BICH 489-500 CACAO
Biocurator Training Session #3
Plan for tonight
1.
2.
3.
4.
Review
Teams… start thinking of a team name
Make pages on GONUTS for proteins
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?
GONUTS
http://gowiki.tamu.edu
What does a GO annotation
consist of?
4 REQUIRED parts of EVERY GO
annotation
GO
Reference
Evidence
code
** I will cover this again!!
Notes (about
evidence)
2 other parts that may be
required…
With/from
Making a protein page on GONUTS
requires a UniProt accession
• UniProt - http://www.uniprot.org
How do you make a new gene
page in GONUTS?
1
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•
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. Experimental
2. Computational
3. Author Statement
4. Curator Assigned
5. Automatically assigned by GO
What are the 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
CACAO biocurators may only use certain experimental and
computational evidence codes
Experimental Evidence Codes
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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
•
•
•
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•
•
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
•
•
•
•
•
•
•
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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
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•
•
•
•
•
•
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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.
2.
In the “Annotation” table on the gene page you just edited
In the table on your user page
http://gowiki.tamu.edu/wiki/index.php/User:Siebenmc
3.
In the table on your team page
http://gowiki.tamu.edu/wiki/index.php/Category:Team_Mu_subunits
4.
As points on the scoreboard
http://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
Assessment” part
1
3
2
Scoreboard
Submitted
Challenges
Moving
through
challenges
Closed
Challenges
http://gowiki.tamu.edu/wiki/index.php/Category:Michigan_State_CACAO
Category:Team
UCL1
Part 2: TEAMS
1.
Maria Gutierrez
&
Mary Hodde
2.
Alex Francis
&
Mark Nentwig
3.
Alberto Florez
&
Mark Kline
4.
Oscar Herrera
&
Mimi Dao
5.
Emilee Larkin
&
Renny Mathew
6.
Thomas McMillin
&
Monica Pinarte
&
Vincent
7.
Austin Tiner
&
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
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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)
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•
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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)
•
•
•
•
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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 topic
Topic: phenylalanine and phenylacetate catabolism in bacteria
Example #3 - from UniProt
• 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
1.
2.
CAN WE USE THIS PAPER?
WHAT EVIDENCE CODE?
Practice Paper #4 - inspiration
from a movie…
• 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