1. GONUTS Community annotation and usage guides for Gene Ontology TAMU GO Workshop 17 May 2010

2. 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

3. 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

4. "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

5. 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

6. 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

7. Create account http://gowiki.tamu.edu Login link on upper right User: XXXX Password: XXXX

8. Create account The Demo user can only create new accounts Get back to the login page to create your own account

9. Create account

10. 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"

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. MOD gene pages Search for a gene Example "SIR3"

19. 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

20. User-created gene pages Annotation pages based on UniProt IDs GONUTS creates a page automatically

21. 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).

22. Editing annotation tables Tables of GO annotations can be edited via our TableEdit interface Table structure tags the entries for data mining

23. 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

24. 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

25. 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

26. 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

27. 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

28. 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

29. 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

30. 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?

31. CACAO coupling 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

32. 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)

33. 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