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ThaleMine v0.9.1 Release

ThaleMine (v0.9.1-Preview2-c1764c1 [2014-05-29 14:00:00]) was put in production on 5/29/2014.

Release Notes:

  • Additional AtGenExp expression datasets (courtesy of BAR) have been loaded into ThaleMine. List of available datasets are as follows: Hormone, Pathogen, Stress, Light Series, Root, Seed, Ecotypes.
  • Publications (from NCBI PubMed) are now available on Gene Report pages as well as Protein pages.
  • Linkouts to other InterMine instances hosting plant genomics datasets. Replaced links to animal mines with MedicMine (Medicago truncatula genome): http://medicmine.jcvi.org/medicmine and PhytoMine (InterMine interface to data from Phytozome): http://phytozome.jgi.doe.gov/phytomine
  • Software upgraded to InterMine v1.3.2
  • Searches via the InterMine quick search interface should now be much faster (due to optimized and reduced index size)

Issues resolved since last release:

  • When creating lists, the search terms that are not of the chosen feature type should now be correctly resolved/converted to the appropriate type. As an example, if a Protein identifier is provided to the List query where the chosen type is 'Gene', then the resolver will convert the IDs to the correct type.
  • Gene to UTR relationship now established properly and should allow users to query for lists of UTRs associated with Gene loci (instead of the Transcript)
  • Genes to Probe Set associations have now been established properly, they are now mutual collections of one another (i.e. a Gene can be associated to multiple Probe Sets and a Probe Set can be associated to multiple Genes)

Araport Preview Release 2

Welcome to the second preview release of the Arabidopsis Information Portal, or "Araport". We hope you will find it useful.

New Features Include:

  • ThaleMine 0.90, an Arabidopsis-specific data warehouse containing TAIR10 functional annotation, interaction and expression data, and ortholog mappings
  • Genome Browsers based on TAIR10 annotations. Both Jbrowse and Gbrowse are offered.
  • The ability to sign up for an Araport account. Some AIP functionality will only be available to logged-in users.
  • Preview versions of "Science Apps" based on modern web service technologies
  • The beginnings of a Developer Zone in support of community-led extension of AIP
  • Site support for posting meetings, conferences, and important web links

Known Issues With This Release:

  • The main Araport page (www.araport.org) and ThaleMine (apps.araport.org/thalemine/) require separate accounts. You may use the same credentials for each, but you will need to manually sign up for both services. This will be addressed in a future release of Araport

Issues Resolved Since Last Release:

  • None, as this is the first public Araport release.

We look forward to receiving your questions, comments, and suggestions at araport@jcvi.org

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