The New Website of the Gene Ontology Consortium

Seth Carbon Chris Mungall, PhD | @chrismungallMonica Munoz-Torres, PhD | @monimunoztoGenomics Division, Lawrence Berkeley National Laboratory16 March, 2014

UNIVERSITY OF CALIFORNIA

Outline1. The New GOC Website

• Numbers, Organization, and Flow.

2. What’s new?• Menus• User Stories• Tags• Outreach Tools

3. Report from Outreach & Multimedia Breakout Group

The New Website of the Gene Ontology Consortium

Outline 2

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 EditorsIncluding 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

5

1.

3.

5.

2.

4.

1. Numbers, Organization, and Flow.

Organization and Flow.

6. Documentation

7. Downloads

8. User Stories

9. Community

10. Tools

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6.

7.8.

9.

10.

1. 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):e1000431.

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 Desk

@News4GO#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?

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• 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

TagsAssist 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.

103. 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. HG002273 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-AC02-05CH11231.

• Images used with permission. NPG Lic. No. 3346711104169.

• 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 http://beta.GeneOntology.org