CACAO TrainingASM-JGI 2012

Transferring information to new genomes

Database

Lists of genes

Known functions ofHomologs or subsets

New knowledge

Curation is rate limiting

Literature

Datasets

Biocurators(rate limiting)

Database

CACAO is growing

Spring 2010 Fall 2010 Spring 2011 Fall 2011 Spring 20120

500

1000

1500

2000

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309

165153

753871

1796

1316

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students

annotations

CACAO biodiversityE.

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Spring 2012

CACAO 2

• CACAO changes the job of the professionals from primary curation to assessment

• Growth in CACAO makes assessment rate limiting

• Solution: Promote CACAO veterans to help with assessment

ecoliwiki@gmail.com

BIOCURATORS

The biocurator training …

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 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.

*

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 (normally 1 week/round, today = 25 mins)

• 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 (normally 1 week/round, today = 20 mins)

• Identify a problem • Suggest correct alternative

• Refinements can be entered by any team (during any challenge week)

Scoreboard & Challengeshttp://gowiki.tamu.edu/wiki/index.php/

Category:ASM_JGI_challenge

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.

Annotation discussion (aka argument)

• 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

ASM-JGI Competition!

• You now have 25 mins to:– Use the assigned paper for your group and …– Find the correct UniProt accession– Make the page for the protein on GONUTS– Make at least one annotation

• You will have 20 mins to challenge other teams’ annotations– What fields are wrong & why?!