v1.0.3

Hot fixes

• [urgent] Merge equivalent hits from different documents #130

General Enhancements

• [enhancement] Add all query elements to Excel output #277
• [enhancement] Add organism filters specific for Input Lists #276

Bug Fixes

• [bug] Fix FAQ example link #278
• [bug] Set appropriate document source in result table #275
• [bug] Fix headings filter field #268
• [bug] Investigate why second example in help page does give an empty result #260
• [bug] Restrict Pie and bar charts to interaction partners actually on the list #205
• [bug] Display fulltext match type in Excel #199
• [bug] Make FamPlex and HGNC group query terms work #174

Miscellaneous Changes

• [closed] Use appropriate Ajax URI creation mechanism #274
• [closed] Handle HTTPS URL issues in Ajax calls #272
• [closed] Help Needed with Installing Neo4j Concepts Server Plugin for GEPI #270
• [closed] Offer API for batch requests for direct download of the result sheet #136
• [closed] Sentence/paragraph: Index abbreviations resolved #127
• [closed] Make sure that the NatCom main result is reproducible #111
• [closed] Add a close button to the input panel #106
• [closed] Remove stupid gene tagging errors #97
• [closed] table 2nd sheet most frequent hits sorted #95
• [closed] Table: give PMC and Medline IDs #93
• [closed] Drop down menu for download format #91
• [closed] feature comparison GNormPlus and BANNER (solely NER) #74
• [closed] Nature methods review #51
• [closed] paper outline #45
• [closed] stat widget #43
• [closed] index restructuring for performance #37
• [closed] API functionality #33
• [closed] GePi webapplication server location #9
• [closed] Organise semedico-app input resources from gene database #7

v1.0.2

General Enhancements

• [enhancement] Add hyperlinks to the ID columns of the table result widget #259
• [enhancement] Add hyperlinks to external gene resources to Excel result sheet #258
• [enhancement] Unify symbol aggregation counts by normalization #242
• [enhancement] Place table paging buttons on top #241

Bug Fixes

• [bug] Fix issue where paragraph URL parameter is not parsed correctly #262
• [bug] Fix broken example on the Help page due to separating gene items with commas #261
• [bug] Fix conceptId pattern in GeneIdService #257
• [bug] Fix null links to external databases #256
• [bug] Discard duplicate items from input mapping table #240

Documentation

• [documentation] Add a license #267
• [documentation] Add documentation for the preprocessing pipelines. #266
• [documentation] Add documentation for the concept database. #265

v1.0.0: Submission to NAR Webserver Issue

Speed Improvements

• [performance] Replace retrieval of all event documents with aggregations #226

General Enhancements

• [enhancement] Use requirements.txt in Docker build #255
• [enhancement] Add helpful descriptions, tooltips etc #248
• [enhancement] Remove interaction limit input field #246
• [enhancement] Show actual number of table pages #243
• [enhancement] Add the publication date to the index #233
• [bug][enhancement] Update argument1 and argument2 index fields with FamPlex, HGNC and equal name aggregate IDs #222
• [enhancement] (re)add fields for ES aggregations to index #208
• [enhancement] Update to ElasticSearch 7.17.8. #197
• [enhancement] Integrate GO -> gene mapping #187
• [enhancement] Integrate HGNC -> gene ID mapping #186

Bug Fixes

• [bug] Fix download crash for fulltext-only data #253
• [bug] Make copy button for download link work on Windows #249
• [bug] Normalize interaction arguments in Excel sheet argument statistics #245
• [bug] Reset retrieval of unary events in new session #236
• [bug] Investigate AKT search behavior #227
• [bug] Update concept manager for gene ontology correction #225
• [bug] Fix download button on the new ResultDownload page #217
• [bug] Take care to avoid AGGREGATE_EQUAL_NAMES nodes when fetching geneInfo #194

Miscellaneous Changes

• [closed] Integrate UniProt Accession or Mnemomic -> NCBI Gene ID mapping #120
• [closed] Integrate ID mapping #117

v0.12.1

General Enhancements

• [enhancement] Add an FAQ page. #224
• [enhancement] Create a (fav)icon or our own #214

Bug Fixes

• [bug] Fix NPE when entering the page via FAQ or Help page #223

v0.12.0

General Enhancements

• [enhancement] Offer a page for delayed results download #213
• [enhancement] Add a service to delete temporary Excel download files after a given amount of time #212

Bug Fixes

• [bug] Fix download file issue "file not found" in production container #220
• [bug] Fix truncated download table due to event download restriction for charts #215

Miscellaneous Changes

• [closed] Download functionality #32

v0.11.2

• [enhancement] Add an input field to allow the user the specification of the number of interactions used for aggregations #207

What's Changed

• Version 0.11.2. Fixes #207,#208. by @khituras in #209

Full Changelog: v0.11.1...v0.11.2

v0.11.1

What's Changed

• Issue68atid fix by @SchSascha in #82
• Rather a formal pull request, just to keep the documentation style up and running by @SchSascha in #87
• Table Download now results in an xls file (realized with apache poi).… by @fmatthies in #90
• 0.2 sankey d3 by @khituras in #109
• 0.2 by @khituras in #110
• Tab sessions by @khituras in #137
• Result paging by @khituras in #142
• State of BioArxiv first version by @khituras in #148
• Add python to the docker image. Fixes #152. by @khituras in #153
• 0.9.0 beta by @khituras in #158
• Fix #200, the pure section heading search crash. by @khituras in #201
• Interactive help by @khituras in #206

Full Changelog: v0.1.1...v0.11.1

v0.11.0-beta

Speed Improvements

• [performance] Add an index document field for aggregations #181

General Enhancements

• [enhancement] Provide search examples #196
• [enhancement] Introduce separate waiting-for-data state for paged requests #193
• [enhancement] Load geneInfo in batch instead of one-by-one #192
• [enhancement] Add a mechanism for GePiFamplexIdAssigner to let GNP decide whether a gene should be mapped to Famplex/HGNC groups or not #191
• [enhancement] Switch FamPlex and HGNC IDs in the index from conceptIds to prefixed original IDs #190
• [enhancement] Extend preferredName normalization to punctuation and white spaces #188
• [enhancement] Add taxIds to index documents and filter on those #185
• [enhancement] Show message when concrete gene IDs and tax IDs are given with contradictions #184
• [enhancement] Make direct links possible #182
• [enhancement] Create index documents for unary events #180
• [enhancement] Filter out duplicates based on abbreviation introduction #179
• [enhancement] Integrate factuality (level of likelihood that an interaction actually takes place) #173
• [enhancement] Add hover effects and tooltips for sankey diagrams #172
• [enhancement] Add 6th Bootstrap grid tier #171
• [enhancement] Distribute widgets relative to breakpoints and available space #170
• [enhancement] Display messages in widges when there is no data #169
• [enhancement] Try to resolve genes by synonym if there is no match by preferredName/symbol #168
• [enhancement] Add bar plot widget #166
• [enhancement] Always show 'others' slice in pie charts when there are too many genes to show #165
• [enhancement] Make sankey diagrams so that their contents are not cropped #155
• [enhancement] Integrate Gene Name -> NCBI Gene ID mapping #118

Bug Fixes

• [bug] Deactivate B list file upload as long as A is empty #147
• [bug] Make the event type filter work for 'phosphorylation' #144
• [bug] Fix issue where b-list cannot be read from file repeatedly #134

Evaluation and Reproducibility

• [evaluation] Add a UIMA BioNLP ST gene merger component #178
• [evaluation] Add code to evaluate BioSem given GNormPlus genes #177
• [evaluation] Add code to reproduce GNormPlus evalution results in the GePI paper #176

Miscellaneous Changes

• [closed] Common partners Sankey: hide non-common edges #167
• [closed] Check if reflexive relations are returned #131
• [closed] Integrate Ensemble ID -> NCBI Gene ID mapping #119
• [closed] Remove the organism restriction of GeNo #112
• [closed] Make diagrams always use up the available space #101

v0.10.1-beta

• [bug] Fix null context with paragraph filter #164

v0.10.0-beta

General Enhancements

• [enhancement] Add tabs to the pie charts widgets to switch between a- and b-counts #162
• [enhancement] Scroll to top upon search submission #161
• [enhancement] Implement AND/OR for sentence and paragraph filters #160
• [enhancement] Fix Pie Chart coloring #156

Bug Fixes

• [bug] Fix fulltext match column #163
• [bug] Fix paged result download #159