1. CACAO Biocurator Training CACAO Fall 2011

2. CACAO Syllabus What is CACAO & why is it important? Training Examples

3. Mutualistic Relationship We want you to get experience with: 1.CRITICALLY reading scientific papers 2.Bioinformatics resources 3.Collaborating with other biocurators 4.Synthesizing functional annotations We want to get high quality functional annotations to contribute back to the GO Consortium and other biological databases

4. What is an annotation? Hint: try looking for a definition on Wikipedia.

5. What is a functional annotation? Process of attaching information from the scientific literature to proteins

6. Growing need for functional annotations Advances in DNA sequencing mean lots of new genomes & metagenomes

7. Classic MODel Literature Datasets Curators (rate limiting) Database

8. Classic MODel is Expensive YIKES!

9. Growing need for high quality functional annotations High quality annotations allow us to infer the function of genes Which allows us to understand the capabilities of genomes and understand the patterns of gene expression

10. Two problems meet How can we get more curators with finite budgets? How can we incorporate more critical analysis into undergraduate education?

11. What does a functional annotation have to do with this course? Process of attaching information from the scientific literature to proteins CACAO will teach you to become a biocurator –you will be adding functional annotations to the biological database GONUTS (http://gowiki.tamu.edu)

12. CACAO Community Assessment - How well can Community - you (with our coaching) Annotation with - assign gene functions Ontologies - using GO?

13. Can students become biocurators? YES! Spring 2010Fall 2010Spring 2011 InstitutionsTAMU UCL TAMU Miami (Ohio) N. Texas Penn State Mich. State Rounds1 round4 rounds5 rounds Annotations* / Submitted 118/153496/753726/1013 1340 GO annotations in 2 & 1/2 semesters!

14. Functional annotation with Gene Ontology Controlled vocabulary with –Term identifiers GO:0000075 –Name cell cycle checkpoint –Definitions "A point in the eukaryotic cell cycle where progress through the cycle can be halted until conditions are suitable for the cell to proceed to the next stage." [GOC:mah, ISBN:0815316194] –Relationships is_a GO:0000074 ! regulation of progression through cell cycle Terms arranged in a Directed Acyclic Graph (DAG)

15. Why use Ontologies? Standardization facilitate comparison across systems facilitate computer based reasoning systems –Good for data mining! leading functional annotation ontology = Gene Ontology (GO)

16. What is GO? Who is the GO Consortium (GOC)? GO = ~30,000 terms for gene product attributes 1.Molecular Function (enzyme activity) 2.Biological Process (pathways) 3.Cellular Component (parts of the cell) GO Consortium - set of biological databases that are involved in developing GO and contributing GO annotations

17. Cellular Component where a gene product acts

18. Molecular Function activities or “jobs” of a gene product glucose-6-phosphate isomerase activity figure from GO consortium presentations

19. Biological Process a commonly recognized series of events cell division Figure from Nature Reviews Microbiology 6, 28-40 (January 2008)

20. Where can we find GO terms? http://gowiki.tamu.edu GONUTS

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

22. Which subontology (MF, BP or CC) would the following terms fit in? GO:0003909 DNA ligase activity GO:0071705 Nitrogen compound transport GO:0007124 Pseudohyphal growth GO:0015123 Acetate transmembrane transporter activity GO:0071514 Genetic imprinting GO:0005773 Vacuole GO:0000312 Plastid small ribosomal subunit

23. Questions? 1. You will be making functional (GO) annotations using GO terms. 2. You can search for GO terms on GONUTS. What do we know so far?

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

25. Why are we using GONUTS? Students can add functional annotations to proteins. It has all the GO terms in it, too. Some of the GO terms have usage notes. It works a lot like Wikipedia, so it’s familiar. It has the ability to keep track of each student’s and team’s annotations. We run it. http://gowiki.tamu.edu

26. REQUIRED parts of a GO annotation GO http://gowiki.tamu.edu/wiki/index.php/ECOLI:LPOB ** I will cover this again!!

27. Parts of a GO annotation (cont) Evidence code

28. Parts of a GO annotation (cont) Reference Notes (about evidence)

29. Questions? 1. You will be making functional (GO) annotations using GO terms. 2. You can search for GO terms on GONUTS. 3. You will be adding your GO annotations to GONUTS. 4. There are 4 required parts to a GO annotation. 5. You have to base your annotation on an experiment published in a scientific paper. What do we know so far?

30. Next week Review of GO & GO annotations More biocurator training – lots of examples – lots of practice BICH 485 & 689 students - please stick around to talk about these courses!

31. Plan for training 1.Synthesizing GO annotations 2.Refinements 3.Judging & Assessment 4.Individual & Team tracking

32. Part 1: Synthesizing GO annotations

33. What can you annotate? Proteins. –Any protein with a record in UniProt (Universal Protein Resource - http://uniprot.org)http://uniprot.org How can you find proteins to annotate? –Think of ways to identify a protein or paper to annotate

34. Choosing a protein to annotate 1. randomly 2. topics of interest (ie efflux pump proteins, biofilms, marine biology) 3. papers you have come across while doing other stuff 4. methods you know or want to learn 5. phenotypes and mutants you are interested in 6. by author 7. by pathway or regulon 8. suggested by another - high ratio of IEA:manual annotations in GONUTS - mentioned in another class 9. current paper mentions another gene product 10. review papers (ie Annual Reviews are excellent sources) 11. Uniprot, GONUTS, WikiPathways, PubMed searches 12. protein annotated by other teams 13. ask a coach

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

36. Practice 1. What is the GO term for GO:0004713? 2. What is the GO identifier for mitosis? 3. How many results (ballpark) do you get when you search for cell division using the Go, Search or G buttons? 4. How many child terms are there for plasma membrane? How many grandchildren? 5. What term is the parent of GO:006825? http://gowiki.tamu.edu

37. Finding a scientific paper on a certain protein Has to be a scientific paper with experimental data in it. –Anything else is a valid reason to challenge! PubMed, PubMed Central, GoogleScholar… No review articles no books, textbooks, wikipedia articles, class notes… You will need the PMID number

38. Practice - searching PubMed 1.How many papers do you get when you search for “coli”? 2.How many of those papers are reviews? 3.What is the title of the oldest paper when you search for “coli AND RNA polymerase”? 4.How many results are there when you search for “GTPase activity and Gene Ontology”? 5.What is the PMID of the paper when you search for “Hu JC AND coli AND lysR AND 2010”? http://pubmed.org

39. Why do we annotate on GONUTS? UniProt (Universal Protein Resource) will not let us annotate protein records on their site. They are a professionally-curated & closed database. GONUTS will. GONUTS pulls the info from the UniProt record when it makes a page for you to edit.

40. UniProt - http://www.uniprot.orghttp://www.uniprot.org UniProt is not community edited, so we can’t add annotations directly to their database Making a protein page on GONUTS requires a UniProt accession

41. Practice - Searching UniProt Find the UniProt accessions for: a)Mouse Lsr protein b)Diptheria toxin from Corynebacterium c)mutS from E. coli K-12 http://uniprot.org

42. 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 & pull all of the annotations from UniProt into a table that you can edit.

43. Practice 1.How many annotations are on the page for the p53 protein from humans? 2.How many different evidence codes are there on the page for the Bub1a protein from mice? 3.Give one of the paper identifiers for an annotation for the LpxK protein from E. coli. http://gowiki.tamu.edu

44. Questions? 1. You will be making functional (GO) annotations using GO terms. 2. You can search for GO terms on GONUTS. 3. You will be adding your GO annotations to GONUTS. 4. There are 4 required parts to a GO annotation. 5. You have to base your annotation on an experiment published in a scientific paper. 6.You can annotate any protein with a record in UniProt. 7.You have to make a page in GONUTS for your protein using the UniProt accession. What do we know so far?

45. 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

46. 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?

47. 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

48. 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

49. 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

50. 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

51. 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!!!

52. Required parts (for every annotation) GO:0004713 PMID:1111 IDA: Inferred from direct assay Figure 2a

53. What you might also have to fill in http://geneontology.org/GO.evidence.shtml

54. Questions? 1. You will be making functional (GO) annotations using GO terms. 2. You can search for GO terms on GONUTS. 3. You will be adding your GO annotations to GONUTS. 4. There are 4 required parts to a GO annotation. 5. You have to base your annotation on an experiment published in a scientific paper. 6.You can annotate any protein with a record in UniProt. 7.You have to make a page in GONUTS for your protein using the UniProt accession. What do we know so far?

55. Practice - Identify the problem annotation(s) & why 1. GO:0003674 PMID:20372022IDA: Inferred from Direct Assay Table 2. 2. GO:0016985 PMID:20372022IMP: Inferred from Mutant Phenotype Table 2. 3. GO:0016985 PMID:20372022IDA: Inferred from Direct Assay 4. GO:0016985 PMID:20372022IDA: Inferred from Direct Assay Table 2. 5. GO:0003674 PMID:20372022IDA: Inferred from Direct Assay Table 2. 6. GO:0016985 PMID:20372002 IGI: Inferred from Genetic Interaction Table 2. 7. GO:0016985 20372022 IDA: Inferred from Direct Assay Table 2. 8. GO:0016985 PMID:20372002 EXP: Inferred from Experiment Table 2. 9. What is the UniProt accession of the protein described/annotated? GO IDReferenceEvidence CodeNotes

56. How is CACAO scored? Points for a complete annotation GO term (right level of specificity) Reference (paper) Evidence code Identify where in the paper the evidence is Refinements used to steal points for incorrect &/or incomplete annotations Identify a problem Suggest correct alternative Refinements can be entered by any team (including the original team)

57. How can you get the annotations required by Rubric #2? 1.Synthesize complete & correct annotations. 2.Correctly refine (challenge & correct) someone else’s annotation. 3.If your annotation gets challenged, offer the best correction.

58. Summary You will be searching literature for experimental evidence for a protein’s function (MF), processes (BP) and location (CC)

59. Where do annotations show up?

60. Refinements & Challenges

61. What can you challenge?

62. Scoreboard

63. Schedule

64. Spring 2011 - Results by organism