Riza Batista-Navarro, PhD

   2016

• Batista-Navarro, R., Carter, J. and Ananiadou, S. (In Press). Argo: Enabling the development of bespoke workflows and services for disease annotation. In: Database: The Journal of Biological Databases and Curation.
• Shardlow, M., Przybyła, P., Batista-Navarro, R., Carter, J., McNaught, J. and Ananiadou, S. (In Press). Facilitating and promoting web annotation with Argo. In: Proceedings of I Annotate 2016.
• Thompson, P., Batista-Navarro, R., Kontonatsios, G., Carter, J., Toon, E., McNaught, J., Timmermann, C., Worboys, M. and Ananiadou, S. (2016). Text Mining the History of Medicine. In: PLOS One, 11(1), e0144717.

   2015

• Batista-Navarro, R., Rak, R. and Ananiadou, S. (2015). Optimising chemical named entity recognition with pre-processing analytics, knowledge-rich features and heuristics. Journal of Cheminformatics, 7(Suppl 1):S6.
• Alnazzawi, N., Thompson, P., Batista-Navarro, R. and Ananiadou, S. (2015). Using text mining techniques to extract phenotypic information from the PhenoCHF corpus. In: BMC Medical Informatics and Decision Making, 15(Suppl. 2), S3.
• Fu, X., Batista-Navarro, R., Rak, R. and Ananiadou, S. (2015). Supporting the Annotation of Chronic Obstructive Pulmonary Disease (COPD) Phenotypes with Text Mining Workflows. In: Journal of Biomedical Semantics, 6:8.
• Batista-Navarro, R. and Ananiadou, S. (2015). Adapting ChER for the recognition of chemical mentions in patents. In: Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Seville, Spain, pp. 149-153.
• Batista-Navarro, R. and Ananiadou, S.. (2015). Augmenting the Medical Subject Headings vocabulary with semantically rich variants to improve disease mention normalisation. In: Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Seville, Spain, pp. 311-316.
• Batista-Navarro, R., Carter, J. and Ananiadou, S. (2015). Development of bespoke machine learning and biocuration workflows in a BioC-supporting text mining workbench. In: Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Seville, Spain, pp. 51-56.
• Batista-Navarro, R., Carter, J. and Ananiadou, S. (2015). Semi-automatic curation of chronic obstructive pulmonary disease phenotypes using Argo. In: Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Seville, Spain, pp. 403-408.
• Batista-Navarro, R., Nawaz, R., Zerva, C. and Ananiadou, S. (2015). Bridging text-mined biomolecular events to pathway models using approximate subgraph matching techniques. In: Proceedings of the 16th International Conference on Systems Biology, Singapore.
• Batista-Navarro, R., Ulate, W., Hammock, J., Kontonatsios, G., Rose-Sandler, T. and Ananiadou, S. (2015). Unlocking knowledge in biodiversity legacy literature through automatic semantic metadata extraction. In: Proceedings of the TDWG 2015 Annual Conference.
• Mihăilă, C., Batista-Navarro, R., Alnazzawi, N., Kontonatsios, G., Korkontzelos, I., Rak, R., Thompson, P. and Ananiadou, S.. (2015). Mining the biomedical literature. In: Healthcare Data Analytics, pages 251-308, CRC Press.

   2014

• Comeau, Donald C., Batista-Navarro, R., Dai, Hong-Jie, Islamaj Doğan, Rezarta, Jimeno Yepes, Antonio, Khare, Ritu, Lu, Zhiyong, Marques, Hernani, Mattingly, Carolyn J., Neves, M., Peng, Yifan, Rak, R., Rinaldi, F., Tsai, Richard Tzong-Han, Verspoor, K., Wiegers, Thomas C., Wu, Cathy H. and Wilbur, W. (2014). BioC interoperability track overview. In: Database: The Journal of Biological Databases and Curation, 2014.
• Rak, R., Batista-Navarro, R., Carter, J., Rowley, A. and Ananiadou, S. (2014). Processing Biological Literature with Customisable Web Services Supporting Interoperable Formats. In: Database: The Journal of Biological Databases and Curation.
• Rak, R., Batista-Navarro, R., Rowley, A., Carter, J. and Ananiadou, S. (2014). Text Mining-assisted Biocuration Workflows in Argo. In: Database: The Journal of Biological Databases and Curation.
• Batista-Navarro, R., Islam, A., Ulate, W., Hammock, J., Soto, A., Ananiadou, S. and Milios, E.. (2014). Enriching the legacy literature with OCR corrections and text-mined semantic metadata. In: Proceedings of the TDWG 2014 Annual Conference.
• Fu, X., Batista-Navarro, R., Rak, R. and Ananiadou, S. (2014). A Strategy for Annotating Clinical Records with Phenotypic Information relating to the Chronic Obstructive Pulmonary Disease. In: Proceedings of the Phenotype day at ISMB 2014 (pp. 1-8).
• Rak, R., Rowley, A., Carter, J., Batista-Navarro, R. and Ananiadou, S. (2014). Interoperability and Customisation of Annotation Schemata in Argo. In: Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC 2014), Reykjavik, Iceland (pp. 3837-3842).

   2013

• Batista-Navarro, R., Rak, R. and Ananiadou, S. (2013). Chemistry-specific Features and Heuristics for Developing a CRF-based Chemical Named Entity Recogniser. In: Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, USA (pp. 55-59).
• Batista-Navarro, R., Rak, R. and Ananiadou, S. (2013). NaCTeM CTD Web Services. In: Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, USA (pp. 85-89).
• Rak, R., Batista-Navarro, R., Rowley, A., Carter, J. and Ananiadou, S. (2013). Customisable Curation Workflows in Argo. In: Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, USA (pp. 270-278).
• Rak, R., Batista-Navarro, R., Rowley, A., Miwa, M., Carter, J. and Ananiadou, S. (2013). NaCTeM's BioC Modules and Resources for BioCreative IV. In: Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, USA (pp. 61-67).
• Batista-Navarro, R., Kontonatsios, G., Mihăilă, C., Thompson, P., Rak, R., Nawaz, R., Korkontzelos, I. and Ananiadou, S. (2013). Facilitating the Analysis of Discourse Phenomena in an Interoperable NLP Platform. Computational Linguistics and Intelligent Text Processing: 14th International Conference, CICLing 2013 (Vol. 7816, pp. 559-571). Springer Berlin Heidelberg.
• Mihăilă, C., Kontonatsios, G., Batista-Navarro, R., Thompson, P., Korkontzelos, I. and Ananiadou, S. (2013). Towards a Better Understanding of Discourse: Integrating Multiple Discourse Annotation Perspectives Using UIMA. In: Proceedings of the 7th Linguistic Annotation Workshop and Interoperability with Discourse, Association for Computational Linguistics, Sofia, Bulgaria (pp. 79-88). Recipient of LAW Challenge Award.
• Kontonatsios, G., Thompson, P., Batista-Navarro, R., Mihăilă, C., Korkontzelos, I. and Ananiadou, S.(2013). Extending an interoperable platform to facilitate the creation of multilingual and multimodal NLP applications. In: Proceedings of the 51st Annual Meeting of the Association for Computational Linguistics: System Demonstrations, Association for Computational Linguistics, Sofia, Bulgaria (pp. 43-48).

   2012

• Mihăilă, C., Batista-Navarro, R. and Ananiadou, S. (2012). Analysing Entity Type Variation across Biomedical Subdomains. In: Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012) (pp. 1-7).
• Mihăilă, C., and Batista-Navarro, R. (2012). What's in a Name? Entity Type Variation across Two Biomedical Subdomains. In: Proceedings of the Student Research Workshop at the 13th Conference of the European Chapter of the Association for Computational Linguistics (pp. 38-45). Association for Computational Linguistics.

   2011

• Wang, X., Rak, R., Restificar, A., Nobata, C., Rupp, C. J., Batista-Navarro, R., Nawaz, R., et al. (2011). Detecting Experimental Techniques and Selecting Relevant Documents for Protein-Protein Interactions from Biomedical Literature. BMC Bioinformatics, 12(Suppl 8), S11.
• Batista-Navarro, R. and Ananiadou, S. (2011). Adapting the Cluster Ranking Supervised Model to Resolve Coreferences in the Drug Literature. In: Proceedings of the Fourth International Symposium on Languages in Biology and Medicine (LBM 2011).
• Batista-Navarro, R. and Ananiadou, S. (2011). Building a Coreference-annotated Corpus from the Domain of Biochemistry. In: Proceedings of BioNLP 2011 (pp. 83-91).
• Batista-Navarro, R. and Ananiadou, S. (2011). Discovering Potential Drugs by Extracting Biological Activities of Natural Products. In: Proceedings of the Workshop on Mining the Pharmacogenomics Literature, Pacific Symopsium on Biocomputing.

   2010

• Wang, X., Rak, R., Restificar, A., Nobata, C., Rupp, C. J., Batista-Navarro, R., Nawaz, R., et al. (2010). NaCTeM Systems for BioCreative III PPI Tasks. In: Proceedings of the BioCreative III Workshop (pp. 142-147).