| 4b963e5 | Dane Bell | 17 February 2016, 20:38:21 UTC | Add 'which' to 'X which is MODIFIED' PTM rules | 17 March 2016, 22:29:56 UTC |
| b7afebb | Dane Bell | 16 February 2016, 23:03:38 UTC | Add PTM rules and tests for 'X that is MODIFIED at SITE' | 17 March 2016, 22:29:10 UTC |
| 2a52ed1 | Dane Bell | 17 March 2016, 22:06:01 UTC | Merge branch 'master' into corefBrat Conflicts: src/main/scala/edu/arizona/sista/coref/CorefUtils.scala | 17 March 2016, 22:06:01 UTC |
| 99392cb | Mihai Surdeanu | 15 March 2016, 22:10:50 UTC | Merge pull request #125 from clulab/issue99 Priority variables | 15 March 2016, 22:10:50 UTC |
| 2c6bed6 | Dane Bell | 15 March 2016, 21:27:46 UTC | Revert "Revert "Use priority variable for all but entity and mod rules"" This reverts commit 0af15a407bc8c2de06a0b1e208df9a248304f2bb. | 15 March 2016, 21:27:46 UTC |
| 6dd64fd | Dane Bell | 15 March 2016, 21:09:42 UTC | Create priorities in master rule files | 15 March 2016, 21:09:42 UTC |
| 0af15a4 | Dane Bell | 15 March 2016, 21:06:33 UTC | Revert "Use priority variable for all but entity and mod rules" This reverts commit 9cc4ecb45adb7990bd35eb5fc20bc3f602e87239. | 15 March 2016, 21:09:00 UTC |
| 9cc4ecb | Dane Bell | 15 March 2016, 20:27:53 UTC | Use priority variable for all but entity and mod rules | 15 March 2016, 20:27:53 UTC |
| 69a7fe4 | Mihai Surdeanu | 15 March 2016, 04:30:54 UTC | Merge pull request #122 from clulab/inducedreg Improved pos_reg rules; Improved resolution of overlap between site_1letter and other ents | 15 March 2016, 04:30:54 UTC |
| 14393d7 | Mihai Surdeanu | 15 March 2016, 04:11:59 UTC | Do not allow overlap between site_1letter and proteins or chemicals. Added unit tests to check for this. | 15 March 2016, 04:11:59 UTC |
| 3d4f82c | Mihai Surdeanu | 15 March 2016, 04:10:58 UTC | Merge pull request #120 from clulab/assembly Sieve-based assembly system used in the March 2016 evaluation | 15 March 2016, 04:10:58 UTC |
| 51ee595 | Mihai Surdeanu | 15 March 2016, 03:35:04 UTC | Extended the pos_reg rules. Made sure the site_1letter runs after NER, because it ambiguous. | 15 March 2016, 03:35:04 UTC |
| d6b221e | Gus Hahn-Powell | 14 March 2016, 23:46:20 UTC | Runnables for generating sieve-based assembly output | 14 March 2016, 23:46:20 UTC |
| f71872d | Gus Hahn-Powell | 14 March 2016, 23:41:51 UTC | Assembly config | 14 March 2016, 23:41:51 UTC |
| 9b15eb4 | Gus Hahn-Powell | 14 March 2016, 23:08:52 UTC | Merge branch 'csvtofriesentry' into assembly | 14 March 2016, 23:08:52 UTC |
| 96be06d | Mihai Surdeanu | 14 March 2016, 19:59:43 UTC | Added CSVParser.toFriesEntries, which converts a CSV file into a sequence of FriesEntry blocks, similar to NxmlReader.readNxml | 14 March 2016, 19:59:43 UTC |
| eacd4b2 | Gus Hahn-Powell | 14 March 2016, 09:22:31 UTC | Added a WH pattern | 14 March 2016, 09:22:31 UTC |
| c6deeea | Gus Hahn-Powell | 14 March 2016, 09:22:16 UTC | Complex is not an event | 14 March 2016, 09:22:16 UTC |
| ec3e751 | Gus Hahn-Powell | 14 March 2016, 08:03:19 UTC | Sieve may encounter Activations | 14 March 2016, 08:03:19 UTC |
| ccceaf1 | Gus Hahn-Powell | 14 March 2016, 08:03:01 UTC | Exporter handles Activations | 14 March 2016, 08:03:01 UTC |
| 3cf1365 | Gus Hahn-Powell | 14 March 2016, 08:01:53 UTC | AM handles more event and entity types Added support for Mentions with label Complex and ActivationEvent | 14 March 2016, 08:01:53 UTC |
| 16b25fe | Gus Hahn-Powell | 14 March 2016, 08:00:53 UTC | Added ComplexEvent -> Regulation & Activation | 14 March 2016, 08:00:53 UTC |
| e0d559f | Gus Hahn-Powell | 14 March 2016, 07:59:07 UTC | Updates to grammar for precedence relations | 14 March 2016, 07:59:23 UTC |
| 8505dc0 | Gus Hahn-Powell | 14 March 2016, 02:06:39 UTC | Merge branch 'master' into assembly | 14 March 2016, 02:06:39 UTC |
| 2071f72 | Gus Hahn-Powell | 14 March 2016, 02:05:33 UTC | Handle config -> contextEngine params in context | 14 March 2016, 02:05:33 UTC |
| d4e28ce | Gus Hahn-Powell | 14 March 2016, 02:04:47 UTC | Added assembly config | 14 March 2016, 02:04:47 UTC |
| a94e1c8 | Gus Hahn-Powell | 14 March 2016, 02:01:05 UTC | Improvements to AssemblyManager Added method for precedence relations Moved isValidMention to companion object | 14 March 2016, 02:01:05 UTC |
| 9aadb8e | Gus Hahn-Powell | 14 March 2016, 02:00:26 UTC | Corrected require | 14 March 2016, 02:00:26 UTC |
| a27db61 | Gus Hahn-Powell | 14 March 2016, 01:59:46 UTC | predecessors and successors of Event are EERs | 14 March 2016, 01:59:46 UTC |
| 03d11e4 | Gus Hahn-Powell | 14 March 2016, 01:59:09 UTC | Improved Sieve and and added Constraints | 14 March 2016, 01:59:09 UTC |
| daa4057 | Gus Hahn-Powell | 14 March 2016, 01:58:19 UTC | Improved rules and corrected label | 14 March 2016, 01:58:19 UTC |
| e79b4d1 | Tom Hicks | 13 March 2016, 21:11:29 UTC | Restore minor output directory change. | 13 March 2016, 21:11:29 UTC |
| fa91dd6 | Gus Hahn-Powell | 13 March 2016, 20:36:02 UTC | Export precededBy EventIDs | 13 March 2016, 20:36:02 UTC |
| 3a98c9a | Gus Hahn-Powell | 13 March 2016, 20:35:44 UTC | AssemblyExporter cleanup | 13 March 2016, 20:35:44 UTC |
| 5f9d894 | Gus Hahn-Powell | 13 March 2016, 04:06:46 UTC | Added SieveUtils includes a method for applying rules to set of existing mentions | 13 March 2016, 04:06:46 UTC |
| ef834a7 | Gus Hahn-Powell | 13 March 2016, 04:05:39 UTC | Added rules for detecting causal precedence | 13 March 2016, 04:06:30 UTC |
| 7807143 | Gus Hahn-Powell | 13 March 2016, 04:04:50 UTC | Added PrecedenceRelations | 13 March 2016, 04:04:50 UTC |
| dbdb8a7 | Gus Hahn-Powell | 13 March 2016, 04:03:54 UTC | Cleanup made LUTs private | 13 March 2016, 04:03:54 UTC |
| ea58558 | Mihai Surdeanu | 13 March 2016, 03:16:44 UTC | Merge pull request #117 from clulab/issue114 Issue114 | 13 March 2016, 03:16:44 UTC |
| 46b5815 | Enrique Noriega Atala | 13 March 2016, 02:21:03 UTC | Unit test extended to test fallback species | 13 March 2016, 02:21:03 UTC |
| bdbf6f1 | Gus Hahn-Powell | 13 March 2016, 02:04:19 UTC | Cosmetic changes variable names were too long. xxEERepresentation => xxEER xxEEReprs => xxEERs etc. | 13 March 2016, 02:08:02 UTC |
| 9537e1f | Enrique Noriega Atala | 13 March 2016, 01:52:36 UTC | Added fallback species to context, if any | 13 March 2016, 01:52:36 UTC |
| 18c880b | Gus Hahn-Powell | 12 March 2016, 05:06:51 UTC | Merge branch 'master' into assembly | 12 March 2016, 05:06:51 UTC |
| 0e778c6 | Gustave Hahn-Powell | 12 March 2016, 05:01:55 UTC | Merge pull request #115 from clulab/gfin Global grounding with species from Context | 12 March 2016, 05:01:55 UTC |
| e5f6be6 | Tom Hicks | 12 March 2016, 04:13:41 UTC | Walk biomentions, match species from context. | 12 March 2016, 04:13:41 UTC |
| b35731e | Tom Hicks | 12 March 2016, 04:03:51 UTC | Remove debugging from ReachSystem. | 12 March 2016, 04:03:51 UTC |
| f80da8e | Tom Hicks | 12 March 2016, 04:02:57 UTC | Replace nsId selectors with species set selectors. | 12 March 2016, 04:02:57 UTC |
| 2d37608 | Tom Hicks | 12 March 2016, 04:02:10 UTC | Return immutable Sets from reverse lookup. | 12 March 2016, 04:02:10 UTC |
| fdfc252 | Gus Hahn-Powell | 12 March 2016, 00:31:34 UTC | Binding Mention => SimpleEvent output of Binding SimpleEvent is a Complex | 12 March 2016, 00:31:34 UTC |
| fc87750 | Mihai Surdeanu | 11 March 2016, 22:54:26 UTC | New binding rule. | 11 March 2016, 22:54:26 UTC |
| 0060df6 | Gus Hahn-Powell | 11 March 2016, 21:15:48 UTC | Added require to tsv output procedure | 11 March 2016, 21:15:48 UTC |
| 4c51493 | Gus Hahn-Powell | 11 March 2016, 18:53:42 UTC | Use DefaultNamespace to detect UAZ groundings | 11 March 2016, 18:53:42 UTC |
| 8503c2c | Gus Hahn-Powell | 11 March 2016, 18:35:37 UTC | Fix: filter out Mentions with UAZ grounding | 11 March 2016, 18:35:37 UTC |
| 0306a0c | Gus Hahn-Powell | 11 March 2016, 18:30:43 UTC | Filter out Mentions with a UAZ grounding | 11 March 2016, 18:30:43 UTC |
| f2bc545 | Gus Hahn-Powell | 11 March 2016, 18:30:21 UTC | Minor changes to EERLUT | 11 March 2016, 18:30:21 UTC |
| d8d755c | Gus Hahn-Powell | 11 March 2016, 17:54:08 UTC | FIXME: Anaphoric require fails on PMC3178447 | 11 March 2016, 17:54:08 UTC |
| bf33153 | Gus Hahn-Powell | 11 March 2016, 08:07:49 UTC | Added MITRE constraints as filter | 11 March 2016, 08:07:49 UTC |
| ed694fa | Gus Hahn-Powell | 11 March 2016, 08:07:34 UTC | papers => docIDs | 11 March 2016, 08:07:34 UTC |
| c999239 | Gus Hahn-Powell | 11 March 2016, 08:06:55 UTC | Fixed Regulation bug | 11 March 2016, 08:06:55 UTC |
| 25fc433 | Tom Hicks | 11 March 2016, 03:44:40 UTC | WIP: begin to match context by nsId. | 11 March 2016, 03:44:40 UTC |
| cfe23d8 | Tom Hicks | 11 March 2016, 03:41:30 UTC | Add Reverse Lookup KB class, factory class, and Reach object. | 11 March 2016, 03:41:30 UTC |
| ab6db2b | Tom Hicks | 11 March 2016, 03:33:07 UTC | NsId logic: move some, add constants, new methods to select, test, and format. Move tsv field validator. | 11 March 2016, 03:33:07 UTC |
| 6e1c9ec | Gus Hahn-Powell | 11 March 2016, 01:17:41 UTC | Bug fix and cleanup | 11 March 2016, 01:17:41 UTC |
| 38dcd4f | Gus Hahn-Powell | 11 March 2016, 01:16:32 UTC | Make use of EER's sourceMention | 11 March 2016, 01:16:32 UTC |
| 724811c | Gus Hahn-Powell | 10 March 2016, 22:26:14 UTC | Simplified EERs to take optional sourceMention | 10 March 2016, 22:26:32 UTC |
| e964168 | Tom Hicks | 10 March 2016, 17:32:48 UTC | Merge lastest master into branch gfin. | 10 March 2016, 17:32:48 UTC |
| 6872de7 | Gus Hahn-Powell | 10 March 2016, 05:25:54 UTC | Fixed text display for SimpleEvent output SimpleEvent outputs have no source Mentions, so retrieving the "representative" text requires some gymnastics | 10 March 2016, 05:25:54 UTC |
| 72cd47d | Gus Hahn-Powell | 10 March 2016, 05:24:58 UTC | Added .getSimpleEntitiesByModification to AM | 10 March 2016, 05:24:58 UTC |
| df7e3b3 | Gus Hahn-Powell | 10 March 2016, 05:24:35 UTC | added .withSameGrounding method to SimpleEntity | 10 March 2016, 05:24:35 UTC |
| 3495c8e | Gus Hahn-Powell | 10 March 2016, 05:24:24 UTC | Fixed docstring for SimpleEntity | 10 March 2016, 05:24:24 UTC |
| 2190b29 | Gus Hahn-Powell | 10 March 2016, 04:37:41 UTC | Fixed text label of input When input has a mention source... Does not work for representations of the output of some SimpleEvent, which do not have source Mentions (i.e., output isn't represented in our mentions) | 10 March 2016, 04:37:41 UTC |
| 17e991e | Gus Hahn-Powell | 10 March 2016, 04:14:58 UTC | Merge branch 'master' into assembly | 10 March 2016, 04:14:58 UTC |
| 93587cb | Gus Hahn-Powell | 10 March 2016, 04:13:43 UTC | Retrieve distinct Events and Entities | 10 March 2016, 04:13:43 UTC |
| ab985c9 | Gus Hahn-Powell | 10 March 2016, 04:13:09 UTC | Fixed Regulation validation | 10 March 2016, 04:13:09 UTC |
| abb890d | Gus Hahn-Powell | 10 March 2016, 04:12:30 UTC | Move to companion object | 10 March 2016, 04:12:30 UTC |
| 957e915 | Gus Hahn-Powell | 10 March 2016, 04:11:13 UTC | Add sites to PTMs in export | 10 March 2016, 04:11:13 UTC |
| 9b88a2e | Gus Hahn-Powell | 10 March 2016, 04:10:29 UTC | Use AssemblyManager's mention resolution method | 10 March 2016, 04:10:29 UTC |
| 344b4ca | Gus Hahn-Powell | 10 March 2016, 04:10:11 UTC | getEventRows | 10 March 2016, 04:10:11 UTC |
| 66f8b76 | Gus Hahn-Powell | 10 March 2016, 04:09:42 UTC | Include expanded evidence? | 10 March 2016, 04:09:42 UTC |
| e51f549 | Gus Hahn-Powell | 10 March 2016, 04:08:42 UTC | Get Event ID | 10 March 2016, 04:08:42 UTC |
| a7136e2 | Gus Hahn-Powell | 10 March 2016, 04:08:22 UTC | Handle entities | 10 March 2016, 04:08:22 UTC |
| 290a04b | Gus Hahn-Powell | 10 March 2016, 04:07:42 UTC | Fixed header and adjusted row sort | 10 March 2016, 04:07:42 UTC |
| 5e5d0fe | Gus Hahn-Powell | 10 March 2016, 04:07:22 UTC | Threshold rows | 10 March 2016, 04:07:22 UTC |
| a38a992 | Gus Hahn-Powell | 10 March 2016, 04:05:13 UTC | Error handling | 10 March 2016, 04:05:13 UTC |
| 777bd70 | Gus Hahn-Powell | 10 March 2016, 04:04:58 UTC | Resolve evidence, if needed | 10 March 2016, 04:04:58 UTC |
| 23de1a1 | Gus Hahn-Powell | 10 March 2016, 04:04:27 UTC | Changed row representation | 10 March 2016, 04:04:27 UTC |
| aa91b43 | Gus Hahn-Powell | 10 March 2016, 04:04:02 UTC | Changed EERLUT | 10 March 2016, 04:04:02 UTC |
| 5c296d1 | Gustave Hahn-Powell | 10 March 2016, 01:17:54 UTC | Merge pull request #111 from clulab/issue110 Issue110 | 10 March 2016, 01:17:54 UTC |
| 88cc006 | Tom Hicks | 09 March 2016, 23:32:23 UTC | Add default sort-by-human for resolutions returned from IMKB. | 09 March 2016, 23:32:23 UTC |
| a8499c3 | Tom Hicks | 09 March 2016, 23:31:40 UTC | Comment out debugging output in TestFamilyResolutions. | 09 March 2016, 23:31:40 UTC |
| 06ddaca | Tom Hicks | 09 March 2016, 23:09:09 UTC | Remove empty junk file someone must have accidentally committed. | 09 March 2016, 23:09:09 UTC |
| 2f7d973 | Tom Hicks | 09 March 2016, 18:43:28 UTC | Redo to propagate ambiguity. | 09 March 2016, 18:43:28 UTC |
| 982c487 | Tom Hicks | 09 March 2016, 18:32:58 UTC | Add resolution filters and default sort-by-human for resolutions returned from IMKB. | 09 March 2016, 18:35:14 UTC |
| 8a01199 | Tom Hicks | 09 March 2016, 18:16:09 UTC | Quiet debugging in ReachSystem, turned on my accident. | 09 March 2016, 18:16:09 UTC |
| ae1bd97 | Tom Hicks | 09 March 2016, 17:40:35 UTC | Comment debugging output in TestFamilyResolutons. | 09 March 2016, 17:40:35 UTC |
| 57f2691 | Gus Hahn-Powell | 09 March 2016, 07:39:04 UTC | Fixed PTM display and TSV writing | 09 March 2016, 07:39:04 UTC |
| 6d0ad6a | Gus Hahn-Powell | 09 March 2016, 07:26:13 UTC | Formatting | 09 March 2016, 07:26:13 UTC |
| e38d788 | Gus Hahn-Powell | 09 March 2016, 07:25:44 UTC | Better entity representation | 09 March 2016, 07:25:44 UTC |
| fddaed0 | Gus Hahn-Powell | 09 March 2016, 07:24:50 UTC | toString => toTSVrow | 09 March 2016, 07:25:04 UTC |
| d92e247 | Gus Hahn-Powell | 09 March 2016, 07:24:05 UTC | Get full sentence for each piece of evidence | 09 March 2016, 07:24:05 UTC |
