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Publications of Pyysalo, S. sorted by journal and type
Bioinformatics
| and , Anatomical Entity Mention Recognition at Literature Scale (2014), in: Bioinformatics, 30:6(868-875) |
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| , , , , , and , A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text (2013), in: Bioinformatics, 29:13(i44-i52) |
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| , , , , and , Event extraction across multiple levels of biological organization (2012), in: Bioinformatics, 28:18(i575-i581) |
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| , , , and , Complex event extraction at PubMed scale (2010), in: Bioinformatics, 26:12(i382-i390) |
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BMC BioInformatics
| , , , , , , , and , Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013 (2015), in: BMC BioInformatics, 16(Suppl 10):Suppl 10(S2) |
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BMC Bioinformatics
| , , and , BioCause: Annotating and Analysing Causality in the Biomedical Domain (2013), in: BMC Bioinformatics, 14:1(2) |
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| , , and , Wide coverage biomedical event extraction using multiple partially overlapping corpora (2013), in: BMC Bioinformatics, 14:175 |
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| , , , , , , , and , 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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| , , , , , , , , , , , , , , , , , , , , , , , , , , and , U-Compare bio-event meta-service: compatible BioNLP event extraction services (2011), in: BMC Bioinformatics, 12(481) |
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| , , , , , and , Medie and Info-pubmed: 2010 update (2010), in: BMC Bioinformatics, 11:Suppl 5(P7) |
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| , , , and , Investigating heterogeneous protein annotations toward cross-corpora utilization (2009), in: BMC Bioinformatics, 10(403) |
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Computational Intelligence
| , , , and , Extracting Bio-Molecular Events From Literature—The BioNLP’09 Shared Task (2011), in: Computational Intelligence, 27:4(513-540) |
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Journal of Bioinformatics and Computational Biology (JBCB)
| , , and , A re-evaluation of biomedical named entity-term relations (2010), in: Journal of Bioinformatics and Computational Biology (JBCB), 8:5(917--928) |
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| , , , , and , Improving the Inter-corpora Compatibility for Protein Annotations (2010), in: Journal of Bioinformatics and Computational Biology (JBCB), 8:5(901-916) |
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Journal of Biomedical Semantics
| , , and , Generalising semantic category disambiguation with large lexical resources for fun and profit (2014), in: Journal of Biomedical Semantics, 5(26) |
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PLOS ONE
| , , , , , , , , , and , Large-scale event extraction from literature with multi-level gene normalization (2013), in: PLOS ONE, 8:4(e55814) |
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PLoS ONE
| , , , , , , , , and , Named Entity Recognition for Bacterial Type IV Secretion Systems (2011), in: PLoS ONE, 6:3(e14780) |
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Proceedings of the Fourth International Symposium on Languages in Biology and Medicine (LBM 2011)
| , , and , Almost Total Recall: Semantic Category Disambiguation Using Large Lexical Resources and Approximate String Matching (2011), in: Proceedings of the Fourth International Symposium on Languages in Biology and Medicine (LBM 2011) |
Trends in Biotechnology
| , , and , Event extraction for systems biology by text mining the literature (2010), in: Trends in Biotechnology, 28:7(381-390) |
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Publications of type Inproceedings
2013
| , , , and , Distributional Semantics Resources for Biomedical Text Processing, in: Proceedings of LBM 2013, pages 39-44, 2013 |
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| , , , , , and , Overview of BioNLP Shared Task 2013, in: Proceedings of the BioNLP Shared Task 2013 Workshop, pages 1--7, Association for Computational Linguistics, 2013 |
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| , and , Overview of the Cancer Genetics (CG) task of BioNLP Shared Task 2013, in: Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, Bulgaria, pages 58-66, Association for Computational Linguistics, 2013 |
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| , , , , , , and , Overview of the Pathway Curation (PC) task of BioNLP Shared Task 2013, in: Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, Bulgaria, pages 67-75, Association for Computational Linguistics, 2013 |
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2012
| , , , , and , 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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| , , , and , 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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