This is a tutorial for the sol genomics network (sgn; http://sgn.cornell.edu/) community annotation database. It guides users step-by-step how to access the locus and phenotype database, search for genes and phenotypes, and annotate online using a simple, shared, web interface.

1. SGN community Annotation Tutorial

7. 3.1 Search for the locus. You can get editor privileges for any locus in the database.

8. 3.1 Search for the locus. You can get editor privileges for any locus in the database.

9. 3.1 Search for the locus. You can get editor privileges for any locus in the database.

10. 3.1 Search for the locus. You can Submit a new locus if you cannot find your gene in the database. You need an SGN submitter account for submitting new loci. If you do not have such account, contact SGN at [email_address] and we will grant you these privileges

11. 3.2 Edit the locus details – you must login and become the locus editor!

12. 3.2 Edit the locus details – click on 'log in' and type your SGN username and password No SGN account? Sign up for one.

13. Create an SGN account. You will receive a confirmation email shortly after. Now you can go back to the locus page.

14. 3.2 Edit the locus details – you must login and become the locus editor! Click here to request editing privileges

15. 3.2 Edit the locus details – when you are logged-in the 'edit' links will become active.

16. 3.2 Edit the locus details – Click 'edit' and a web-form will open. Store the details instantly in the database.

17. No! Only editors can edit the locus detail, but anyone can annotate any locus with publications, sequences, phenotypes, and more! A submitter account is required. contact [email_address] and we will grant you submit-privileges. You can contribute to the following locus features without being the official 'locus editor' : 4. Do I have to be a locus editor?

18. 4. This is how the locus page looks like when a submitter who is not the editor is logged-in. Notice the highlighted links

19. 4.1 Submit synonyms

20. 4.2 Upload figures

21. 4.2 Upload figures. Image files and PDFs are supported. You are the copyright owner, and can edit/delete your file.

22. 4.3 Associate accessions from the phenotype database with the locus. You may want to add a phenotype first (see 'submit phenotypes' section)

23. 4.4 Create gene networks by associating other loci and specifying relationship type

24. 4.5 Add new alleles and edit existing allele information

25. 4.5 Add new alleles and edit existing allele information. Each allele has an information page.

26. 4.6 SolCyc is a database of biochemical pathways ( http://solcyc.sgn.cornell.edu ) . Add a unigene to your locus, and the related SolCyc reaction will be imported (this feature is updated periodically by SGN staff)

27. 4.7 Associate an SGN-Unigene. A link back to the locus page will show on the unigene page ( http://sgn.cornell.edu/search/direct_search.pl?search=unigene )

28. 4.8 Associate GenBank accessions

29. 4.8 Associate GenBank accessions

30. 4.8 Associate GenBank accessions

31. 4.9 Add literature references

32. 4.9 Add literature references- from PubMed

33. 4.9 Add literature references- from PubMed

34. 4.9 Add literature references not in PubMed

35. 4.9 Add literature references not in PubMed

36. 4.9 Add literature references – from automated text indexing

37. 4.9 Add literature references – from automated text indexing. This list is generated daily from the SGN publication database

38. 4.10 Add ontology annotations

39. 4.10 Ontologies are structured controlled vocabulary terms ( http://www.obofoundry.org/ )

40. You might also want to browse some of the ontologies SGN uses for annotating different datatypes (loci, phenotypes, QTLs, Unigenes)

41. Search ontology terms using SGN's ontology browser Search Select a term from the search results View the term in the ontology tree. Click it to see the detail page

42. Ontology term page shows its details and all annotations (including objects annotated with any child terms)

43. 4.11 Back to locus community annotation. You may add comments. No special 'submitter' privileges required. Create an SGN account, and start posting comments.

44. 4.11 Add page comments

46. 5.1 Search the phenotype database

47. 5.2 If you uploaded this accession, you can edit the phenotype page.

48. 5.2 Submit a new accession.

49. 5.2 You can contribute to any phenotyped accession after logging-in with your submitter account. Link to loci Literature annotation Ontology annotation Add comments

51. SGN is funded by SGN is located at the Boyce Thompson Institute for Plant Research Please cite SGN using Mueller et al (2005). The SOL Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond. Plant Physiology 138:1310-1317. More SGN publications http://sgn.cornell.edu/help/publications.pl