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helpful handouts for students

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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 - [1] or Jim.

Help for Students

Downloadable Handouts

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.

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

Since 2019, CACAO has transitioned to using ECO codes for evidence.

  • Additionally, ECO codes can be searched at QuickGO.

Introductory & Practice Material

Intro/Practice Material

Training #1 Paper:

  • PMID:8227000 Escherichia coli topoisomerase IV. Purification, characterization, subunit structure, and subunit interactions

Training #2 Paper:

Practice to identify where in the paper the info came from:

  • PMID:21586683 There are several annotations, as seen on TAIR:LQY1, that have been made using this paper. Note that the annotators used C, P, and F terms for the same paper.
  • PMID:9288922, see the annots to SGD:AAT2

Training #3 Paper:

Example of a Bad-for-CACAO paper on Disease:

From this paper's introduction, also in the abstract: Now, in our present study, we have investigated whether ZA induced growth inhibition and apoptosis in PC-3 and DU-145 may be enhanced by the combination with CA or OA, through inhibition of serine/threonine phosphatases in prostate cancer cells. This investigates the affects of zoledronic acid on specific processes, not the native function of ZA (which is not a protein, but a drug). It would be better to open it and look at the references to find where the serine/threonine phosphatases are ORIGINALLY characterised.