OntoGene
Text Mining for Biomedical Literature
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.
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.
NEWS!
April 2010: The Swiss National Science Foundation (SNF) has approved the project SASEBio (Semi-Automated Semantic Enrichment of the Biomedical Literature). Duration: 3 years. Funding: 3 post-docs. Additional financial and practical
support provided by Novartis Pharma AG, NITAS, Text Mining Services,
CH-4002, Basel, Switzerland.
January 2010: We have successfully completed the SNF - funded project Detection of Biological Interactions from Biomedical Literature (grant 100014-118396/1).
October 2009: Our participation to the BioCreative II.5 competitive evaluation of biomedical text mining systems resulted in the best run for the detection of protein-protein interactions (according to the AUC iP/R metric). Our system was overall considered as one of the best three (look for system T37 in the graph to the left).
February 2009 : One of our papers at CICLING has been selected for a Best Paper Award! See paper (3) in the list of selected papers below.
Selected publications
- Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess, Martin Romacker. An environment for relation mining over richly annotated corpora: the case of GENIA. BMC Bioinformatics 2006, 7(Suppl 3):S3. doi:10.1186/1471-2105-7-S3-S3
- Fabio Rinaldi, Thomas Kappeler, Kaarel Kaljurand, Gerold Schneider, Manfred Klenner, Simon Clematide, Michael Hess, Jean-Marc von Allmen, Pierre Parisot, Martin Romacker, Therese Vachon. OntoGene in BioCreative II. Genome Biology, 2008, 9:S13.
- Gerold Schneider, Kaarel Kaljurand, Thomas Kappeler, Fabio Rinaldi.
Detecting protein-protein interactions in biomedical texts using a parser and linguistic resources. CICLING 2009. - Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Simon Clematide, Thérèse Vachon, Martin Romacker, "OntoGene in BioCreative II.5," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 17 May. 2010. IEEE computer Society Digital Library. IEEE Computer Society, <http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.50>
Notes
This is the new web site of the OntoGene Project. If you are looking for the old web site (no longer mantained), click here.
NB: OntoGene is a non-commercial research project. We have nothing to do with a commercial product of the same name. We neither endorse nor recommend such a product.