GONUTS

Community annotation and usage guides for Gene Ontology

TAMU GO Workshop

17 May 2010

Why GONUTS?

• GONUTS = Gene Ontology Normal Usage Tracking System– Not an official GOC component– But we are used by the GOC for a variety of purposes

• GONUTS = Community wiki for– Recording usage notes at the level of GO terms– Curating to the GO annotation of gene products– Comparing annotations of sets of gene products

GO is only as useful as the quality and coverage of the annotations

• Traditional models of centralized curation don't scale well– Too many genomes

• Bee, beetle, paramecium, platypus, sea urchin, dog, cat, chicken, turkey, cow, grape, truffle, zebrafinch, Neandertal ...

– Rise of clade-oriented and metagenome databases

• Graminae, vertebrates, “Atlantic Ocean,” “thermal vent”, "human microbiome"

– Communities too small and fragmented to support classic MODs

• not enough money or expertise to support experiments and curators

• Need a mechanism to enlist expert communities to contribute to GO and GO annotation

"Wikifying" Genome Annotation

• The need for ongoing annotation and reannotation is accelerating

• Expertise is distributed across broad communities of scientists

• The need for ongoing annotation and reannotation is accelerating

• Expertise is distributed across broad communities of scientists

Plan for the demo

• Create accounts• Browsing GO with GONUTS

– Usage notes– Getting to and from Amigo/Sourceforge

• Gene pages– Viewing annotations from GOC MOD examples– Creating a gene page

• Annotation jamborees– Reference Genomes Project– CACAO - integrating GO annotation with undergraduate teaching

Accounts

• You don't need an account to browse GONUTS• You do need an account to

– edit GONUTS– create watchlists– track your contributions– customize your views

• Registered users can create new registered users– Unless they are student accounts

Create account

• http://gowiki.tamu.edu• Login link on upper right • User: XXXX• Password: XXXX

Create account

• The Demo user can only create new accounts

• Get back to the login page to create your own account

Create account

Create account

• Fill in your desired username• Fill in the password you want to use• Fill in your email• Fill in your real name• Click either "Create account" or "by email"

Plan for the demo

• Create accounts• Browsing GO with GONUTS

– Usage notes– Getting to and from Amigo/Sourceforge

• Gene pages– Viewing annotations from GOC MOD examples– Creating a gene page

• Annotation jamborees– Reference Genomes Project– CACAO - integrating GO annotation with undergraduate teaching

Search for a GO term

• Go tries to go directly to a matching page

• Search shows you all matching results

• G uses Google instead of the built-in mediawiki search

GONUTs has a page for every GO term

• Upper box: information from the GO ontology file– updated

weekly

• Usage notes: more extensive explanation from users

• References

GONUTs has a page for every GO term

• Child terms– expand and

collapse

• Genes annotated with this term– note that this

does not include genes annotated to child terms

Adding to Usage Notes

• What we want– When to use a term vs

alternatives– Assays used to assess

whether a term should be used

– Links to the literature about what the term describes

– etc.

• You can add uploaded figures

• Wiki philosophy: Let the user community decide what to add or delete

Usage notes are linked from AmiGO

• Others will use them!

• A web service from GONUTS counts how many times the page has been saved– excludes

robots

Plan for the demo

• Create accounts• Browsing GO with GONUTS

– Usage notes– Getting to and from Amigo/Sourceforge

• Gene pages– Viewing annotations from GOC MOD examples– Creating a gene page

• Annotation jamborees– Reference Genomes Project– CACAO - integrating GO annotation with undergraduate teaching

MOD gene pages

• Search for a gene

• Example "SIR3"

MOD gene pages

• Basic information

• Editable table with the GO annotations for that gene– Sort– Filter

• Helps us think of properties to check when annotating homologs

User-created gene pages

• Annotation pages based on UniProt IDs

• GONUTS creates a page automatically

User-created gene pages

• Annotation pages based on UniProt IDs

• GONUTS creates a page automatically

• We can also add pages for you– Example:

Chicken Reactome targets added for Carl Schmidt (Univ. of Delaware).

Editing annotation tables

• Tables of GO annotations can be edited via our TableEdit interface

• Table structure tags the entries for data mining

Plan for the demo

• Create accounts• Browsing GO with GONUTS

– Usage notes– Getting to and from Amigo/Sourceforge

• Gene pages– Viewing annotations from GOC MOD examples– Creating a gene page

• Annotation jamborees– Reference Genomes Project– CACAO - integrating GO annotation with undergraduate teaching

Reference genomes project

• Goals– Generate sets of high-quality literature-based annotations

for sets of orthologous genes from well-characterized organisms

• E. coli, yeast, Dictyostelium, C. elegans, Drosophila, Arabidopsis, Zebrafish, Rat, Mouse, Chicken, Human

– Support annotation transfer by orthology– Improve annotation consistency

• Monthly lists of ~30 ortholog sets are annotated by all groups

• Every few months, an "Electronic jamboree" held to focus on 2-3 ortholog sets

Annotation Jamborees in Cyberspace

• Groups of genes are marked with a category to put them in a group to compare

• Wiki tools mine the annotations on the individual pages and make summary tables and figures

Annotation Jamborees in Cyberspace

• Groups of genes are marked with a category to put them in a group to compare

• Wiki tools mine the annotations on the individual pages and make summary tables and figures

Annotation Jamborees in Cyberspace

• Each wiki page has an associated discussion page

• Embed a chat room to record discussion between remote locations

• Or coordinate with conference calls

Making your own Annotation Jamboree

• Not just for the RefGenome project

• Make a category tag and tag your genes of interest

• Create a jamboree page using our template

Making your own Annotation Jamboree

• Not just for the RefGenome project

• Make a category tag and tag your genes of interest

• Create a jamboree page using our template

• Example:– Complement comparison

page

Participation is still the major challenge

• People are busy• GO annotation is even more complicated than

entering information in EcoliWiki• What's in it for community members?

– Does improving the wiki help your own research enough?– Does it help with funding?– Does it help with promotion?

CACAOcoupling annotation to teaching credit

Community

Assessment of

Community

Annotation with

Ontologies

• Teams of students curate• Faculty supervision• Support from our team• Intramural or Intercollegiate competition• Distributed annotation jamborees• Assessment via surveys and wiki data-

mining

Important features of wikis/GONUTS

• Content evolves. It's a large-scale, long-term collaboration

• There is no overall gatekeeper• Every revision is saved• Every version has a permanent URL link• You can set pages to be watched• We welcome new uses• We're funded to help (ecoliwiki@gmail.com)

Acknowledgements

• EcoliWiki/GONUTS Team– Dave Clements– Gwen Knapp– Nathan Liles– Brenley McIntosh– Debby Siegele– Daniel Renfro– Amanda Supak– Anand Venkatraman– Adrienne Zweifel

• EcoliHub• GO consortium• Chris Elsik

• Funding NIGMS