Areas of Interest
Information extraction, named entity recognition, named entity relationship extraction, extractive summarisation, knowledge representation, natural language processing, text mining and resource curation platforms.
Experience and Education
Please visit the LinkedIn profile
- Europe PubMed Central
A collaboration with the European Bioinformatics Institute (EBI), MIMAS and the British Library on a European version of the PubMed Central paper repository. NaCTeM's contribution include the applications of text mining to enhance information retrieval and knowledge discovery.
A web-based workbench for the collaborative development of text-processing workflows and semi-automatic curation of textual resources.
Recently Completed Projects
- BioCreative IV: Critical Assessment of Information Extraction in Biology challenge
Our team participated in 4 out of 5 tracks and our solutions were top-ranked in several evaluation setups.
- KISTI Pathway
Supporting the curation of pathway models by automatically analysing literature relevant to pathway reactions.
- Infectious diseases
A National Institute of Health (NIH) project in collaboration 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.
- Clinical trials
A search application that applies text mining and data mining to enriching clinical trials with metadata and recommending inclusion and exclusion criteria for new trials.
For a more complete list of publications please visit the Google Scholar profile and NaCTeM's publications website where you can also find pointers to full text.
- Rak, R., Batista-Navarro, R. T. B., Rowley, A., Carter, J. and Ananiadou, S. Text Mining-assisted Biocuration Workflows in Argo. Database: The Journal of Biological Databases and Curation, 2014
- Rak, R., Batista-Navarro, R. T. B., Carter, J., Rowley, A. and Ananiadou, S. Processing Biological Literature with Customisable Web Services Supporting Interoperable Formats. Database: The Journal of Biological Databases and Curation, 2014
Batista-Navarro, R. T. B., Rak, R. and Ananiadou, S. Chemistry-specific Features and Heuristics for Developing a CRF-based Chemical Named Entity Recogniser. In Proc. of Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, USA, pp. 55-59, 2013
Ohta, T., Pyysalo, S., Rak, R., Rowley, A., Chun, H.-W., Jung, S. -J., Choi, S. -P. and Ananiadou, S. Overview of the Pathway Curation (PC) task of BioNLP Shared Task 2013. In Proc. of BioNLP Shared Task 2013 Workshop, Association for Computational Linguistics, Sofia, Bulgaria, pp. 67-75, 2013
Rak, R. and Ananiadou, S. Making UIMA Truly Interoperable with SPARQL. In Proc. of the 7th Linguistic Annotation Workshop & Interoperability with Discourse, Sofia, Bulgaria, In press
Rak, R., Rowley, A., Carter, J. and Ananiadou, S. Development and Analysis of NLP Pipelines in Argo. In: Proceedings of the System Demonstration Session at The 51st Annual Meeting of the Association for Computational Linguistics, Association for Computational Linguistics, Sofia, Bulgaria, In press
Miwa, M., Ohta, T., Rak, R., Rowley, A., Kell, D. B., Pyysalo, S. and Ananiadou, S. A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. Bioinformatics, 29(13), i44-i52, 2013
Rak, R., Kolluru, B. and Ananiadou, S.
Building trainable taggers in a web-based, UIMA-supported NLP
In Proc. of the 50th Annual Meeting of the Association for Computational Linguistics,
Pyysalo, S., Ohta, T., Rak, R., Sullivan, D., Mao, C., Wang, C., Sobral, B., Tsujii, J. and Ananiadou, S.
Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011.
BMC Bioinformatics, 13(Suppl. 11), S2, 2012
Rak, R., Rowley, A. and Ananiadou, S.
Collaborative Development and Evaluation of Text-processing Workflows in a UIMA-supported Web-based Workbench.
In Proc. of the Eighth International Conference on Language Resources and Evaluation (LREC 2012), pp. 2971-2976, Istanbul, Turkey, May 2012.
Rak, R., Rowley, A., Black, W.J. and Ananiadou, S.
Argo: an integrative, interactive, text mining-based workbench supporting curation.
Database: The Journal of Biological Databases and Curation, 2012
Wang, X., Rak, R., Restificar, A., Nobata, C., Rupp, C. J., Batista-Navarro, R. T. B., Nawaz, R. and Ananiadou, S.
Detecting Experimental Techniques and Selecting Relevant Documents for Protein-Protein Interactions from Biomedical Literature.
BMC Bioinformatics, 12(Suppl 8), S11, 2011.
Rak, R., Kurgan, L., and Reformat, M.
A tree-projection-based algorithm for multi-label recurrent-item associative-classification rule generation.
Data and Knowledge Engineering, 64(1):171-197, 2008.
Rak, R., Kurgan, L., and Reformat, M.
Multilabel associative classification categorization of MEDLINE articles into MeSH keywords.
IEEE Engineering in Medicine and Biology Magazine,
University of Manchester
- Text Mining (COMP61332); Instructor; 2011, 2012, 2013, 2014
University of Alberta
- Principles of Software Implementation (CMPE210); Principal Instructor; 2008
- Principles of Software Implementation (CMPE210); Lab Instructor; 2006, 2007
- Introduction to Software Engineering Process (CMPE300); Lab Instructor; 2006, 2007, 2008
- Computer Programming for Engineers (ENCMP100); Teaching Assistant; 2006, 2007, 2008, 2009
- Software Systems Design Project (CMPE440); Teaching Assistant; 2005
Manchester Institute of Biotechnology
131 Princess Street, Manchester M1 7DN, UK