Infectious Diseases

In September 2009, the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), awarded a 5-year contract to to support the biomedical research community's work on infectious diseases.

As part of the contract, NaCTeM is collaborating with Virginia Bioinformatics Insititute (VBI) to integrate vital information on pathogens, provide key resources and tools to scientists, and help researchers to analyze genomic, proteomic and other data arising from infectious disease research. The new contract supports the development of the PathoSystems Resource Integration Center (PATRIC); providing rich data and analysis tools for all bacterial species in the selected NIAID category A-C priority pathogens list. NaCTeM is providing literature-based text mining capability and services.

Relevant Software/Websites

Project Team

Prinicipal Investigator: Prof. Sophia Ananiadou
Project team: Dr Rafal Rak, Dr Sampo Pyysalo, Dr Tomoko Ohta,
Prof. Jun'ichi Tsujii.

BioNLP 2011 Shared Task

Extraction of event in full-text papers concerning the molecular mechanisms involved in infectious diseases will feature as one of the main tasks in the BioNLP 2011 Shared Task. The task follows the basic setup of the BioNLP'09 shared task, with biomolecular events concerning genes and gene products as the core information extraction target. The task and corpora will be prepared as a collaborative effort by NaCTeM, the Tsujii laboratory (Japan) and Virginia Bioinformatics Institute (USA).


Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Dan Sullivan, Chunhong Mao, Chunxia Wang, Bruno Sobral, Jun'ichi Tsujii and Sophia Ananiadou (2012), Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. BMC Bioinformatics 13(Suppl 11):S2.

Sampo Pyysalo, Tomoko Ohta, Han-Cheol Cho, Dan Sullivan, Chunhong Mao, Bruno Sobral, Jun'ichi Tsujii, Sophia Ananiadou (2010). Towards Event Extraction from Full Texts on Infectious Diseases. In Proceedings of the 2010 Workshop on Biomedical Natural Language Processing (BioNLP 2010), ACL, pp. 132-140