1. Modifying GO How changes are made to GO, and how you can be involved

2. Modifying GO: • Why we have to make changes to GO • How changes are made to GO • The GO editorial office • How you can make changes to GO • SourceForge • Interest groups • Content meetings

3. Why we have to make changes to GO • Why not just keep it the same?

4. Why we have to make changes to GO • Why not just keep it the same? • annotations would never need fixing

5. Why we have to make changes to GO • Why not just keep it the same? • annotations would never need fixing • wouldn’t need an editorial office

6. Why we have to make changes to GO • Because GO reflects current knowledge of biology

7. Why we have to make changes to GO • Because GO reflects current knowledge of biology • biology always changing

8. Why we have to make changes to GO • Because GO reflects current knowledge of biology • biology always changing • New organisms being added makes existing terms arrangements incorrect • we generally only add terms in response to annotation needs • if organism not being annotated, terms won’t be present in GO

9. Why we have to make changes to GO • Because GO reflects current knowledge of biology • biology always changing • New organisms being added makes existing terms arrangements incorrect • we generally only add terms in response to annotation needs • if organism not being annotated, terms won’t be present in GO • Not everything perfect from the outset

10. Growth of GO

11. Evolution of GO • Original GO • FlyBase (Drosophila) • MGI (Mouse) • SGD (S. cerevisae) • Later • TAIR (Arabadopsis) • TIGR (microbes including prokaryotes) • SWISS-PROT (several thousand species inc. human) • PSU (P. falciparum) • Recent additions • PAMGO (plant pathogens)

12. Example - parasites • Original GO:

13. Example - parasites • Annotation of P. falciparum • protozoan cellular parasite • intracellular infection (erythrocytes) • Parasite proteins located in host nucleus • What cellular component term to annotate to? • ‘nucleus’ refers to parasite nucleus when annotating parasite

14. Example - parasites • Added new term ‘host’:

15. Example - parasites parasite gene products located in parasite nucleus annotated here parasite gene products located in host nucleus annotated here

16. Improving GO • Some parts of GO need expanding/improving • In progress: • immunology • cell cycle • development • fungal toxin metabolism • Still to do: • transporters and transport • signal transducer/signalling pathways

17. Improving GO - example • Interactions between organisms • e.g. symbiosis, host/pathogen interaction, biofilm formation • Not well covered in GO • very few terms • some inconsistencies • PAMGO developed node last year

18. Improving GO - example

19. Editing GO • Logistics • file formats • DAG-Edit • cvs • Communication • monthly reports • diff emails • updating annotations • mailing lists

20. Editing GO - file formats • GO available in different formats: • OBO flat file (terms & definitions only) • GO flat file (terms & definitions only) • XML (terms & definitions only) • OWL (terms & definitions only) • MySQL (terms, definitions & annotations) • OBO flat file primary editing format for ontologies

21. GO file formats • Different formats different update times: • OBO flat file: every 30 minutes • GO flat file, XML, OWL: daily • MySQL: weekly without IEAs, monthly with IEAs • AmiGO runs from MySQL database so will not show new terms immediately • QuickGO updates weekly

22. Editing GO - DAG-Edit • Generic ontology editing tool developed by GO consortium • Java-based stand-alone tool • Used to do almost all ontology edits • demo • Downloading DAG-Edit: http://sourceforge.net/project/showfiles.php?group_id=36855 • DAG-Edit help: http://www.godatabase.org/dev/java/dagedit/docs/index.html

23. Editing GO example: adding new term • Suggestion of new term from annotator: • Check whether term exists under another name • search terms and synonyms • Determine if valid GO term • e.g. disease process, individual gene products not allowed • Decide on placement in ontology

24. Editing GO example: adding new term • Write definition if not provided • from biological dictionaries, experts, papers, online sources • some types of terms e.g. metabolism have standardised definitions, see: http://www.geneontology.org/GO.function.guidelines.shtml?all#defs http://www.geneontology.org/GO.process.guidelines.shtml • Add term with new id in DAG-Edit • Inform annotator of new term name and id

25. Editing GO - cvs • Amended ontology file committed to cvs (concurrent versions system) repository located at Stanford • cvs prevents changes being overwritten by other editors • Allows files to be reverted to former versions • log files detailing changes • Anonymous cvs available: http://www.geneontology.org/GO.downloads.shtml?all#cvs

26. Editing GO - monthly reports • Every month a full report released with all changes made to ontologies that month: http://www.geneontology.org/MonthlyReports/ • Generated with set of Perl scripts available on GO FTP site • Includes: • new terms • term name changes • new definitions • term movements • term obsoletions • SF items closed • overall statistics

27. Editing GO - diff files • Daily email with all changes made to file that day • Subscribe to go-diff mailing list: http://www.geneontology.org/GO.mailing.lists.shtml?all#godiff • Example diff:

28. Mailing lists • Several GO mailing lists: • GO (main) • discussion of ontology development • general queries/error reporting • high-traffic • GO-friends • mainly announcements • low-traffic • annotation • all annotation issues • GO-diff • GO-database • all database/techy issues

29. Mailing lists • All mailing lists archived: http://www.geneontology.org/GO.contents.archives.mail.shtml?all • Subscribe: http://www.geneontology.org/GO.mailing.lists.shtml • Interest group mailing lists

30. Editing GO - updating annotations • Annotations become out-of-sync with ontologies • term name changes • term obsoletions • term merges • Databases have individual strategies for flagging • 2 week notice given on obsoletions, provided no objections • Example email: http://www.geneontology.org/email-go/go-arc/go-2005/0012.html

31. The GO editorial office • Located at European Bioinformatics Institute, Cambridge UK • Four full-time editors of the ontologies: • Midori Harris • Jane Lomax • Amelia Ireland • Jennifer Clark

32. The GO editorial office • Primary responsibility to edit ontologies in response to community needs • Also: • website • documentation • outreach • GO in other systems • new annotation groups • training

33. Requesting changes to GO • Curator requests tracker • demo of how to add an item • types of changes • new terms • errors - tpvs • obsolete terms • Interest groups • Content meetings

34. Requesting changes to GO - curator requests tracker • Web-based tracking system hosted at SourceForge.net • Tracker item for each new request or question • Allows requests/suggestions/comments to be added by anyone • Daily digest of new tracker items goes to GO mailing list

35. Curator requests tracker

36. Requesting changes to GO - curator requests tracker • Common different types of changes suggested: • new term request https://sourceforge.net/tracker/index.php?func=detail&aid=1207105&group_id=36855&atid=440764 • reporting errors https://sourceforge.net/tracker/index.php?func=detail&aid=1206995&group_id=36855&atid=440764 • obsoletion/merge requests https://sourceforge.net/tracker/index.php?func=detail&aid=1200109&group_id=36855&atid=440764 • add synonym https://sourceforge.net/tracker/index.php?func=detail&aid=1202748&group_id=36855&atid=440764 • queries • term move

37. Requesting changes to GO - curator requests tracker • Obtaining a SourceForge account • demo: https://sourceforge.net/

38. Requesting changes to GO - curator requests tracker • Submitting a request • demo: https://sourceforge.net/tracker/?atid=440764&group_id=36855&func=browse

39. Requesting changes to GO - curator requests tracker • Things to bear in mind when submitting a request: • Have you given us enough information? • useful things to include are references to papers, name/id of gene being annotated, EC numbers • if you’re requesting an e.g. obsoletion or merge, have you put a reason? • Have you included a definition? • very useful where requests very organism-specific or if you’re an expert • source of definition, PubMed id, ISBN etc. • Are there any synonyms you would like included for a new term? What type? • synonym types are exact, broader and narrower • Have you suggested parentage for a new term?

40. Tracker volume • average 65.9 new items/month

41. Tracker volume • 24.5 days to complete on average

42. Other trackers • Listed at: http://www.geneontology.org/GO.sourceforge.links.shtml?all#track • annotation • website • integrity checks • big ideas

43. Content meetings • Short meetings aimed at developing specific areas of GO ontology content • proposals defined and discussed before meeting • small number of people • invited experts • specific topics

44. Next content meeting - November? • Possible topics for discussion: • immunology • transport/transporters • cell cycle • signal transduction/signal transducer activity • response to/defense terms

45. Interest groups • Groups of experts for a specific topic • e.g. development, cell cycle, plants • Includes GO curators/annotators and external experts • Communicate by mailing lists and at meetings

46. Interest groups • We actively encourage annotators to join interest groups for their field • Complete list of groups: http://www.geneontology.org/GO.interests.shtml?all

47. GO documentation • Much documentation: http://www.geneontology.org/GO.contents.doc.shtml

48. Acknowledgements: The GO Consortium