Release Notes

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ThaleMine 1.4 Release

ThaleMine was updated to version 1.4 on 03 March 2015. ThaleMine is available at https://apps.araport.org/thalemine/

Release Notes

Major Changes

  • ThaleMine 1.4 incorporates Curated Gene Reference Into Function (GeneRIF) annotation of gene records from the NCBI gene database [MINE-388].
  • ThaleMine 1.4 incorporates metabolic pathway data from Reactome (release v49.0) and KEGG (release 20150202) [MINE-66].

Minor Changes

  • ThaleMine 1.4 runs InterMine 1.4.2, the latest version of that software [MINE-410].
  • ThaleMine 1.4 is faster to resolve links to specific detail pages. This fixes a problem that took up to 8 seconds to resolve links from other sites [MINE-367]. Please provide links to ThaleMine within your web site! Follow the instructions here: https://www.araport.org/linking-araport.
  • On ThaleMine detail pages, in the Interactions stripe, the “Export” button is fixed. It now exports the interaction graph in the output format (image, XML, etc.) selected [MINE-175]. Also, the “Toggle” button now displays the full list of participating interactors [MINE-422].
  • On ThaleMine detail pages, in the Publications stripe, the author names are now displayed when the author is a consortium [MINE-300].
  • ThaleMine protein detail pages now have a protein FASTA download link [MINE-267].
  • The ThaleMine home page was redesigned slightly to add collaborator logos, remove the API box, and update links to Araport [MINE-83].

ThaleMine 1.2.1 Release

ThaleMine was updated to version 1.2.1 on 07 Jan 2015. ThaleMine is available at https://apps.araport.org/thalemine/

Release Notes

Database Changes

  • ThaleMine incorporates TAIR curated data through 12/31/2013 (the latest public release). Compared to ThaleMine 1.2, this version has 260 new gene symbols, 202 new gene descriptions, 19 new or updated curator summary fields, and 6 new or updated computational description fields.
  • GO annotations from geneontology.org, update to release 11/10/2014
  • Curated (SwissProt) and Computationally derived (trEMBL) protein data from Uniprot, updated to release 2014_11
  • Protein domain data from InterPro, updated to release v49.0. Protein domains now include coordinates (signatures) from InterPro protein2ipr.
  • Homology data from Panther, updated to release v9.0
  • Gene-to-publication mapping from NCBI gene2pubmed, updated to release 12/10/2014

ThaleMine 1.2 Release

ThaleMine was upgraded to version 1.2 on 30 Oct 2014. ThaleMine is available at https://apps.araport.org/thalemine/

Release Notes

Major Changes

  • In Search, append tilde [~] to any term to invoke fuzzy matches. [MINE-356]
  • In List Analysis, mouse-over a data cell to open pop-up with further details. [MINE-147]
  • Gene pages have an enhanced GO term display, similar to MouseMine. [MINE-141]
  • Gene pages now include co-regulation data from atted. [MINE-68]

Minor Changes

  • Gene pages have more external links (Aracyc, Aramemnon, AtcisDB, Ensembl Plant, Gramene, PIR).
  • Gene page external links to NCBI now hit the full gene report. [MINE-181]
  • Protein FASTA button, previously on gene pages only, now on protein pages. [MINE-325]
  • Protein EC number now decorated with description and link. [MINE-269]
  • Protein domain names now display with their UniProt descriptions [MINE-357]
  • Search was not finding publications given their full title. Fixed. [MINE-361]

Known Issues not yet Resolved

  • Generic links to ThaleMine genes from external sites can be slow to resolve. [MINE-367]
  • Co-regulation visualization on gene pages (in development). [MINE-68]
  • Graphical display of protein 2D structure (planned). [MINE-309]
  • Include data providers as searchable data. [MINE-254]
  • Display authors when paper's first author is a consortium. [MINE-300]
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