Release Notes

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ThaleMine 1.7.1 Release

ThaleMine was updated to version 1.7.1 on 27 October 2015. ThaleMine is available at https://apps.araport.org/thalemine/

Release Notes

Minor Changes

  • On ThaleMine Gene report pages, the overlapping features displayer was re-instated based on a user request [FEED-569]
  • On the ThaleMine API console, several missing web service descriptions were re-instated [MINE-1069]

ThaleMine 1.7.0 Release featuring #Araport11 annotation data

ThaleMine was updated to version 1.7.0 on 16 October 2015. ThaleMine is available at https://apps.araport.org/thalemine/

JBrowse was updated on 16 October 2015. JBrowse is available at https://apps.araport.org/jbrowse/?data=arabidopsis

Release Notes

Major Changes

  • ThaleMine 1.7.0 added the following new data contents:
    • Araport11 Pre-Release 2 (10/2015) gene structure and functional annotation for the Col-0 genome generated by Araport (submitted to NCBI) [MINE-955]
    • Plant Ontology (PO) annotations showing plant anatomical and developmental stages from TAIR public data release 09/30/2014 [MINE-1033]
    • Physical and genetic protein-protein interactions from BioGRID v3.4.128 and IntAct release 08/22/2015 [MINE-840]
    • Consolidation of curated gene-to-publication mappings from NCBI, UniProt and TAIR (09/30/2014) available via the Gene report [MINE-1033]
    • AGI gene locus history, tracking information about gene splits/merges, deletions and addition of novel gene loci available via the Gene report [MINE-1034]
  • ThaleMine 1.7.0 added a dynamic “Data Sources” page, summarizing annotated genome features as well as data source/set information [MINE-1020]. For more detailed information about datasets available via ThaleMine, please see: https://www.araport.org/thalemine/data-statistics
  • ThaleMine 1.7.0 runs InterMine 1.5.5, the latest version of the software [MINE-850]
  • JBrowse added the following new datasets:
    • Araport11 Pre-Release 2 (10/2015) gene structure and functional annotation for the Col-0 genome generated by Araport (submitted to NCBI) [MINE-1029]
    • VISTA whole genome alignment plots against other Brassicaceae species, retrieved via web services from Phytozome [MINE-1048]
    • For more detailed information about datasets available via JBrowse, please see: https://www.araport.org/jbrowse/data-statistics

Minor Changes

  • ThaleMine pages use a new and improved color scheme [MINE-245, MINE-1031]
  • On ThaleMine gene report pages, publications mapping to Transcript/Protein entities are now transitively mapped to the parent Gene entity [MINE-1013]
  • On ThaleMine gene report pages, the overlapping features stripe has been disabled since the data is represented in other stripes [MINE-976, FEED-470]

ThaleMine 1.6.3 Release

ThaleMine was updated to version 1.6.3 on 02 September 2015. ThaleMine is available at https://apps.araport.org/thalemine/

Release Notes

Minor Changes

  • On ThaleMine List Analysis pages, clicking on the column of matches within an enrichment widget (like Publication, GO, Pathway) now provides access to the full list of features pertaining to the enriched entity [FEED-459, FEED-519, MINE-964]
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