Category:CACAO Spring 2012

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Announcements Welcome to the SUPER BOWL ROUND - The final round of CACAO for the Spring 2012 competition. Annotations can be added from 6pm CST Sunday April 8th until 5:59pm CST Sunday April 15th. Challenges can be entered from 6pm CST Sunday April 15th until 5:59pm CST Sunday April 22nd.

CACAO Spring 2012

CACAO Materials

Student and instructor resources (including many listed on this page) can be found HERE.

• download the Powerpoint presentation used for training here or the training as a pdf here
• This Guide to Evidence Codes is an at-a-glance-overview to the codes you can use for CACAO and how/when they are used
• The helpful handouts for students page also has several VERY USEFUL documents that address PubMed searches, Evidence Codes, a guide to making annotations, and more.
• The Rules page has a quick-guide to the competition rules, as well as a link to the official rules. Make sure you read over these, and keep them handy- especially during challenge weeks!
• Scoring of challenges: Judges, and very attentive competitors, may find this general guide to point distribution useful.
• Finally, the links at the bottom of the page (under Pages in category "CACAO Spring 2012") may be helpful.
• FAQs about the protein pages used for the competition

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. IEP: Inferred from Expression Pattern
5. ISO: Inferred from Sequence Orthology - requires with/from field to be filled in
6. ISA: Inferred from Sequence Alignment - requires with/from field to be filled in
7. ISM: Inferred from Sequence Model - requires with/from field to be filled in
8. IGC: Inferred from Genomic Context

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

NEW CALENDAR FOR ROUNDS

How the annotations will be checked

If any of these conditions are not met, the GO annotation will be marked as incorrect and will not be submitted to UniProt or other databases.

1. Is the annotation on the right protein’s page? (Is the paper about the right protein and the right organism/strain?)
2. Is the annotation complete? Does it have the 4 required parts? Does the annotation require either of the additional 2 fields (i.e. does the annotation use an evidence code that needs the with/from field filled in)?
3. Has the student used information NOT allowed by the CACAO rules (i.e. evidence code or binding terms)?
4. Do the notes point to a figure/table that supports the annotation? (i.e. is the paper a peer-reviewed article (not a review article)? Is the figure or table experimental data (no models or crystal structures)?) And do all parts of the figure apply to the term (eg, is part B using a different organism or only showing component when the annotation was for a process term)?
5. Is there a more suitable GO term (more or less specific)?
6. Does the evidence code fit with the experiment described?
7. For IGI, ISO, or ISA have they entered the correct accession in the with/from field?
8. For ISO & ISA, does the protein in the with/from field have a GO annotation that has experimental evidence for that GO term? (i.e. Does the annotation maintain a direct chain of evidence?)
9. Is the annotation complete, correct and accurate based on the paper? (i.e. will it be submitted to UniProt?)

Class Information

• The class syllabus is here as well as past syllabi (just in case old students need it!)
• For TAMU students:
  • list of review articles Bren gave to previous TAMU CACAO students

Participating Schools

• Michigan State Univ.
• North Dakota State.
• Texas A&M Univ.
• Univ. of Central Florida
• Univ. of North Texas
• University of Wisconsin Parkside