Category:CACAO II Spring 2012

Judging

Verify for EVERY Annotation

• For each annotation, the default is incorrect until you have verified EVERY one of the following:

1. Paper
2. Protein (organism & strain)
3. Qualifier
4. GO term
5. Evidence code
6. With/from field
7. Notes
8. Duplicate annotation

Judging QuickList

This is a partial list of the most obvious things that need to be checked:

1. Is the annotation on the right protein’s page? (Is the paper about the right protein and the right organism?)
2. Is the annotation original? Check to make sure that PMID hasn't been used for the same GO & EC, that is, that they didn't just copy an existing row or IEA. Also remember that a GO term implies all of its "parents", so if a more specific GO has been or can be obtained, the annotation is redundant and shouldn't be accepted.
3. 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)?
4. Has the student used information NOT allowed by the CACAO rules (i.e. evidence code or binding terms)?
5. 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)?
6. Is there a more suitable GO term (more or less specific)?
7. Does the evidence code fit with the experiment described?
8. For IGI, ISO, or ISA have they entered the correct accession in the with/from field?
9. 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?)
10. Is the annotation complete, correct and accurate based on the paper? (i.e. will it be submitted to UniProt?)

Scoring Challenges

• Scoring_of_challenges

Sample Annotations for Judges

These are past annotations that have been evaluated to have problems. See if you can identify the issue. Bonus points to anyone that can identify problems the original judges missed!!

1. BACSU:FEUA
2. STRCO:HISX
3. ROSDO:Q16DS5
4. BACSU:LCTP
5. BACSU:RSBX
6. ECOLI:DCUR
7. ECOLI:BASR
8. HUMAN:DDX6
9. ECOLI:NTRB Challenge question!

Feedback

Sample Feedback for CACAO I students

Suggesting a change to a GO term & other papers to look for annotations

Hi,
I'm emailing with a bit of feedback, mostly on PMID:16790015.
1.  Be sure to stay away from the "illegal" evidence codes for CACAO (such as EXP or IPI) and only choose from the 8 listed below the 
   scoreboard on GONUTS.   Also, be sure to not annotate using any binding terms - these are "illegal" for CACAO since they were abused to pump 
 up scores in a previous semester.
2.  For PMID:16790015, I see where you were going, but I don't think fig 1 actually shows NifJ is transferring electrons.  The authors are 
assaying for nitrogenase activity, but they are not assigning that function to NifJ.   The nifJ- mutant has the same level of nitrogenase 
activity as the wild type by the time you factor in the error bars, which means that you cannot make an annotation for NifJ here.  However, 
you could certainly annotate fixX since cells with a mutation in fixX have a dramatically less nitrogenase activity.  I think that I 
would look at GO:0009399 instead of an activity term since it appears FixX has something to do with regulating the nitrogenase activity in 
these cells.  Make sense?
3.  I would look at the refs from the intro, including: Edgren & Nordlund, 2004 and Edgren & Nordlund, 2005.  They look promising to 
annotate based on what is mentioned in the intro.
Email me with any questions & keep annotating!

Changing evidence codes and binding terms & Offering other annotations

Hi,
I'm emailing with some feedback, mostly for PMID:20148901.
1.  EXP is not a permitted evidence code for CACAO.  There is a list on GONUTS below the scoreboard of the 8 you may choose from, so you 
 will have to change this before the challenge week starts.  
2.  I also don't allow annotations to any binding terms, so you'll have to change the GO term/annotation or delete your annotation on 
RHORU:P72322. I know it sucks, but I banned all binding terms after they were abused by competitors in a previous semester to pad their 
score.
3.  I like the annotation to GO:0050765 - it looks excellent.
4.  There are other annotations in this paper as well - I found GO:0043087 & if you look at the children of this term, you might recognize 
GO:0032318 or maybe GO:0032319 *hint - look at Fig 3.  Don't forget that the authors are studying 2 proteins - YopE & SptP and you can 
use this paper to annotate both as long as there is evidence!  Also, you might get an annotation out of this paper for GO:0009405.
Email me with questions & keep annotating!

Changing evidence codes, binding terms & using ISA properly

Hi,
I'm emailing with a bit of feedback, mostly for PMID:8402691.
1.  EXP is not an evidence code you can choose for your annotations.  The 8 you can choose from are on GONUTS below your scoreboard. 
 Be sure to change your evidence code before the challenge period begins.
2.  There are also no binding terms allowed for CACAO.  Unfortunately, students in previous semesters abused these terms to pad their 
 scores, so I have banished them.  You will have to find a different GO term or annotation for RHORT:CYCP.  I know it sucks, but we had to 
just eliminate their use altogether.
3.  Be careful with your ISA annotation because it will need some changes - I haven't looked at the paper, but the GO Consortium requires a 
 GO annotation to be no further than 1 step away from an annotation supported by an experiment.  ISA requires you to put the UniProt 
 accession for the protein yours is similar to in the with/from, but that "similar" protein MUST have an annotation using one of the 
 experimental evidence codes to that term.  It's a bit tricky, but here's a link to more 
 documentation: http://www.geneontology.org/GO.evidence.shtml#isa.  If this doesn't make sense, email me & I'll help you.
4.  For PMID:8402691, don't forget to change the evidence code (I would suggest IDA).  I would also use Table 1 to annotate to GO:0030284 
 since the authors show that the ER protein is the receptor for estrogen.  
Email me if you have any questions & keep annotating!

Fixing PMID formatting & removing a qualifier

Hi,
I am emailing with a bit of feedback, mostly for PMID:10648524.
1.  First, be sure to get the PMID numbers for your papers - we cannot submit anything else in the reference field & I will agree with any 
 challenge that identifies the correct PMID for any PMC paper.  That would really suck since you've put all the work into the 
annotation, so be sure you change this.
2.  Be sure to stay away from the "illegal" evidence codes for CACAO (the permitted ones are listed below the scoreboard on GONUTS) and also 
from any binding terms.  They were abused to pump up scores in a previous semester, so I do not allow any annotation to a binding term.
3.  For PMID:10648524, your annotation does not need a qualifier - contributes_to is only valid with function terms, but I like your GO 
term.  You might consider annotating NifA similarly.
Email me with any questions & keep annotating!

CACAO II Reference Materials

Student resources (including much of what is listed on this page) and more can be found 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.
• Scoring of challenges: This is the general guide to point distribution.
• Finally, the links at the bottom of the page (under Pages in category "CACAO II Spring 2012") may be helpful.

Class Information

• The class syllabus is here (as well as other current/past syllabi)
• Calendar of rounds *will be updated soon!*