v0.9.0-beta

Speed Improvements

• [performance] Implement paged result retrieval for closed search #151
• [performance] Avoid complete result download after each search #150

General Enhancements

• [enhancement] Avoid freezing on result download #157
• [enhancement] Re-enable the common partners Sankey #149
• [enhancement] Make the table Ajax-Enabled #143
• [enhancement] Implement paged result retrieval from ES #138

Bug Fixes

• [bug] Fix bug where events are duplicated #133

Miscellaneous Changes

• [closed] Add highlighting to table #129
• [closed] Allow sentence and paragraph filters to contain compounds/phrases #125
• [closed] Add paragraph filter options to GepiInput #124
• [closed] Make paragraph text information available for all events #123

v0.8.0-beta2

• [bug] Fix download table creation #152

v0.8.0-beta (bioRxiv upload)

GePI v0.8.0-beta

This is the state of GePI right after the publication of the first bioRxiv version.

bug

• [bug] references are missing (got deleted to aid sentence splitter) #92
• [bug] atid shown in results instead of gene symbol #68
• [bug] events.argumentsearch does not recognise atids. #60
• [bug] multiple line entries #15

closed

• [closed] Add pipeline to create test data. #139
• [closed] Create specific argument1 and argument2 fields. #132
• [closed] Allow all events to be retrieved filtered on sentence/paragraph #126
• [closed] Update to Java 11 #121
• [closed] Erik Changelog 0.1.18-43 #99
• [closed] Erik Changelog 0.1.18-42 #98
• [closed] Erik Changelog 0.1.18-41 #96
• [closed] Integrate search for relation type #94
• [closed] General changelog #86
• [closed] Come up with a solution for the problem of gene db data export #83
• [closed] Bernd changelog 0.1.17-49 #80
• [closed] Sascha changelog 0.1.17-49 #78
• [closed] explicitely evaluate Sankey plot with common partners #77
• [closed] remove bar plot/widget #75
• [closed] extract neo4jDB concept project #73
• [closed] Add main event type to result table #71
• [closed] Add resource versioning #70
• [closed] Allow to download table also in format xls #64
• [closed] order of mentioned gene events #62
• [closed] clean up gepi neo4j build up scripts #57
• [closed] Download feature for table #54
• [closed] provide filter possibilities to narrow down search / for search exploration #49
• [closed] Provide article id in resulting table per sentence #41
• [closed] Search box entries A|B should automatically be extended to all homologous genes #39
• [closed] proper Inject usage for googleChartManager #38
• [closed] correct table resizing #31
• [closed] Input list recoverable from left side #30
• [closed] pie chart resizing #29
• [closed] Full index gepi available on coling servers #28
• [closed] complete medline & pmc index #27
• [closed] working demo on Sascha's laptop #26
• [closed] workable A - B Search #25
• [closed] input field - responsiveness #24
• [closed] bar diagram - numbers #23
• [closed] Table pager #22
• [closed] elasticsearch index: pmid/pmcid fields wrong? #21
• [closed] event class - atid order in meaningful order? #20
• [closed] Switch to an event-centric index structure #19
• [closed] Add index field for number of arguments #17
• [closed] es_query - no pmc hits #16
• [closed] atid's #14
• [closed] Result Portal #13
• [closed] PMC XMI Parsing issue: Maximum attribute size limit exceeded #11
• [closed] Problematic Medline Document: 23700993 #10
• [closed] Point to missing and useful documentation #8
• [closed] Build Gene Database #6
• [closed] jpp: jules-longdocument-skipper (jls) #5
• [closed] Who does what? #4
• [closed] Current status of modules relevant for GePi #3
• [closed] Write FieldsGenerator #2
• [closed] result pane small #1

enhancement

• [enhancement] Support multiple sources for relations and genes #146
• [enhancement] Support event indexing for multiple IDs per gene #145
• [enhancement] Add a PieChart again #141
• [enhancement] Enable section heading filter #140
• [enhancement] Add filter terms to the Excel frontpage #135

urgent

• [urgent] Update data download to the format used in latest data deliveries #115