Publications

2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | Complete list


2011

  1. Thomas, J., McNaught, J., & Ananiadou, S. (2011). Applications of text mining within systematic reviews. Research Synthesis Methods, 2(1), 1-14. DOI: 10.1002/jrsm.27. Publication link: 67ce1683-00ed-4b70-999a-522ba95b77e6
  2. Thompson, P., Nawaz, R., McNaught, J., & Ananiadou, S. (2011). Enriching a biomedical event corpus with meta-knowledge annotation. BMC Bioinformatics, 12, [393]. DOI: 10.1186/1471-2105-12-393. Publication link: 7164ecd5-2af4-44a5-bac6-2d8e6b6e7d61
  3. Thompson, P., McNaught, J., Montemagni, S., Calzolari, N., del Gratta, R., Lee, V., ... Ananiadou, S. (2011). The BioLexicon: A large-scale terminological resource for biomedical text mining. BMC Bioinformatics, 12, [397]. DOI: 10.1186/1471-2105-12-397. Publication link: 959e688d-8ae6-4522-ad7c-5a84525b8129
  4. Thompson, P., Kano, Y., McNaught, J., Pettifer, S., Attwood, T., Keane, J., & Ananiadou, S. (2011). Promoting Interoperability of Resources in META-SHARE. In C. N, I. T, P. S, & S. V (Eds.), IJCNLP 2011 Proceedings of the Workshop on Language Resources,Technology and Services in the Sharing Paradigm. (pp. 50-58). Asian Federation of Natural Language Processing. . Publication link: 1fd6fc11-3f33-43e2-8695-2aab079e467f
  5. Ananiadou, S., Thompson, P., Kano, Y., McNaught, J., Attwood, T., Day, P. J. R., ... Pettifer, S. (2011). Towards Interoperability of European Language Resources. Ariadne, 67. . Publication link: 3defeb41-695d-44b8-8044-5654c807c6e5
  6. McEntyre, J. R., Ananiadou, S., Andrews, S., Black, W. J., Boulderstone, R., Buttery, P., ... Vaughan, P. (2011). UKPMC: A full text article resource for the life sciences. Nucleic acids research., 39(1), D58-D65. DOI: 10.1093/nar/gkq1063. Publication link: c4788750-2941-4d51-b3b8-95aa852153c9 | PubMed:21062818
  7. Kontonasios, G., Korkontzelos, I., Kolluru, B. K., & Ananiadou, S. (2011). Adding text mining workflows as web services to the BioCatalogue. In SWAT4LS 2011 : 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences. (pp. 50-57). London: ACM. DOI: 10.1145/2166896.2166913. Publication link: bb071873-732f-4e2a-a2f5-1914c15934a4
  8. Ananiadou, S., & Batista-Navarro, R. T. (2011). Discovering Potential Drugs by Extracting Biological Activities of Natural Products. In Workshop on Mining the Pharmacogenomics Literature, Pacific Symopsium on Biocomputing 2011.. Publication link: b402d53f-b5af-474e-8c7c-6841df2136f2
  9. Ananiadou, S., Sullivan, D., Black, W., Levow, G. A., Gillespie, J. J., Mao, C., ... Sobral, B. (2011). Named entity recognition for bacterial type IV secretion systems. PLoS ONE, 6(3), [e14780]. DOI: 10.1371/journal.pone.0014780. Publication link: b6538b0f-1fec-4a41-af37-acd0378aeb40
  10. McEntyre, J. R., Ananiadou, S., Andrews, S., Black, W. J., Boulderstone, R., Buttery, P., ... Vaughan, P. (2011). UKPMC: A full text article resource for the life sciences. Nucleic acids research., 39(1), D58-D65. DOI: 10.1093/nar/gkq1063. Publication link: c4788750-2941-4d51-b3b8-95aa852153c9 | PubMed:21062818
  11. Stenetorp, P., Pyysalo, S., Ananiadou, S., & Tsujii, J. (2011). Almost Total Recall: Semantic Category Disambiguation Using Large Lexical Resources and Approximate String Matching. Proceedings of the Fourth International Symposium on Languages in Biology and Medicine (LBM 2011). . Publication link: c4a92cda-f3a2-41d9-b29d-a94054fa0210
  12. Ohta, T., Pyysalo, S., Ananiadou, S., & Tsujii, J. (2011). Pathway Curation Support as an Information Extraction Task. In host publication.. Publication link: 9f0811f7-0bbe-4b23-ab36-9ab14f0785b9
  13. Kolluru, B., Nakjang, S., Hirt, R. P., Wipat, A., & Ananiadou, S. (2011). Automatic extraction of microorganisms and their habitats from free text using text mining workflows. In Journal of integrative bioinformatics|J Integr Bioinform. (Vol. 8, pp. 184). Publication link: a7ea0ac9-8837-4255-aef1-402f838dbfb2
  14. Kano, Y., Björne, J., Ginter, F., Salakoski, T., Buyko, E., Hahn, U., ... Tsujii, J. (2011). U-Compare bio-event meta-service: Compatible BioNLP event extraction services. BMC Bioinformatics, 12(1), [481]. DOI: 10.1186/1471-2105-12-481. Publication link: aa23b36e-56e9-429a-a5ef-c2b82a116349
  15. Sasaki, Y., Wang, X., & Ananiadou, S. (2011). Extracting secondary bio-event arguments with extraction constraints. Computational Intelligence, 27(4), 702-721. DOI: 10.1111/j.1467-8640.2011.00406.x. Publication link: e70325f1-95f2-4c46-8256-0af7831cf1e4
  16. Rosner, M., Attard, A., Thompson, P., Gatt, A., & Ananiadou, S. (2011). Extending a Tool Resource Framework with U-Compare. In Proceedings of the 5th Language \& Technology Conference (LTC'2011).. Publication link: c89c5f6e-8252-4fb0-80b1-edcbe59e507e
  17. Pyysalo, S., Ohta, T., & Ananiadou, S. (2011). Anatomical Entity Recognition with Open Biomedical Ontologies. In host publication.. Publication link: ca355534-8d92-46b4-ad29-adcb76506075
  18. Kocbek, S., Saetre, R., Stiglic, G., Kim, J-D., Pernek, I., Tsuruoka, Y., ... Tsujii, J. (2011). Analysis of gene ranking algorithms with extraction of relevant biomedical concepts from Pubmed publications. In Proceedings of the 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS).. Publication link: cc136286-e6fc-4cfe-8a80-43b4fd01c8d1
  19. Thomas, J., McNaught, J., & Ananiadou, S. (2011). Applications of text mining within systematic reviews. Research Synthesis Methods, 2(1), 1-14. DOI: 10.1002/jrsm.27. Publication link: 67ce1683-00ed-4b70-999a-522ba95b77e6
  20. Kolluru, B., Hawizy, L., Murray-Rust, P., Tsujii, J., & Ananiadou, S. (2011). Using workflows to explore and optimise named entity recognition for chemistry. PLoS ONE, 6(5), [e20181]. DOI: 10.1371/journal.pone.0020181. Publication link: 66762b7e-59ac-4cd6-824c-41c1274e0429
  21. Thompson, P., Nawaz, R., McNaught, J., & Ananiadou, S. (2011). Enriching a biomedical event corpus with meta-knowledge annotation. BMC Bioinformatics, 12, [393]. DOI: 10.1186/1471-2105-12-393. Publication link: 7164ecd5-2af4-44a5-bac6-2d8e6b6e7d61
  22. Batista-Navarro, R. T., & 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). (pp. 71-77). Publication link: 5f00c3f7-71e2-498f-a1d5-6f5e796785f1
  23. Batista-Navarro, R. T., Cohen, K. (Ed.), Demner-Fushman, D. (Ed.), Ananiadou, S. (Ed.), Pestian, J. (Ed.), Tsujii, J. (Ed.), & Webber, B. (Ed.) (2011). Building a coreference-annotated corpus from the domain of biochemistry. In K. Cohen, D. Demner-Fushman, S. Ananiadou, J. Pestian, J. Tsujii, & B. Webber (Eds.), Proceedings of the 2011 Workshop on Biomedical Natural Language Processing, ACL-HLT 2011. (pp. 83-91). Association for Computational Linguistics. . Publication link: 5257013d-10a8-42cd-9335-177b797e6e0c
  24. Kocbek, S., Sætre, R., Stiglic, G., Kim, J. D., Pernek, I., Tsuruoka, Y., ... Tsujii, J. (2011). AGRA: Analysis of gene ranking algorithms. Bioinformatics, 27(8), 1185-1186. [btr097]. DOI: 10.1093/bioinformatics/btr097. Publication link: 76202ab2-c254-4c8a-a10f-fe48c65b1741
  25. Pyysalo, S., Ohta, T., Rak, R., Sullivan, D., Mao, C., Wang, C., ... Ananiadou, S. (2011). Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011. In host publication.. Publication link: 79174087-2411-45e1-83ed-82d0c8a0b558
  26. Thompson, P., McNaught, J., Montemagni, S., Calzolari, N., del Gratta, R., Lee, V., ... Ananiadou, S. (2011). The BioLexicon: A large-scale terminological resource for biomedical text mining. BMC Bioinformatics, 12, [397]. DOI: 10.1186/1471-2105-12-397. Publication link: 959e688d-8ae6-4522-ad7c-5a84525b8129
  27. Wang, X., Rak, R., Restificar, A., Nobata, C., Rupp, C. J., Batista-Navarro, R. T. B., ... Ananiadou, S. (2011). Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature. BMC Bioinformatics, 12(8), [S11]. DOI: 10.1186/1471-2105-12-S8-S11. Publication link: 919e4258-3458-4108-939a-94ea5251902e
  28. Korkontzelos, I., Mu, T., Restificar, A., & Ananiadou, S. (2011). Text mining for efficient search and assisted creation of clinical trials. In International Conference on Information and Knowledge Management, Proceedings|Int Conf Inf Knowledge Manage. (pp. 43-50). DOI: 10.1145/2064696.2064706. Publication link: 24e7831c-1e3a-4341-a170-4059299c9f93
  29. Kolluru, B., Nakjang, S., Hirt, R. P., Wipat, A., & Ananiadou, S. (2011). Automatic extraction of microorganisms and their habitats from free text using text mining workflows.Journal of integrative bioinformatics, 8(2), 184. . Publication link: 26460ed3-d0c0-49e9-a851-a01c2df405d1
  30. Soldatova, L. N., Kolluru, B., King, R. D., Qi, D., & Ananiadou, S. (2011). An ontology-based disambiguation of terms. In Proceedings of the Workshop on Mining the Pharmacogenomics Literature, Pacific Symopsium on Biocomputing.. Publication link: 20a441ad-c79b-448f-9c33-a83bb4077ab2
  31. Thompson, P., Kano, Y., McNaught, J., Pettifer, S., Attwood, T., Keane, J., & Ananiadou, S. (2011). Promoting Interoperability of Resources in META-SHARE. In C. N, I. T, P. S, & S. V (Eds.), IJCNLP 2011 Proceedings of the Workshop on Language Resources,Technology and Services in the Sharing Paradigm. (pp. 50-58). Asian Federation of Natural Language Processing. . Publication link: 1fd6fc11-3f33-43e2-8695-2aab079e467f
  32. Wang, X., McKendrick, I., Barrett, I., Dix, I., French, T., Tsujii, J., & Ananiadou, S. (2011). Automatic Extraction of Angiogenesis Bio-Process from Text. Bioinformatics. . Publication link: 113d104a-58a0-426b-a01c-dff9ee988a64
  33. Tsuruoka, Y., Miwa, M., Hamamoto, K., Tsujii, J., & Ananiadou, S. (2011). Discovering and visualizing indirect associations between biomedical concepts. Bioinformatics, 27(13), 111-119. [btr214]. DOI: 10.1093/bioinformatics/btr214. Publication link: 0912070f-0ced-4733-8075-7e14447fa76b
  34. Ananiadou, S., Thompson, P., Kano, Y., McNaught, J., Attwood, T., Day, P. J. R., ... Pettifer, S. (2011). Towards Interoperability of European Language Resources. Ariadne, 67. . Publication link: 3defeb41-695d-44b8-8044-5654c807c6e5
  35. Kano, Y., Miwa, M., Cohen, K. B., Hunter, L. E., Ananiadou, S., & Tsujii, J. (2011). U-Compare: A modular NLP workflow construction and evaluation system. IBM Journal of Research and Development, 55(3). DOI: 10.1147/JRD.2011.2105691. Publication link: 3fac9ed4-95d5-446e-8dad-92ad164a9a6b
  36. Nobata, C., Dobson, P. D., Iqbal, S. A., Mendes, P., Tsujii, J., Kell, D. B., & Ananiadou, S. (2011). Mining metabolites: Extracting the yeast metabolome from the literature. Metabolomics, 7(1), 94-101. DOI: 10.1007/s11306-010-0251-6. Publication link: 4c0af9ba-5794-461b-a55a-c00bf439892b
  37. Ananiadou, S., Thompson, P., Kano, Y., McNaught, J., Attwood, T. K., Day, P. J. R., ... Pettifer, S. (2011). Towards Interoperability of European Language Resources. Ariadne, 67. . Publication link: 2fc4e197-f049-449e-9ba3-8e07c5dfcba1
  38. Tsuruoka, Y., Miwa, M., Hamamoto, K., Tsujii, J., & Ananiadou, S. (2011). Discovering and visualizing indirect associations between biomedical concepts. Bioinformatics, 27(13), 111-119. [btr214]. DOI: 10.1093/bioinformatics/btr214. Publication link: 0912070f-0ced-4733-8075-7e14447fa76b
  39. Kano, Y., Miwa, M., Cohen, K. B., Hunter, L. E., Ananiadou, S., & Tsujii, J. (2011). U-Compare: A modular NLP workflow construction and evaluation system. IBM Journal of Research and Development, 55(3). DOI: 10.1147/JRD.2011.2105691. Publication link: 3fac9ed4-95d5-446e-8dad-92ad164a9a6b
  40. Nobata, C., Dobson, P. D., Iqbal, S. A., Mendes, P., Tsujii, J., Kell, D. B., & Ananiadou, S. (2011). Mining metabolites: Extracting the yeast metabolome from the literature. Metabolomics, 7(1), 94-101. DOI: 10.1007/s11306-010-0251-6. Publication link: 4c0af9ba-5794-461b-a55a-c00bf439892b
  41. Kolluru, B., Hawizy, L., Murray-Rust, P., Tsujii, J., & Ananiadou, S. (2011). Using workflows to explore and optimise named entity recognition for chemistry. PLoS ONE, 6(5), [e20181]. DOI: 10.1371/journal.pone.0020181. Publication link: 66762b7e-59ac-4cd6-824c-41c1274e0429
  42. Kocbek, S., Sætre, R., Stiglic, G., Kim, J. D., Pernek, I., Tsuruoka, Y., ... Tsujii, J. (2011). AGRA: Analysis of gene ranking algorithms. Bioinformatics, 27(8), 1185-1186. [btr097]. DOI: 10.1093/bioinformatics/btr097. Publication link: 76202ab2-c254-4c8a-a10f-fe48c65b1741
  43. Ananiadou, S., Sullivan, D., Black, W., Levow, G. A., Gillespie, J. J., Mao, C., ... Sobral, B. (2011). Named entity recognition for bacterial type IV secretion systems. PLoS ONE, 6(3), [e14780]. DOI: 10.1371/journal.pone.0014780. Publication link: b6538b0f-1fec-4a41-af37-acd0378aeb40
  44. Kano, Y., Björne, J., Ginter, F., Salakoski, T., Buyko, E., Hahn, U., ... Tsujii, J. (2011). U-Compare bio-event meta-service: Compatible BioNLP event extraction services. BMC Bioinformatics, 12(1), [481]. DOI: 10.1186/1471-2105-12-481. Publication link: aa23b36e-56e9-429a-a5ef-c2b82a116349
  45. Baran, J., Gerner, M., Haeussler, M., Nenadic, G., & Bergman, C. M. (2011). pubmed2ensembl: A resource for mining the biological literature on genes. PLoS ONE, 6(9), [e24716]. DOI: 10.1371/journal.pone.0024716. Publication link: 5afdc557-0d00-4b48-a78c-88f86b92e966 | PubMed:21980353
  46. Afzal, H., Eales, J., Stevens, R., & Nenadic, G. (2011). Mining Semantic Networks of Bioinformatics e-Resources from the Literature. Journal of Biomedical Semantics, 2(Suppl. 1). DOI: 10.1186/2041-1480-2-S1-S4. Publication link: 9e17947f-033f-4940-a829-e871b463874b
  47. Hakenberg, J., Gerner, M., Haeussler, M., Solt, I., Plake, C., Schroeder, M., ... Bergman, C. M. (2011). The GNAT library for local and remote gene mention normalization. Bioinformatics, 27(19), 2769-2771. [btr455]. DOI: 10.1093/bioinformatics/btr455. Publication link: 966b3222-110f-46ef-8f60-6e8f17e5a663 | PubMed:21813477
  48. Pataky, T. C., Bosch, K., Mu, T., Keijsers, N. L. W., Segers, V., Rosenbaum, D., & Goulermas, J. Y. (2011). An anatomically unbiased foot template for inter-subject plantar pressure evaluation. Gait & Posture, 33(3), 418-422. . Publication link: 1b759459-c88b-46b5-97b9-e068e69d38d2
  49. Wang, X., Rak, R., Restificar, A., Nobata, C., Rupp, C. J., Batista-Navarro, R. T. B., ... Ananiadou, S. (2011). Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature. BMC Bioinformatics, 12(8), [S11]. DOI: 10.1186/1471-2105-12-S8-S11. Publication link: 919e4258-3458-4108-939a-94ea5251902e
  50. Batista-Navarro, R. T., Cohen, K. (Ed.), Demner-Fushman, D. (Ed.), Ananiadou, S. (Ed.), Pestian, J. (Ed.), Tsujii, J. (Ed.), & Webber, B. (Ed.) (2011). Building a coreference-annotated corpus from the domain of biochemistry. In K. Cohen, D. Demner-Fushman, S. Ananiadou, J. Pestian, J. Tsujii, & B. Webber (Eds.), Proceedings of the 2011 Workshop on Biomedical Natural Language Processing, ACL-HLT 2011. (pp. 83-91). Association for Computational Linguistics. . Publication link: 5257013d-10a8-42cd-9335-177b797e6e0c
  51. Batista-Navarro, R. T., & 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). (pp. 71-77). Publication link: 5f00c3f7-71e2-498f-a1d5-6f5e796785f1
  52. Ananiadou, S., & Batista-Navarro, R. T. (2011). Discovering Potential Drugs by Extracting Biological Activities of Natural Products. In Workshop on Mining the Pharmacogenomics Literature, Pacific Symopsium on Biocomputing 2011.. Publication link: b402d53f-b5af-474e-8c7c-6841df2136f2
▲ Up to the top