Publications

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2015

  1. McNaught, J., & AlGahtani, S. (2015). Joint Arabic segmentation and part-of-speech tagging. In N. Habash, S. Vogel, & K. Darwish (Eds.), Proceedings of the Second Workshop on Arabic Natural Language Processing. (pp. 108-117). Stroudsburg, USA: Association for Computational Linguistics. . Publication link: fdfcf5e4-0bf6-4204-8122-d86938064082
  2. Almagrabi, H., Malibari, A., & McNaught, J. (2015). A survey of quality prediction of product reviews. International Journal of Advanced Computer Science and Applications, 6(11), 49-58. [7]. DOI: 10.14569/IJACSA.2015.061107. Publication link: 30562523-51ea-42f8-9351-e0dca4c8e773
  3. O'Mara-Eves, A., Thomas, J., McNaught, J., Miwa, M., & Ananiadou, S. (2015). Using text mining for study identification in systematic reviews: a systematic review of current approaches. Systematic Reviews, 4(5). DOI: 10.1186/2046-4053-4-5. Publication link: 195249ea-380c-4499-9132-b5401626d4a2
  4. Ananiadou, S., Thompson, P., Nawaz, R., McNaught, J., & Kell, D. (2015). Event-based text mining for biology and functional genomics. Briefings in Functional Genomics, 14(3), 213-30. DOI: 10.1093/bfgp/elu015. Publication link: 9284975e-2b46-4311-b108-476722f296f5 | PubMed:24907365
  5. Korkontzelos, I., Piliouras, D., Dowsey, A. W., & Ananiadou, S. (2015). Boosting Drug Named Entity Recognition Using an Aggregate Classifier. Artificial Intelligence in Medicine, 65(2), 145–153. DOI: 10.1016/j.artmed.2015.05.007. Publication link: bbe69443-386a-46bd-8378-fadc7f56ef3a
  6. Batista-Navarro, R. T., Carter, J., & 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. (pp. 51-56). Seville, Spain. . Publication link: bf59c608-d8be-4cf9-bfc8-cbe0c881926a
  7. Batista-Navarro, R. T., & Ananiadou, S. (2015). Adapting ChER for the recognition of chemical mentions in patents. In Proceedings of the Fifth BioCreative Challenge Evaluation Workshop. (pp. 149-153). Seville, Spain. . Publication link: b1983e8a-58cf-40b6-b536-d9a9cc4e4851
  8. Ananiadou, S., Kevin, C. (Ed.), Dina, D-F. (Ed.), Ananiadou, S. (Ed.), & Jun-ichi, T. (Ed.) (2015). Event Extraction in pieces: tackling the partial event identification problem on unseen corpora. In C. Kevin, D-F. Dina, A. Sophia, & T. Jun-ichi (Eds.), Biomedical Natural Language Processing. (pp. 31-41). ACL. . Publication link: e8d9ba07-9a62-454e-a111-5341b6e5beb8
  9. Xu, Y., Chen, L., Wei, J., Ananiadou, S., Fan, Y., Qian, Y., ... Tsujii, J. (2015). Bilingual term alignment from comparable corpora in English discharge summary and Chinese discharge summary. B M C Bioinformatics, 16, [149]. DOI: 10.1186/s12859-015-0606-0. Publication link: daecf9c4-1897-42e9-bcf2-937613e6fee2
  10. Batista-Navarro, R. T., Carter, J., & Ananiadou, S. (2015). Semi-automatic curation of chronic obstructive pulmonary disease phenotypes using Argo. In Proceedings of the Fifth BioCreative Challenge Evaluation Workshop. (pp. 406-408). Seville, Spain. . Publication link: cd5f1641-f268-4bf0-b57e-d4ba558fc25a
  11. Batista-Navarro, R. T., & 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. (pp. 311-316). Seville, Spain. . Publication link: cb6633d1-0c2c-446c-bf4c-880326e9dc1d
  12. Miwa, M., & Ananiadou, S. (2015). Adaptable, High Recall, Event Extraction System with Minimal Configuration. B M C Bioinformatics, 16(10:S7), [PMID: 26201408]. DOI: 10.1186/1471-2105-16-S10-S7. Publication link: d00e2b91-d57d-423e-9cdc-1b0a875ee606
  13. Batista-Navarro, R., Rak, R., & Ananiadou, S. (2015). Optimising chemical named entity recognition with pre-processing analytics, knowledge-rich features and heuristics. Journal of Cheminformatics, 7((Suppl 1): S6). DOI: 10.1186/1758-2946-7-S1-S6. Publication link: 1be8bd84-6a17-4df5-a952-b3ee1760ff48
  14. O'Mara-Eves, A., Thomas, J., McNaught, J., Miwa, M., & Ananiadou, S. (2015). Using text mining for study identification in systematic reviews: a systematic review of current approaches. Systematic Reviews, 4(5). DOI: 10.1186/2046-4053-4-5. Publication link: 195249ea-380c-4499-9132-b5401626d4a2
  15. Batista-Navarro, R. T., Ulate, W., Hammock, J., Kontonatsios, G., Rose-Sandler, T., & Ananiadou, S. (2015). Unlocking knowledge in biodiversity legacy literature through automatic semantic metadata extraction. In Proceedings of the TDWG 2015 Annual Conference.. Publication link: 07e7da04-a24a-4718-b591-9206bdc0c1fe
  16. Batista-Navarro, R. T., Nawaz, R., Zerva, C., & 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.. Publication link: 11067846-5932-4dbd-9792-7a91358036bb
  17. Mo, Y., Kontonatsios, G., & Ananiadou, S. (2015). Supporting Systematic Reviews Using LDA-based Document Representations. Systematic Reviews, 24(6). . Publication link: 399dd8b4-8ca6-41a3-93fa-8dc96c4e35bf
  18. Bollegala, D., Kontonatsios, G., & Ananiadou, S. (2015). A Cross-lingual Similarity Measure for Detecting Biomedical Term Translations. P L o S One. DOI: 10.1371/journal.pone.0126196. Publication link: 35dfb126-e11a-43d0-8647-cd542339633f
  19. Alnazzawi, N., Thompson, P., Batista-Navarro, R. T., & Ananiadou, S. (2015). Using text mining techniques to extract phenotypic information from the PhenoCHF corpus. B M C Medical Informatics and Decision Making, 15(Suppl 2). DOI: 10.1186/1472-6947-15-S2-S3, 10.1186/1472-6947-15-S2-S3. Publication link: 433dafb1-91ec-4b66-bfbe-43d5ca1c0f8a
  20. Ananiadou, S., Thompson, P., Nawaz, R., McNaught, J., & Kell, D. (2015). Event-based text mining for biology and functional genomics. Briefings in Functional Genomics, 14(3), 213-30. DOI: 10.1093/bfgp/elu015. Publication link: 9284975e-2b46-4311-b108-476722f296f5 | PubMed:24907365
  21. Mihaila, C., Batista-Navarro, R. T., Alnazzawi, N., Kontonatsios, G., Korkontzelos, I., Rak, R., ... Ananiadou, S. (2015). Mining the biomedical literature. In Healthcare Data Analytics. (pp. 251-308). CRC Press. . Publication link: 9128e5ac-2e04-4ebb-91ec-9599153ecf77
  22. Fu, X., Batista-Navarro, R. T., Rak, R., & Ananiadou, S. (2015). Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows. Journal of Biomedical Semantics, 6(8). DOI: 10.1186/s13326-015-0004-6. Publication link: 69394412-3296-438f-8fd7-8c0933e53755
  23. Rosner, M., Attard, A., Thompson, P., Gatt, A., & Ananiadou, S. (2015). Extending a Tool Resource Framework with U-Compare. In Human Language Technology Challenges for Computer Science and Linguistics. (Vol. 8387, pp. 315-326). (Lecture Notes in Computer Science). Springer Verlag. . Publication link: 5211e123-ef8c-4d21-b47a-d49152269011
  24. Stoney, R., Ames, R., Nenadic, G., Robertson, D., & Schwartz, J. M. (2015). Disentangling the multigenic and pleiotropic nature of molecular function. BMC Systems Biology, 9(Suppl 6), S3. DOI: 10.1186/1752-0509-9-S6-S3. Publication link: 847f8679-0c1d-4cff-908d-3adb6d55947e | PubMed:26678917
  25. Nenadic, G. (2015). Contextualisation of Biomedical Knowledge through Large-scale Processing of Literature, Clinical Narratives and Social Media. Lecture Notes in Computer Science, 9105, 7-9. DOI: 10.1007/978-3-319-19551-3_2. Publication link: 98f5e4bb-75b1-4747-add6-141899c150a8
  26. Filannino, M., & Nenadic, G. (2015). Temporal expression extraction with extensive feature type selection and a posteriori label adjustment. Data & Knowledge Engineering, 100(A), 19-33. DOI: 10.1016/j.datak.2015.09.002. Publication link: 4f946106-37c0-4127-8426-60c9219f832d
  27. Wu, C., Schwartz, J. M., Brabant, G., Peng, S. L., & Nenadic, G. (2015). Constructing a molecular interaction network for thyroid cancer via large-scale text mining of gene and pathway events.BMC Systems Biology, 9(Suppl 6), S5. DOI: doi:10.1186/1752-0509-9-S6-S5. Publication link: 00b827f0-9f30-4f9a-9e10-31cd100ba003 | PubMed:26679379
  28. Milosevic, N., Gregson, C., Hernandez, R., & Nenadic, G. (2015). Supporting clinical trial data curation from literature with table mining. Poster session presented at Postgraduate Summer Research Showcase 2015, Withworth Hall, .. Publication link: 0fe69da9-1f9e-4fb0-bdd8-5d40ce11afb2
  29. Dehghan, A., Kovacevic, A., Karystianis, G., Keane, J. A., & Nenadic, G. (2015). Combining knowledge- and data-driven methods for de-identification of clinical narratives. Journal of Biomedical Informatics, 58(Supplement), S53-S59. DOI: 10.1016/j.jbi.2015.06.029. Publication link: 4bf61a22-35af-41f8-9b2c-33bda9c2e992
  30. Karystianis, G., Dehghan, A., Kovacevic, A., Keane, J. A., & Nenadic, G. (2015). Using local lexicalized rules to identify heart disease risk factors in clinical notes. Journal of Biomedical Informatics, 58(Supplement), S183-S188. DOI: 10.1016/j.jbi.2015.06.013. Publication link: c8074d16-f3b3-4dfc-aa0d-774c8e135b90
  31. Duck, G., Kovacevic, A., Robertson, D. L., Stevens, R., & Nenadic, G. (2015). Ambiguity and variability of database and software names in bioinformatics. Journal of Biomedical Semantics, 6, [29]. DOI: 10.1186/s13326-015-0026-0. Publication link: dd026a12-fa1c-4cf8-9f87-934e4f36c739
  32. Bollegala, D., Mu, T., & Goulermas, J. Y. (2015). Cross-Domain Sentiment Classification Using Sentiment Sensitive Embeddings. IEEE Transactions on Knowledge and Data Engineering (TKDE), 28(2), 398-410. DOI: 10.1109/TKDE.2015.2475761. Publication link: 4a66a6ad-246c-41ee-a162-c47d3b745ab0
  33. Batista-Navarro, R. T., Carter, J., & 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. (pp. 51-56). Seville, Spain. . Publication link: bf59c608-d8be-4cf9-bfc8-cbe0c881926a
  34. Batista-Navarro, R. T., & Ananiadou, S. (2015). Adapting ChER for the recognition of chemical mentions in patents. In Proceedings of the Fifth BioCreative Challenge Evaluation Workshop. (pp. 149-153). Seville, Spain. . Publication link: b1983e8a-58cf-40b6-b536-d9a9cc4e4851
  35. Batista-Navarro, R. T., Carter, J., & Ananiadou, S. (2015). Semi-automatic curation of chronic obstructive pulmonary disease phenotypes using Argo. In Proceedings of the Fifth BioCreative Challenge Evaluation Workshop. (pp. 406-408). Seville, Spain. . Publication link: cd5f1641-f268-4bf0-b57e-d4ba558fc25a
  36. Batista-Navarro, R. T., & 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. (pp. 311-316). Seville, Spain. . Publication link: cb6633d1-0c2c-446c-bf4c-880326e9dc1d
  37. Fu, X., Batista-Navarro, R. T., Rak, R., & Ananiadou, S. (2015). Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows. Journal of Biomedical Semantics, 6(8). DOI: 10.1186/s13326-015-0004-6. Publication link: 69394412-3296-438f-8fd7-8c0933e53755
  38. Mihaila, C., Batista-Navarro, R. T., Alnazzawi, N., Kontonatsios, G., Korkontzelos, I., Rak, R., ... Ananiadou, S. (2015). Mining the biomedical literature. In Healthcare Data Analytics. (pp. 251-308). CRC Press. . Publication link: 9128e5ac-2e04-4ebb-91ec-9599153ecf77
  39. Batista-Navarro, R., Rak, R., & Ananiadou, S. (2015). Optimising chemical named entity recognition with pre-processing analytics, knowledge-rich features and heuristics. Journal of Cheminformatics, 7((Suppl 1): S6). DOI: 10.1186/1758-2946-7-S1-S6. Publication link: 1be8bd84-6a17-4df5-a952-b3ee1760ff48
  40. Batista-Navarro, R. T., Ulate, W., Hammock, J., Kontonatsios, G., Rose-Sandler, T., & Ananiadou, S. (2015). Unlocking knowledge in biodiversity legacy literature through automatic semantic metadata extraction. In Proceedings of the TDWG 2015 Annual Conference.. Publication link: 07e7da04-a24a-4718-b591-9206bdc0c1fe
  41. Batista-Navarro, R. T., Nawaz, R., Zerva, C., & 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.. Publication link: 11067846-5932-4dbd-9792-7a91358036bb
  42. Alnazzawi, N., Thompson, P., Batista-Navarro, R. T., & Ananiadou, S. (2015). Using text mining techniques to extract phenotypic information from the PhenoCHF corpus. B M C Medical Informatics and Decision Making, 15(Suppl 2). DOI: 10.1186/1472-6947-15-S2-S3, 10.1186/1472-6947-15-S2-S3. Publication link: 433dafb1-91ec-4b66-bfbe-43d5ca1c0f8a
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