Post on 17-Feb-2016
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CACAO TrainingFall 2012
Community Assessment ofCommunity Annotation with Ontologies (CACAO)
Spring 2010 Fall 2010 Spring 2011 Fall 2011
Institutions TAMU TAMUUCL
TAMUMiami (Ohio)North TexasPenn StateMichigan State
TAMUUCLSwarthmoreMississippi StateHofstraHouston BaptistNorth Dakota StateWisconsinWisconsin-Parkside
# Rounds 1 round 4 rounds 5 rounds 5 rounds
Annotations/Submitted
118/153 496/753 723/1018 Not finished with assessments/1524
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!
Annotation
Annotation: a note that is made while reading any form of text
For scientists,1. Nucleotide level: Where the genes are in
the genome 2. Protein level: What their functions are
From Wikipedia
Annotation
Annotation: a note that is made while reading any form of text
For scientists,1. Nucleotide level: Where the genes are in
the genome 2. Protein level: What their functions are
From Wikipedia
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
Functional Annotations• Allow us to:
– Infer the function of genes• Related by common descent• Related by similar expression patterns• Related by phylogenetic profiles• …
• Allow us to:– Understand the capabilities of organisms’ genomes– Understand patterns of gene expression
• In different environments• In different tissues• In disease states• …
Functional Annotations
• Finding genes faster than we can understand them
Functional Annotations
• >21 million peer-reviewed articles in PubMed• Many millions of proteins recorded in UniProt
http://www.uniprot.org
Who classically makes functional annotations?
Literature
Datasets
Biocurators(rate limiting)
Database
Functional Annotations
• Accurate functional annotation for as many genes as possible
• A system of assigning function that allows both humans and computers to compare, contrast, analyze, and predict gene function
• Curators to make and/or check these assignments– For CACAO, we will train you to be
biocurators.
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
GO (Gene Ontology) Annotations• 3 aspects (ontologies) for
describing protein attributes:1. Biological Process2. Molecular Function3. Cellular Component
• Controlled vocabulary– Everyone uses the same terms– Terms have 7 digit IDs that computers can
understand
• Relationships between terms
GO:0005886
Molecular Function• activities or “jobs” of a gene product
GO:0004347 hexokinase activity
From PMID:9341134, rndsystems.com
GO:0016301 Kinase activity
Biological Process• a commonly recognized series of events
GO:0051301 cell division
From ridge.icu.ac.jp, edtech.clas.pdx.edu, scielosp.org
GO:0006351 transcription, DNA dependent
GO:0009405 pathogenesis
Cellular Component• where a gene product acts
From visualphotos.com, epmm.group.shef.ac.uk, http://www.cellsignal.com/products/2415.html
GO:0005739 mitochondrion
GO:0009274 peptidoglycan-based
cell wall
GO:0005840 ribosome
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
What do you actually need once you have found the correct term?
GO:0004713
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
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 wikipedia articles, no class notes…
• You will need the PMID number
22110029
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
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
Why do you need an accession from UniProt (http://www.uniprot.org)?
1. UniProt is not editable by the community, but GONUTS is.2. GONUTS can make a page that has the annotations from UniProt for
any protein using it’s UniProt accession.3. Correct & complete annotations at the end of the competition will be
submitted back to UniProt.
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How do you make a new protein page in GONUTS?
1
2
• 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!
Annotations
edit table
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
Annotations
edit table
Form for your annotation (when you edit the table)
4 REQUIRED parts of EVERY GO annotation
GOEvidence
code
ReferenceNotes (about evidence)
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
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
4 REQUIRED parts of EVERY GO annotation
GOEvidence
code
ReferenceNotes (about evidence)
2 other parts that may rarely be required…
With/From
Qualifier
How is CACAO scored? Rounds
• Points for a complete AND correct annotation (1 week/round)• 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 (1 week/round)
• Identify a problem • Suggest correct alternative
• Refinements can be entered by any team (during any challenge week)
Scoreboard & Challenges
Team & Individual Pages
challenge
Challenges
1. Enter the reason for your challenge here. - (i.e. What’s wrong)
2. Provide the fix(es) for it.
I don’t think IGI is appropriate for this annotation. IGI uses multiple strains or organisms to compare. The evidence listed is just showing mutations in the protein and it’s effects on Dynamin-1, endophilin, and GluR1. The evidence code should be changed to IMP instead, and the other two annotations will probably need to be deleted.
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Example Challenge
Multiple Challenges = Potentially More Points!
Scoreboard
• 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