Ananiadou, S. - NaCTeM Publications - Aigaion 2.0

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First name(s):	S.
Last name(s):	Ananiadou

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Kontonatsios, G., Korkontzelos, I., Kolluru, B., Thompson, P. and Ananiadou, S., Deploying and Sharing U-Compare Workflows as Web Services (2013), in: Journal of Biomedical Semantics, 4(7)

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Pyysalo, S., Ohta, T., Miwa, M., Cho, H. -C., Tsujii, J. and Ananiadou, S., Event extraction across multiple levels of biological organization (2012), in: Bioinformatics, 28:18(i575-i581)

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Selected articles from the BioNLP Shared Task 2011, 2012

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Rak, R., Kolluru, B. and Ananiadou, S., Building trainable taggers in a web-based, UIMA-supported NLP workbench, in: Proceedings of the 50th Annual Meeting of the Association for Computational Linguistics (ACL 2012), pages 121-126, 2012

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Wang, X., Rak, R., Restificar, A., Nobata, C., Rupp, C. J., Batista-Navarro, R., Nawaz, R. and Ananiadou, S., NaCTeM Systems for BioCreative III PPI Tasks, in: Proceedings of the BioCreative III Workshop, pages 142-147, 2010

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Stenetorp, P., Pyysalo, S., Ohta, T., Ananiadou, S. and Tsujii, J., Bridging the Gap Between Scope-based and Event-based Negation/Speculation Annotations: A Bridge Not Too Far, in: Proceedings of ExProM 2012, pages 47-56, 2012

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Ohta, T., Pyysalo, S., Tsujii, J. and Ananiadou, S., Open-domain Anatomical Entity Mention Detection, in: Proceedings of the ACL Workshop on Detecting Stucture in Scholarly Discourse (DSSD), pages 27-36, 2012

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Pyysalo, S., Stenetorp, P., Ohta, T., Kim, J.-D. and Ananiadou, S., New Resources and Perspectives for Biomedical Event Extraction, in: Proceedings of BioNLP 2012, pages 100-108, 2012

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BjÃ¶rne, J., Van Landeghem, S., Pyysalo, S., Ohta, T., Ginter, F., Van de Peer, Y., Ananiadou, S. and Salakoski, T., PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations, in: Proceedings of BioNLP 2012, pages 82-90, 2012

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Liakata, M., Thompson, P., de Waard, A., Nawaz, R., Pander Maat, H. and Ananiadou, S., A three-way perspective on scientiï¬c discourse annotation for knowledge extraction, in: Proceedings of the ACL Workshop on Detecting Structure in Scholarly Discourse (DSSD), pages 37-46, 2012

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Korkontzelos, I., Mu, T. and Ananiadou, S., ASCOT: a text mining-based web-service for efficient search and assisted creation of clinical trials (2012), in: BMC Medical Informatics and Decision Making, 12:Suppl 1(S3)

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Miwa, M., Thompson, P. and Ananiadou, S., Boosting automatic event extraction from the literature using domain adaptation and coreference resolution (2012), in: Bioinformatics, 28:13(1759-1765)

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Miwa, M., Thompson, P., McNaught, J., Kell, D. B. and Ananiadou, S., Extracting semantically enriched events from biomedical literature (2012), in: BMC Bioinformatics, 13(108)

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Nawaz, R., Thompson, P. and Ananiadou, S., Meta-Knowledge Annotation at the Event Level: Comparison between Abstracts and Full Papers, in: Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012), pages 24-31, 2012

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Kontonatsios, G., Korkontzelos, I. and Ananiadou, S., Developing Multilingual Text Mining Workflows in UIMA and U-Compare, in: Proceedings of the 17th International conference on Applications of Natural Language Processing to Information Systems, Groningen, Netherlands, pages 82 - 93, Springer, 2012

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MihÄƒilÄƒ, C., Batista-Navarro, R. and Ananiadou, S., Analysing Entity Type Variation across Biomedical Subdomains, in: Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012), Istanbul, Turkey, pages 1-7, 2012

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Black, W.J., Procter, R., Gray, S. and Ananiadou, S., A data and analysis resource for an experiment in text mining a collection of micro-Âblogs on a political topic, in: Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012), pages 2083-2088, 2012

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Pyysalo, S., Ohta, T., Rak, R., Sullivan, D., Mao, C., Wang, C., Sobral, B., Tsujii, J. and Ananiadou, S., Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011 (2012), in: BMC Bioinformatics, 13:Suppl. 11(S2)

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Rak, R., Rowley, A. and Ananiadou, S., Collaborative Development and Evaluation of Text-processing Workflows in a UIMA-supported Web-based Workbench, in: Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012), pages 2971-2976, 2012

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Rak, R., Rowley, A., Black, W.J. and Ananiadou, S., Argo: an integrative, interactive, text mining-based workbench supporting curation (2012), in: Database: The Journal of Biological Databases and Curation, 2012

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Wang, X., Thompson, P. and Ananiadou, S., Biomedical Chinese-English CLIR Using an Extended CMeSH Resource to Expand Queries, in: Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012), pages 1148-1155, 2012

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Nawaz, R., Thompson, P. and Ananiadou, S., Identification of Manner in Bio-Events, in: Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012), pages 3505-3510, 2012

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Stenetorp, P., Pyysalo, S., TopiÄ‡, G., Ohta, T., Ananiadou, S. and Tsujii, J., brat: a Web-based Tool for NLP-Assisted Text Annotation, in: Proceedings of the Demonstrations at the 13th Conference of the European Chapter of the Association for Computational Linguistics, Avignon, France, pages 102-107, Association for Computational Linguistics, 2012

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Mu, T., Goulermas, J. Y, Tsujii, J. and Ananiadou, S., Proximity-based Frameworks for Generating Embeddings from Multi-Output Data (2012), in: IEEE Transactions on Pattern Analysis and Machine Intelligence

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Kano, Y., BjÃ¶rne, J., Ginter, F., Salakoski, T., Buyko, E., Hahn, U., Cohen, K. B., Verspoor, K., Roeder, C., Hunter, L., Kilicoglu, H., Bergler, S., Van Landeghem, S., Van Parys, T., Van de Peer, Y., Miwa, M., Ananiadou, S., Neves, M., Pascual-Montano, A., Ozgur, A., Radev, D. R., Riedel, S., SÃ¦tre, R., Chun, H.-W., Kim, J.-D., Pyysalo, S., Ohta, T. and Tsujii, J., U-Compare bio-event meta-service: compatible BioNLP event extraction services (2011), in: BMC Bioinformatics, 12(481)

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