The Spring 2012 season of CACAO has started!
Category:CACAO
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 is developed and is currently run at Texas A&M University, along with many other institutions.
If you are interested in participating, please email us - Brenley or Jim.
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About CACAO
The rapid advances in genomics technology mean that we are discovering genes faster than we can figure out what they do. For most new sequences, gene function will be inferred by comparison with well-studied systems that have published experimental data. This means that the quality of functional annotation for these systems is very important for the future of biology. This course aims to remedy the problem of available curators by leveraging undergraduates -- teaching them how to critically read scientific literature and make useful and correct annotations. We think that the large number of biology-related undergraduates at world-renowned institutions are a vast untapped resource for biocuration.
Help for students
General
If you're having any issues, first make sure you are still logged into GONUTS!
- 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!
- The class syllabus is here as well as past syllabi (just in case old students need it!)
- Rubrics include the judge's point-assignment guidelines and rubrics for instructors pertaining to group work, quality of annotations and challenges, etc.
- The helpful handouts for students page has several documents that address PubMed searches, Evidence Codes, a guide to making annotations, and more.
- The Gene Ontology Help page is an alternative, general explanation to just what you're doing, why it's important, and what's involved. Read over this short guide if you're still completely lost as to what CACAO is all about, and don't worry- talk to Brenley for more help.
- Finally, the links at the bottom of the page (under Pages in category "CACAO") may be helpful.
Evidence codes
- The helpful handouts for students page also has several handouts including the Evidence Code Decision Tree and a "Sampler" sheet listing experiments that are typically used to support each evidence code
- This Guide to Evidence Codes is an at-a-glance-guide to the codes you can use for CACAO and how/when they are used
- The Official GO Consortium documentation is a great resource if the CACAO guide brushes over what you were looking for, or you want to be absolutely certain about the evidence code for a challenge or your annotation
- Please note this details all of the codes used for annotating, including ones that are OFF-LIMITS for CACAO. Although you are encouraged to read over the whole document, remember you (and your peers) can only use the 8 CACAO codes.
- Here's the 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
- IEP: Inferred from Expression Pattern
- 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
Papers/PubMed
- List of review articles: Some reviews that mention MANY potential targets to annotate. Look up the appropriate reference(s) in each review for the gene you're interested in annotating, and remember you cannot use these reviews as your annotation "reference"- but most of the papers the reviews referenced are great sources or leads.
- 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
How 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.
- Is the annotation on the right protein’s page? (Is the paper about the protein?)
- 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)?
- Has the student used information NOT allowed by the CACAO rules (i.e. evidence code or binding terms)?
- Do the notes point to a figure/table that supports the annotation? (i.e. is the paper a peer-reviewed article (no review article)? Is the figure or table experimental data (no models or crystal structures)?)
- Is there a more suitable GO term (more or less specific)?
- Does the evidence code fit with the experiment described?
- For IGI, ISO, or ISA have they entered the correct accession in the with/from field?
- 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?)
- Is the annotation complete, correct and accurate based on the paper? (i.e. will it be submitted to UniProt?)
Course Materials
For Instructors
Instructors may find the following resources helpful.
- CACAO Learning Objectives
- Instructors Manual A pdf of the manual for instructors
- Help:CACAO: This page is intended to be a reference for setting up a new session for CACAO on GONUTS.
- Group work assessment
- Calendar of rounds
Biocurator Training Powerpoints
- File:Biocurator Training 1.ppt
- File:Biocurator training 2.ppt
- File:Biocurator Training 3.ppt
- File:CACAO remote training.ppt
Past Semesters
Spring 2010
We ran a pilot competition in the Spring of 2010 with 20 volunteer undergraduates from Texas A&M University. This was run on our sister site, EcoliWiki.
Fall 2010
See the main article at: Category:CACAO_Fall_2010
After the initial test-run and a lot of positive feedback from the students, the competition was set up as a multi-national competition in the Fall of 2010 with the addition of teams from University College London.
Spring 2011
See the main article at: Category:CACAO_Spring_2011
We completed a second full semester-long competition in Spring 2011 with teams from TAMU, UNT, Miami Univ (Ohio), Penn State & Michigan State using GONUTS.
Fall 2011
See the main article at: Category:CACAO_Fall_2011
We finished the Fall 2011 competition that had students from TAMU, North Dakota State, Hofstra, Swarthmore, Houston Baptist, Mississippi State, Wisconsin, Wisconsin-Parkside and University College, London. A team from UCL won the competition with teams from TAMU & Hofstra close behind.
Spring 2012
See the main article at: Category:CACAO_Spring_2012
For the scoreboard, calendar, team listing, and other specific information, see the Spring 2012 page.
Links and Other Resources
- The Daily Scan Genome Web report on CACAO Yay! CACAO in the news!
- CACAO on UCL Participants at UCL
Subcategories
This category has the following 14 subcategories, out of 14 total.
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