ThaleMine 1.8.0 Release

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ThaleMine was updated to version 1.8.0 on 14 December 2015. ThaleMine is available at https://apps.araport.org/thalemine/

JBrowse was updated on 14 December 2015. JBrowse is available at https://apps.araport.org/jbrowse/?data=arabidopsis

Release Notes

Major Changes

  • ThaleMine 1.8.0 added the following new data contents:
    • Araport11 Pre-Release 3 (12/2015) gene structure and functional annotation for the Col-0 genome generated by Araport (submitted to NCBI) [MINE-955]
    • Arabidopsis Germplasm and Seed stocks and their associated Phenotypes with links to the ABRC and NASC stock ordering systems [MINE-988]
  • ThaleMine 1.8.0 includes the following updated datasets:
    • Gene-to-publication mapping from NCBI gene2pubmed, updated to release 11/30/2015 [MINE-1103]
    • Curated Gene Reference Into Function (GeneRIF) annotation of gene records from the NCBI gene database, updated to release 11/30/2015 [MINE-1103]
    • GO annotations from geneontology.org, update to release 11/02/2015 [MINE-1103]
    • Protein domain data from InterPro, updated to release v54.0. Protein domains now include coordinates (signatures) from InterPro protein2ipr [MINE-1103]
    • Curated (SwissProt) and Computationally derived (trEMBL) protein data from Uniprot, updated to release 2015_11 [MINE-1103]
  • ThaleMine 1.8.0 now features public gene lists for loss-of-function mutants collected by Lloyd and Meinke 2012 [MINE-1126]
  • ThaleMine 1.8.0 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 1.8.0 runs InterMine 1.6.0, the latest version of the software [MINE-1073]
  • JBrowse added the following new datasets:
    • Araport11 Pre-Release 3 (10/2015) gene structure and functional annotation for the Col-0 genome generated by Araport (submitted to NCBI) [MINE-955]
    • Variants generated by the 1001 Genomes project along with metadata retrieved via web services from the Gregor Mendel Institute [MINE-1096]
    • Araport runs JBrowse 1.12.0, the latest version of the software
    • For more detailed information about datasets available via JBrowse, please see: https://www.araport.org/jbrowse/data-statistics

Minor Changes

  • On ThaleMine gene report pages, missing/broken links to Data Sources were fixed [MINE-1122]
  • On JBrowse displays, a button is now available to toggle on/off the track labels [MINE-1068]