1. BICH 489-500 - CACAO Biocurator Training Session #3

2. Plan for tonight 1.Review 2.Teams… start thinking of a team name 3.Make pages on GONUTS for proteins 4.Practice!

3. Search for GO terms on GONUTS http://gowiki.tamu.edu

4. What do you actually need once you have found the correct term? GO:0004713

5. Where are we adding GO annotations? http://gowiki.tamu.edu GONUTS

6. What does a GO annotation consist of?

7. 4 REQUIRED parts of EVERY GO annotation GO ** I will cover this again!! Evidence code Reference Notes (about evidence)

8. 2 other parts that may be required… With/from

10. UniProt - http://www.uniprot.orghttp://www.uniprot.org Making a protein page on GONUTS requires a UniProt accession

11. How do you make a new gene page in GONUTS? 1 2 Use a UniProt accession to make a page on GONUTS that you can add your own annotations to. GoPageMaker will: - Check if the page exists in GONUTS & take you there if it does. - Make a page if it does not exist in GONUTS already & pull all of the annotations from UniProt into a table that you can edit.

12. … 1.You cannot mess up GONUTS by making lots of protein pages! Feel free to make a protein page on GONUTS, even if you don’t end up annotating it. 2.You would be wise if you find a potentially good paper to make the protein page on GONUTS and check to see if the paper has already been annotated.

13. Practice making protein pages on GONUTS For the protein I gave you as you came into class: Find protein on UniProt & get the accession Make a page for that protein on GONUTS

14. What are evidence codes? Describe the type of work or analysis done by the authors 5 general categories of evidence codes: 1.Experimental 2.Computational 3.Author Statement 4.Curator Assigned 5.Automatically assigned by GO

15. Describe the type of work or analysis done by the authors 5 general categories of evidence codes: 1.Experimental 2.Computational 3.Author Statement 4.Curator Assigned 5.Automatically assigned by GO CACAO biocurators may only use certain experimental and computational evidence codes What are the evidence codes?

16. Experimental Evidence Codes IDA: Inferred from Direct Assay IMP: Inferred from Mutant Phenotype IGI: Inferred from Genetic Interaction IEP: Inferred from Expression Pattern IPI: Inferred from Physical Interaction EXP: Inferred from Experiment

17. Experimental Evidence Codes IDA: Inferred from Direct Assay IMP: Inferred from Mutant Phenotype IGI: Inferred from Genetic Interaction IEP: Inferred from Expression Pattern IPI: Inferred from Physical Interaction EXP: Inferred from Experiment http://geneontology.org/GO.evidence.shtml

18. Computational Evidence Codes ISS: Inferred from Sequence or Structural Similarity ISO: Inferred from Sequence Orthology ISA: Inferred from Sequence Alignment ISM: Inferred from Sequence Model IGC: Inferred from Genomic Context IBA: Inferred from Biological Aspect of Ancestor IBD: Inferred from Biological Aspect of Descendant IKR: Inferred from Key Residues IRD: Inferred from Rapid Divergence RCA: Inferred from Reviewed Computational Analysis http://geneontology.org/GO.evidence.shtml

19. Computational Evidence Codes ISS: Inferred from Sequence or Structural Similarity ISO: Inferred from Sequence Orthology ISA: Inferred from Sequence Alignment ISM: Inferred from Sequence Model IGC: Inferred from Genomic Context IBA: Inferred from Biological Aspect of Ancestor IBD: Inferred from Biological Aspect of Descendant IKR: Inferred from Key Residues IRD: Inferred from Rapid Divergence RCA: Inferred from Reviewed Computational Analysis http://geneontology.org/GO.evidence.shtml

20. Summary of Evidence Codes for CACAO IDA: Inferred from Direct Assay IMP: Inferred from Mutant Phenotype IGI: Inferred from Genetic Interaction IEP: Inferred from Expression Pattern ISO: Inferred from Sequence Orthology ISA: Inferred from Sequence Alignment ISM: Inferred from Sequence Model IGC: Inferred from Genomic Context If it’s not one of these 8, your annotation is incorrect!!! CHALLENGE!

21. Where will your annotation now show up? 1.In the “Annotation” table on the gene page you just edited 2.In the table on your user page http://gowiki.tamu.edu/wiki/index.php/User:Siebenmc 3.In the table on your team page http://gowiki.tamu.edu/wiki/index.php/Category:Team_Mu_subunits 4.As points on the scoreboard http://gowiki.tamu.edu/wiki/index.php/Category:CACAO_Spring_2011 5.If challenged, it will show up in the “Submitted Challenges” table (below the scoreboard)

22. Community Assessment CACAO - the “Community Assessment” part …

24. 1 2 3

25. Scoreboard Submitted Challenges Closed Challenges Moving through challenges http://gowiki.tamu.edu/wiki/index.php/Category:Michigan_State_CACAO

26. Category:Team UCL1

29. Part 2: TEAMS 1.Maria Gutierrez 2.Alex Francis 3.Alberto Florez 4.Oscar Herrera 5.Emilee Larkin 6.Thomas McMillin 7.Austin Tiner & Mary Hodde & Mark Nentwig & Mark Kline &Mimi Dao &Renny Mathew & Monica Pinarte & Vincent &Chris P.& Lilly

30. Part 3: PRACTICE!

31. Practice Example #1 - Starting from a review paper I read a review article - Double-strand break end resection and repair pathway choice (Symington & Gautier, 2011). - One protein mentioned is yeast MRE11. - Look up UniProt record for this & find references - First reference looks promising - PMID:7789757 - Make page for yeast MRE11 on GONUTS - First reference has already been annotated. - Fifth reference looks promising - PMID:7625279 What is the UniProt accession of this protein? How do you make the page for this protein on GONUTS?

32. Practice Example #1 cont PMID:7625279 - Functions of the yeast meiotic recombination genes, MRE11 and MRE12. –Mutant is defective in meiotic recombination & viable spore formation, but proficient in mitotic recombination. –Mutant doesn’t form double-stranded breaks necessary for meiotic recombination & is sensitive to DNA damaging agents (MMS) What is a suitable GO term? What evidence code? How do you add your GO annotation? 42138

33. MEIOSIS?!

34. Practice Example #1 cont PMID:7625279 - Functions of the yeast meiotic recombination genes, MRE11 and MRE12. –Mutant is defective in meiotic recombination & viable spore formation, but proficient in mitotic recombination. –Mutant doesn’t form double-stranded breaks necessary for meiotic recombination & is sensitive to DNA damaging agents (MMS) What is a suitable GO term? What evidence code? Where is the evidence for this annotation in the paper? How do you add your GO annotation? HOW MANY OTHER ANNOTATIONS COULD YOU GET OUT OF THIS 1 PAPER?! 42138

35. Example #2 - starting from a topic Topic: phenylalanine and phenylacetate catabolism in bacteria

36. Example #3 - from UniProt 1.CAN WE USE THIS PAPER? 2.WHAT EVIDENCE CODE? I searched UniProt for “allergen” and found the dust mite protein, Der p 1. http://www.ncbi.nlm.nih.gov/pubmed/3335830 http://www.ncbi.nlm.nih.gov/pubmed/3335830 –Sequence Analysis of cDNA coding for a major house dust mite allergen, Der p 1

37. Inspiration = “Contagion” Searched for pig (Sus scrofa) Picked the first protein record (Q9TV69) –paper listed under references = PMID:2018468 –Made page on GONUTS for this protein & checked if paper has already been annotated Practice Paper #4 - inspiration from a movie…