015, 00:50:48 UTC | Modify output structure to list of index cards. | 03 May 2015, 00:50:48 UTC |
| 2bd487e | Tom Hicks | 03 May 2015, 00:24:16 UTC | Fake doc ID in developement driver. | 03 May 2015, 00:24:16 UTC |
| 471f231 | Marco Antonio Valenzuela Escárcega | 02 May 2015, 21:54:36 UTC | keep original text in document | 02 May 2015, 21:54:36 UTC |
| 7b72381 | Tom Hicks | 02 May 2015, 21:13:48 UTC | Tweak JSON write method. | 02 May 2015, 21:13:48 UTC |
| db4f02d | Tom Hicks | 02 May 2015, 21:05:42 UTC | Begin JSON output. | 02 May 2015, 21:05:42 UTC |
| deca780 | Tom Hicks | 02 May 2015, 20:21:30 UTC | Pull Doc.id change from branch 'master' into frexport. | 02 May 2015, 20:21:30 UTC |
| 84fa100 | Tom Hicks | 02 May 2015, 20:20:42 UTC | Start building output. | 02 May 2015, 20:20:42 UTC |
| 33ba901 | Tom Hicks | 02 May 2015, 20:20:20 UTC | Change output file extension. | 02 May 2015, 20:20:20 UTC |
| 0412d83 | Marco Antonio Valenzuela Escárcega | 02 May 2015, 19:31:51 UTC | add id to document | 02 May 2015, 19:31:51 UTC |
| 17196bd | Tom Hicks | 01 May 2015, 22:13:42 UTC | Add existing Java DateUtils class. | 01 May 2015, 22:13:42 UTC |
| bf0dcb3 | Gus Hahn-Powell | 01 May 2015, 22:06:35 UTC | Merge branch 'master' of github.com:sistanlp/reach | 01 May 2015, 22:06:35 UTC |
| 8965fd8 | Tom Hicks | 01 May 2015, 20:47:33 UTC | Pull changes from 'master' into frexport. | 01 May 2015, 20:47:33 UTC |
| 34216f4 | Tom Hicks | 01 May 2015, 20:45:18 UTC | Update UniprotKB with gene names and synonyms. | 01 May 2015, 20:45:18 UTC |
| f7264f2 | Tom Hicks | 01 May 2015, 20:32:11 UTC | Ignore script by-products in src/test/resources/inputs/nxml. | 01 May 2015, 20:32:11 UTC |
| af7040f | Tom Hicks | 01 May 2015, 14:43:25 UTC | All classes must use same resolution method: speciated KB accessors. | 01 May 2015, 14:43:25 UTC |
| 9038d6f | Tom Hicks | 01 May 2015, 14:04:37 UTC | Add and use speciated KB accessor trait. | 01 May 2015, 14:04:37 UTC |
| 06f674e | Tom Hicks | 01 May 2015, 04:13:42 UTC | Add initial FRIES output stub files. | 01 May 2015, 04:13:42 UTC |
| 49e0d10 | Tom Hicks | 01 May 2015, 03:20:49 UTC | Merge recent changes from branch 'master' into frexport. | 01 May 2015, 03:20:49 UTC |
| 35f320f | Tom Hicks | 01 May 2015, 02:16:51 UTC | Add serialized papers and NXML inputs in src/test/resources/inputs. | 01 May 2015, 02:16:51 UTC |
| d3cdb54 | Tom Hicks | 01 May 2015, 02:14:33 UTC | Update for move of KBs to subdirectory. | 01 May 2015, 02:14:33 UTC |
| 1981a42 | Gus Hahn-Powell | 01 May 2015, 00:43:20 UTC | Added documentation. | 01 May 2015, 00:43:20 UTC |
| 57dc21d | Gus Hahn-Powell | 01 May 2015, 00:34:34 UTC | Merge branch 'master' of github.com:sistanlp/reach | 01 May 2015, 00:34:34 UTC |
| 3220063 | Gus Hahn-Powell | 01 May 2015, 00:32:57 UTC | Added code to construct Iterator from gz files. | 01 May 2015, 00:32:57 UTC |
| c106be1 | Tom Hicks | 30 April 2015, 23:48:57 UTC | Add gitignore for NXML dir, remove gitkeep for export/fries dir. | 30 April 2015, 23:48:57 UTC |
| f947ef8 | Marco Antonio Valenzuela Escárcega | 30 April 2015, 23:34:10 UTC | keep original text | 30 April 2015, 23:34:10 UTC |
| c9a67e7 | Tom Hicks | 30 April 2015, 23:24:06 UTC | Merge branch 'master' into frexport | 30 April 2015, 23:24:06 UTC |
| fd4b453 | Marco Antonio Valenzuela Escárcega | 30 April 2015, 21:24:24 UTC | added support for custom config files | 30 April 2015, 21:24:24 UTC |
| 3aaae6e | Gus Hahn-Powell | 30 April 2015, 20:28:17 UTC | Reorganized kb resources and brought in PathFinder | 30 April 2015, 20:28:17 UTC |
| c0e1669 | Tom Hicks | 30 April 2015, 04:22:03 UTC | Add 2 NXML files to test inputs. | 30 April 2015, 04:22:03 UTC |
| 10bc711 | Tom Hicks | 30 April 2015, 04:18:51 UTC | Add 4 pre-processed (serialized) files to test resources for testing. | 30 April 2015, 04:18:51 UTC |
| 233e16f | Tom Hicks | 30 April 2015, 04:00:02 UTC | Port extern/inward from processors. Create extern/export dirs. | 30 April 2015, 04:00:02 UTC |
| 2f0ff16 | Marco Antonio Valenzuela Escárcega | 30 April 2015, 00:37:06 UTC | revert scala version | 30 April 2015, 00:37:06 UTC |
| 83b2b77 | Marco Antonio Valenzuela Escárcega | 29 April 2015, 22:29:41 UTC | use paths relative to user's home | 29 April 2015, 22:29:41 UTC |
| 2304f50 | Marco Antonio Valenzuela Escárcega | 29 April 2015, 22:12:57 UTC | ignore citations | 29 April 2015, 22:12:57 UTC |
| d5116b8 | Marco Antonio Valenzuela Escárcega | 29 April 2015, 22:00:06 UTC | added RunSystem | 29 April 2015, 22:00:06 UTC |
| 7d0b64c | Marco Antonio Valenzuela Escárcega | 29 April 2015, 19:27:52 UTC | moved tests | 29 April 2015, 19:27:52 UTC |
| 6275ee3 | Marco Antonio Valenzuela Escárcega | 29 April 2015, 19:21:22 UTC | fixed deprecation warnings | 29 April 2015, 19:21:22 UTC |
| 9a58172 | Marco Antonio Valenzuela Escárcega | 29 April 2015, 19:18:56 UTC | updated processors | 29 April 2015, 19:18:56 UTC |
| 2c6e41b | Marco Antonio Valenzuela Escárcega | 29 April 2015, 19:07:54 UTC | copied project files | 29 April 2015, 19:07:54 UTC |
| 4984b82 | Marco Antonio Valenzuela Escárcega | 29 April 2015, 18:53:11 UTC | fixed deprecation warning | 29 April 2015, 18:53:11 UTC |
| 724bb56 | Marco Antonio Valenzuela Escárcega | 29 April 2015, 18:30:04 UTC | deleted erroneous import | 29 April 2015, 18:30:04 UTC |
| 1d2f593 | Marco Antonio Valenzuela Escárcega | 29 April 2015, 05:28:02 UTC | added scalac options | 29 April 2015, 18:08:18 UTC |
| f3a8f6d | enoriega | 19 March 2015, 23:06:47 UTC | Update to BratOutput.scala to include text bound mentions | 19 March 2015, 23:06:47 UTC |
| 6957af4 | enoriega | 18 March 2015, 19:36:43 UTC | Continuing development of the brat output feature | 18 March 2015, 19:36:43 UTC |
| 883d716 | enoriega | 18 March 2015, 19:10:52 UTC | Continuing development of the brat output feature | 18 March 2015, 19:10:52 UTC |
| e7c69f4 | Enrique Noriega | 18 March 2015, 19:07:05 UTC | New output script that creates a brat standoff with the Built-in functionality | 18 March 2015, 19:07:05 UTC |
| 1daf3bc | Tom Hicks | 04 March 2015, 21:34:50 UTC | Update dependencies and sbt. | 04 March 2015, 21:34:50 UTC |
| 69ff350 | Marco Antonio Valenzuela Escárcega | 25 February 2015, 22:11:24 UTC | Reverting changes Experimental code was merged into master by mistake. This commit reverts the changes to what we had for the darpa eval. | 25 February 2015, 22:11:24 UTC |
| faae499 | Marco Antonio Valenzuela Escárcega | 25 February 2015, 21:02:44 UTC | Updated imports | 25 February 2015, 21:02:44 UTC |
| 96448bd | Gus Hahn-Powell | 19 February 2015, 21:06:59 UTC | Merge branch 'biorulelearning' Conflicts: src/main/resources/edu/arizona/sista/bionlp/extractors/default_entities.yml | 19 February 2015, 21:06:59 UTC |
| 6267f3d | Gus Hahn-Powell | 19 February 2015, 21:02:53 UTC | Imports now reflect new version of processors. | 19 February 2015, 21:02:53 UTC |
| cf16048 | Gus Hahn-Powell | 19 February 2015, 21:00:23 UTC | Imports now reflect new layout of processors. | 19 February 2015, 21:00:23 UTC |
| 067b63a | enoriega | 18 February 2015, 21:07:30 UTC | Merge branch 'master' of https://github.com/sistanlp/reach | 18 February 2015, 21:07:30 UTC |
| 654ce95 | Dane Bell | 18 February 2015, 20:23:34 UTC | Now gives evaluable BioNLP output | 18 February 2015, 20:23:34 UTC |
| ec20bce | Mihai Surdeanu | 17 February 2015, 22:00:28 UTC | Cleaned up unit tests. | 17 February 2015, 22:00:28 UTC |
| c465b42 | enoriega | 12 February 2015, 01:12:00 UTC | Added the CommandLineOutput ruler | 12 February 2015, 01:12:00 UTC |
| 2cef20d | Dane Bell | 11 February 2015, 22:33:52 UTC | dump output to BioNLP format, plus evaluation scripts | 11 February 2015, 22:33:52 UTC |
| 8abd070 | Marco Antonio Valenzuela Escárcega | 08 February 2015, 22:14:30 UTC | changed scala version | 08 February 2015, 22:14:30 UTC |
| 517f289 | Gus Hahn-Powell | 08 February 2015, 21:48:39 UTC | Commented out problematic site rule. | 08 February 2015, 21:48:39 UTC |
| 67c187b | Gus Hahn-Powell | 03 February 2015, 07:00:07 UTC | Merge branch 'master' of github.com:sistanlp/reach | 03 February 2015, 07:00:07 UTC |
| 9893f5c | Gus Hahn-Powell | 03 February 2015, 06:59:50 UTC | Added a site rule. | 03 February 2015, 06:59:50 UTC |
| ed1341e | Marco Antonio Valenzuela Escárcega | 27 January 2015, 23:20:58 UTC | Merge branch 'master' of https://github.com/sistanlp/reach | 27 January 2015, 23:20:58 UTC |
| d046da6 | Marco Antonio Valenzuela Escárcega | 27 January 2015, 23:17:56 UTC | add support for 'keep' rule field | 27 January 2015, 23:17:56 UTC |
| fc280b8 | Gus Hahn-Powell | 22 January 2015, 20:20:15 UTC | Phospho themes cannot be Sites. If we're not explicit about this, coref gets triggered within the action. | 22 January 2015, 20:20:15 UTC |
| 1d61d9d | Gus Hahn-Powell | 22 January 2015, 19:15:51 UTC | Merge branch 'master' of github.com:sistanlp/reach | 22 January 2015, 19:15:51 UTC |
| 61b0149 | Enrique Noriega | 22 January 2015, 19:15:15 UTC | Fix a transcription rules bug | 22 January 2015, 19:15:15 UTC |
| 56e8c80 | Gus Hahn-Powell | 22 January 2015, 18:54:30 UTC | Fixed some mention patterns to avoid crazy coref. | 22 January 2015, 18:54:30 UTC |
| c6988f3 | Gus Hahn-Powell | 22 January 2015, 18:42:06 UTC | Merge branch 'master' of github.com:sistanlp/reach | 22 January 2015, 18:42:06 UTC |
| d594db3 | Gus Hahn-Powell | 22 January 2015, 18:39:29 UTC | Removed bad protein_with_site rule. | 22 January 2015, 18:39:29 UTC |
| 614ed0f | Marco Antonio Valenzuela Escárcega | 22 January 2015, 18:28:48 UTC | added entity variation | 22 January 2015, 18:28:48 UTC |
| 42ec330 | Gus Hahn-Powell | 22 January 2015, 18:27:12 UTC | Merge branch 'master' of github.com:sistanlp/reach | 22 January 2015, 18:27:12 UTC |
| 633fd75 | Gus Hahn-Powell | 22 January 2015, 18:25:46 UTC | modification to syntax_2_verb patterns | 22 January 2015, 18:25:46 UTC |
| 9c95be7 | Marco Antonio Valenzuela Escárcega | 22 January 2015, 18:02:09 UTC | added required entity | 22 January 2015, 18:02:09 UTC |
| 0dea011 | Gus Hahn-Powell | 22 January 2015, 18:00:15 UTC | Adjusted syntax_2_verb rule pattern for cause. | 22 January 2015, 18:00:15 UTC |
