Annotation Outreach Working Group Who are we and What do we do?

1. Annotation Outreach Working Group Who are we and What do we do?

2. The Group: Jennifer Clark, Evelyn Camon, Karen Christie, Alex Diehl, Pascale Gaudet, Michelle Gwinn Giglio, Ranjana Kishore, Harold Drabkin.

3. We exist to solve this problem:

4. These groups already annotate:

5. Many more do not:

6. Biologists like these would like to annotate. But the learning curve is steep.

7. Dear Professor Newham, …may I ask if you have considered Gene Ontology annotation… Dear Professor Hurst, …may I ask if you have considered Gene Ontology annotation… Dear Professor Logan, …may I ask if you have considered Gene Ontology annotation… Dear Professor Setz, …may I ask if you have considered Gene Ontology annotation… Dear Dr Zoidberg, …may I ask if you have considered Gene Ontology annotation… Dear Professor Brand, …may I ask if you have considered Gene Ontology annotation… Dear Professor Smith, …may I ask if you have considered Gene Ontology annotation… Dear Professor Jones, …may I ask if you have considered Gene Ontology annotation… Dear Professor Campbell, …may I ask if you have considered Gene Ontology annotation… Dear Professor Kurt, …may I ask if you have considered Gene Ontology annotation… What are we doing about it?

8. Better documentation and tools. • Feedback on how systems can be more user friendly

9. 2006 GO Annotation Camp

10. Outreach at meetings…

11. Keeping track of progress to minimize duplication of effort…

13. PAMGO • PAMGO is funded and up and running • Initial term set (Jan. 2005) • >500 more terms from a jamboree held at TIGR this past summer • Annotation will proceed at full speed when final details on new terms are worked out

14. PAMGO term jamboree at TIGR, July 2006 Left to right: Bryan Biehl, Trudy Torto-Alalibo Michelle Gwinn Giglio Candace Collmer Jane Lomax Marcus Chibucos Amelia Ireland and of course, TIGR’s tiger

15. Training workshops • TIGR hosts regularly scheduled prokaryotic annotation courses 4 times per year since 2002 • GO is a very significant part of that course • ~150 scientists trained in the last 2 years alone • eukaryotic course is set to begin March, 2007 • Ask me for brochures if you are interested

16. Follow-Up • Need to see how many of these folks are actually annotating with GO now • surveys • check publications • Haven’t done that yet…..

17. Additional activities • Workshop and booth at PAG • PAMGO/AgBase sessions during GO workshop • PAG booth • Meeting with Jim Hu • Not quite a traditional MOD • they may use TIGR’s infrastructure

18. Ready-to-go annotation systems greatly facilitate the process • Annotation Engine • TIGR’s service that provides automatic annotation, Manatee, and database infrastructure to anyone with a prokaryotic genome • Manatee • free, open source • makes GO annotation easier • GO plans for tools?

19. The Manatee Gene Curatation Page

20. GO terms and evidence Auto Fill-ins Follow the arrows to see which fields are filled in by clicking the various GO “evidence” and “add” buttons around the GCP (only appears when there are TMHMM hits for a protein,this pull-down will be to the right of the other term pull-downs for process, component, and function)

21. A sampling of the GO Search tools built into Manatee

22. The 1st Eurofungbase Annotation Jamboree on Aspergillus nidulans (Run by Jennifer Wortman of TIGR, and the staff of Eurofungbase.) Ingredients for a successful annotation jamboree...

23. One Framework 7 Collective Action Grant

24. One wiki:

26. One genome: 45 willing biologists

27. One computer room.

28. Good Preparation… 500 new manual Annotations in two days.

29. The Annotation Outreach Working Group Jennifer Clark, Evelyn Camon, Karen Christie, Alex Diehl, Pascale Gaudet, Michelle Gwinn Giglio, Ranjana Kishore, Harold Drabkin.