Release 4.0

Major changes to layout and content of summary pages. These pages can now display the results of template queries inline to give immediate access to data. The http://www.flymine.org home page now shows aspect icons and query options. Many other interface improvements. Addition of Arbeitman et al, 2002 Drosophila time course microarray data and human disease gene matches from Homophila.

  • Data
    • NEW: microarray data from “Gene Expression During the Life Cycle of Drosophila melanogaster“, Arbeitman et al 2002.
    • NEW: added data human disease gene matches from Homophila (http://superfly.ucsd.edu/homophila/).
    • NEW: more protein interaction experiments from IntAct – see Protein Interaction aspect.
    • NEW: Gene now has an “allGoAnnotation” collection that contains the term assigned to a gene plus all the parents of the term. Using this collection to find genes with a particular term will find all genes with that term *and* any with a more specific term.
    • ENHANCEMENT: MRNA now references threePrimeUTR and fivePrimeUTR.
    • ENHANCEMENT: D. melanogaster translation symbols now set from FlyBase.
    • ENHANCEMENT: D. melanogaster chromosome bands now loaded from FlyBase.
    • UPDATE: D. melanogaster genome annotation updated from 4.2 to 4.2.1.
    • UPDATE: GO annotation and UniProt proteins updated.
    • FIX: D. melanogaster regulatory regions from FlyBase now have chromosome location.
    • FIX: D. melanogaster insertion sites and point mutations from FlyBase reference genes correctly.
    • FIX: A. gambiae genes from Ensembl and InParanoid orthologues now merged correctly.
  • Tools
    • NEW: a graph of interacting proteins on protein summary pages.
    • NEW: graphs of D. melanogaster time course expression on gene details pages (Arbeitman et al, 2002).
    • NEW: FASTA retrieval icon to access sequence of all features with sequence.
    • FIX: insertion sites now displayed correctly on GBrowse.
  • User Interface
    • NEW: Template queries are now viewable inline on object summary pages.
    • NEW: bags saved in history can now be subtracted from one another.
    • NEW: Query constraint logic can now be manipulated within the query builder – can constrain A AND B/A OR B.
    • NEW: Added Run query link to run a query directly from the History page.
    • NEW: Template queries can now include a choice of several different output formats.
    • ENHANCEMENT: Template search terms are highlighted in results lists.
    • ENHANCEMENT: Template building integrated into query builder interface.
  • Known issues
    • DATA: Protein interactions from Formstecher et al, 2005 (PubMed: 15710747) are incorrectly assigned to Rain et al, 2001 (PubMed: 11196647) which in IntAct is a secondary reference.
    • DATA: OMIM disease names contain the same text repeated multiple times.
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