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Curiosity and Computers Leads to Innovative, Visual Database for Plant Scientists

July 27, 2017

Richard Linchangco

Graduate student Richard Linchangco shares his role in developing a new online, knowledgebase as part of the Plant Pathways Elucidation Project (P2EP) at the NC Research Campus.

When Richard Linchangco finished his undergraduate degree in biology at the University of Illinois at Chicago, he found himself interested in combining biology and computer science. His curiosity led him to a Master’s degree and soon, a PhD, both in bioinformatics from UNC Charlotte.

His graduate studies were not on the main campus of UNC Charlotte. He instead worked at the Bioinformatics Services division (BiSD) at the North Carolina Research Campus (NCRC) in Kannapolis, just north of Charlotte. He joined BiSD just as the Plant Pathway Elucidation Project (P2EP) was launching. He became one of the first graduate mentors to help lead the research and scientific training program. P2EP involves multiple research centers at the NCRC. They focus on plant science and genomics while training undergraduates and graduates students for careers in science.

“I had a thirst to dive deeper into the field of bioinformatics,” Linchangco explained. “I was introduced to the P2EP program and jumped at the opportunity to learn and research cutting-edge subfields of bioinformatics, such as text mining and knowledge-based discovery.”

Now in his fourth year with P2EP, Linchangco has been instrumental in the development of the P2EP knowledgebase, a data warehouse and knowledge discovery tool that combines agricultural and biomedical data from around the world, both from the public domain and from research conducted by P2EP students.

Linchangco explained that “scientists can access the knowledgebase to see what chemicals plants are making, how plants are making them, and how these different chemicals might be affecting human health. By taking in all of this information, we can start making connections between different sets of data that we might not have seen before.”

The goal is to help crop breeders generate better crops by knowing how phytochemicals are produced and used in the plants as well as understanding how they improve human health. Phytochemicals, such as polyphenols or antioxidants, are non-essential components that are known to improve human health by preventing certain diseases.

“Suppose I am a scientist interested in a certain plant. I want to know the human genes affected by that plant, or I may want to know the plant’s phytochemical profile,” Linchangco said. “Those types of generalized queries are already prepared for people to use.”

The knowledgebase is continuously updated so that scientists can make inquiries and see visual representations of phytochemicals found in plants, phytochemical effects on human genes or pathways influenced by genes to describe their effects on disease.

“The power of the knowledgebase is that it is creating visualizations to help our collaborators make associations they have never made before,” Linchangco said. “P2EP is one of the most collaborative opportunities on campus, and now we are trying to advance genomic resources for crops of interest and understand how they are affecting human health at the molecular level.”

During the summer of 2017, Linchangco and student interns participating in P2EP will work on developing an exploratory interface that allows researchers to access the knowledgebase and begin making queries. Soon after the interface is completed, it will be available for scientists to use.

“Being the inaugural PhD student working on this, he has taken it from concept to actual implementation,” said Cory Brouwer, PhD, BiSD director and P2EP leader. “So he’s really been able to make the vision happen.”

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