OntoGene 

OntoGene is a research project based at the Institute of Computational Linguistics (Department of Computer Science) of the University of Zurich. Please check our publications.

Our work focuses on the extraction of semantic relations between specific biological entities (such as Genes and Proteins) from the scientifical literature (e.g. PubMed).

Our approach is based upon high-precision robust syntactic parsing of the target documents. Please check our applications. A good documentation of our original application can be found in the paper (1) below.

NEWS!!!!

09/02/21 : One of our papers at CICLING has been selected for a Best Paper Award!!!!

Gerold Schneider, Kaarel Kaljurand, Thomas Kappeler, Fabio Rinaldi.
Detecting protein-protein interactions in biomedical texts using a parser and linguistic resources. CICLING 2009.

SNF - funded project

Detection of Biological Interactions from Biomedical Literature (grant 100014-118396/1), funded by the Swiss National Science Foundation (SNF). The project started on 01.04.2008 and will last 18 months. Additional financial and practical support is provided by Novartis Pharma AG, NITAS, Text Mining Services, CH-4002, Basel, Switzerland. See here for more details.

BioCreative participation 

In 2006/2007 we participated in the 2nd BioCreative competition, obtaining very good results in the tasks of detecting protein interactions, and detecting experimental methods. A detailed description of the setting of the competition and our own contribution and results can be found in article (2) below.