Publications

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2010

  1. Rupp, C., Thompson, P., Black, W., McNaught, J., & Ananiadou, S. (2010). A Specialised Verb Lexicon as the Basis of Fact Extraction in the Biomedical Domain. In Proceedings of interdisciplinary workshop on verbs: the identification and representation of verb features (Verb 2010). (pp. 6pp). Pisa. . Publication link: 755c5d11-8793-4408-9886-3b204a358a85
  2. Ananiadou, S., Thompson, P., Thomas, J., Mu, T., Oliver, S., Rickinson, M., ... McNaught, J. (2010). Supporting the education evidence portal via text mining. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 368(1925), 3829-3844. DOI: 10.1098/rsta.2010.0152. Publication link: 833b310c-a637-4957-a28d-a5bfbbfcae1a
  3. Black, W., Rupp, C., Nobata, C., McNaught, J., Tsujii, J., & Ananiadou, S. (2010). High-Precision Semantic Search by Generating and Testing Questions. In Proceedings of the UK e-Science All Hands Meeting. (pp. 3pp). Publication link: 4c8ee5f9-503e-47d3-b46b-5581d885e2f3
  4. Nawaz, R., Thompson, P., McNaught, J., & Ananiadou, S. (2010). Meta-knowledge annotation of bio-events. In Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC2010). (pp. 2498-2505). Paris: European Language Resources Association. . Publication link: 111f9cdb-d727-4a00-a733-2b08198f8594
  5. Sasaki, Y., McNaught, J., & Ananiadou, S. (2010). The value of an in-domain lexicon in genomics QA. Journal of Bioinformatics and Computational Biology, 8(1), 147-161. DOI: 10.1142/S0219720010004513. Publication link: 1f2e81a0-b85c-454f-af67-5cc5d62e0a3f
  6. Ananiadou, S., McNaught, J., Thomas, J., & Oliver, S. (2010). Evaluating a text mining based educational search portal. In Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC2010). (pp. 3344-3350). Paris: European Language Resources Association. . Publication link: c0a62f05-5dad-4fa9-a351-28fa4649a63a
  7. Thew, S., Sutcliffe, A., De Bruijn, O., McNaught, J., Procter, R., Jarvis, P., & Buchan, I. (2010). Supporting creativity and appreciation of uncertainty in exploring geo-coded public health data. Methods of Information in Medicine, 50(2), 158-165. DOI: 10.3414/ME09-01-0070. Publication link: d04859ac-547e-414e-bb69-7c25db758d5d
  8. Wang, X., Rak, R., Restificar, A., Nobata, C., Rupp, C. J., Batista-Navarro, R. T., ... Ananiadou, S. (2010). NaCTeM Systems for BioCreative III PPI Tasks. In Proceedings of the BioCreative III Workshop. (pp. 142-147). Publication link: ee085f53-f48a-49e0-a6e8-73e48197d597
  9. Mu, T., & Ananiadou, S. (2010). Proximity-based graph embeddings for multi-label classification. In KDIR 2010 - Proceedings of the International Conference on Knowledge Discovery and Information Retrieval|KDIR - Proc. Int. Conf. Knowl. Discov. Inf. Retr.. (pp. 74-84). Publication link: df0f420b-f95f-47f8-bf0a-92d41a2e3b33
  10. Ananiadou, S., Pyysalo, S., Tsujii, J., & Kell, D. B. (2010). Event extraction for systems biology by text mining the literature. Trends in Biotechnology, 28(7), 381-390. DOI: 10.1016/j.tibtech.2010.04.005. Publication link: e13e6cc1-8f55-4bbb-bbbb-88953d8c05c4
  11. Ananiadou, S., Kano, Y., Dorado, R., McCrochon, L., & Tsujii, J. (2010). U-Compare: An integrated language resource evaluation platform including a comprehensive UIMA resource library. In host publication. (pp. 428-434). Publication link: ba19f411-ab27-4852-95c8-e95119d719f9
  12. Ananiadou, S., McNaught, J., Thomas, J., & Oliver, S. (2010). Evaluating a text mining based educational search portal. In Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC2010). (pp. 3344-3350). Paris: European Language Resources Association. . Publication link: c0a62f05-5dad-4fa9-a351-28fa4649a63a
  13. Ananiadou, S., Nawaz, R., & Thompson, P. (2010). Evaluating a meta-knowledge annotation scheme for bio-events. In host publication. (pp. 69-77). Publication link: bd03317a-6fbb-4124-bde0-0b9ed06c71e3
  14. Sasaki, Y., McNaught, J., & Ananiadou, S. (2010). The value of an in-domain lexicon in genomics QA. Journal of Bioinformatics and Computational Biology, 8(1), 147-161. DOI: 10.1142/S0219720010004513. Publication link: 1f2e81a0-b85c-454f-af67-5cc5d62e0a3f
  15. Ananiadou, S., & Wang, X. (2010). A task oriented extension of the Chinese MeSH Concepts Hierarchy. In host publication. (pp. 23-30). Publication link: 09c88411-10df-44cb-b33e-b7708b8856e0
  16. Nawaz, R., Thompson, P., McNaught, J., & Ananiadou, S. (2010). Meta-knowledge annotation of bio-events. In Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC2010). (pp. 2498-2505). Paris: European Language Resources Association. . Publication link: 111f9cdb-d727-4a00-a733-2b08198f8594
  17. Kemper, B., Matsuzaki, T., Matsuoka, Y., Tsuruoka, Y., Kitano, H., Ananiadou, S., & Tsujii, J. (2010). PathText: A text mining integrator for biological pathway visualizations. Bioinformatics, 26(12), 374-381. [btq221]. DOI: 10.1093/bioinformatics/btq221. Publication link: 0ef7f56e-d0ad-49e3-8e03-250e5ca01813
  18. Mu, T., Wang, X., Tsujii, J., & Ananiadou, S. (2010). Imbalanced classification using dictionary-based prototypes and hierarchical decision rules for entity sense disambiguation. In Coling 2010 - 23rd International Conference on Computational Linguistics, Proceedings of the Conference|Coling - Int. Conf. Comput. Linguist., Proc. Conf.. (Vol. 2, pp. 851-859). ACL. . Publication link: 4161c716-aedf-4ba3-b4b0-f7a3dcf68f9f
  19. Ananiadou, S., Nawaz, R., & Thompson, P. (2010). Event Interpretation: A Step towards Event-Centred Text Minin. In host publication. (pp. 103-107). Publication link: 4d7a9f0f-90fa-4a2a-ad68-9e3414d57354
  20. Black, W., Rupp, C., Nobata, C., McNaught, J., Tsujii, J., & Ananiadou, S. (2010). High-Precision Semantic Search by Generating and Testing Questions. In Proceedings of the UK e-Science All Hands Meeting. (pp. 3pp). Publication link: 4c8ee5f9-503e-47d3-b46b-5581d885e2f3
  21. Ananiadou, S., Pyysalo, S., Ohta, T., Cho, H-C., Sullivan, D., Mao, C., ... Tsujii, J. (2010). Towards Event Extraction from Full Texts on Infectious Diseases. In host publication. (pp. 132-140). Publication link: 2a16dc6e-d120-4f2d-a6bb-32950ce10d44
  22. Ananiadou, S., Thompson, P., & Nawaz, R. (2010). Improving search through Event-based Biomedical Text Mining. 1st Automated Motif Discovery in Cultural Heritage and Scientific Communication Texts (AMICUS) workshop, Vienna, .. Publication link: 2c64dea1-335d-47b3-a91b-9e16a3a6c6b3
  23. Wang, X., Tsujii, J., & Ananiadou, S. (2010). Disambiguating the species of biomedical named entities using natural language parsers. Bioinformatics, 26(5), 661-667. [btq002]. DOI: 10.1093/bioinformatics/btq002. Publication link: 50d1efb5-d8f6-4b91-a71c-90a21e04a449
  24. Ananiadou, S., Thompson, P., Thomas, J., Mu, T., Oliver, S., Rickinson, M., ... McNaught, J. (2010). Supporting the education evidence portal via text mining. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 368(1925), 3829-3844. DOI: 10.1098/rsta.2010.0152. Publication link: 833b310c-a637-4957-a28d-a5bfbbfcae1a
  25. Rupp, C., Thompson, P., Black, W., McNaught, J., & Ananiadou, S. (2010). A Specialised Verb Lexicon as the Basis of Fact Extraction in the Biomedical Domain. In Proceedings of interdisciplinary workshop on verbs: the identification and representation of verb features (Verb 2010). (pp. 6pp). Pisa. . Publication link: 755c5d11-8793-4408-9886-3b204a358a85
  26. Okazaki, N., Ananiadou, S., & Tsujii, J. (2010). Building a high-quality sense inventory for improved abbreviation disambiguation. Bioinformatics, 26(9), 1246-1253. [btq129]. DOI: 10.1093/bioinformatics/btq129. Publication link: 98d0669e-2673-4a98-8104-0c53806bd18d
  27. Mu, T., Wang, X., Tsujii, J., & Ananiadou, S. (2010). Imbalanced classification using dictionary-based prototypes and hierarchical decision rules for entity sense disambiguation. In Coling 2010 - 23rd International Conference on Computational Linguistics, Proceedings of the Conference|Coling - Int. Conf. Comput. Linguist., Proc. Conf.. (Vol. 2, pp. 851-859). ACL. . Publication link: 4161c716-aedf-4ba3-b4b0-f7a3dcf68f9f
  28. Black, W., Rupp, C., Nobata, C., McNaught, J., Tsujii, J., & Ananiadou, S. (2010). High-Precision Semantic Search by Generating and Testing Questions. In Proceedings of the UK e-Science All Hands Meeting. (pp. 3pp). Publication link: 4c8ee5f9-503e-47d3-b46b-5581d885e2f3
  29. Kemper, B., Matsuzaki, T., Matsuoka, Y., Tsuruoka, Y., Kitano, H., Ananiadou, S., & Tsujii, J. (2010). PathText: A text mining integrator for biological pathway visualizations. Bioinformatics, 26(12), 374-381. [btq221]. DOI: 10.1093/bioinformatics/btq221. Publication link: 0ef7f56e-d0ad-49e3-8e03-250e5ca01813
  30. Wang, X., Tsujii, J., & Ananiadou, S. (2010). Disambiguating the species of biomedical named entities using natural language parsers. Bioinformatics, 26(5), 661-667. [btq002]. DOI: 10.1093/bioinformatics/btq002. Publication link: 50d1efb5-d8f6-4b91-a71c-90a21e04a449
  31. Okazaki, N., Ananiadou, S., & Tsujii, J. (2010). Building a high-quality sense inventory for improved abbreviation disambiguation. Bioinformatics, 26(9), 1246-1253. [btq129]. DOI: 10.1093/bioinformatics/btq129. Publication link: 98d0669e-2673-4a98-8104-0c53806bd18d
  32. Ananiadou, S., Pyysalo, S., Tsujii, J., & Kell, D. B. (2010). Event extraction for systems biology by text mining the literature. Trends in Biotechnology, 28(7), 381-390. DOI: 10.1016/j.tibtech.2010.04.005. Publication link: e13e6cc1-8f55-4bbb-bbbb-88953d8c05c4
  33. Rebholz-Schuhmann, D., & Nenadic, G. (2010). Biomedical Semantics: The Hub for Biomedical Research 2.0. Journal of Biomedical Semantics, 1, [1]. DOI: 10.1186/2041-1480-1-1. Publication link: fd30bfef-2019-438e-a00b-02d638bdf906
  34. Nenadic, G., Gerner, M., & Bergman, C. M. (2010). An Exploration of Mining Gene Expression Mentions and their Anatomical Locations from Biomedical Text. In Proceedings of the BioNLP 2010 Workshop.. Publication link: f7584a04-f9eb-4e83-bfb0-c110930e79c4
  35. Nenadic, G., Stivaros, S., Zeng, X., Gledson, A., Hutchinson, C., Keane, J., & Jackson, A. (2010). Early Phase Validation of a Decision Support System within the Exemplar of Aneurysmal Subarachnoid Haemorrhage. In Proceedings of British Society of NeuroRadiologists Annual Conference (BSNR 2010).. Publication link: e1173257-6623-4ead-8d97-d3a19338c649
  36. Sarafraz, F., & Nenadic, G. (2010). Identification of negated regulation events in the literature: Exploring the feature space. 134-138. Poster session presented at 4th International Symposium on Semantic Mining in Biomedicine, SMBM 2010, Cambridge, .. Publication link: e70f7cab-be24-4764-a594-79e2ed14fc5d
  37. Nenadic, G., Latif, S., & Wood, M. M. (2010). Improving Clustering of Noisy Documents through Automatic Summarisation. Poster session presented at International Conference on Intelligent Text Processing and Computational Linguistics (CICLing), Iasi, Romania, .. Publication link: 1857a8f3-7e51-4f84-8f5c-e3934887aa65
  38. Nenadic, G., Stivaros, S., Zeng, X., Laitt, R., Hughes, D., Williams, T., ... Jackson, A. (2010). Development of a Computerized Decision Support System for Treatment Planning and Outcome Prediction in Aneurysmal Subarachnoid Haemorrhage. In Proceedings of American Society of NeuroRadiologists 48th Annual Meeting.. Publication link: 421fb3d6-cbdf-440e-9572-f747fea57a22
  39. Nenadic, G., & Sarafraz, F. (2010). Using SVMs with the Command Relation Features to Identify Negated Events in Biomedical Literature. In Proceedings of the Workshop on Negation and Speculation in Natural Language Processing, 2010.. Publication link: 2a0b30fa-afe8-4574-9615-6d332bbdfdeb
  40. Nenadic, G., Baran, J., Gerner, M., Haeussler, M., & Bergman, C. (2010). pubmed2ensembl: Linking Publications and Genes. Poster session presented at Genome Informatics (UK) 2010, Hinxton, UK, .. Publication link: 8d851035-1a5d-4755-82a6-2f0e95e3e0c0
  41. Gerner, M., Nenadic, G., & Bergman, C. M. (2010). LINNAEUS: A species name identification system for biomedical literature. BMC Bioinformatics, 11, [85]. DOI: 10.1186/1471-2105-11-85. Publication link: 9d9f91c4-a7a1-49b2-951a-8b3f36b4ed7f | PubMed:20149233
  42. Nenadic, G., Solt, I., Gerner, M., Thomas, P., Bergman, C. M., Leser, U., & Hakenberg, J. (2010). Gene mention normalization in full texts using GNAT and LINNAEUS. In Proceedings of the BioCreative III Workshop.. Publication link: 98e228b8-27fc-4278-94c6-71a3286dfd41
  43. Mu, T., Pataky, T. C., Findlow, A. H., Aung, M. S. H., & Goulermas, J. Y. (2010). Automated nonlinear feature generation and classification of foot pressure lesions. IEEE Transactions on Information Technology in Biomedicine, 14(2), 418-424. . Publication link: 7fa09867-feb2-4f90-9945-38371e3bdeec
  44. Ananiadou, S., Thompson, P., Thomas, J., Mu, T., Oliver, S., Rickinson, M., ... McNaught, J. (2010). Supporting the education evidence portal via text mining. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 368(1925), 3829-3844. DOI: 10.1098/rsta.2010.0152. Publication link: 833b310c-a637-4957-a28d-a5bfbbfcae1a
  45. Rodriguez-Martinez, E., Goulermas, J. Y., Mu, T., & Ralph, J. F. (2010). Automatic induction of projection pursuit indices. IEEE Transactions on Neural Networks, 21(8), 1281-1295. . Publication link: 9f129bc0-b3ac-443c-94df-9f8b672d5cd3
  46. Wang, X., Rak, R., Restificar, A., Nobata, C., Rupp, C. J., Batista-Navarro, R. T., ... Ananiadou, S. (2010). NaCTeM Systems for BioCreative III PPI Tasks. In Proceedings of the BioCreative III Workshop. (pp. 142-147). Publication link: ee085f53-f48a-49e0-a6e8-73e48197d597
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