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 host nucleus annotated here parasite gene products located in parasite 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=4 40764  reporting errors https://sourceforge.net/tracker/index.php?func=detail&aid=1206995&group_id=36855&atid=4 40764  obsoletion/merge requests https://sourceforge.net/tracker/index.php?func=detail&aid=1200109&group_id=36855&atid=4 40764  add synonym https://sourceforge.net/tracker/index.php?func=detail&aid=1202748&group_id=36855&atid=4 40764  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