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