helpful annotation examples

Unacceptable GO annotations

For CACAO I students, here are some examples of some GO annotations that I would mark as unacceptable

• I would mark this annotation wrong because the authors aren't characterizing the PROTEIN in this figure. The figure is a Northern blot measuring a change in the mRNA levels and doesn't characterize anything specifically about the PROTEIN.

• Here's one I would mark wrong for having an qualifier that is unnecessary. We already assume a protein contributes_to a bioloigcal process, so there is NO NEED for a qualifier on this annotation.

Acceptable GO annotations

• If you see a paper that looks like it is about an enzyme (i.e. ends in -ase), see if the authors assay or give the activity or specific activity or kinetics or enzyme kinetics for the protein. It might look like this in a paper:

• Here is an EXCELLENT annotation made by Schal007 during the UW-Parkside competition in the Fall 2011 semester. On the page for the Mouse ADA17 protein (Mouse:ADA17), this student added the annotation using PMID:20610799.

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

Downloadable handouts

• Step by step instructions on adding an annotation to GONUTS
• Experiments and their evidence codes
• Useful urls for students
• Hints for searching PubMed efficiently
• Evidence code decision tree