Help for Students
Decision Tree: Experimental Codes (IMP, IDA, IGI, ISS)
Decision Tree: Sequence/Structure Codes (ISS, ISA, ISO, ISM)
Step by step instructions on adding an annotation
ECs for common experiments
List of useful/helpful sites
CACAO students, please print out/bookmark the starred entries (★); you will likely need to refer to them often. These links are identical to the gallery above, but have more detailed descriptions:
★ Experimental evidence code decision tree: A chart that, with yes/no questions, that can be very useful in determining what EXPERIMENTAL evidence code to use: IDA, IMP, IGI.
★ Step by step instructions on adding an annotation to GONUTS: An ILLUSTRATED guide for the whole process, from GO terms and finding accessions to the final annotation!
- Table Edit Help is another illustrated and very detailed guide that is specific to entering information into tables.
- Experiments and their evidence codes: A list of some types of experiments and the evidence codes that are usually associated with them. This is good as a starting point if you're not quite sure what the experiment is showing, but remember, one type of experiment may support different evidence codes; for example what shows an IMP for a process term could possibly be an IDA for a component term as well.
★ Hints for searching PubMed efficiently: This lists some pointers that allow you to spend less time searching PubMed for papers, and tips on how to select papers to read.
★ Hints for searching UniProt efficiently: What the gold stars mean, how to do basic/advances searches, and how to narrow down your options.
- The Gene Ontology has an EXCELLENT guide on transcription terms.
- Useful urls for students: Lists practically all the sites you will use or might find helpful, info if you need to contact help, and some links that are pretty fun to explore if you are interested or are looking for a place to start.
- How to request new GO Terms: New terms are sometimes needed, but they are handled by a group other than GONUTS. Here are directions on how to access the Ontology Tracker site. We usually offer some incentive to encourage the submission of new terms, please ask your instructor for more details.
Acceptable Evidence Codes
Here's a list of the evidence codes that CACAO students may use:
- IDA: Inferred from Direct Assay
- IMP: Inferred from Mutant Phenotype
- IGI: Inferred from Genetic Interaction - requires with/from field to be filled in
- ISS: Inferred from Sequence or Structural Similarity - almost always requires with/from field to be filled in
- ISO: Inferred from Sequence Orthology - requires with/from field to be filled in
- ISA: Inferred from Sequence Alignment - requires with/from field to be filled in
- ISM: Inferred from Sequence Model - requires with/from field to be filled in
- IGC: Inferred from Genomic Context