Outreach & Dissemination Progress Report December 2015

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Outreach and Usability:



AmiGO: the GOC’s tool for querying, browsing, and visualizing the GO database, continues to be updated regularly with many improvements and increased documentation. This year’s upgrades continued to expand on the variety of search modes, graph traversals (and visualization), as well as availability of data types. Over 80 tickets have been closed, such as improved filtering, bringing experimental results for human genes to the top of the results lists for gene products, and loading of PANTHER family data. Largely, all these feature refinements were accomplished without disruption to services (hot swap). Access to the GO enrichment tool has likewise been greatly improved.

Public servers of GO

Considerable work has been carried out in preparation for the transition of all GO services to Berkeley, including an increased number of unit tests and improved status reporting. For example, load balancing was improved so that users never experience discontinuity during sessions that coincide with regular reloading is occurring (which takes ~one hour).

GOC website

Throughout this year we have continued to improve the documentation on our website, refining content for both clarity and brevity. Before these focused efforts, some areas of our documentation were lacking important details, and others contained related information dispersed throughout two or more pages; these made some pages at times complementary, but more often redundant. Going through sections and updating the information, we have achieved documentation pages that both offer complete and more concise information, as well as aggregate previously dispersed details. This facilitates ease of finding and usability. For example, researchers willing to contribute to the Gene Ontology Consortium (GOC), by either providing suggestions for updating the ontology or by providing annotations, can do so when they review the options we offer on our pages about “Contributing to GO” (http://geneontology.org/page/contributing-go) and “Submitting GO Annotations” (http://geneontology.org/page/submitting-go-annotations).


FAQ: A total of 83 frequently asked questions (FAQs) are now available on the GO website, covering a variety of topics from annotation, to analysis, to mappings. Special emphasis was also given to improving documentation on how to conduct term enrichment analyses using tools supported by the GOC as well as third-party tools, and documentation on how to submit annotations and contribute to the ontology.

GO Help Desk

In 2015, members of the GO Help Desk team responded to 298 requests for information and help while resolving and closing 317 tickets (between 2015-01-01 and 2015-11-16).

User Survey

We devised and implemented a GO user survey to query our users about their needs and collect their feedback, so we can implement better solutions. To this aim, we consulted with User Experience specialists at one of the partner institutions and collated feedback from several rounds of internal testing. We sent out the survey to a broad but targeted array of mailing lists (for a total of 11 different survey collectors), and received ~600 responses.

First GO Symposium Day

In August 2015, as part of the annual meeting of the Gene Ontology Consortium in Washington, DC, we organized a day of talks and discussions centered around the GO. The GO Symposium day was open to the general public, and attendees included researchers, faculty, and students from local institutions as well as NIH senior personnel. The sessions included two talks and two workshops. The talks were offered by our guest speakers [Dr. Dona Slonim] and Dr. Trey Ideker. The workshop on Annotation included details on the use and implementation of GOC standards and tools. Lastly, the second workshop was focused on Term Enrichment Analysis using the resources of the GOC. Further details regarding the symposium are available from the agenda website].

Plans for coming year

  • Release AmiGO 2.4
  • Develop additional improvements to Term Enrichment
  • Continue to improve website usability
  • Continue to provide user support
  • Continue to improve the AmiGO interface
  • Continue to support online web services