News
[Invited Talk] OntoGene & SASEBio: biomedical text mining research at UZH
News Announcements Published December 11, 2013Date: 2013.12.16 (Mon.) 9:30
Venue: Lecture Room Blue (B301), KI Bldg.
Host: Jong C. Park
Speaker:
Fabio Rinaldi, University of Zurich, Switzerland
Title:
OntoGene & SASEBio: biomedical text mining research at UZH
Abstract:
In this talk I will describe text mining activities conducted by the OntoGene research group (www.ontogene.org) at the University of Zurich (UZH). The OntoGene group is supported by the Swiss National Science Foundation (project SASEBIO: Semi-Automated Semantic Enrichment of the Biomedical Literature) and by the Scientific Information Management group at Roche Pharmaceuticals. The SASEBio project focuses in particular on applications of text mining technologies to the process of biomedical database curation.
The OntoGene text mining system is based on a scalable entity recognition component with a semi-automated organism-based disambiguation module, an in-house dependency parser, and a flexible relation mining approach. The OntoGene team has participated in several biomedical text mining challenges (BioCreative, BioNLP, CALBC), obtaining competitive results in all of them. Some of these results will be discussed in the talk.
The OntoGene Document Inspector (ODIN) is an interactive tool which allows database curators to leverage upon the results of the OntoGene text mining system and use them in their curation tasks. One recent version of the system has been tested in the curation process of the Pharmacogenomics Knowledge Base (PharmGKB), and another version adapted for the Comparative Toxicogenomics Database in the context of a BioCreative challenge.
Speaker Bio:
Fabio Rinaldi is the leader of the OntoGene research group at the University of Zurich and the principal investigator of the SASEBio project. He holds an MSc in Computer Science (University of Udine, Italy) and a PhD in Computational Linguistics (University of Zurich, Switzerland). He is author or co-author of 100+ scientific publications (including 19 journal papers) dealing with topics such as Ontologies, Text Mining, Text Classification, Document and Knowledge Management, Language Resources and Terminology.
