Indika Kahanda Asst Professor candidate - Automated Prediction and Curation of Bio-Ontology Terms
- Monday, May 8, 2017 from 4:10pm to 5:00pm
- Barnard Hall, 59717-3880 - view map
Automated Prediction and Curation of Bio-Ontology Terms
A key component of Precision Medicine is to take into account the individual variability in genes for disease treatment. The successes of this process is highly dependent on the reliability of large-scale biological databases. Typically, these databases are manually curated by professional biocurators who extract the information on biological entities from biomedical literature in the form of standard vocabularies called bio-ontologies. However, this process is highly resource consuming and thus leads to the incompleteness of these databases. Furthermore, wet-lab experiments that are used to generate evidence on many different biological entities such as proteins are also highly resource consuming in nature. We identify these as two of the major bottlenecks of this pipeline and attempt to find answers to (1) can we develop accurate high-throughput computational tools for predicting bio-ontology terms?, and (2) can we automate the process of biocuration using natural language processing techniques?. In this talk, I will describe two projects, involving automated prediction and curation of Human Phenotype Ontology (HPO) and Gene Ontology (GO) terms, that attempt to provide answers to these questions.
Dr. Indika Kahanda is an Assistant Teaching Professor in the Gianforte School of Computing at Montana State University. His research interests include Bioinformatics and Biomedical Natural Language Processing. He works on the application of machine learning, data mining and natural language processing techniques for solving problems related to large-scale biological data. His current work focuses on predicting mental illness categories for biomedical literature, protein function prediction and protein-function relation extraction from biomedical literature. He received his Ph.D. in Computer Science from Colorado State University in 2016 in the area of Bioinformatics, a Master of Science in Computer Engineering from Purdue University in 2010, and a Bachelor of Science in Computer Engineering from University of Peradeniya, Sri Lanka in 2007.