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

Accomplishments

The AmiGO Ontology and Annotation Browser

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).

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.

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200 HTML files from the outdated site.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)