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CACAO Training

CACAO Training. Fall 2012. C ommunity A ssessment of C ommunity A nnotation with O ntologies (CACAO). Annotation. Annotation: a note that is made while reading any form of text For scientists, Nucleotide level: Where the genes are in the genome

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CACAO Training

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  1. CACAO Training Fall 2012

  2. Community Assessment of Community Annotation with Ontologies (CACAO)

  3. 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

  4. 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

  5. Who classically makes functional annotations? Literature Database Biocurators (rate limiting) Datasets

  6. 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

  7. 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. Do this first in case the paper has already been used to make GO annotations.

  8. Annotations edit table

  9. Practice – find a protein on UniProt (uniprot.org) • Make a page for it on GONUTS (gowiki.tamu.edu) • ARE YOU LOGGED IN?! • Once you’ve made the page, click on “edit Table” • Scroll down & “add row” • Cancel, cancel to get out of TableEditor

  10. 4 REQUIRED parts of EVERY GO annotation Reference GO Notes (about evidence) Evidence code

  11. 2 other parts that may rarely be required… Qualifier With/From

  12. 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

  13. How do you know what GO term to search for or use? • How do the authors describe the attributes of the protein? • Is there a key word (i.e. check the title of the paper) you can search GONUTS for? • After you make the page for the protein, is there a suitable term already used in an annotation in the Annotation table? (*** Also make sure your paper hasn’t already been annotated***) • Stuck? Ask for help.

  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:0004396 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. 4 REQUIRED parts of EVERY GO annotation Reference GO Notes (about evidence) Evidence code

  19. 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

  20. 2 other parts that may rarely be required… Qualifier With/From IGI: Inferred from Genetic Interaction ISO: Inferred from Sequence Orthology ISA: Inferred from Sequence Alignment ISM: Inferred from Sequence Model

  21. Team & Individual Pages challenge

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

  23. 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

  24. CACAO I • Go to UniProt & look for more interesting proteins • What is your favorite microorganism? • What topics are in interested in? • What proteins have you heard about in classes? • Make pages for them on GONUTS • Look for papers about the proteins on PubMed • Has to have experimental data in it! • Look for a suitable GO term • What terms are already in the Annotations table? • If not, try searching based on a keyword in the paper • Add an annotation

  25. CACAO II • We will collectively decide on some challenges & we will assess other GO annotations http://gowiki.tamu.edu/wiki/index.php/ BOMMO:Q3LFR2

  26. What to look for: • Is the annotation on the right protein’s page? (Is the paper about the protein?) • Is the annotation complete? Does it have the 4 required parts? Does the annotation require either of the additional 2 fields (i.e. does the annotation use an evidence code that needs the with/from field filled in)? • Has the student used information NOT allowed by the CACAO rules (i.e. evidence code or binding terms)? • Do the notes point to a figure/table that supports the annotation? (i.e. no review articles, no model figures, no crystal structures, etc) • Is there a more suitable GO term (more or less specific)? • Does the evidence code fit with the experiment described? • For IGI, ISO, or ISA have they entered the correct accession in the with/from field? • For ISO & ISA, does the protein in the with/from field have a GO annotation that has experimental evidence for that GO term? (i.e. Does the annotation maintain a direct chain of evidence?) • Is the annotation complete, correct and accurate based on the paper? (i.e. will it be submitted to UniProt?)

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