CBS students sweep Stanford in gene-annotation competition

06/13/13

UC Davis biology students soundly thumped Stanford this quarter in a gene-annotation competition that runs in a select number of labs in the United States and around the world.

Assistant Professor Siobhan Brady led College of Biological Sciences students in the spring 2013 class, which participated in CACAO—Community Assessment of Community Annotation with Ontologies. The quarter was structured as a joint competition between multiple teams at UC Davis and a class at Stanford, with the mission of annotating genes whose function had been identified electronically but for which there is no primary literature proof.

Brady said that the process was very useful for the students to learn to assess the literature critically and to sort out the hierarchical relationships between gene functions.

“It was tough, but they feel like they can all read papers pretty well and critically now,” Brady said. “And from my end, I realized the distinction between assumed knowledge from my years of experience versus data actually presented in a paper.”

The competition involved four two-week rounds, each with one annotation week followed by a challenge week. Final results: Davis’ three teams claimed the top spots, with Team Database Backend taking first with 387 points, Team Quaternary Structure finishing with 304, and Team G’nUnit earning 168.

During annotation weeks, teams hunted for genes whose function has been annotated electronically but for which there is no primary literature proof. The next step was to find literature and the specific assay demonstrating that this gene has said function, or is involved in a biological process or is located in a particular part of a cell.

Finally, students had to find the correct Gene Ontology Database annotation describing this function, process or cellular component and enter all that information on a web page for each protein.

Then came the challenge weeks, when all the annotations were assessed and, if found incorrect, could be discounted by other teams. Challenge winners took points from losers.

Students said that they found the competition very fun but also surprisingly difficult.

“The fun part was that assembling an annotation was as if building a puzzle where each piece needs to be correct in order for the annotation to be correct. The challenging part of the competition was the starting point and finding which piece (Gene Ontology term or protein) would be the correct piece,” senior Sharon Wei said.

And the challenge weeks sometimes taught the students even more.

“I thought I had no problem doing it until my first round of annotation turned out almost all wrong,” said Chenling Xu, a junior who will graduate in fall 2013. “The most important thing I learned is how bad many annotations are. I am now much more cautious towards studies that use Gene Ontology terms enrichment to make inferences.”

Participants also noted that the team-based competition increased their communications skills, something that isn’t always highlighted in science courses.

“I've learned a great deal not only about genome annotations and the process of scientific research, but also collaboration and the importance of teamwork in success,” senior Betty Wu said. “The most important lesson I received was in learning how to communicate with my classmates to compete against Stanford.”

And the benefits of the competition were a two-way street between students and the field of genetics: Brady noted that CACAO competitions add to the scientific literature, in that students’ approved annotations go directly from the course to gene databases.

“Normally database curators have PhDs,” Brady said. “This is allowing our students to make a very real impact on currently underfunded databases.”

More information

For more about the CACAO competition in general, go to http://gowiki.tamu.edu/wiki/index.php/Category:CACAO; to see Davis’ final standings against Stanford, visit http://gowiki.tamu.edu/wiki/index.php/Category:CACAO_Plants_2013.