Why biocuration?

The rapid advances in genomics technology mean that we are discovering genes faster than we can figure out what their gene products do. For most new sequences, gene function will be inferred by comparison with genes from well-studied organisms that have published experimental data. This means that the quality of functional annotation for genes from these systems is very important for the future of biology. The CACAO project aims to remedy the problem of not enough available curators by tapping into a vast resource: the large number of undergraduates studying biology-related fields at world-renowned institutions who can biocurate.

A Short History

The original Community Assessment of Community Annotation with Ontologies (CACAO) project started as a multi-institution student competition allowing large-scale manual community annotation of gene function using the Gene Ontology. CACAO was developed and run at Texas A&M University by the research team of Dr. Jim Hu, with participation from many other institutions. An initial publication described the MediaWiki framework used for hosting competitions and browsing the Gene Ontology. A later publication described the scientific impact of the hundreds of participants over more than a decade.

How does it work?

In CACAO, teams of students get points for making correct annotations or by correcting their competitors ungraded annotations. Annotations that are judged to be correct will be submitted to the GO Consortium for incorporation into the overall annotation of gene products in major databases. Scientists worldwide use these databases daily to perform large-scale gene set analyses. The scope of CACAO annotation can be any protein in UniProt where students can find experimental literature supporting appropriate GO annotations. Therefore, CACAO teams can be run as courses or as club activities across numerous biological fields.

The Present

In 2024, CACAO re-launched as Creating Annotations through Critical Analysis of Original research, a lab course at Texas A&M with a microbiology theme led by Dr. Jolene Ramsey and Dr. Debby Siegele. Both were deeply involved in the original implementation of CACAO. This course is rooted in giving students authentic practice developing essential disciplinary skills like reading primary scientific literature and contributing their work products back to the scientific community for use in research investigations. A&M undergraduates can participate by enrolling in Howdy under course: BIOL489 SPTP Crit Anal.