Release Notes

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ThaleMine 1.10.1 Release

ThaleMine was updated to version 1.10.1 on 21 December 2016. ThaleMine is available at https://apps.araport.org/thalemine/

Release Notes

Major Changes

Minor Changes

  • On ThaleMine gene report pages, there is now a convenient link-out to related homologous genes in Phytozome, via automatically generated FriendlyMine links to PhytoMine
  • On all ThaleMine pages, the footer was updated to show additional information about the project, such as Citation, Funding Information, Links to other mines and Link to the InterMine Android App download page

ThaleMine 1.10.0 Release

ThaleMine was updated to version 1.10.0 on Sep 7, 2016. ThaleMine is available at https://apps.araport.org/thalemine/

Release Notes

Major Changes

  • ThaleMine 1.10.0 added the following new data contents:
    • Insertional mutatnts identified by TDNA-seq from segregating SALK, SAIL and WiscDsLox lines
  • ThaleMine 1.10.0 includes the following updated datasets:
    • TAIR curated data (gene symbols, aliases, curator summary and computational descriptions) from TAIR public data release 06/30/2016
    • Curated (SwissProt) and Computationally derived (trEMBL) protein data from Uniprot, updated to release 2016_07
    • Protein domain data from InterPro, updated to release v58.0. Protein domains now include coordinates (signatures) from InterPro protein2ipr
    • Gene-to-publication mapping from NCBI gene2pubmed, updated to release 08/12/2016
    • Curated Gene Reference Into Function (GeneRIF) annotation of gene records from the NCBI gene database, updated to release 08/12/2016
    • GO annotations from geneontology.org, update to release 08/01/2016
    • Plant Ontology (PO) annotations showing plant anatomical and developmental stages from TAIR public data release 06/30/2016
    • Homology data from Panther, updated to release v11.0
  • For more detailed information about datasets available via ThaleMine, please see: https://www.araport.org/thalemine/data-statistics
  • ThaleMine 1.10.0 runs InterMine 1.6.7, the latest version of the software

Minor Changes

  • On ThaleMine gene/transcript report pages, the embedded JBrowse displayer now uses the fixed InterMine populate-child-features post-processor and JBrowse REST API endpoint(s) to retrieve and visualize the spliced gene structure

ThaleMine 1.9.1 Release

ThaleMine was updated to version 1.9.1 on June 21 2016. ThaleMine is available at https://apps.araport.org/thalemine/

JBrowse was updated on June 21 2016. JBrowse is available at https://apps.araport.org/jbrowse/?data=arabidopsis

Release Notes

Major Changes

  • ThaleMine 1.9.1 includes the following updated datasets:
    • Araport11 Official Release (06/2016) gene structure and functional annotation for the Col-0 genome generated by Araport (accepted by NCBI) [MINE-1196]
    • Homolog data from Panther DB, restricted only to orthologs from Human and Yeast and paralogs from Arabidopsis thaliana [MINE-1223]
    • For more detailed information about datasets available via ThaleMine, please see: https://www.araport.org/thalemine/data-statistics
  • JBrowse added/updated the following new datasets:
    • Araport11 Official Release (06/2016) gene structure and functional annotation for the Col-0 genome generated by Araport (accepted by NCBI) [MINE-1196]
    • 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, external Friendly Mine links to HumanMine and YeastMine have been reinstated [FEED-1110, MINE-1227]
  • On ThaleMine report pages, the FASTA sequence of the Pseudogene feature is now correctly reported [MINE-1225]
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