The OntoGene literature mining web service

Abstract

Text mining technologies are increasingly providing an effective response to the growing demand for faster access to the vast amounts of information hidden in the literature. Several tools are becoming available which offer the capability to mine the literature for specific information, such as for example protein-protein interactions or drug-disease relationships. The biomedical text mining community regularly verifies the progress of such systems through competitive evaluations, such as BioCreative, BioNLP, i2b2, CALBC, CLEF-ER, BioASQ, etc.

The OntoGene system is a text mining system which specialises in the detection of entities and relationships from selected categories, such as proteins, genes, drugs, diseases, chemicals. The quality of the system has been tested several times through participation in some of the community-organised evaluation campaigns.

In order to make the advanced text mining capabilities of the OntoGene system more widely accessible without the burden of installation of complex software, we are setting up a web service that will allow any remote user to submit arbitrary documents. The results of the mining service (entities and relationships) are then delivered back to the user as XML data, or optionally can be inspected via a flexible web interface.