InterMine 1.6.4

#1221 - Template queries in my mine: can't export

InterMine 1.6.3

#1236 - Keyword Search: don't show entire index if no keyword provided.
#1179 - PDB fix
#1190 - Atlas express source

InterMine 1.6.2

#1228 - Fix tutorial, remove interpro
#1184 - Keyword search: first search takes you to home page
#1168 - PSI-Complexes -- allow for more data types
#1154 - Web services: tags for templates

InterMine 1.6.1

#1205 - Cytoscape fix for protein report page
#1209 - Fix Panther for Drosophila
#1216 - Make region.start and end integers instead of strings

InterMine 1.6

We are happy to announce the latest release of InterMine!

This release contains some new tools and updates to others, as well as lots of bug fixes and improvements.

There are also data model changes for interactions and protein domains. The model has been updated to add complex and protein interactions, and protein domain regions.

See the upgrade instructions for details.

Interactions

Model changes

We updated the data model for interactions to allow for more data types to be loaded.

Current Model

New Model

• interaction.gene1 gene2 changed to be interaction.participant1 participant2
  • allows for protein and molecular interactions
  • was dumb not to do this first why didn’t anyone stop me
• interaction.relationship type is a string instead of an ontology term
  • e.g. "physical association"
  • easier to query, understand if just a string instead of a separate object
• interactionDetail.all interactors contains Interactor type instead of Gene
  • need to associate biological role (e.g. bait, prey) with the interactor not the gene / protein

New data

You can now load complex interacton data from IntAct into your mine. See the docs for details.

New and improved visualisation tools

- We've updated to Cytoscape JS - New [EsyN network editor tool](http://intermine.readthedocs.org/en/latest/webapp/third-party-tools/esyn/) - Display and edit interaction data - Works on report and list analysis pages

Protein Domains

We added protein domain regions to the data model. Proteins now have a proteinDomainRegions collection which then have a reference to the InterPro protein domain.

See the upgrade instructions for details on the data model and here for information on how to load these data.

Notes

- The UniProt data source no longer creates protein domains because the data file does not include locations. - Issues with Tomcat 8 have been fixed.

Data

#1125 - UniProt: add publications to genes too
#1116 - Make protein isoforms collection
#1035 - VCF data parser for InterMine

Bug Fixes

#1187 - GO enrichment widget -- gene length normalisation error
#1164 - GO enrichment widget -- background change error
#1163 - QueryBuilder: error querying for NULL relationships
#1150 - IntegrationWriterDataTrackingImplTest failing tests, sometimes.
#1147 - Web service: speed up requests
#1124 - CORS issues
#1121 - Query Builder: cannot query for disease names because of trailing whitespace
#1114 - YeastMine: serial number not being reset
#1108 - Point Mutations: new index doesn't seem to handle features of size = 1;
#1103 - FlyMine: bad locations being created when there are no gaps between features
#1102 - Result table preview with many collections overflows off screen.
#1095 - FlyMine: Queries using overlaps are failing
#1094 - Code generation not updating in result tables in Safari 8
#1079 - Panther not parsing homologues parameter correctly
#1072 - Counts missing from templates on report / list pages
#1071 - Complexes - fails for human
#1067 - More queries link in summary area on http://www.flymine.org/ fails
#1065 - FlyMine: flyfish failed on dull pointer exception
#1063 - FASTA: error loading locations
#1053 - Simple objects fail to show in results tables with outer joins
#1032 - CORS issue - www.humanmine.org and humanmine.org
#1019 - Duplicate BioGrid interaction data
#992 - Build fails silently on misconfiguration of keyword search properties. Should fail loudly.
#968 - Reduce tracker table size
#962 - Interaction region not a Bioentity causing problems in located features collection
#919 - Unhelpful error when no database connections available
#912 - Better error message for running out of connections
#896 - keyword search task aborts silently if it encounters an error
#834 - Fresh install on beta has issues with java 8
#745 - Update for Tomcat 8
#652 - Add class keys for sequence feature
#420 - Save XML button gives "Bad URL" in Safari

InterMine 1.5.6

#1075 - Fix mising template row counts.

InterMine 1.5.5

Minor fixes, plus new esyN displayer.

#1027 - Outer joins break the results table
#1020 - Manage columns labels gone
#1017 - Panther - didn't load yeast orthologues
#1000 - GeneLenghtCorrectionCoefficient misspelled
#988 - Download script failed on a few sources
#986 - JS tests failing
#980 - FlyMine: genes not being merged correctly
#978 - template with lookup failing if selecting the organism
#967 - Java client code gen errors
#957 - Homologues need to merge

InterMine 1.5.4

A small patch to fix a widget issue.

#1021 - View on widgets opens a blank window
#1013 - OBO converter - fails on creating synonyms.
#967 - Java client code gen errors
#948 - Error during ant build-db on bio/test-all/dbmodel
#931 - Logo for human InterMine
#866 - Panther - rat genes
#865 - Delete mystery properties
#846 - InterPro - description text is too long for index
#824 - Duplicate human genes in data file
#722 - Table cell previews display too many fields
#591 - Links to FlyMine contain release number
#152 - Use ontology for data sources

InterMine 1.5.3

InterMine 1.5.3

#1022 - Widget download fix

InterMine 1.5.2

#996 - Inheritance in webconfig-model.xml is inconsistant
#976 - Portal doesn't correctly process homologues
#963 - Download link for Java client is broken
#958 - improve error message when creating list from set operation
#957 - Homologues need to merge
#955 - UniProt fails to parse multiple Ensembl genes
#937 - Travis isn't checking bio packages.
#851 - Adding numerical constraint in results filter does not accept minus values

InterMine 1.5.1

#978 - template with lookup failing if selecting the organism
#950 - Escape list description
#943 - results table no longer supports removing a filter
#935 - Query results - popups don't work after paging
#800 - Angle bracket issue in column summary dialog
#799 - Allow editing logic expression
#796 - Support one/none of operator
#795 - Support option lists in 'add filter' dialog
#794 - Allow subtype constraints in results table dialogs
#779 - Export correct strand on FASTA output with extension
#778 - Manage Columns needs to allow addition of multiple columns
#753 - Query results - onhover the cell embiggens
#744 - expand/collapse-all sub-tables does not work in 1.6.x
#679 - Tomcat reports a memory leak on stopping a webapp
#641 - Results table - Boolean column not filterable if it contains NULLs
#628 - Results tables - column summary disappears on second click
#521 - results tables default code option
#436 - Query results - add link to query builder
#420 - Save XML button gives "Bad URL" in Safari
#374 - Result table download modifications
#311 - Filter dialogue - list of fields overlaps cancel button
#200 - Safari bug - mouseovers on results tables not working correctly
#167 - Need a 'Creating list..' warning when creating large lists from results tables.
#141 - Column headers for download