BICH 489-500 - CACAO

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

2. Plan for tonight • Review • Teams… start thinking of a team name • Make pages on GONUTS for proteins • 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? GONUTS http://gowiki.tamu.edu

6. What does a GO annotation consist of?

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

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

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

11. How do you make a new gene page in GONUTS? 2 1 • 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. 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. 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: • Experimental • Computational • Author Statement • Curator Assigned • Automatically assigned by GO

15. What are the evidence codes? • Describe the type of work or analysis done by the authors • 5 general categories of evidence codes: • Experimental • Computational • Author Statement • Curator Assigned • Automatically assigned by GO • CACAO biocurators may only use certain experimental and computational 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? • In the “Annotation” table on the gene page you just edited • In the table on your user page http://gowiki.tamu.edu/wiki/index.php/User:Siebenmc • In the table on your team page http://gowiki.tamu.edu/wiki/index.php/Category:Team_Mu_subunits • As points on the scoreboard http://gowiki.tamu.edu/wiki/index.php/Category:CACAO_Spring_2011 • If challenged, it will show up in the “Submitted Challenges” table (below the scoreboard)

22. CACAO - the “Community Assessment” part …

24. 1 3 2

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

26. Category:Team UCL1

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

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

37. Practice Paper #4 - inspiration from a movie… • 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