Software Group progress report for 2009

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Progress report for the software group, 2009


  • Released OBO-Edit 2.0
  • Improvements in the following components:
    • Cross Product Editor
    • Assert Implied Links Panel (used frequently as part of regulates work)
    • Remove Redundant Links Panel
    • Parent Editor
    • Graph Editor -- Improved editing and display features
  • Hands on-training for working with Cross-products in OBO-Edit
    • Finding xp terms, searching, recognizing, constructing and manipulating xps
  • Reasoner improvements
    • Rewrote reasoner to handle relation chain axioms for regulates
    • Ability to perform incremental reasoning and step-wise reasoning on large ontologies.
  • Saving
    • added save-isa-closure option (required for Cross-Products
    • Ability to save filtered OBO files based on user defined constraints.
  • November 2009: Working on version 2.1beta2 and plan to implement a two week release cycle December 2009 onwards.

List of Bug fixes: Tracker on sourceforge:


  • AmiGO_1_6 released.
    • Community annotation / GONUTs integration
    • RefG support
    • various misc.
  • AmiGO_1_7 released.
    • uses Google analytics
    • IEA support
    • new graphics backend, integrated with term enrichment
    • various new requested features, bug fixes
    • OpenSearch plugins
  • AmiGO_1_8 - in beta, many prototype components are in use
    • Matrix queries
    • Lucene-based search


  • Starting to replace old infrastructure with new (graphing)
  • More work on:
    • core perl API
    • JSAPI


  • prototyped web-based implementation of PAINT viewer



  • Answered queries on go-help
  • Provided custom SQL queries for GOC members for use in GOOSE
  • Extensive reasoner / scripting support for regulates work. 1000s of broken links fixed
  • Maintenance of news site

Software/Ontology cross-over

  • Ongoing work on cross-products
    • Cross-products paper published as ICBO proceedings and submitted as full article to JBI
    • Writing custom scripts to detect GO/CHEBI inconsistencies
    • Cross-product work used in 2 papers from Hunter Lab:
  • Ongoing work on improving Reactome-GO integration
    • Using XPs to partially automate assigning GO-Reactome xrefs


  • IEAs from main organisms now loaded into AmiGO database