SGN community Annotation Tutorial

1. SGN community Annotation Tutorial

2. SGN community annotation tutorial <ul><ul><ul><ul><li>What is community annotation? </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Why should I submit data to SGN? </li></ul></ul></ul></ul><ul><ul><ul><ul><li>How do I annotate my favourite gene? </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Do I have to be a locus editor? </li></ul></ul></ul></ul><ul><ul><ul><ul><li>How do I submit phenotypes to SGN? </li></ul></ul></ul></ul><ul><ul><ul><ul><li>More tools and feedback. </li></ul></ul></ul></ul>

3. <ul><ul><li>The concept of community annotation is a growing discipline for achieving participation of the research community in depositing up-to-date knowledge in biological databases . </li></ul></ul><ul><ul><li>We are amid a revolution in how people use computers to share data on the Web, as evidenced by the recent success of social networking sites that have made sharing user-generated content popular. </li></ul></ul>1. What is community annotation?

4. <ul><ul><li>One of the major efforts at SGN is linking Solanaceae phenotype information with the underlying genes, and subsequently the genome. </li></ul></ul><ul><ul><li>As part of this goal, SGN has introduced a database for locus names and descriptors, and phenotypes of natural and induced variation. </li></ul></ul><ul><ul><li>SGN is the first among the major plant databases to put the control of the information directly in the hands of community experts . As a result, SGN annotations are more up to date and richer with detailed descriptions, images, and several levels of gene-to-phenotype cross-links, than would otherwise be possible without a large curatorial staff. </li></ul></ul>1. What is community annotation?

5. <ul><ul><li>SGN is the bioinformatics hub for Solanaceae genomics and genetics. </li></ul></ul><ul><ul><li>Gives you control over the way your favorite genes are named, described, and annotated. </li></ul></ul><ul><ul><li>Easy, quick way for submitting updates on your work and sharing with the research community. </li></ul></ul><ul><ul><li>All contributions are accredited and acknowledged on the relevant web page. We also promote featured locus and publication on the SGN homepage, usually of community-annotated genes. </li></ul></ul>2. Why should I submit data to SGN?

6. <ul><ul><li>Search the locus database </li></ul></ul><ul><ul><li>Login with your 'submitter' account (or contact SGN) </li></ul></ul><ul><ul><li>Edit your favorite gene online, or submit a new locus </li></ul></ul><ul><ul><li>Submit annotations: </li></ul></ul><ul><ul><ul><li>synonyms, images, phenotypes, gene networks, sequences, publications, ontology terms, and comments. </li></ul></ul></ul>The process in a nutshell 3. How do I annotate my favourite gene?

7. 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

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

45. <ul><ul><li>Search the phenotype database. </li></ul></ul><ul><ul><li>Login with your 'submitter' account (or contact SGN). </li></ul></ul><ul><ul><li>Edit your phenotyped 'accession' online, or submit a new one. </li></ul></ul><ul><ul><li>Submit annotations: </li></ul></ul><ul><ul><ul><li>Link loci, publications, ontology terms, and comments. </li></ul></ul></ul><ul><ul><ul><li>More: large populations, QTLs measurements and map locations can be batch-submitted. See http://sgn.cornell.edu/content/phenotype_submissions.pl </li></ul></ul></ul>It works just like the locus database 5. How do I submit phenotypes to SGN?

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

50. <ul><ul><li>Check out SGN's QTL Analyzer tool http://sgn.cornell.edu/search/direct_search.pl?search=cvterm_name </li></ul></ul><ul><ul><li>For submissions of large datasets, such as phenotyping experiments, QTLs, images, gene identifiers, etc. please contact us by email [email_address] </li></ul></ul><ul><ul><li>SGN software, code, and data are completely free to use and download! ftp://ftp.sgn.cornell.edu </li></ul></ul><ul><ul><li>Most SGN components can be downloaded as a virtual machine and adapted for other clades. </li></ul></ul>6. More tools and feedback

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

SGN community Annotation Tutorial

Naama Menda

SGN community Annotation Tutorial