Download - BICH 489-500 - CACAO
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BICH 489-500 - CACAO
Biocurator Training Session #3
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Plan for tonight
1. Review
2. Teams… start thinking of a team name
3. Make pages on GONUTS for proteins
4. Practice!
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Search for GO terms on GONUTS
http://gowiki.tamu.edu
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What do you actually need once you have found the correct term?
GO:0004713
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What does a GO annotation consist of?
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4 REQUIRED parts of EVERY GO annotation
GO
** I will cover this again!!
Evidencecode
Reference Notes (about evidence)
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2 other parts that may be required…
With/from
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• UniProt - http://www.uniprot.org
Making a protein page on GONUTS requires a UniProt accession
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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.
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…
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.
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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
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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
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• 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?
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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
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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
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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
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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
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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!
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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)
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CACAO - the “Community Community AssessmentAssessment” part
…
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1
2
3
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Scoreboard
Submitted Challenges
Closed Challenges
Moving through challenges
http://gowiki.tamu.edu/wiki/index.php/Category:Michigan_State_CACAO
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Category:Team UCL1
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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
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Part 3: PRACTICE!
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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?
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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
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MEIOSIS?!
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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
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Example #2 - starting from a topicTopic: phenylalanine and phenylacetate catabolism in bacteria
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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
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• 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…
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