Outreach & Dissemination Progress Report December 2014

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We will provide annotations and ontologies to the broad genetics community, supporting the use of the Gene Ontology resources.


The AmiGO Ontology and Annotation Browser

AmiGO 1.x

  • We provided continued support and maintenance of AmiGO 1.x legacy code to cover any use cases not yet covered by AmiGO 2 for our large user base;
  • We provided continuing support for the legacy databases, including exploration of simplifying the pipeline using modern software (OWLTools).

AmiGO 2.x

  • We successfully released AmiGO 2, with an accelerated ‘GOlr’ backend based on Solr/Lucene technology:
  • GOlr’s new fast text and facet searching makes it possible for users to interactively search the data and filter away unwanted results;
  • The initial production release was thoroughly tested for stability and improved the performance over AmiGO 1, by orders of magnitude in some cases;
  • Berkeley coordinated testing and phased rollout of the new AmiGO 2 stack, with its simplified and refactored codebase, and oversaw its deployment with the production team at Stanford;
  • AmiGO 2 has been continuously enhanced with new user-requested features and enhancements since its initial release (AmiGO 2.1), as well as fixing problems encountered by users;
  • Since the initial production release we have continued to increase the number and detail of fields and personalities offered to users;
  • We now have in development numerous pre-beta tools, with both novel and user requested functionality.

GO Web Site

  • Carried out design, implementation, and deployment of a new and improved website for the Gene Ontology Consortium. The new design involved:
    1. Ensuring that all content is up-to-date (and can easily be maintained that way),
    2. Ensuring that terms of licensing and usage are upgraded and visible;
    3. Making the site more dynamic and interactive;
    4. Encouraging participation from the research community while enforcing workflows to most effectively capture their input;
    5. Adding many new features - new layout, skin, and dynamic content;
    6. Added a dynamic protein family tree viewer for display of PAINT annotations as a part of the upcoming release to public website (scheduled for 2nd quarter 2015)
  • Carried out a major push to migration of content from legacy site, including:
    1. Reorganization of content in a hierarchical manner to make it consistent throughout the site,
    2. Staging and testing of pages as content was transferred. We edited and pushed content for approx. 80% of >200 HTML files from the outdated site.
    3. Training and creating editing documentation for eight additional editors who worked on the remaining ~20% of the pages, and coordinated and revised their contributions. The current version of the website contains approximately 150 pages of updated and reorganized information.
  • The new website was successfully deployed to production in June, 2014.
  • Members of the software group are active “gatekeepers” and coordinators of content for the GOC website.


  • Supported GO aims through special software and data requests by consortium
  • OWLTools: incremental improvements to loading software to add functionality for automatically loading the full NCBI Taxonomy ontology and all GOA IEA annotations. (AmiGO 2)


  • Wrote biannual NAR paper about the GO [authored by Munoz-Torres and Drabkin 2014]
  • Are taking the initiative to plan and implement an education portal for the GOC (work in progress).
  • GO Helpdesk
    • Continuously supporting the GO user community responding to inquiries received via the GO Helpdesk (http://geneontology.org/form/contact-go)
    • Staff: Rama Balakrishnan, Rachael Huntley, Monica Muñoz-Torres, Harold Drabkin, Jane Lomax, Kimberly Van Auken, Tanya Berardini, Rebecca Foulger, Prudence Mutowo-Meullenet, Poala Roncaglia, David Osumi-Sutherland. We have also recruited 4 new curators to join the GO-help rotation.
  • FAQ was published on the GOC website to point users to some of the common questions about GO.


  • The Gene Ontology Consortium. 2014. Gene Ontology Consortium: Going Forward. Nucleic Acids Res., In Press (doi: 10.1093/nar/gku1179)