SGN community Annotation Tutorial
SGN community annotation tutorial <ul><ul><ul><ul><li>What is community annotation? </li></ul></ul></ul></ul><ul><ul><ul><...
<ul><ul><li>The concept of  community annotation  is a growing discipline for achieving participation of the research comm...
<ul><ul><li>One of the major efforts at SGN is linking Solanaceae phenotype information with the underlying genes, and sub...
<ul><ul><li>SGN is the bioinformatics hub for Solanaceae genomics and genetics.  </li></ul></ul><ul><ul><li>Gives  you  co...
<ul><ul><li>Search the locus database </li></ul></ul><ul><ul><li>Login with your 'submitter' account (or contact SGN)  </l...
3.1 Search for the locus.  You can get editor privileges for any locus in the database.
3.1 Search for the locus.  You can get editor privileges for any locus in the database.
3.1 Search for the locus.  You can get editor privileges for any locus in the database.
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 submi...
3.2 Edit the locus details – you must login and become the locus editor!
3.2 Edit the locus details – click on 'log in' and type your SGN username and password No SGN account? Sign up for one.
Create an SGN account. You will receive a confirmation email shortly after. Now you can go back to the locus page.
3.2 Edit the locus details – you must login and become the locus editor! Click here to request editing privileges
3.2 Edit the locus details – when you are logged-in the 'edit' links will become active.
3.2 Edit the locus details – Click 'edit' and a web-form will open. Store the details instantly in the database.
No! Only editors can edit the locus detail, but  anyone  can annotate any locus with publications, sequences, phenotypes, ...
4. This is how the locus page looks like when a submitter who is not the editor is logged-in. Notice the  highlighted links
4.1 Submit synonyms
4.2 Upload figures
4.2 Upload figures. Image files and PDFs are supported. You are the copyright owner, and can edit/delete your file.
4.3 Associate accessions from the phenotype database with the locus. You may want to add a phenotype first (see 'submit ph...
4.4 Create gene networks by associating other loci and specifying relationship type
4.5 Add new alleles and edit existing allele information
4.5 Add new alleles and edit existing allele information. Each allele has an information page.
4.6  SolCyc is a database of biochemical pathways ( http://solcyc.sgn.cornell.edu ) .  Add a unigene to your locus, and th...
4.7 Associate an SGN-Unigene. A link back to the locus page will show on the unigene page ( http://sgn.cornell.edu/search/...
4.8 Associate GenBank accessions
4.8 Associate GenBank accessions
4.8 Associate GenBank accessions
4.9 Add literature references
4.9 Add literature references- from PubMed
4.9 Add literature references- from PubMed
4.9 Add literature references not in PubMed
4.9 Add literature references not in PubMed
4.9 Add literature references – from automated text indexing
4.9 Add literature references – from automated text indexing. This list is generated daily from the SGN publication database
4.10 Add ontology annotations
4.10 Ontologies are structured controlled vocabulary terms ( http://www.obofoundry.org/ )
You might also want to browse some of the ontologies SGN uses for annotating different datatypes (loci, phenotypes, QTLs, ...
Search ontology terms using SGN's ontology browser Search Select a term from the search results View the term in the ontol...
Ontology term page shows its details and all annotations (including objects annotated with any child terms)
4.11 Back to locus community annotation. You may add comments.  No special 'submitter' privileges required. Create an SGN ...
4.11 Add page comments
<ul><ul><li>Search the phenotype database. </li></ul></ul><ul><ul><li>Login with your 'submitter' account (or contact SGN)...
5.1 Search the  phenotype database
5.2  If you uploaded this accession, you can edit the phenotype page.
5.2  Submit a new accession.
5.2  You can contribute to any phenotyped accession after logging-in with your submitter account. Link to loci Literature ...
<ul><ul><li>Check out SGN's  QTL Analyzer  tool   http://sgn.cornell.edu/search/direct_search.pl?search=cvterm_name   </li...
SGN is funded by SGN is located at the Boyce Thompson Institute for Plant Research Please cite SGN using Mueller et al (20...
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SGN community Annotation Tutorial

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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.

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SGN community Annotation Tutorial

  1. 1. SGN community Annotation Tutorial
  2. 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. 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. 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. 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. 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. 7. 3.1 Search for the locus. You can get editor privileges for any locus in the database.
  8. 8. 3.1 Search for the locus. You can get editor privileges for any locus in the database.
  9. 9. 3.1 Search for the locus. You can get editor privileges for any locus in the database.
  10. 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. 11. 3.2 Edit the locus details – you must login and become the locus editor!
  12. 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. 13. Create an SGN account. You will receive a confirmation email shortly after. Now you can go back to the locus page.
  14. 14. 3.2 Edit the locus details – you must login and become the locus editor! Click here to request editing privileges
  15. 15. 3.2 Edit the locus details – when you are logged-in the 'edit' links will become active.
  16. 16. 3.2 Edit the locus details – Click 'edit' and a web-form will open. Store the details instantly in the database.
  17. 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. 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. 19. 4.1 Submit synonyms
  20. 20. 4.2 Upload figures
  21. 21. 4.2 Upload figures. Image files and PDFs are supported. You are the copyright owner, and can edit/delete your file.
  22. 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. 23. 4.4 Create gene networks by associating other loci and specifying relationship type
  24. 24. 4.5 Add new alleles and edit existing allele information
  25. 25. 4.5 Add new alleles and edit existing allele information. Each allele has an information page.
  26. 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. 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. 28. 4.8 Associate GenBank accessions
  29. 29. 4.8 Associate GenBank accessions
  30. 30. 4.8 Associate GenBank accessions
  31. 31. 4.9 Add literature references
  32. 32. 4.9 Add literature references- from PubMed
  33. 33. 4.9 Add literature references- from PubMed
  34. 34. 4.9 Add literature references not in PubMed
  35. 35. 4.9 Add literature references not in PubMed
  36. 36. 4.9 Add literature references – from automated text indexing
  37. 37. 4.9 Add literature references – from automated text indexing. This list is generated daily from the SGN publication database
  38. 38. 4.10 Add ontology annotations
  39. 39. 4.10 Ontologies are structured controlled vocabulary terms ( http://www.obofoundry.org/ )
  40. 40. You might also want to browse some of the ontologies SGN uses for annotating different datatypes (loci, phenotypes, QTLs, Unigenes)
  41. 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. 42. Ontology term page shows its details and all annotations (including objects annotated with any child terms)
  43. 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. 44. 4.11 Add page comments
  45. 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. 46. 5.1 Search the phenotype database
  47. 47. 5.2 If you uploaded this accession, you can edit the phenotype page.
  48. 48. 5.2 Submit a new accession.
  49. 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. 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. 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

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