Gene Ontology Consortium: Website & COmmunity

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Monica Munoz-Torres

A brief update for the GOC2016 meeting.

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GENE ONTOLOGY CONSORTIUM
WEBSITE & COMMUNITY
A BRIEF UPDATE
MONI MUNOZ-TORRES, SETH CARBON, PAUL THOMAS.
GOC2016 MEETING, GENEVA, SWITZERLAND | 16 APRIL 2016

GO HELP ROTATION TEAM FOR 2016
• David Osumi-Sutherland
• Donghui Li
• Edith Wong
• Harold Drabkin
• Kimberly Van Auken
• Helen Attrill *
• Melanie Courtot
• Moni Munoz-Torres
• Paola Roncaglia
• Petra Fey *
• Rachael Huntley *
• Rebecca Foulger *
• Tanya Berardini
• Victoria Petri *
• Rob Nash
* rotate twice a year. Everyone
else rotates four times a year.

THE GO HELP ROTATION TEAM: PRODUCTIVITY
Number of issues created vs. number of
issues resolved since September 2015.
215
167

THE GO HELP ROTATION TEAM: PRODUCTIVITY
Since September 2015 an average of 20 issues
have been created each month.
Of those, approx. 3 issues remain open each
month. That is, these still need further feedback
from user or helper in charge.
Tanya & Moni addressed stagnant issues older
than 12 months. Only 21 issues remain currently
open, the oldest one (July 2015) was last
updated ~3 weeks ago.

AFTER
Gone the way of the buggy whip:
• Photo carousel
• User Stories
• Highlighted GO term

UPDATED CONTRIBUTIONS PAGE
http://geneontology.org/page/contributing-go

STILL TO BE ADDED
• Suggested by some of you, most recently Ruth & Val:
• Teaching materials:
• training slides,
• videos,
• competitions

SUGGESTIONS WELCOME!
https://github.com/geneontology/go-site

FOR YOUR ATTENTION, THANK YOU.
Berkeley Bioinformatics Open
Source Projects - BBOP
• Suzanna Lewis – Principal Investigator
• Chris Mungall
• Seth Carbon
• Heiko Dietze
• Nathan Dunn
• Monica Munoz-Torres
• Jeremy Nguyen Xuan
FUNDING
• BBOP work for GOC is supported by NIH grant
5U41HG002273-14 from NHGRI.
• 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

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Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests. The i5k, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community. This presentation is an introduction to Apollo for the members of the i5K Pilot Project working on species of the order Calanoida (copepod).

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Scientific research is inherently a collaborative task; in our case it is a dialog among different researchers to reach a shared understanding of the underlying biology. To facilitate this dialog we have developed two web-based annotation tools: Apollo (http://genomearchitect.org/), a genomic feature editor, designed to support structural annotation of gene models, and Noctua (http://noctua.berkeleybop.org/), a biological-process model builder designed for describing the functional roles of gene products. Here we wish to outline an inventory of essential requirements that, in our experience, enable an annotation tool to meet the needs of both professional biocurators as well as other members of the research community. Here are the general requirements, beyond specific functional requirements, that any annotation tool must satisfy.

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Comparative genome analysis requires high quality annotations of all genomic elements. Today’s sequencing projects face numerous challenges including lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Precise elucidation of the many different biological features encoded in any genome requires careful examination and review. We need genome annotation editing tools to modify and refine the location and structure of the genome elements that predictive algorithms cannot yet resolve automatically. During the manual annotation process, curators identify elements that best represent the underlying biology and eliminate elements that reflect systemic errors of automated analyses. Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Researchers from nearly one hundred institutions worldwide are currently using Apollo for distributed curation efforts in over sixty genome projects across the tree of life: from plants to arthropods, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog.

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Gene Ontology Consortium: Website & COmmunity

1. GENE ONTOLOGY CONSORTIUM WEBSITE & COMMUNITY A BRIEF UPDATE MONI MUNOZ-TORRES, SETH CARBON, PAUL THOMAS. GOC2016 MEETING, GENEVA, SWITZERLAND | 16 APRIL 2016

2. GO HELP ROTATION TEAM FOR 2016 • David Osumi-Sutherland • Donghui Li • Edith Wong • Harold Drabkin • Kimberly Van Auken • Helen Attrill * • Melanie Courtot • Moni Munoz-Torres • Paola Roncaglia • Petra Fey * • Rachael Huntley * • Rebecca Foulger * • Tanya Berardini • Victoria Petri * • Rob Nash * rotate twice a year. Everyone else rotates four times a year.

3. THE GO HELP ROTATION TEAM: PRODUCTIVITY Number of issues created vs. number of issues resolved since September 2015. 215 167

4. THE GO HELP ROTATION TEAM: PRODUCTIVITY Since September 2015 an average of 20 issues have been created each month. Of those, approx. 3 issues remain open each month. That is, these still need further feedback from user or helper in charge. Tanya & Moni addressed stagnant issues older than 12 months. Only 21 issues remain currently open, the oldest one (July 2015) was last updated ~3 weeks ago.

5. Twitter @news4go #geneontology

6. FACEBOOK STATISTICS FOR GO

7. UPDATED HOME PAGE WWW.GeneOntology.ORG

8. BEFORE

9. AFTER Gone the way of the buggy whip: • Photo carousel • User Stories • Highlighted GO term

10. UPDATED CONTRIBUTIONS PAGE http://geneontology.org/page/contributing-go

11. PAGES: CONTRIBUTING TO GO BEFORE…

12. PAGES: CONTRIBUTING TO GO NOW...

13.

14.

15.

16. PAGES: CONTRIBUTING TO GO NOW...

17.

18. STILL TO BE ADDED • Suggested by some of you, most recently Ruth & Val: • Teaching materials: • training slides, • videos, • competitions

19.

20. SUGGESTIONS WELCOME! https://github.com/geneontology/go-site

21. FOR YOUR ATTENTION, THANK YOU. Berkeley Bioinformatics Open Source Projects - BBOP • Suzanna Lewis – Principal Investigator • Chris Mungall • Seth Carbon • Heiko Dietze • Nathan Dunn • Monica Munoz-Torres • Jeremy Nguyen Xuan FUNDING • BBOP work for GOC is supported by NIH grant 5U41HG002273-14 from NHGRI. • 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

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