Release Notes

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ThaleMine 1.9.0 Release

ThaleMine was updated to version 1.9.0 on May 13, 2016. ThaleMine is available at https://apps.araport.org/thalemine/

JBrowse was updated on May 13, 2016. JBrowse is available at https://apps.araport.org/jbrowse/?data=arabidopsis

Release Notes

Major Changes

  • ThaleMine 1.9.0 added the following new data contents:
    • RNA-seq based gene expression levels (Transcripts per Million, TPM) quantified by Salmon on the Araport11 Release (04/2016) transcript dataset [MINE-1138]
    • Heatmap displayer for the RNA-seq based gene expression data, visible on the Gene/Transcript Report and Gene List Analysis pages [MINE-1138, MINE-1191]
  • ThaleMine 1.9.0 includes the following updated datasets:
    • Araport11 Pre-Release (04/2016) gene structure and functional annotation for the Col-0 genome generated by Araport (submitted to NCBI) [MINE-1196]
    • Curated (SwissProt) and Computationally derived (trEMBL) protein data from Uniprot, updated to release 2016_02 [MINE-1196]
    • Protein domain data from InterPro, updated to release v55.0. Protein domains now include coordinates (signatures) from InterPro protein2ipr [MINE-1196]
    • Gene-to-publication mapping from NCBI gene2pubmed, updated to release 03/15/2016 [MINE-1196]
    • Curated Gene Reference Into Function (GeneRIF) annotation of gene records from the NCBI gene database, updated to release 03/15/2016 [MINE-1196]
    • GO annotations from geneontology.org, update to release 04/15/2016 [MINE-1196]
    • Homolog data from Panther DB, restricted only to paralogs from Arabidopsis thaliana [MINE-1196]
  • For more detailed information about datasets available via ThaleMine, please see: https://www.araport.org/thalemine/data-statistics
  • ThaleMine 1.9.0 runs InterMine 1.6.5, the latest version of the software [MINE-1202]
  • JBrowse added/updated the following new datasets:
    • Araport11 Pre-Release (04/2016) gene structure and functional annotation for the Col-0 genome generated by Araport (submitted to 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, there is now a convenient link-out to the NCBI GeneRIF submission page, which pre-populates the submission form with relevant information extracted from ThaleMine [ED-159]
  • On ThaleMine transcript report pages, the FASTA sequence/length being reported was incorrect (entire genomic region), instead of excluding the intronic regions [MINE-1203, FEED-677]
  • On ThaleMine gene/protein report pages, Araport11 and UniProt protein entities are now correctly integrated together based on protein sequence similarity [MINE-1213]
  • On ThaleMine gene report pages, the Alleles and Stocks stripes feature a new displayer with improved pagination, to speed up report page loading [MINE-1177]
  • On ThaleMine gene report pages, the Array Expression stripe now reports log2 expression ratio value in addition to average ratio [MINE-1110, MINE-1137]

ThaleMine 1.8.1 Release

ThaleMine was updated to version 1.8.1 on 27 January 2016. ThaleMine is available at https://apps.araport.org/thalemine/

Release Notes

Minor Changes

  • On ThaleMine Gene report pages, the real-time Phytozome Homologs displayer was fixed to support the Phytozome services switch from HTTP to secure HTTP (https) [MINE-1152]
  • On ThaleMine Gene report pages, the Interactions Displayer was disabled for genes without any interaction data [MINE-1133]
  • On ThaleMine Gene report pages, external links were added to GeneVisible and Agrisera websites [MINE-1149, MINE-1150]

ThaleMine 1.8.0 Release

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]
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