Cacao rules

	CACAO the intercollegiate annotation competition!

The Community Assessment of Community Annotation with Ontologies (CACAO) is a competition for teams of undergrads around the world to improve the functional annotation of genes. CACAO was developed and is currently run at Texas A&M University, along with many other institutions. If you are interested in participating, please email us - Suzi or Jim.

CACAO RULES

The rules outlined in the following document are the ultimate basis for the competition and will be used to settle any dispute.

• Rules for the competition can be accessed here:

Rules for CACAO

• If you are stuck and need some help with annotation conventions, click here.
• If you are stuck on how to use the evidence codes correctly, click here. Don't forget, you may only use IDA, IMP, IGI, ISA, ISO, ISM, IGC.

• Biocurators should annotate to the most specific GO term; if a parent and child annotation appear on the same gene page, the parent annotation should be challenged (assuming that the child annotation is appropriate).

Quick Guide (see The Rules Document for all rules)

Important rules to follow (see the complete Rules for CACAO!!!):

1. Annotations must be complete and accurate to get points (at a minimum - GO term, evidence term, reference & brief description of evidence; possibly with/from field and/or qualifier)
2. Only 7 evidence codes are permitted, 4 of which require the with/from field to be filled in correctly (see section below)
3. No annotations to binding terms or response to terms will be accepted
4. Qualifiers must be used correctly - see the GO page about using qualifiers
5. No high throughput papers - email Suzi if you're still not sure after you've checked the rules document (see link to doc above)
6. Your reference must be a PMID for a peer-reviewed scientific paper. No reviews, no class notes, no hypothetical modeling papers, etc.
7. Your evidence for the Notes section must be to a figure with the experimental or computational evidence in it, not a model or summary figure.
   • Although not a condition for disqualification, it is highly recommended that you include a brief description of why your figure is pertinent/applicable conditions (specific tissue? temperature?) etc.
8. Any team member can refine/challenge any annotation from another team & do so more than once. The more complex the refinements, the more points at stake!

4 ways to get a "perfect" annotation

There are 4 ways to have a “perfect” annotation that counts towards the total number of annotations required by an instructor:

1. Synthesize a complete and accurate annotation.
2. Challenge someone else’s incomplete/inaccurate annotation and correct the problems with the annotation entirely.
3. If one of their own annotations was challenged, but not fully corrected by the challenges, the original author may enter a challenge to the challenge and entirely fix the annotation.
4. Identify term(s) missing in the GO, request the term(s) from the GO Consortium using SourceForge and get the term(s) accepted by the GOC. Each accepted term is equivalent to 1 complete/accurate annotation.

Assessment Status

Allowable Evidence Codes

• Here's a list of the evidence codes that CACAO students may use:

1. IDA: Inferred from Direct Assay
2. IMP: Inferred from Mutant Phenotype
3. IGI: Inferred from Genetic Interaction - requires with/from field to be filled in
4. ISO: Inferred from Sequence Orthology - requires with/from field to be filled in
5. ISA: Inferred from Sequence Alignment - requires with/from field to be filled in
6. ISM: Inferred from Sequence Model - requires with/from field to be filled in
7. IGC: Inferred from Genomic Context

More Evidence Code Help

For more help on evidence codes, see helpful handouts for students or the GO Consortium documentation at: http://www.geneontology.org/GO.evidence.shtml