The New Website of the Gene Ontology Consortium Seth Carbon Chris Mungall, PhD Monica Munoz-Torres, PhD Genomics Division, Lawrence Berkeley National Laboratory 16 March, 2014 UNIVERSITY OF CALIFORNIA

Outline 1.The New GOC Website Numbers, Organization, and Flow. 2. What’s new? Menus User Stories Tags Outreach Tools 1.Report from Outreach & Multimedia Breakout Group The New Website of the Gene Ontology Consortium Outline2

GOC Website 1. Numbers, Organization, and Flow.3 Reorganized Consistent Up to date New licensing (CC-BY 4.0) and usage Interactive and dynamic Search and enrichment Statistics Remote content Enforced workflows Easy to maintain/update Push content Project pages Highlighted terms This is your site!

GO Website in Numbers 1. Numbers, Organization, and Flow.4 Starting material >200 HTML files >250 image files 10 Editors Including David OS, Jane, Kimberly, Paola, Rama, Ruth, and Tanya. 143 Pages Information Articles, News External Projects Highlighted Terms

Organization and Flow. 1.Tools 2.Information 3.Articles, News 4.External Projects 5.Highlighted Terms Numbers, Organization, and Flow.

Organization and Flow. 6.Documentation 7.Downloads 8.User Stories 9.Community 10.Tools Numbers, Organization, and Flow.

Community 1. Organization and Flow.7 The Reference Genome Annotation Project: AmiGO displays Comparison Graph for genes present in homolosets. PLoS Comput. Biol.. Jul 2009;5(7):e Wiki The work of the GOC is only possible thanks to collaborations among members of a very active research community. GO Projects Related Projects GO Forums GO Wiki Web Feeds Help #GeneOntology

What’s New? User Stories Represent a way of looking at the information that the Gene Ontology offers. Everybody Biocurator Bioinformatician Domain Specialist Software Developer Industry 82. What’s New?

What Else Is New? 9 Analysis Evidence Formats Guide Navigation Ontology Software Announcement Event (Conference, Course/workshop, Meeting) Feature (gene of the quarter, term of the month, publication, tip, tutorial) Report Software Jobs Warning Tags Assist in organizing and finding content. Change with content type. 2. What’s New? Information Page Article

Outreach & Multimedia Breakout To explain features in our websites and cover case studies, in videos that differentially address general and specialized scientific audiences. Example questions: - What is a GO annotation and who makes a GO annotation? - How to use AmiGO 2. - Mechanics of Term Enrichment. - What the GO can offer, the types of available data, and how to access them. - What are Evidence Codes and how are they used? - Filtering with GO slims Outreach & Multimedia

More from Seth and Chris. New Documentation Pages, Exports of GO, and Retiring GO. (Mike, Seth, Chris) Tool Registry and Enrichment Analysis. (Chris) How to find tools How to register tools Term Enrichment More from Seth and Chris.11

Acknowledgments Berkeley Bioinformatics Open-source Projects (BBOP), Lawrence Berkeley National Laboratory. Suzanna Lewis (PI). The Gene Ontology Consortium is supported by the U41 grant No. HG from NHGRI (NIH). BBOP is also supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH Images used with permission. NPG Lic. No For your attention, thank you! Acknowledgments.12 The Gene Ontology Team Seth Carbon Heiko Dietze Suzi Lewis Chris Mungall Moni Munoz-Torres BBOP Test drive the new GO Website at