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CACAO Training

CACAO Training. ASM-JGI 2012. Transferring information to new genomes. Lists of genes. Database. New knowledge. Known functions of Homologs or subsets. Curation is rate limiting. Literature. Database. Biocurators (rate limiting). Datasets. CACAO is growing. CACAO biodiversity.

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CACAO Training

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  1. CACAO Training ASM-JGI2012

  2. Transferring information to new genomes Lists of genes Database New knowledge Known functions of Homologs or subsets

  3. Curation is rate limiting Literature Database Biocurators (rate limiting) Datasets

  4. CACAO is growing

  5. CACAO biodiversity Spring 2012 Annotations

  6. CACAO 2 • CACAO changes the job of the professionals from primary curation to assessment • Growth in CACAO makes assessment rate limiting • Solution: Promote CACAO veterans to help with assessment

  7. BIOCURATORS ecoliwiki@gmail.com

  8. The biocurator training …

  9. What’s in it for you? • We hope you will • learn how we think about protein function • gain skills that will help your future career • enjoy contributing to a resource used by people all over the world • have fun!

  10. Annotation Annotation: a note that is made while reading any form of text For scientists, • Nucleotide level: Where the genes are in the genome • Protein level: What their functions are From Wikipedia

  11. Annotation Annotation: a note that is made while reading any form of text For scientists, • Nucleotide level: Where the genes are in the genome • Protein level: What their functions are From Wikipedia

  12. Functional Annotation Annotation: a note that is made while reading any form of text Functional Annotation: a note in a specific format that is made based on evidence in a peer-reviewed paper about the attributes of a protein

  13. Functional Annotation Functional Annotation: a note in a specific format that is made based on evidence in a peer-reviewed paper about the attributes of a protein • Specific format = GO (Gene Ontology) Annotation

  14. GO (Gene Ontology) Annotations • 3 aspects (ontologies) for describing protein attributes: 1. Biological Process 2. Molecular Function 3. Cellular Component • Controlled vocabulary • Everyone uses the same terms • Terms have 7 digit IDs that computers can understand • Relationships between terms GO:0005886

  15. Molecular Function • activities or “jobs” of a gene product GO:0004347 hexokinase activity GO:0016301 Kinase activity From PMID:9341134, rndsystems.com

  16. Biological Process • a commonly recognized series of events GO:0009405 pathogenesis GO:0006351 transcription, DNA dependent GO:0051301 cell division From ridge.icu.ac.jp, edtech.clas.pdx.edu, scielosp.org

  17. Cellular Component • where a gene product acts GO:0009274 peptidoglycan-based cell wall GO:0005840 ribosome GO:0005739 mitochondrion From visualphotos.com, epmm.group.shef.ac.uk, http://www.cellsignal.com/products/2415.html

  18. Where can you search for GO terms? GONUTS (gowiki.tamu.edu) • http://gowiki.tamu.edu • http://www.ebi.ac.uk/QuickGO • http://amigo.geneontology.org

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

  20. Functional Annotation Functional Annotation: a note in a specific format that is made based on evidence in a peer-reviewed paper about the attributes of a protein • Specific format = GO (Gene Ontology) Annotation • Peer-reviewed paper

  21. Finding a scientific paper • Has to be a scientific paper with experimental data in it. (Anything else is a valid reason to challenge!!) • No review articles, no books, no textbooks, no wikipediaarticles, no class notes… • You will need the PMID number 22110029

  22. Functional Annotation Functional Annotation: a note in a specific format that is made based on evidence in a peer-reviewed paper about the attributes of a protein • Specific format = GO (Gene Ontology) Annotation • Peer-reviewed paper • Protein

  23. What can you annotate? Proteins. • PubMed for papers on a specific topic or protein or GO term • Search UniProt for something interesting (i.e. allergen) or a protein of interest (i.e. PcnB) • Check the references in the paper you are currently reading No matter what, you will need to find the protein’s accession on UniProt (http://uniprot.org) Use that accession to make a page for that protein on GONUTS (http://gowiki.tamu.edu) Add your GO annotations to the protein’s page on GONUTS

  24. Why do you need an accession from UniProt (http://www.uniprot.org)? * UniProt is not editable by the community, but GONUTS is. GONUTS can make a page that has the annotations from UniProt for any protein using it’s UniProt accession. Correct & complete annotations at the end of the competition will be submitted back to UniProt.

  25. How do you make a new protein page in GONUTS? 2 1 • 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. • Make as many protein pages as you would like!

  26. Annotations edit table

  27. Functional Annotation Functional Annotation: a note in a specific format that is made based on evidence in a peer-reviewed paper about the attributes of a protein • Specific format = GO (Gene Ontology) Annotation • Peer-reviewed paper • Protein

  28. Annotations edit table

  29. Form for your annotation (when you edit the table)

  30. 4 REQUIRED parts of EVERY GO annotation Reference GO Notes (about evidence) Evidence code

  31. Summary of Evidence Codes for CACAO Evidence codes describe the type of work or analysis done by the authors • IDA: Inferred from Direct Assay • IMP: Inferred from Mutant Phenotype • IGI: Inferred from Genetic Interaction • 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 7, your annotation is incorrect!!! http://gowiki.tamu.edu/wiki/index.php/evidence_codes

  32. Functional Annotation Functional Annotation: a note in a specific format that is made based on evidence in a peer-reviewed paper about the attributes of a protein • Specific format = GO (Gene Ontology) Annotation • Peer-reviewed paper • Protein • Evidence code

  33. 4 REQUIRED parts of EVERY GO annotation Reference GO Notes (about evidence) Evidence code

  34. 2 other parts that may rarely be required… Qualifier With/From

  35. How is CACAO scored? Rounds • Points for a complete AND correct annotation (normally 1 week/round, today = 25 mins) • 4 necessary parts • May be additional parts • NOTE: We will take away points if the annotation is not correct when assessed by an experienced CACAO biocurator • Challenges are used to steal points for incorrect &/or incomplete annotations (normally 1 week/round, today = 20 mins) • Identify a problem • Suggest correct alternative • Refinements can be entered by any team (during any challenge week)

  36. Scoreboard & Challenges http://gowiki.tamu.edu/wiki/index.php/Category:ASM_JGI_challenge

  37. Team & Individual Pages challenge

  38. Challenges • Enter the reason for your challenge here. • - (i.e. What’s wrong) • 2. Provide the fix(es) for it.

  39. Annotation discussion (aka argument)

  40. UniProt – http://uniprot.org • Find your protein(s) here (UniProt accession required) • PubMed – http://pubmed.org • Find your papers about the protein’s attributes (molecular function, biological process, cellular component) • GONUTS – http://gowiki.tamu.edu • Search for GO terms • Make page for your protein on GONUTS (using UniProt accession) • Add your annotation to the protein’s Annotation table during first (Annotation) week of any round • Review and challenge competitors’ annotations during the second (challenge) week of any round

  41. ASM-JGI Competition! • You now have 25 mins to: • Use the assigned paper for your group and … • Find the correct UniProt accession • Make the page for the protein on GONUTS • Make at least one annotation • You will have 20 mins to challenge other teams’ annotations • What fields are wrong & why?!

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