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Modifying GO

Modifying GO. How changes are made to GO, and how you can be involved. 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. Why we have to make changes to GO.

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Modifying GO

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  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

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