Publications by John McNaught

Papers by John McNaught at NaCTeM, newest first. All publications

2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 1995 | 1990

72 publications

2018

Przybyła, P., Brockmeier, A., Kontonatsios, G., Pogam, M. L., McNaught, J., von Elm, E., Nolan, K. and Ananiadou, S., Prioritising references for systematic reviews with RobotAnalyst: a user study, in: Research Synthesis Methods, pages 470–488, 2018 [DOI] [URL] [Pure]
Shardlow, M., Nguyen, N., Owen, G., Turner, S., Leach, A., O'Donovan, C., McNaught, J. and Ananiadou, S., A New Corpus to Support Text Mining for the Curation of Metabolites in the ChEBI Database, in: Proceedings of the Eleventh International Conference on Language Resources and Evaluation, Miyazaki, Japan, 7/05/18, pages 280–285, 2018 [URL] [Pure]
Shardlow, M., Ju., M., Li, M., O'Reilly, C., Iavarone, E., McNaught, J. and Ananiadou, S., A Text Mining Pipeline Using Active and Deep Learning for Curating Information in Computational Neuroscience, in: Neuroinformatics, 2018 [DOI] [URL]
Almagrabi, H., Malibari, A. and McNaught, J., Corpus Analysis and Annotation for Helpful Sentences in Product Reviews, in: Computer and Information Science, 11:2(76-87), 2018 [DOI] [URL]
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

Kontonatsios, G., Brockmeier, A., Przybyla, P., McNaught, J., Mu, T., Goulermas, J. Y. and Ananiadou, S., A semi-supervised approach using label propagation to support citation screening, in: Journal of Biomedical Informatics, pages 67–76, 2017 [DOI] [URL] [Pure]
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]

2016

Przybyla, P., Shardlow, M., Aubin, S., Bossy, R., de Castilho, R. E., Piperidis, S., McNaught, J. and Ananiadou, S., Text Mining Resources for the Life Sciences, in: Database, 2016 [DOI] [URL] [Pure]
Black, W., Rowley, A., Miwa, M., McNaught, J. and Ananiadou, S., Text Mining for Semantic Search in Europe PubMed Central Labs, in: Working with Text, pages 111–131, 2016 [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]
Shardlow, M., Przybyla, P., Batista-Navarro, R. T., Carter, J., McNaught, J. and Ananiadou, S., Facilitating and promoting web annotation with Argo, in: Proceedings of I Annotate 2016, 2016 [Pure]

2015

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]
O'Mara-Eves, A., Thomas, J., McNaught, J., Miwa, M. and Ananiadou, S., Using text mining for study identification in systematic reviews: a systematic review of current approaches, in: Systematic Reviews, 2015 [DOI] [URL] [Pure]
Almagrabi, H., Malibari, A. and McNaught, J., A Survey of Quality Prediction of Product Reviews, in: International Journal of Advanced Computer Science and Applications, 6:11(49-58), 2015 [URL]

2014

Gou, Y., Graff, F., Rossiter, P., Talo, F., Vartak, V., Coleman, L., Hawkins, C., Kinsey, A., Mansoor, S., Morris, V., Rowbotham, R., Chapman, D., Kilian, O., MacIntyre, R., Patel, Y., Ananiadou, S., Black, W., McNaught, J., Rak, R., Rowley, A., Kafkas, S., Katuri, J., Kim, J., Marinos, N., McEntyre, J., Morrison, A. and Pi, X., Europe PMC: a full-text literature database for the life sciences and platform for innovation, in: Nucleic acids research, pages 1–7, 2014 [DOI] [Pure]
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]
Sutcliffe, A., de Bruijn, O., Thew, S., Buchan, I., Jarvis, P., McNaught, J. and Procter, R., Developing visualization-based decision support tools for epidemiology, in: Information Visulization, 13:1(3 -17), 2014 [DOI] [URL]

2013

Thomas, J., O'Mara-Eves, A., McNaught, J. and Ananiadou, S., The potential of text mining to reduce screening workload in systematic reviews: a retrospective evaluation, in: 21st Cochrane Colloquium, Quebec, 19/09/13, pages 5–5, 2013 [Pure]
Alhazmi, S., Black, W.J. and McNaught, J., Arabic SentiWordNet in Relation to SentiWordNet 3.0, in: International Journal of Computational Linguistics, 4:1(1-11), 2013 [URL]
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]

2012

Sutcliffe, A., de Bruijn, O., Thew, S., Buchan, I., Jarvis, P., McNaught, J. and Procter, R., Developing visualization-based decision support tools for epidemiology, in: Information Visualization, 2012 [DOI] [URL]
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]
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]
Thomas, J., McNaught, J. and Ananiadou, S., Applications of text mining within systematic reviews, in: Research Synthesis Methods, pages 1–14, 2011 [DOI] [URL] [Pure]
McEntyre, J. R., Ananiadou, S., Andrews, S., Black, W. J., Boulderstone, R., Buttery, P., Chaplin, D., Chevuru, S., Cobley, N., Coleman, L. A., Davey, P., Gupta, B., Haji-Gholam, L., Hawkins, C., Horne, A., Hubbard, S. J., Kim, J. H., Lewin, I., Lyte, V., MacIntyre, R., Mansoor, S., Mason, L., McNaught, J., Newbold, E., Nobata, C., Ong, E., Pillai, S., Rebholz-Schuhmann, D., Rosie, H., Rowbotham, R., Rupp, C. J., Stoehr, P. and Vaughan, P., UKPMC: A full text article resource for the life sciences, in: Nucleic acids research., pages D58–D65, 2011 [DOI] [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]
Ananiadou, S., McNaught, J., Thomas, J. and Oliver, S., Evaluating a text mining based educational search portal, in: Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC2010), pages 3344–3350, 2010 [URL] [Pure]
Sasaki, Y., McNaught, J. and Ananiadou, S., The value of an in-domain lexicon in genomics QA, in: Journal of Bioinformatics and Computational Biology, pages 147–161, 2010 [DOI] [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]
Black, W., Rupp, C., Nobata, C., McNaught, J., Tsujii, J. and Ananiadou, S., High-Precision Semantic Search by Generating and Testing Questions., in: Proceedings of the UK e-Science All Hands Meeting, pages 3pp, 2010 [URL] [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]
Thew, S., Sutcliffe, A., de Bruijn, O., McNaught, J., Procter, R. and Buchan, I., Supporting Creativity and Appreciation of Uncertainty in Exploring Geo-coded Public Health Data, in: Methods of Information in Medicine, 49, 2010 [DOI] [URL]
Sutcliffe, A., Thew, S., de Bruijn, O., Buchan, I., Jarvis, P., McNaught, J. and Procter, R., User Engagement by User-Centred Design in e-Health, in: Philosophical Transactions of the Royal Society A, 368:1926(4209-4224), 2010 [DOI] [URL]

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]
Piao, S., Rea, B., McNaught, J. and Ananiadou, S., Improving full text search with text mining tools, in: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pages 301–302, 2009 [DOI] [PDF] [Pure]
Thew, S., Sutcliffe, A., Procter, R., de Bruijn, O., McNaught, J., Venters, C.C. and Buchan, I., Requirements Engineering for E-science: Experiences in Epidemiology, in: IEEE Software, 26:1(80-87), 2009 [PDF]
Ananiadou, S., Sasaki, Y. and McNaught, J., The Value of an In-Domain Lexicon in Genomics QA, in: host publication, pages 47–55, 2009 [URL] [Pure]
Sasaki, Y., McNaught, J. and Ananiadou, S., The Value of an In-Domain Lexicon in Genomics QA, in: Proceedings of 3rd International Symposium on Languages in Biology and Medicine (LBM-2009), pages 47–55, 2009 [URL]
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

Sasaki, Y., Tsuruoka, Y., McNaught, J. and Ananiadou, S., How to make the most of NE dictionaries in statistical NER, in: BMC Bioinformatics, 2008 [DOI] [PDF] [Pure]
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]
Piao, S., McNaught, J. and Ananiadou, S., Clustering Related Terms with Definitions, in: Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008), pages 2013–2019, 2008 [PDF] [Pure]
Tsuruoka, Y., McNaught, J. and Ananiadou, S., Normalizing biomedical terms by minimizing ambiguity and variability, in: BMC Bioinformatics, 2008 [DOI] [PDF] [Pure]
Sasaki, Y., Montemagni, S., Pezik, P., Rebholz-Schuhmann, D., McNaught, J. and Ananiadou, S., BioLexicon: A Lexical Resource for the Biology Domain, in: Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland, Turku Centre for Computer Science (TUCS), pages 109–116, 2008 [PDF]
Rebholz-Schuhmann, D., Pezik, P., Lee, V., Kim, J., del Gratta, R., Sasaki, Y., McNaught, J., Montemagni, S., Monachini, M., Calzolari, N. and Ananiadou, S., 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), 2008 [PDF] [Pure]
Splendiani, A., Piao, S., Sasaki, Y., Ananiadou, S., McNaught, J. and Burgun, A., Compositional Enrichment of Bio-Ontologies, in: Proceedings of 11th Annual Bio-Ontologies Meeting, at the Intelligent Systems for Molecular Biology 2008 Conference (ISMB-2008), 2008 [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]
Thew, S., Sutcliffe, A., de Bruijn, O., McNaught, J., Procter, R., Venters, C.C. and Buchan, I., Experience in e-Science Requirements Engineering, pages 277-282, 2008 [PDF]
Sasaki, Y., Tsuruoka, Y., McNaught, J. and Ananiadou, S., How to Make the Most of NE Dictionaries in Statistical NER, in: Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing (BioNLP 2008), Association for Computational Linguistics, pages 63–70, 2008 [PDF]

2007

Tsuruoka, Y., McNaught, J., Tsujii, J. and Ananiadou, S., Learning string similarity measures for gene/protein name dictionary look-up using logistic regression, in: Bioinformatics, pages 2768–2774, 2007 [DOI] [PDF] [Pure]
Hahn, U., Buyko, E., Tomanek, K., Piao, S., McNaught, J., Tsuruoka, Y. and Ananiadou, S., An annotation type system for a data-driven NLP pipeline, in: ACL 2007: The LAW - Proceedings of The Linguistic Annotation Workshop, pages 33–40, 2007 [PDF] [Pure]
Piao, S., Buyko, E., Tsuruoka, Y., Tomanek, K., Kim, J., McNaught, J., Hahn, U., Su, J. and Ananiadou, S., BOOTStrep Annotation Scheme: Encoding Information for Text Mining, in: Proceedings of the 4th Corpus Linguistics Conference (CL2007), 2007 [PDF] [Pure]
Piao, S., Ananiadou, S. and McNaught, J., Integrating Annotation Tools into UIMA for Interoperability, in: Proceedings of the UK e-Science AHM Conference 2007, pages 575–582, 2007 [PDF] [Pure]
Piao, S., Ananiadou, S., Tsuruoka, Y., Sasaki, Y. and McNaught, J., Mining Opinion Polarity Relations of Citations, in: Proceedings of the 7th International Workshop on Computational Semantics, pages 366–371, 2007 [PDF] [Pure]

2006

Ananiadou, S. and McNaught, J., Introduction to Text Mining for Biology and Biomedicine, in: Text Mining for Biology and Biomedicine, pages 1–12, 2006 [Pure]
Ananiadou, S. and McNaught, J., Introduction to Text Mining in Biology, in: Text Mining for Biology and Biomedicine, pages 1–12, 2006 [Pure]

2005

Spasic, I., Ananiadou, S., McNaught, J. and Kumar, A., Text mining and ontologies in biomedicine: Making sense of raw text, in: Briefings in Bioinformatics, pages 239–251, 2005 [DOI] [PDF] [Pure]
Ananiadou, S., Chruszcz, J., Keane, J., McNaught, J. and Watry, P., The National Centre for Text Mining: Aims and Objectives, in: Ariadne, 2005 [URL] [Pure]
Tsuruoka, Y., Tateishi, Y., Kim, J. D., Ohta, T., McNaught, J., Ananiadou, S. and Tsujii, J., Developing a robust part-of-speech tagger for biomedical text, in: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pages 382–392, 2005 [DOI] [PDF] [Pure]

2004

Nenadic, G., Ananiadou, S. and McNaught, J., Enhancing automatic term recognition through recognition of variation, in: Proceedings of COLING 2004, pages 604–610, 2004 [PDF] [Pure]

1995

Ananiadou, S. and McNaught, J., Terms are not alone: Aids for term choice and choice terms, in: Aslib Proceedings, pages 47–60, 1995 [DOI] [Pure]

1990

Ananiadou, S. and Mcnaught, J., Treatment of compounds in a transfer-based MT system, in: Proc. 3rd Int. Conf. on Theoretical and Methodological Issues in Machine Translation, pages 57–63, 1990 [Pure]