Publications

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2008

  1. Thompson, P., Venturi, G., McNaught, J., Montemagni, S., & Ananiadou, S. (2008). Categorising Modality in Biomedical Texts. In Proceedings of the LREC 2008 Workshop on Building and Evaluating Resources for Biomedical Text Mining.. (pp. 27-34). Publication link: edf5928a-d14d-4776-9edb-8d35bfa66804
  2. Thew, S., Sutcliffe, A., De Bruijn, O., McNaught, J., Procter, R., Venters, C., & Buchan, I. (2008). Experience in e-Science Requirements Engineering. In Proceedings of the 16th IEEE International Requirements Engineering Conference, RE'08|Proc. IEEE Int. Requir. Eng. Conf., RE. (pp. 277-282). IEEE Explore Digital Library: IEEE. DOI: 10.1109/RE.2008.34. Publication link: cd0eb4bc-ccb2-4f1b-a43b-df51e458f7b5
  3. Splendiani, A., Piao, S., Sasaki, Y., Ananiadou, S., McNaught, J., & Burgun, A. (2008). Compositional Enrichment of Bio-Ontologies. In Proceedings of 11th Annual Bio-Ontologies Meeting, at the Intelligent Systems for Molecular Biology 2008 Conference (ISMB-2008).. Publication link: b3453455-66e0-4836-97f1-57ad3743a5ca
  4. Sasaki, Y., Thompson, P., Cotter, P., McNaught, J., & Ananiadou, S. (2008). Event frame extraction based on a gene regulation corpus. In Coling 2008 - 22nd International Conference on Computational Linguistics, Proceedings of the Conference|Coling - Int. Conf. Comput. Linguist., Proc. Conf.. (Vol. 1, pp. 761-768). Publication link: bc1538ab-c503-41f8-8332-0fc022f509a3
  5. Piao, S., McNaught, J., & Ananiadou, S. (2008). Clustering Related Terms with Definitions. In Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008). (pp. 2013-2019). Publication link: 489f9211-0249-4ff1-829d-e95152ed24de
  6. Thompson, P., Cotter, P., McNaught, J., Ananiadou, S., Montemagni, S., Trabucco, A., & Venturi, G. (2008). Building a Bio-Event Annotated Corpus for the Acquisition of Semantic Frames from Biomedical Corpora. In Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008). (pp. 2159-2166). Publication link: 31279678-6483-4bd3-8f19-92520bc7b6eb
  7. Sasaki, Y., Tsuruoka, Y., McNaught, J., & Ananiadou, S. (2008). How to make the most of NE dictionaries in statistical NER. BMC Bioinformatics, 9(supplement 11), [S5]. DOI: 10.1186/1471-2105-9-S11-S5. Publication link: 73853d1b-b031-4a70-b7f2-21638f3122fb
  8. Sasaki, Y., Thompson, P., Cotter, P., McNaught, J., & Ananiadou, S. (2008). Event frame extraction based on a gene regulation corpus. 761-768. Paper presented at 22nd International Conference on Computational Linguistics, Coling 2008, Manchester, .. Publication link: 70c53b33-a3e6-4117-adb3-0f3e8fb124e0
  9. Tsuruoka, Y., McNaught, J., & Ananiadou, S. (2008). Normalizing biomedical terms by minimizing ambiguity and variability. BMC Bioinformatics, 9(3), [S2]. DOI: 10.1186/1471-2105-9-S3-S2. Publication link: 54a10e04-30d1-4db5-bb77-88f9899f66c8
  10. Rebholz-Schuhmann, D., Pezik, P., Lee, V., Kim, J-J., del Gratta, R., Sasaki, Y., ... Ananiadou, S. (2008). BioLexicon: Towards a Reference Terminological Resource in the Biomedical Domain. In Proceedings of the of the 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB-2008).. Publication link: 5c971568-c602-4bd1-890f-5906fb138124
  11. Kano, Y., Nguyen, N., SÆtre, R., Yoshida, K., Miyao, Y., Tsuruoka, Y., ... Tsujii, J. (2008). Filling the gaps between tools and users: A tool comparator, using protein-protein interaction as an example. In Pacific Symposium on Biocomputing 2008, PSB 2008|Pac. Symp. Biocomputing, PSB. (pp. 616-627). Publication link: 6f48e3f8-0872-4c65-a649-fef7d8da6f27
  12. Sasaki, Y., Thompson, P., Cotter, P., McNaught, J., & Ananiadou, S. (2008). Event frame extraction based on a gene regulation corpus. 761-768. Paper presented at 22nd International Conference on Computational Linguistics, Coling 2008, Manchester, .. Publication link: 70c53b33-a3e6-4117-adb3-0f3e8fb124e0
  13. Sasaki, Y., Tsuruoka, Y., McNaught, J., & Ananiadou, S. (2008). How to make the most of NE dictionaries in statistical NER. BMC Bioinformatics, 9(supplement 11), [S5]. DOI: 10.1186/1471-2105-9-S11-S5. Publication link: 73853d1b-b031-4a70-b7f2-21638f3122fb
  14. Tsuruoka, Y., McNaught, J., & Ananiadou, S. (2008). Normalizing biomedical terms by minimizing ambiguity and variability. BMC Bioinformatics, 9(3), [S2]. DOI: 10.1186/1471-2105-9-S3-S2. Publication link: 54a10e04-30d1-4db5-bb77-88f9899f66c8
  15. Rebholz-Schuhmann, D., Pezik, P., Lee, V., Kim, J-J., del Gratta, R., Sasaki, Y., ... Ananiadou, S. (2008). BioLexicon: Towards a Reference Terminological Resource in the Biomedical Domain. In Proceedings of the of the 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB-2008).. Publication link: 5c971568-c602-4bd1-890f-5906fb138124
  16. Thompson, P., Cotter, P., McNaught, J., Ananiadou, S., Montemagni, S., Trabucco, A., & Venturi, G. (2008). Building a Bio-Event Annotated Corpus for the Acquisition of Semantic Frames from Biomedical Corpora. In Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008). (pp. 2159-2166). Publication link: 31279678-6483-4bd3-8f19-92520bc7b6eb
  17. Okazaki, N., Tsuruoka, Y., Ananiadou, S., & Tsujii, J. (2008). A discriminative candidate generator for string transformations. In EMNLP 2008 - 2008 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference: A Meeting of SIGDAT, a Special Interest Group of the ACL|EMNLP - Conf. Empir. Methods Nat. Lang. Process., Proc. Conf.: Meet. SIGDAT, Spec. Interest Group ACL. (pp. 447-456). Publication link: 34ff11d5-325e-4779-8edd-7308db6348d7
  18. Sætre, R., Kemper, B., Oda, K., Okazaki, N., Matsuoka, Y., Kikuchi, N., ... Tsujii, J. (2008). Connecting Text Mining and Pathways using the PathText Resource. In Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008). (pp. 1736-1740). Publication link: 34f87ca2-41e0-4d3a-a324-4f1f50a39c28
  19. Piao, S., McNaught, J., & Ananiadou, S. (2008). Clustering Related Terms with Definitions. In Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008). (pp. 2013-2019). Publication link: 489f9211-0249-4ff1-829d-e95152ed24de
  20. Meziane, F., Athanasakis, N., & Ananiadou, S. (2008). Generating Natural Language specifications from UML class diagrams. Requirements Engineering, 13(1), 1-18. DOI: 10.1007/s00766-007-0054-0. Publication link: 3cfe77a9-f51d-41fb-b485-e488c7078513
  21. Sætre, R., Kemper, B., Oda, K., Okazaki, N., Matsuoka, Y., Kikuchi, N., ... Tsujii, J. (2008). PathText: Text Mining Tools Integrated with Biological Pathway. In host publication.. Publication link: 1716b0f0-c6c9-48c5-95e8-68c1190a222a
  22. Splendiani, A., Piao, S., Sasaki, Y., Ananiadou, S., McNaught, J., & Burgun, A. (2008). Compositional Enrichment of Bio-Ontologies. In Proceedings of 11th Annual Bio-Ontologies Meeting, at the Intelligent Systems for Molecular Biology 2008 Conference (ISMB-2008).. Publication link: b3453455-66e0-4836-97f1-57ad3743a5ca
  23. Sasaki, Y., Thompson, P., Cotter, P., McNaught, J., & Ananiadou, S. (2008). Event frame extraction based on a gene regulation corpus. In Coling 2008 - 22nd International Conference on Computational Linguistics, Proceedings of the Conference|Coling - Int. Conf. Comput. Linguist., Proc. Conf.. (Vol. 1, pp. 761-768). Publication link: bc1538ab-c503-41f8-8332-0fc022f509a3
  24. Tsuruoka, Y., Tsujii, J., & Ananiadou, S. (2008). FACTA: A text search engine for finding associated biomedical concepts. Bioinformatics, 24(21), 2559-2560. DOI: 10.1093/bioinformatics/btn469. Publication link: acf90ade-6c5a-4720-8ac1-25f3d307cd10
  25. Tsuruoka, Y., Tsujii, J. I., & Ananiadou, S. (2008). Accelerating the annotation of sparse named entities by dynamic sentence selection. In BMC Bioinformatics|BMC Bioinform.. (Vol. 9). DOI: 10.1186/1471-2105-9-S11-S8. Publication link: caf93649-ec0b-4474-887f-3005b40f4864
  26. Kano, Y., Nguyen, N., Sætre, R., Fukamachi, K., Yoshida, K., Miyao, Y., ... Tsujii, J. (2008). Sharable type system design for tool inter-operability and combinatorial comparison. In Proceedings of the First International Conference on Global Interoperability for Language Resources (ICGL). (pp. 122-129). Publication link: e67ff010-207c-421f-ba85-e87c894f661e
  27. Kano, Y., Nguyen, N., Sætre, R., Yoshida, K., Fukamachi, K., Miyao, Y., ... Tsujii, J. (2008). Towards Data And Goal Oriented Analysis: Tool Inter-Operability And Combinatorial Comparison. In Proceedings of the 3rd International Joint Conference on Natural Language Processing (IJCNLP-2008). (pp. 859-864). Publication link: de8a38ed-b4c5-485a-945e-cd24b16e03d7
  28. Hirohata, K., Okazaki, N., Ananiadou, S., & Ishizuka, M. (2008). Identifying Sections in Scientific Abstracts using Conditional Random Fields. In Proceedings of the 3rd International Joint Conference on Natural Language Processing (IJCNLP 2008). (pp. 381-388). Publication link: ebf03d48-4bed-45a5-ab15-d277ff5729d1
  29. Thompson, P., Venturi, G., McNaught, J., Montemagni, S., & Ananiadou, S. (2008). Categorising Modality in Biomedical Texts. In Proceedings of the LREC 2008 Workshop on Building and Evaluating Resources for Biomedical Text Mining.. (pp. 27-34). Publication link: edf5928a-d14d-4776-9edb-8d35bfa66804
  30. Tsuruoka, Y., Tsujii, J. I., & Ananiadou, S. (2008). Accelerating the annotation of sparse named entities by dynamic sentence selection. In BMC Bioinformatics|BMC Bioinform.. (Vol. 9). DOI: 10.1186/1471-2105-9-S11-S8. Publication link: caf93649-ec0b-4474-887f-3005b40f4864
  31. Tsuruoka, Y., Tsujii, J., & Ananiadou, S. (2008). FACTA: A text search engine for finding associated biomedical concepts. Bioinformatics, 24(21), 2559-2560. DOI: 10.1093/bioinformatics/btn469. Publication link: acf90ade-6c5a-4720-8ac1-25f3d307cd10
  32. Kano, Y., Nguyen, N., SÆtre, R., Yoshida, K., Miyao, Y., Tsuruoka, Y., ... Tsujii, J. (2008). Filling the gaps between tools and users: A tool comparator, using protein-protein interaction as an example. In Pacific Symposium on Biocomputing 2008, PSB 2008|Pac. Symp. Biocomputing, PSB. (pp. 616-627). Publication link: 6f48e3f8-0872-4c65-a649-fef7d8da6f27
  33. Okazaki, N., Tsuruoka, Y., Ananiadou, S., & Tsujii, J. (2008). A discriminative candidate generator for string transformations. In EMNLP 2008 - 2008 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference: A Meeting of SIGDAT, a Special Interest Group of the ACL|EMNLP - Conf. Empir. Methods Nat. Lang. Process., Proc. Conf.: Meet. SIGDAT, Spec. Interest Group ACL. (pp. 447-456). Publication link: 34ff11d5-325e-4779-8edd-7308db6348d7
  34. Nenadic, G., & Afzal, H. (2008). Mining bioinformatics services terminology from literature. Poster session presented at MIB Interdisciplinary Research Conference, Manchester, .. Publication link: 67541270-9629-4f44-9df7-3b9f115977e9
  35. Yang, H., Nenadic, G., & Keane, J. A. (2008). Identification of transcription factor contexts in literature using machine learning approaches. In BMC Bioinformatics|BMC Bioinform.. (Vol. 9). BioMed Central. DOI: 10.1186/1471-2105-9-S3-S11. Publication link: 7607fa8a-e0e7-4dd9-a1f5-6032eef3b793
  36. Ananiadou, S., Monachini, M., Nenadic, G., & Su, J. (2008). Building and Evaluating Resources for Biomedical Text Mining. In host publication.. Publication link: 57ecad82-d6f7-4b26-ac63-9a5191ba105e
  37. Stivaros, S., Nenadic, G., Zeng, X., Keane, J., & Jackson, A. (2008). Decision support system for treatment planning and outcome prediction in aneurysmal subarachnoid haemorrhage. Poster session presented at Computer Assisted Radiology and Surgery 2008, Barcelona, .. Publication link: 5dd887c5-d2ef-48ee-97e3-1f7c0178f34f
  38. Stivaros, S., Nenadic, G., Zeng, X., Keane, J., & Jackson, A. (2008). Computational Treatment Prediction of Subarachnoid Haemorrhage. Poster session presented at British Society of Neuroradiologists (BSNR) 2008, Manchester, .. Publication link: 8f2f743c-d075-4572-ac63-1ec6a563963e
  39. Greenwood, M., & Nenadic, G. (2008). Lexical Profiling of Existing Web Directories to Support Fine-grained Topic-Focused Web Crawling. In host publication. (pp. 42-49). London, UK: BCS. . Publication link: 3fe98beb-f72f-49d1-bd1e-0f92c73ea6c9
  40. Yang, H., Spasic, I., Keane, J., & Nenadic, G. (2008). Combining Lexical Profiling, Rules and Machine Learning for Disease Prediction from Hospital Discharge Summaries. In Proc. of i2b2 Obesity Challenge 2008. (pp. online). Publication link: 0f437b46-e627-4c04-bc14-0dcaaa367695
  41. Nenadic, G., & Spasic, I. (2008). Towards Terminology Extraction in Serbian. In Formal Description of Slavic Languages: The Fifth Conference. Frankfurt am Main: Peter Lang. . Publication link: 116d2890-e171-4b20-a75c-1464b7b949a3
  42. Yang, H., Nenadic, G., & Keane, J. A. (2008). Identification of transcription factor contexts in literature using machine learning approaches. BMC Bioinformatics, 9(3), [S11]. DOI: 10.1186/1471-2105-9-S3-S11. Publication link: a68d5907-218c-40ae-abd4-a77a259f91d0
  43. Afzal, H., Stevens, R., & Nenadic, G. (2008). Towards semantic annotation of bioinformatics services: Building a controlled vocabulary. In 3rd International Symposium on Semantic Mining in Biomedicine, SMBM 2008 - Proceedings|Int. Symp. Semantic Min. Biomed., SMBM - Proc.. (pp. 5-12). Publication link: c82e7c71-d3cf-48e0-aec0-c31029c75009
  44. Rebholz-Schuhmann, D., & Nenadic, G. (2008). Towards standardisation of named-entity annotations in the life science literature. In 3rd International Symposium on Semantic Mining in Biomedicine, SMBM 2008 - Proceedings|Int. Symp. Semantic Min. Biomed., SMBM - Proc.. (pp. 167-169). Publication link: dae1def3-49e1-451f-be3d-4c484922669e
  45. Nenadic, G., Stivaros, S. M., Zeng, X., Keane, J., & Jackson, A. (2008). Development of a Language-based Bayesian Decision Support System for Treatment Planning and Outcome Prediction in Aneurysmal Subarachnoid Haemorrhage. Poster session presented at BSNR 2008, London, UK, .. Publication link: ff55d4f0-54e6-4cda-9e4a-a2330c280985
  46. Mu, T., Nandi, A. K., & Rangayyan, R. M. (2008). Screening of knee-joint vibroarthrographic signals using the strict 2-surface proximal classifier and genetic algorithm. Computers in Biology and Medicine, 38(10), 1103-1111. . Publication link: 8183c20b-1d3d-4b5f-811d-869164253672
  47. Mu, T., Nandi, A. K., & Rangayyan, R. M. (2008). Classification of breast masses using selected shape, edge-sharpness, and texture features with linear and kernel-based classifiers. Journal of Digital Imaging, 21(2), 153-169. . Publication link: 7ba861fc-d5df-42b7-8602-b40d1be5d015
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