BICH 489-500 - CACAO

Biocurator Training Session #3

Plan for tonight

1. Review

2. Teams… start thinking of a team name

3. Make pages on GONUTS for proteins

4. Practice!

Search for GO terms on GONUTS

http://gowiki.tamu.edu

What do you actually need once you have found the correct term?

GO:0004713

Where are we adding GO annotations?

http://gowiki.tamu.edu

GONUTS

What does a GO annotation consist of?

4 REQUIRED parts of EVERY GO annotation

GO

** I will cover this again!!

Evidencecode

Reference Notes (about evidence)

2 other parts that may be required…

With/from

• UniProt - http://www.uniprot.org

Making a protein page on GONUTS requires a UniProt accession

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.

…

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.

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

What are evidence codes?

• Describe the type of work or analysis done by the authors

• 5 general categories of evidence codes:1. Experimental2. Computational3. Author Statement4. Curator Assigned5. Automatically assigned by GO

• Describe the type of work or analysis done by the authors• 5 general categories of evidence codes:

1. Experimental2. Computational3. Author Statement4. Curator Assigned5. Automatically assigned by GO

• CACAO biocurators may only use certain experimental and computational evidence codes

What are the evidence codes?

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

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

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

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

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!

Where will your annotation now show up?

1. In the “Annotation” table on the gene page you just edited2. In the table on your user page

http://gowiki.tamu.edu/wiki/index.php/User:Siebenmc

3. In the table on your team pagehttp://gowiki.tamu.edu/wiki/index.php/Category:Team_Mu_subunits

4. As points on the scoreboardhttp://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)

CACAO - the “Community Community AssessmentAssessment” part

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1

2

3

Scoreboard

Submitted Challenges

Closed Challenges

Moving through challenges

http://gowiki.tamu.edu/wiki/index.php/Category:Michigan_State_CACAO

Category:Team UCL1

Part 2: TEAMS1. 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

Part 3: PRACTICE!

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?

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

MEIOSIS?!

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

Example #2 - starting from a topicTopic: phenylalanine and phenylacetate catabolism in bacteria

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

–Sequence Analysis of cDNA coding for a major house dust mite allergen, Der p 1

• 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…