Publications by Paul Thompson

Papers by Paul Thompson at NaCTeM, newest first. All publications

2025 | 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008

70 publications

2025

Liu, Z., Thompson, P., Rong, J. and Ananiadou, S., ConspEmoLLM-v2: A robust and stable model to detect sentiment-transformed conspiracy theories, in: Proceedings of the 14th Conference on Prestigious Applications of Intelligent Systems (PAIS-2025), pages 5311–5318, 2025 [URL]
Yang, K, Leng, Y., Zhang, X., Zhang, T., Thompson, P., Keavney, B., Tomaszewski, M. and Ananiadou, S., Natural Language Processing for Cardiology: A Narrative Review, in: arXiv, 2025 [DOI] [URL]

2024

Liu, Z., Liu, B, Thompson, P., Yang, K and Ananiadou, S., ConspEmoLLM: Conspiracy Theory Detection Using an Emotion-Based Large Language Model, in: Proceedings of the 13th International Conference on Prestigious Applications of Intelligent Systems (PAIS-2024), pages 4649–4656, 2024 [DOI] [URL]
Liu, Z., Zhang, T., Yang, K., Thompson, P., Yu, Z. and Ananiadou, S., Emotion detection for misinformation: A review, in: Information Fusion, 2024 [DOI] [Pure]
Thompson, P., Ananiadou, S., Basinas, I., Brinchmann, B. C., Cramer, C., Galea, K. S., Ge, C., Georgiadis, P., Kirkeleit, J., Kuijpers, E., Nguyen, N. T. H., Nuñez, R., Schlünssen, V., Stokholm, Z. A., Taher, E. A., Tinnerberg, H., van Tongeren, M. and Xie, Q., Supporting the working life exposome: Annotating occupational exposure for enhanced literature search, in: PLoS ONE, 19:8(e0307844), 2024 [DOI] [URL]

2023

Liu, B., Schlegel, V., Thompson, P., Batista-Navarro, R. T. and Ananiadou, S., Global information-aware argument mining based on a top-down multi-turn QA model, in: Information Processing & Management, 2023 [DOI] [URL] [Pure]

2022

Inan, E., Thompson, P., Christopoulou, F., Yates, T. and Ananiadou, S., Knowledge Graph Enrichment of a Semantic Search System for Construction Safety, in: Intelligent Systems and Applications. IntelliSys 2022., Springer, Cham, pages 33-52, 2022 [DOI] [URL]

2021

Inan, E., Thompson, P., Yates, T. and Ananiadou, S., HSEarch: semantic search system for workplace accident reports, in: Proceedings of the 43rd European Confererence on Information Retrieval (ECIR 2021), pages 514-519, 2021 [URL]

2020

Thompson, P., Yates, T., Inan, E. and Ananiadou, S., Semantic Annotation for Improved Safety in Construction Work, in: Proceedings of LREC 2020, pages 1983‑1992, 2020 [URL]

2019

Ju, M., Short, A., Thompson, P., Bakerly, N. D., Gkoutos, G., Tsaprouni, L. and Ananiadou, S., Annotating and Detecting Phenotypic Information for Chronic Obstructive Pulmonary Disease, in: Journal of the American Medical Informatics Association, 2019 [DOI] [URL] [Pure]

2018

Thompson, P., Daikou, S., Ueno, K., Batista-Navarro, R. T., Tsujii, J. and Ananiadou, S., Annotation and Detection of Drug Effects in Text for Pharmacovigilance, in: Journal of Cheminformatics, 2018 [DOI] [URL] [Pure]
Thompson, P. and Ananiadou, S., Extracting Gene-Disease Relations from Text to Support Biomarker Discovery, in: Digital Health 2017: Global Public Health, Personalised Medicine, and Emergency Medicine in the Age of Big Data, 2018 [DOI] [URL] [Pure]
Thompson, P. and Ananiadou, S., HYPHEN: A flexible, hybrid method to map phenotype concept mentions to terminological resources, in: Terminology, pages 91–121, 2018 [DOI] [URL] [Pure]
Shardlow, M., Batista-Navarro, R., Thompson, P., Nawaz, R., McNaught, J. and Ananiadou, S., Identification of Research Hypotheses and New Knowledge from Scientific Literature, in: BMC Medical Informatics and Decision Making, 18(46), 2018 [DOI] [URL]

2017

Thompson, P., Nawaz, R., McNaught, J. and Ananiadou, S., Enriching News Events with Meta-knowledge Information, in: Language Resources and Evaluation, pages 409–438, 2017 [DOI] [URL] [Pure]
Ananiadou, S. and Thompson, P., Supporting Biological Pathway Curation Through Text Mining, in: Communications in Computer and Information Science, pages 59–73, 2017 [DOI] [URL] [Pure]
Thompson, P., Boylan, K., Freemont, A. and Ananiadou, S., Supporting biomarker discovery using text mining, in: Proceedings of Informatics for Health 2017, 2017 [URL]
Thompson, P., Ananiadou, S. and Tsujii, J., The GENIA Corpus: Annotation Levels and Applications, in: Handbook of Linguistic Annotation, Springer, pages 1395-1432, 2017 [DOI] [URL]

2016

Alnazzawi, N., Thompson, P. and Ananiadou, S., Mapping Phenotypic Information in Heterogeneous Textual Sources to a Domain- Specific Terminological Resource, in: PLoS One., 2016 [DOI] [URL] [Pure]
Rehm, G., Uszkoreit, H., Garabik, R., Grobelnik, M., García-Mateo, C., van Genabith, J., Hajič, J., Hernáez, I., Judge, J., Koeva, S., Krek, S., Krstev, C., Ananiadou, S., Lindén, K., Magnini, B., Mariani, J., McNaught, J., Melero, M., Monachini, M., Moreno, A., Odijk, J., Ogrodniczuk, M., Pęzik, P., Bel, N., Piperidis, S., Przepiórkowski, A., Rögnvaldsson, E., Rosner, M., Pedersen, B. S., Skadiņa, I., Smedt, K. D., Tadíc, M., Thompson, P., Tufiș, D., Bielevičiené, A., Váradi, T., Vasiļjevs, A., Vider, K., Zabarskaitė, J., Borin, L., Branco, A., Budin, G., Calzolari, N. and Daelemans, W., The strategic impact of META-NET on the regional, national and international level, in: Language Resources and Evaluation, pages 351–374, 2016 [DOI] [URL] [Pure]
Thompson, P., McNaught, J. and Ananiadou, S., Customised OCR correction for historical medical text, in: 2015 Digital Heritage, pages 35–41, 2016 [DOI] [URL] [Pure]
Thompson, P., Carter, J., McNaught, J. and Ananiadou, S., Semantically enhanced search system for historical medical archives, in: 2015 Digital Heritage, pages 387–390, 2016 [DOI] [URL] [Pure]
Thompson, P., Batista-Navarro, R. T., Kontonatsios, G., Carter, J., Toon, E., McNaught, J., Timmermann, C., Worboys, M. and Ananiadou, S., Text mining the history of medicine, in: P L o S One, 2016 [DOI] [URL] [Pure]
Korkontzelos, I., Thompson, P. and Ananiadou, S., Identifying content types of messages related to Open Source Software projects, in: Proceedings of LREC 2016, pages 1837-1844, 2016 [URL]

2015

Alnazzawi, N., Thompson, P., Batista-Navarro, R. T. and Ananiadou, S., Using text mining techniques to extract phenotypic information from the PhenoCHF corpus, in: B M C Medical Informatics and Decision Making, 2015 [DOI] [URL] [Pure]
Ananiadou, S., Thompson, P., Nawaz, R., McNaught, J. and Kell, D., Event-based text mining for biology and functional genomics, in: Briefings in functional genomics, pages 213–30, 2015 [DOI] [URL] [Pure]
Rosner, M., Attard, A., Thompson, P., Gatt, A. and Ananiadou, S., Extending a Tool Resource Framework with U-Compare, in: Human Language Technology Challenges for Computer Science and Linguistics, pages 315–326, 2015 [Pure]
Mihaila, C., Batista-Navarro, R. T., Alnazzawi, N., Kontonatsios, G., Korkontzelos, I., Rak, R., Thompson, P. and Ananiadou, S., Mining the biomedical literature, in: Healthcare Data Analytics, pages 251–308, 2015 [URL] [Pure]

2014

Rehm, G., Uszkoreit, H., Ananiadou, S., Bel, N., Bielevičiené, A., Borin, L., Branco, A., Budin, G., Calzolari, N., Daelemans, W., Garabik, R., Grobelnik, M., García-Mateo, C., van Genabith, J., Hajič, J., Hernáez, I., Judge, J., Koeva, S., Krek, S., Krstev, C., Lindén, K., Magnini, B., Mariani, J., McNaught, J., Melero, M., Monachini, M., Moreno, A., Odijk, J., Ogrodniczuk, M., Pęzik, P., Piperidis, S., Przepiórkowski, A., Rögnvaldsson, E., Rosner, M., Pedersen, B. S., Skadiņa, I., Smedt, K. D., Tadíc, M., Thompson, P., Tufiș, D., Váradi, T., Vasiļjevs, A., Vider, K. and Zabarskaitė, J., The Strategic Impact of META-NET on the Regional, National and International Level, in: Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14), pages 1517–1524, 2014 [URL] [Pure]
Alnazzawi, N., Thompson, P. and Ananiadou, S., Building a semantically annotated corpus for congestive heart and renal failure from clinical records and the literature, in: Proceedings of the 5th International Workshop on Health Text Mining and Information Analysis (Louhi), pages 69–74, 2014 [URL] [Pure]
Kontonatsios, G., Mihăilă, C., Korkontzelos, I., Thompson, P. and Ananiadou, S., A hybrid approach to compiling bilingual dictionaries of medical terms from parallel corpora, in: Statistical Language and Speech Processing, Second International Conference, SLSP 2014, pages 57–69, 2014 [DOI] [Pure]
Miwa, M., Thompson, P., Korkontzelos, I. and Ananiadou, S., Comparable Study of Event Extraction in Newswire and Biomedical Domains, in: Proceedings of Coling 2014, pages 2270–2279, 2014 [URL] [Pure]

2013

Mihaila, C., Kontonatsios, G., Thompson, P., Batista-Navarro, R. T., Mihaila, C., Korkontzelos, I. and Ananiadou, S., Extending an interoperable platform to facilitate the creation of multilingual and multimodal NLP applications, in: Proceedings of the System Demonstration Session at The 51st Annual Meeting of the Association for Computational Linguistics, pages 43–48, 2013 [URL] [PDF] [Pure]
Mihaila, C., Kontonatsios, G., Batista-Navarro, R. T., Thompson, P., Korkontzelos, I. and Ananiadou, S., Towards a Better Understanding of Discourse: Integrating Multiple Discourse Annotation Perspectives Using UIMA, in: Proceedings of the 7th Linguistic Annotation Workshop and Interoperability with Discourse, pages 79–88, 2013 [URL] [PDF] [Pure]
Nawaz, R., Thompson, P. and Ananiadou, S., Negated BioEvents: Analysis and Identification, in: BMC Bioinformatics, 2013 [DOI] [URL] [Pure]
Kontonatsios, G., Korkontzelos, I., Kolluru, B., Thompson, P. and Ananiadou, S., Deploying and Sharing U-Compare Workflows as Web Services, in: Journal of Biomedical Semantics, 4(7), 2013 [DOI] [URL]
Ananiadou, S., Thompson, P. and Nawaz, R., Enhancing Search: Events and their Discourse Context, in: Computational Linguistics and Intelligent Text Processing, pages 318–334, 2013 [DOI] [URL] [Pure]
Batista-Navarro, R. T., Kontonatsios, G., Mihǎilǎ, C., Thompson, P., Rak, R., Nawaz, R., Korkontzelos, I. and Ananiadou, S., Facilitating the analysis of discourse phenomena in an interoperable NLP platform, in: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pages 559–571, 2013 [DOI] [URL] [Pure]
Ananiadou, S., Thompson, P. and Nawaz, R., Mining events from the literature for bioinformatics applications, in: ACM SIGWEB Newsletter, 2013 [URL] [Pure]
Thompson, P., Nawaz, R., Korkontzelos, I., Black, W., McNaught, J. and Ananiadou, S., News search using discourse analytics, in: Proceedings of the DigitalHeritage 2013 - Federating the 19th Int'l VSMM, 10th Eurographics GCH, and 2nd UNESCO Memory of the World Conferences, Plus Special Sessions fromCAA, Arqueologica 2.0 et al., pages 597–604, 2013 [DOI] [URL] [PDF] [Pure]
Nawaz, R., Thompson, P. and Ananiadou, S., Something old, something new: identifying knowledge source in bio-events, in: International Journal of Computational Linguistics and Applications, 4:1(129-144), 2013 [URL]
Batista-Navarro, R. T., Kontonatsios, G., Mihaila, C., Thompson, P., Nawaz, R., Korkontzelos, I. and Ananiadou, S., Supporting Discourse Phenomena in an Interoperable NLP Framework, in: host publication, 2013 [Pure]
Nawaz, R., Thompson, P. and Ananiadou, S., Towards Event-based Discourse Analysis of Biomedical Text, in: International Journal of Computational Linguistics and Applications, pages 101–120, 2013 [URL] [Pure]

2012

Liakata, M., Thompson, P., de Waard, A., Nawaz, R., Maat, H. P. and Ananiadou, S., A Three-Way Perspective on Scientific Discourse Annotation for Knowledge Extraction, in: Proceedings of the ACL Workshop on Detecting Structure in Scholarly Discourse (DSSD), pages 37–46, 2012 [Pure]
Miwa, M., Thompson, P. and Ananiadou, S., Boosting automatic event extraction from the literature using domain adaptation and coreference resolution, in: Bioinformatics, pages 1759–1765, 2012 [DOI] [URL] [Pure]
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 [URL] [Pure]
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 [URL]
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 [URL] [Pure]
Miwa, M., Thompson, P., McNaught, J., Kell, D. and Ananiadou, S., Extracting semantically enriched events from biomedical literature., in: BMC Bioinformatics, 2012 [DOI] [URL] [Pure]
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 [URL] [Pure]
Ananiadou, S., McNaught, J. and Thompson, P., The English Language in the Digital Age, in: White Paper Series, 2012 [URL] [Pure]

2011

Thompson, P., Nawaz, R., McNaught, J. and Ananiadou, S., Enriching a biomedical event corpus with meta-knowledge annotation, in: BMC Bioinformatics, 2011 [DOI] [URL] [Pure]
Thompson, P., McNaught, J., Montemagni, S., Calzolari, N., del Gratta, R., Lee, V., Marchi, S., Monachini, M., Pezik, P., Quochi, V., Rupp, C., Sasaki, Y., Venturi, G., Rebholz-Schuhmann, D. and Ananiadou, S., The BioLexicon: A large-scale terminological resource for biomedical text mining, in: BMC Bioinformatics, 2011 [DOI] [URL] [Pure]
Rosner, M., Attard, A., Thompson, P., Gatt, A. and Ananiadou, S., Extending a Tool Resource Framework with U-Compare, in: Proceedings of the 5th Language & Technology Conference (LTC'2011), 2011
Rosner, M., Attard, A., Thompson, P., Gatt, A. and Ananiadou, S., Extending a Tool Resource Framework with U-Compare, in: Proceedings of the 5th Language & Technology Conference (LTC'2011), 2011 [URL] [Pure]
Thompson, P., Kano, Y., McNaught, J., Pettifer, S., Attwood, T., Keane, J. and Ananiadou, S., Promoting Interoperability of Resources in META-SHARE, in: IJCNLP 2011 Proceedings of the Workshop on Language Resources,Technology and Services in the Sharing Paradigm, pages 50–58, 2011 [URL] [Pure]
Ananiadou, S., Thompson, P., Kano, Y., McNaught, J., Attwood, T. K., Day, P. J. R., Keane, J., Jackson, D. and Pettifer, S., Towards Interoperability of European Language Resources, in: Ariadne, 2011 [URL] [Pure]

2010

Ananiadou, S., Thompson, P., Thomas, J., Mu, T., Oliver, S., Rickinson, M., Sasaki, Y., Weissenbacher, D. and McNaught, J., Supporting the education evidence portal via text mining, in: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, pages 3829–3844, 2010 [DOI] [URL] [Pure]
Rupp, C., Thompson, P., Black, W., McNaught, J. and Ananiadou, S., 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), pages 6pp, 2010 [URL] [Pure]
Ananiadou, S., Nawaz, R. and Thompson, P., Evaluating a meta-knowledge annotation scheme for bio-events, in: host publication, pages 69–77, 2010 [URL] [Pure]
Ananiadou, S., Nawaz, R. and Thompson, P., Event Interpretation: A Step towards Event-Centred Text Minin, in: host publication, pages 103–107, 2010 [PDF] [Pure]
Ananiadou, S., Thompson, P. and Nawaz, R., Improving search through Event-based Biomedical Text Mining, in: 1st Automated Motif Discovery in Cultural Heritage and Scientific Communication Texts (AMICUS) workshop, Vienna, 1/01/24, 2010 [PDF] [Pure]
Nawaz, R., Thompson, P., McNaught, J. and Ananiadou, S., Meta-knowledge annotation of bio-events, in: Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC2010), pages 2498–2505, 2010 [URL] [Pure]

2009

Thompson, P., Iqbal, S. A., McNaught, J. and Ananiadou, S., Construction of an annotated corpus to support biomedical information extraction, in: BMC Bioinformatics, 2009 [DOI] [URL] [Pure]
Sasaki, Y., Thompson, P., McNaught, J. and Ananiadou, S., Biological event recognition with textual induction, in: Proceedings of the 3rd International Symposium on Languages in Biology and Medicine (LBM-2009), pages 91–96, 2009 [URL] [Pure]
Venturi, G., Montemagni, S., Marchi, S., Sasaki, Y., Thompson, P., McNaught, J. and Ananiadou, S., Bootstrapping a verb lexicon for biomedical information extraction, in: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pages 137–148, 2009 [DOI] [URL] [Pure]
Sasaki, Y., Thompson, P., McNaught, J. and Ananiadou, S., Three BioNLP Tools Powered by the BioLexicon, in: Proceeedings of EACL 2009, pages 61–64, 2009 [URL] [Pure]

2008

Thompson, P., Cotter, P., McNaught, J., Ananiadou, S., Montemagni, S., Trabucco, A. and Venturi, G., 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), pages 2159–2166, 2008 [PDF] [Pure]
Thompson, P., Venturi, G., McNaught, J., Montemagni, S. and Ananiadou, S., Categorising Modality in Biomedical Texts, in: Proceedings of the LREC 2008 Workshop on Building and Evaluating Resources for Biomedical Text Mining., pages 27–34, 2008 [PDF] [Pure]
Sasaki, Y., Thompson, P., Cotter, P., McNaught, J. and Ananiadou, S., Event frame extraction based on a gene regulation corpus, in: Coling 2008 - 22nd International Conference on Computational Linguistics, Proceedings of the Conference, pages 761–768, 2008 [PDF] [Pure]