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School of Computer Science

Stevens Publications

  • Full publications list
  • Best paper and prize winning publications
  • google scholar citation page
  • Publications on dBLP.
  • Articles from the Ontogenesis knowledgeblog
    • Full publication list

      [1]
      Oscar Flórez-Vargas, Andy Brass, George Karystianis, Michael Bramhall, Robert Stevens, Sheena Cruickshank, and Goran Nenadic. Bias in the reporting of sex and age in biomedical research on mouse models. eLife, 5:e13615, 2016. [ DOI | http ]
      [2]
      Theofilos Papadopoulos, Magdalena Krochmal, Katryna Cisek, Marco Fernandes, Holger Husi, Robert Stevens, Jean-Loup Bascands, Joost P. Schanstra, and Julie Klein. Omics databases on kidney disease: where they can be found and how to benefit from them. Clinical Kidney Journal, 2016. [ DOI | arXiv | http ]
      [3]
      J. Malone, R. Stevens, S. Jupp, T. Hancocks, H. Parkinson, and C. Brooksbank. Ten simple rules for selecting a bio-ontology. PLoS Computational Biology, 12(2):e1004743, 2016. [ DOI | http ]
      [4]
      Warren Read, George Demetriou, Goran Nenadic, Noel Ruddock, Robert Stevens, and Jerry Winter. The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing. In Semantic Web Applications and Tools for LifeSciences (SWAT4LS), Cambridge, UK, 2015.
      [5]
      Robert Stevens and Adam Nogradi. OBOPedia: An Encyclopaedia of Biology Using OBOOntologies. In Semantic Web Applications and Tools for Life Sciences (SWAT4LS), cambridge, UK, 2015. [ .pdf ]
      [6]
      C. Maria Keet, Agnieszka ?awrynowicz, Claudia d’Amato, Alexandros Kalousis, Phong Nguyen, Raul Palma, Robert Stevens, and Melanie Hilario. The Data Mining OPtimization Ontology. Journal of Web Semantics, 32:43-53, 2015. [ DOI | http | .pdf ]
      [7]
      Geraint Duck, Aleksandar Kovacevic, DavidL Robertson, Robert Stevens, and Goran Nenadic. Ambiguity and variability of database and software names in bioinformatics. Journal of Biomedical Semantics, 2015. [ DOI | .pdf | .pdf ]
      [8]
      Manuel Quesada-Martínez, Jesualdo Tomás Fernández-Breis, and Robert Stevens. Lexical Characterisation of Bio-Ontologies by the Inspection of Regularities in Labels. Current Bioinformatics, 10(2):165-176, 2015. [ DOI | .pdf ]
      [9]
      Artemis Parvizi, Yuan Ren, Markel Vigo, Kees van Deemter, Chris Mellish, Jeff Z Pan, Robert Stevens, and Caroline Jay. Ontology Authoring Inspired By Dialogue. In Language and Ontologies, page 8, 2015. [ .pdf ]
      [10]
      Michael Bramhall, Oscar Flórez-Vargas, Robert Stevens, Andy Brass, and Sheena Cruickshank. Quality of Methods Reporting in Animal Models of Colitis. Inflammatory Bowel Diseases, 21(6):1248-1259, 2015. [ DOI | http | .pdf ]
      [11]
      Markel Vigo, Caroline Jay, and Robert Stevens. Constructing conceptual knowledge artefacts: Activity patterns in the ontology authoring process. In Proceedings of the 33rd Annual ACM Conference on Human Factors in Computing Systems, CHI '15, pages 3385-3394, New York, NY, USA, 2015. ACM. [ DOI | http ]
      [12]
      M Quesada-Martínez, E Mikroyannidi, J. T. Fernández-Breis, and R. Stevens. Approaching the axiomatic enrichment of the Gene Ontology from a lexical perspective. Artificial Intelligence in Medicine, 2014. [ DOI ]
      [13]
      Markel Vigo, Caroline Jay, and Robert Stevens. Protégé4us: Harvesting ontology authoring data with protégé. In Valentina Presutti, Eva Blomqvist, Raphael Troncy, Harald Sack, Ioannis Papadakis, and Anna Tordai, editors, The Semantic Web: ESWC 2014 Satellite Events, Lecture Notes in Computer Science, pages 86-99. Springer International Publishing, 2014. [ DOI | http ]
      [14]
      Colin R. Batchelor, Christian Y. A. Brenninkmeijer, Christine Chichester, Mark Davies, Daniela Digles, Ian Dunlop, Chris T. A. Evelo, Anna Gaulton, Carole A. Goble, Alasdair J. G. Gray, Paul T. Groth, Lee Harland, Karen Karapetyan, Antonis Loizou, John P. Overington, Steve Pettifer, Jon Steele, Robert Stevens, Valery Tkachenko, Andra Waagmeester, Antony Williams, and Egon L. Willighagen. Scientific lenses to support multiple views over linked chemistry data. In The Semantic Web - ISWC 2014 - 13th International Semantic Web Conference, Riva del Garda, Italy, October 19-23, 2014. Proceedings, Part I, pages 98-113, 2014. [ DOI | http ]
      [15]
      Janna Hastings, Andy Brass, Colin Caine, Caroline Jay, and Robert Stevens. Evaluating the emotion ontology through use in the self-reporting of emotional responses at an academic conference. Journal of Biomedical Semantics, 5(1):38, 2014. [ DOI | http ]
      [16]
      A. G. Castro, C. Lange, P. W. Lord, and R. Stevens, editors. Proceedings of the 4th Workshop on Semantic Publishing Co-located with the 11th Extended Semantic Web Conference (ESWC 2014), volume 1155 of CEUR Workshop Proceedings - SePublica 2014. CEUR-WS.org, 2014. [ http ]
      [17]
      G. Duck, G. Nenadic, A. Brass, D. L. Robertson, and R. Stevens. Extracting Patterns of Database and Software Usage from the Bioinformatics Literature. Bioinformatics, 30(17):i601-i608, 2014. [ DOI | http ]
      [18]
      M. Vigo, S. Bail, C. Jay, and R. Stevens. Overcoming the Pitfalls of Ontology Authoring: Strategies and Implications for Tool Design. International Journal of Human-Computer Studies, 72(12):835 - 845, 2014. [ DOI | http ]
      [19]
      R. Hoehndorf, M. Haendel, R. Stevens, and D. Rebholz-Schuhmann. Thematic Series on Biomedical Ontologies in JBMS: Challenges and New Directions. Journal of Biomedical Semantics, 5(1):15, 2014. Series: Biomedical Ontologies. [ DOI | http ]
      [20]
      M Bramhall, O Flórez-Vargas, R Stevens, J Wilson, S Cruickshank, and A Brass. LB-006 Quality of Methods Reporting in Colitis Experiments and the Subsequent Impact on the Development of A Gut Knowledge Base. Gut, 63(Suppl. 1):e3, 2014. [ DOI | http ]
      [21]
      M. Vigo, C. Jay, and R. Stevens. Protégé4US: Harvesting Ontology Authoring Data with Protégé. In H. Paulheim, M. Voigt, A. Mitschick, and R. Garcia, editors, 2nd Workshop on Human-Semantic Web Interaction Workshop (HSWI14), 2014. [ http ]
      [22]
      R. Stevens, N Matentzoglu, U. Sattler, and M. Stevens. A Family History Knowledge Base in OWL 2. In S. Bail, B. Glimm, E. Jiménez-Ruiz, N. Matentzoglu, B. Parsia, and A. Steigmiller, editors, Proceedings of the 3rd International Workshop on OWL Reasoner Evaluation (ORE'14), volume 1207 of CEUR Workshop Proceedings, pages 71-76. CEUR-WS.org, 2014. [ .pdf ]
      [23]
      O. Flórez-Vargas, M. Bramhall, H. Noyes, S. Cruickshank, R. Stevens, and A. Brass. The Quality of Methods Reporting in Parasitology Experiments. PLoS ONE, 9(7):e101131, 2014. [ DOI | http ]
      [24]
      J. Malone, A. Brown, A. Lister, J. Ison, D. Hull, H. Parkinson, and R. Stevens. The Software Ontology (SWO): A Resource for Reproducibility in Biomedical Data Analysis, Curation and Digital Preservation. Journal of Biomedical Semantics, 5(1):25, 2014. [ DOI | http ]
      [25]
      Y. Ren, A. Parvizi, C. Mellish, J. Z. Pan, Kees van Deemter, and R. Stevens. Towards Competency Question-Driven Ontology Authoring. In V. Presutti, C. d'Amato, F. Gandon, M. d'Aquin, S. Staab, and A. Tordai, editors, Proceedings of 11th Conference on The Semantic Web: Trends and Challenges (ESWC 2014)., volume 8465 of Lecture Notes in Computer Science (LNCS), pages 752-767. Springer, 2014. [ DOI | http ]
      [26]
      M. Vigo, C. Jay, and R. Stevens. Design Insights for the Next Wave Ontology Authoring Tools. In M. Jones, P. A. Palanque, A. Schmidt, and T. Grossman, editors, Proceedings of the 32nd Annual ACM Conference on Human Factors in Computing Systems, CHI '14, pages 1555-1558. ACM, 2014. [ DOI | http ]
      [27]
      Eleni Mikroyannidi, Manuel Quesada-Martínez, Dmitry Tsarkov, JesualdoTomás Fernández Breis, Robert Stevens, and Ignazio Palmisano. A Quality Assurance Workflow for Ontologies Based on Semantic Regularities. In Krzysztof Janowicz, Stefan Schlobach, Patrick Lambrix, and Eero Hyvönen, editors, Knowledge Engineering and Knowledge Management, volume 8876 of Lecture Notes in Computer Science, pages 288-303. Springer International Publishing, 2014. [ DOI | http ]
      [28]
      K. Wolstencroft, S. Owen, M. Horridge, S. Jupp, O. Krebs, J. L. Snoep, F. B. du Preez, W. Mueller, R. Stevens, and C. A. Goble. Stealthy Annotation of Experimental Biology by Spreadsheets. Concurrency and Computation: Practice and Experience - Special Issue Paper : Combined Special Issues on eScience 2010 and Euro-Par 2011, 25(4):467-480, 2013. [ DOI | http ]
      [29]
      A. Brown, R. Stevens, and S. Pettifer. Making Graph-Based Diagrams Work in Sound: The Role of Annotation. Human-Computer Interaction, 28(3):193-221, 2013. [ DOI | http ]
      [30]
      A. G. Castro, C. Lange, P. W. Lord, and R. Stevens, editors. Proceedings of the 3rd Workshop on Semantic Publishing (SePublica'13), volume 994 of CEUR Workshop Proceedings - Semantic Publishing. CEUR-WS.org, 2013. [ http ]
      [31]
      M. Copeland, R. S. Goncalves, B. Parsia, U. Sattler, and R. Stevens. Finding Fault: Detecting Issues in a Versioned Ontology. In P. Cimiano, M. Fernández, V. Lopez, S. Schlobach, and J. Völker, editors, Proceedings of the 10th Extended Semantic Web Conference : The Semantic Web (ESWC'13) Satellite Events, volume 7955 of Lecture Notes in Computer Science (LNCS), pages 113-124. Springer, 2013. [ DOI ]
      [32]
      S. F. Liang, D. Scott, R. Stevens, and A. Rector. OntoVerbal: a Generic Tool and Practical Application to SNOMED CT. International Journal of Advanced Computer Science and Applications (IJACSA), 4(6):227-239, 2013. [ DOI ]
      [33]
      A. Parvizi, C. Jay, C. Mellish, J. Z. Pan, Y. Ren, R. Stevens, and Kees van Deemter. A Pilot Experiment in Knowledge Authoring as Dialogue. In Proceedings of the 10th International Conference on Computational Semantics (IWCS 2013) - Short Papers, pages 376-382. Association for Computational Linguistics, 2013. [ http ]
      [34]
      C. Y. A. Brenninkmeijer, I Dunlop, C. Goble, A. J. G. Gray, S. Pettifer, and R. Stevens. Computing Identity Co-Reference Across Drug Discovery Datasets. In A. Paschke, A. Burger, P. Romano, M. S. Marshall, and A. Splendiani, editors, Proceedings of the 6th International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS), volume 1114 of CEUR Workshop Proceedings - Semantic Web Applications and Technologies for Life sciences (SWAT4LS). CEUR-WS.org, 2013. [ .pdf ]
      [35]
      M. Quesada-Martínez, J. T. Fernández-Breis, and R. Stevens. Analysis and Classification of Bio-ontologies by the Structure of their Labels. In I. Rojas and F. M. Ortuño-Guzman, editors, Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, (IWBBIO 2013), pages 713-720. Copicentro Editorial, 2013.
      [36]
      P. Moulos, J. Klein, S. Jupp, R. Stevens, J. Bascands, and J. Schanstra. The KUPNetViz: A Biological Network Viewer for Multiple-omics Datasets in Kidney Diseases. BMC Bioinformatics, 14(1):235, 2013. [ DOI | http ]
      [37]
      M. Quesada-Martínez, J. T. Fernández-Breis, and R. Stevens. Lexical Characterization and Analysis of the BioPortal Ontologies. In N. Peek, R. M. Morales, and M. Peleg, editors, Proceedings of the 14th Conference on Artificial Intelligence in Medicine, AIME 2013, volume 7885 of Lecture Notes in Computer Science (LNCS), pages 206-215. Springer, 2013. [ DOI | http ]
      [38]
      G. Duck, G. Nenadic, A. Brass, D. Robertson, and R. Stevens. bioNerDS: Exploring Bioinformatics' Database and Software Use Through Literature Mining. BMC Bioinformatics, 14(1):194, 2013. [ DOI | http ]
      [39]
      E. Mikroyannidi, R. Stevens, and L. Iannone. Tradeoffs in Measuring Entity Similarity for Pattern Detection in OWL Ontologies. In M. Rodriguez-Muro, S. Jupp, and K. Srinivas, editors, Proceedings of the 10th International Workshop on OWL Experiences and Directions (OWLED'13) co-located with 10th Extended Semantic Web Conference (ESWC'13), volume 1080 of CEUR Workshop Proceedings. CEUR-WS.org, 2013. [ http | .pdf ]
      [40]
      Maria Copeland, Rafael S Gonçalves, Bijan Parsia, Uli Sattler, and Robert Stevens. Finding fault: Detecting Issues in a Versioned Ontology. In P. Lambrix, G. Qi, M. Horridge, and B. Parsia, editors, Proceedings of the Second International Workshop on Debugging Ontologies and Ontology Mappings (WoDOOM 2013), volume 999 of CEUR Workshop Proceedings, pages 9-20. CEUR-WS.org, 2013. [ http ]
      [41]
      A. Duque-Ramos, J. T. Fernãndez-Breis, M. Iniesta, M. Dumontier, M. E. Aranguren, S. Schulz, N. Aussenac-Gilles, and R. Stevens. Evaluation of the OQuaRE Framework for Ontology Quality. Expert Systems with Applications, 40(7):2696-2703, 2013. [ DOI | http ]
      [42]
      J. Klein, J. Eales, P. Zürbig, A. Vlahou, H. Mischak, and R. Stevens. Proteasix: A Tool for Automated and Large-scale Prediction of Proteases Involved in Naturally Occurring Peptide Generation. PROTEOMICS, 13(7):1077-1082, 2013. [ DOI | http ]
      [43]
      J. Malone and R. Stevens. Measuring the Level of Activity in Community Built Bio-Ontologies. Journal of Biomedical Informatics, 46(1):5-14, 2013. [ DOI | arXiv | http ]
      [44]
      Geraint Duck, Goran Nenadic, David L Robertson, and Robert Stevens. What is bioinformatics made from?, 2013. [ http ]
      [45]
      R. Cornet and R. Stevens, editors. Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO'12), volume 897 of CEUR Workshop Proceedings - KR-MED : ICBO'12. CEUR-WS.org, 2012. [ http ]
      [46]
      A. R. González, J. Pathak, M. Wilkinson, N. Shah, R. Stevens, R. D. Boyce, and A. Garciá-Crespo, editors. Proceedings of the Joint Workshop on Semantic Technologies Applied to Biomedical Informatics and Individualized Medicine in Conjunction with the 11th International Semantic Web Conference 2012 (ISWC 2012), volume 930 of CEUR Workshop Proceedings - SATBI+SWIM 2012. CEUR-WS.org, 2012.
      [47]
      S. Jupp, M. Horridge, L. Iannone, J. Klein, S. Owen, J. Schanstra, K. Wolstencroft, and R. Stevens. Populous: A Tool for Building OWL Ontologies from Templates. BMC Bioinformatics, 13(Suppl. 1):S5, 2012. [ DOI | http ]
      [48]
      M. Quesada-Martínez, J. T. Fernández-Breis, and R. Stevens. Enrichment of OWL Ontologies: A Method for Defining Axioms from Labels. In L. Moss and D. Sleeman, editors, Proceedings of the First International Workshop on Capturing and Refining Knowledge in the Medical Domain (K-MED'12) - Co-located with The 18th International Conference on Knowledge Engineering and Knowledge Management (EKAW 2012), pages 1-10, 2012. [ .pdf ]
      [49]
      J. Siwy, C. Zoja, J. Klein, A. Benigni, W. Mullen, B. Mayer, H. Mischak, J. Jankowski, R. Stevens, A. Vlahou, S. Kossida, P. Perco, and F.H. Bahlmann. Evaluation of the Zucker Diabetic Fatty (ZDF) Rat as a Model for Human Disease Based on Urinary Peptidomic Profiles. PLoS One, 7(12):e51334, 2012. [ DOI ]
      [50]
      E. Mikroyannidi, R. Stevens, L. Iannone, and A. Rector. Analysing Syntactic Regularities and Irregularities in SNOMED-CT. Journal of Biomedical Semantics, 3(1):8, 2012. [ DOI | http ]
      [51]
      M. Quesada-Martínez, J. T. Fernández-Breis, and R. Stevens. Extraction and Analysis of the Structure of Labels in Biomedical Ontologies. In C. Tao and M. Bouamrane, editors, Proceedings of the 2nd International Workshop on Managing Interoperability and compleXity in Health Systems, MIXHS '12, pages 7-16. ACM, 2012. [ DOI | http ]
      [52]
      C. Brenninkmeijer, C. Evelo, C. Goble, A. J. G. Gray, P. Groth, S. Pettifer, R. Stevens, A. J. Williams, and E. L. Willighagen. Scientific Lenses over Linked Data: An Approach to Support Task Specific Views of the Data. A Vision. In Proceedings of the 2nd International Workshop on Linked Science 2012 Tackling Big Data (LISC'12) co-located with 11th International Semantic Web Conference (ISWC'12), 2012. [ .pdf ]
      [53]
      P. Lord, S. Cockell, and R. Stevens. Three Steps to Heaven: Semantic Publishing in a Real World Workflow. Future Internet, 4(4):1004-1015, 2012. [ DOI | http ]
      [54]
      K. Wolstencroft, S. Owen, M. Horridge, S. Jupp, O. Krebs, J. Snoep, F. du Preez, W. Mueller, R. Stevens, and C. Goble. Stealthy Annotation of Experimental Biology by Spreadsheets. Concurrency and Computation: Practice and Experience, 25(4):467-480, 2012. [ DOI | http ]
      [55]
      G. Duck, R. Stevens, D. Robertson, and G. Nenadic. Ambiguity and Variability of Database and Software Names in Bioinformatics. In S. Ananiadou, S. Pyysalo, D. Rebholz-Schuhmann, F. Rinaldi, and T. Salakoski, editors, Proceedings of the 5th International Symposium on Semantic Mining in Biomedicine (SMBM'12), pages 2-9., 2012. [ http | .pdf ]
      [56]
      A. Rector, S. Brandt, N. Drummond, M. Horridge, C. Puleston, and R. Stevens. Engineering use cases for modular development of ontologies in OWL. Applied Ontology, 7(2):113-132, 2012. [ DOI | .pdf ]
      [57]
      M. Copeland, A. Brown, H. Parkinson, R. Stevens, and J. Malone. The SWO Project: A Case Study of Applying Agile Ontology Engineering Methods in Community Driven Ontologies. In R. Cornet and R. Stevens, editors, Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO'12), volume 897 of CEUR Workshop Proceedings - KR-MED: ICBO'12. CEUR-WS.org, 2012. [ .pdf ]
      [58]
      S. Jupp, A. Gibson, J. Malone, H. Parkinson, and R. Stevens. Taking a View on Bio-Ontologies. In R. Cornet and R. Stevens, editors, Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO'12), volume 897 of CEUR Workshop Proceedings - KR-MED. CEUR-WS.org, 2012. [ http | .pdf ]
      [59]
      P. Seyed, A. Rector, U. Sattler, B. Parsia, and R. Stevens. Representation of Part-Whole Relationships in SNOMED CT. In R. Cornet and R. Stevens, editors, Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO'12), volume 897 of CEUR Workshop Proceedings - KR-MED. CEUR-WS.org, 2012.
      [60]
      E. Mikroyannidi, L. Iannone, R. Stevens, and A. Rector. RIO: The Regularities Inspector for Ontologies Plugin for Protege. In R. Cornet and R. Stevens, editors, Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO'12), volume 897 of CEUR Workshop Proceedings - KR-MED Series. CEUR-WS.org, 2012. [ .pdf ]
      [61]
      S. F. Liang, R. Stevens, D. Scott, and A. Rector. OntoVerbal: A Protege Plugin for Verbalising Ontology Classes. In R. Cornet and R. Stevens, editors, Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO'12), volume 897 of CEUR Workshop Proceedings - KR-MED. CEUR-WS.org, 2012. [ .pdf ]
      [62]
      R. Stevens and P. Lord. Semantic Publishing of Knowledge about Amino Acids. In A. G. Castro, C. Lange, F. van Harmelen, and B. Good, editors, Proceedings of the 2nd Workshop on the Semantic Publishing (SePublica 2012), held in conjunction with ESWC 2012, volume 903 of CEUR Workshop Proceedings - Semantic Publishing, pages 45-48. CEUR-WS.org, 2012. [ .pdf ]
      [63]
      P. Lord, S. Cockell, and R. Stevens. Three Steps to Heaven: Semantic Publishing in a Real World Workflow. In A. G. Castro, C. Lange, F. van Harmelen, and B. Good, editors, Proceedings of the 2nd Workshop on the Semantic Publishing (SePublica'12), volume 903 of CEUR Workshop Proceedings - Semantic Publishing, pages 23-34. CEUR-WS.org, 2012. [ http ]
      [64]
      S. Jupp, R. Stevens, and R. Hoehndorf. Logical Gene Ontology Annotations (GOAL): Exploring Gene Ontology Annotations with OWL. Journal of Biomedical Semantics, 3(Suppl. 1):S3, 2012. This article is part of the supplement: Proceedings of the Bio-Ontologies Special Interest Group 2011. [ DOI ]
      [65]
      J. Hastings, D. Magka, C. Batchelor, L. Duan, R. Stevens, M. Ennis, and C. Steinbeck. Structure-based Classification and Ontology in Chemistry. Journal of Cheminformatics, 4(1):8, 2012. [ DOI | http ]
      [66]
      N. A. A. Manaf, S. Bechhofer, and R. Stevens. The Current State of SKOS Vocabularies on the Web. In Proceedings of the 9th Extended Semantic Web Conference (ESWC'12), volume 7295 of Lecture Notes in Computer Science (LNCS), pages 270-284. Springer, 2012. [ DOI | http ]
      [67]
      Nor Azlinayati Abdul Manaf, Sean Bechhofer, and Robert Stevens. Common Modelling Slips in SKOS Vocabularies. In P. Klinov and M. Horridge, editors, Proceedings of OWL: Experiences and Directions Workshop 2012 (OWLED'12), volume 849 of CEUR Workshop Proceedings. CEUR-WS.org, 2012.
      [68]
      E. Mikroyannidi, N. A. A. Manaf, L. Iannone, and R. Stevens. Analysing Syntactic Regularities in Ontologies. In P. Klinov and M. Horridge, editors, Proceedings of OWL: Experiences and Directions Workshop 2012 (OWLED'12), volume 849 of CEUR Workshop Proceedings. CEUR-WS.org, 2012. [ http ]
      [69]
      J. Klein, S. Jupp, P. Moulos, M. Fernandez, B. Buffin-Meyer, A. Casemayou, R. Chaaya, A. Charonis, J. Bascands, R Stevens, and J. P. Schanstra. The KUPKB: A Novel Web Application to Access Multi-Omics Data on Kidney Disease. FASEB Journal, 26(5):2145-2153, 2012. [ DOI | .pdf ]
      [70]
      L. Kalankesh, R. Stevens, and A. Brass. The Language of Gene Ontology: A Zipf's Law Analysis. BMC Bioinformatics, 13(1):127, 2012. [ DOI | http ]
      [71]
      S. Jupp, M. Horridge, L. Iannone, J. Klein, S. Owen, J. Schanstra, K. Wolstencroft, and R. Stevens. Populous: A Tool for Building OWL Ontologies from Templates. BMC Bioinformatics, 13(Suppl 1):S5, 2011. This article is part of the supplement: Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2010. [ DOI | http ]
      [72]
      V. Mironov, E. Antezana, M. Egaña, W. Blondé, B. De Baets, M. Kuiper, and R. Stevens. Flexibility and Utility of the Cell Cycle Ontology. Applied Ontology, 6(3):247-261, 2011. [ DOI | http ]
      [73]
      E. Mikroyannidi, L. Iannone, R. Stevens, and A. Rector. Inspecting regularities in ontology design using clustering. In Proceedings of the 10th International Semantic Web Conference (ISWC) 2011, volume 7031 of Lecture Notes in Computer Science LCNS, pages 438-453. Springer, 2011. [ DOI | .pdf ]
      [74]
      E. Mikroyannidi, R. Stevens, and A. Rector. Identifying Ontology Design Styles with Metrics. In Proceedings of the 7th International Workshop on Semantic Web Enabled Software Engineering (SWESE), 2011. [ .pdf ]
      [75]
      S. Jupp, J. Klein, P. Moulos, J. Schanstra, and R. Stevens. Ontologies Come of Age with the iKUP Browser. In G. C. Alexander, K. Baclawski, J. Bateman, K. Viljanen, and C. Lange, editors, Proceedings of the Workshop Ontologies Come of Age in the Semantic Web, ISWC'11, volume 809 of CEUR Workshop Proceedings, pages 25-28. CEUR-WS.org, 2011. [ .pdf ]
      [76]
      J. Eales, G. Demetriou, and R. Stevens. Creating A Focused Corpus of Factual Outcomes from Biomedical Experiments. In Proceedings of the Mining Complex Entities from Biomedical Data (MIND 2011), A Workshop held in Conjuction with PKDD 2011), 2011. [ .pdf ]
      [77]
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      E. Antezana, W. Blondé, M. Egaña, A. Rutherford, R. Stevens, B. De Baets, V. Mironov, and M. Kuiper. Structuring the life science resourceome for Semantic Systems Biology: lessons from the BioGateway project. In A. Burger, A. Paschke, P. Romano, and A. Splendiani, editors, Proceedings of the Workshop on Semantic Web Applications and Tools for the Life Sciences: (SWAT4LS'08), volume 435 of CEUR Workshop Proceedings. CEUR-WS.org, 2008. [ .pdf ]
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      A. Rector, R. Stevens, and N. Drummond. What Causes Pneumonia? The Case for a Standard Semantics for “may” in OWL. In C. Dolbear, A. Ruttenberg, and U. Sattler, editors, Proceedings of the 5th OWLED Workshop on OWL: Experiences and Directions, collocated with the 7th International Semantic Web Conference (ISWC'08), volume 432 of CEUR Workshop Proceedings. CEUR-WS.org, 2008. Long Paper in Volume 432. [ http ]
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      Alan Rector and Robert Stevens. Barriers to the use of OWL in Knowledge Driven Applications. In C. Dolbear, A. Ruttenberg, and U. Sattler, editors, Proceedings of the 5th OWLED Workshop on OWL: Experiences and Directions, collocated with the 7th International Semantic Web Conference (ISWC'08), volume 432 of CEUR Workshop Proceedings. CEUR-WS.org, 2008. Short papers. [ http ]
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      H. Afzal, R. Stevens, and G. Nenadic. Towards Semantic Annotation of Bioinformatics Services: Building a Controlled Vocabulary. In Proceedings of the 3rd International Symposium on Semantic Mining in Biomedicine, 2008. [ .pdf ]
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      G. Diallo, P. Kostkova, G. Jawaheer, S. Jupp, and R. Stevens. Process of Building a Vocabulary for the Infection Domain. In Proceedings of the 21st IEEE International Symposium on Computer-Based Medical Systems (CBMS'08), pages 308-313. IEEE, 2008. [ DOI | http ]
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      Jenny Ure, Rob Proctor, Maryann Martone, David Porteous, Sharon Lloyd, Stephen Lawrie, Dominic Job, Richard Baldock, Alistair Philp, Dave Liewald, Frank Rakebrand, Alan Blaikie, Clare McKay, Stuart Anderson, John Ainsworth, Jano van Hemert, Ignacio Blanquer, Richard Sinnott, Christian Barillot, Frank Bernard Gibaud, Alan Williams, Mark Hartswood, Paul Watson, Leslie Smith, Albert Burger, Jessie Kennedy, Horacio Gonzalez-Velez, Robert Stevens, Oscar Coecho, Robin Morton, Pamela Linksted, Mylene Deschenne, Mark McGilchrist, Paul Johnson, Alex Vossi, Renate Gertz, and Joanna Wardlaw. Data Integration in eHealth: A Domain/Disease Specific Roadmap. Studies Health Technol Inform, 126:144-153, 2007.
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      Y. Yesilada, R. Stevens, S. Harper, and C. A. Goble. Evaluating DANTE: Semantic Transcoding for Visually Disabled Users. ACM Transactions on Computer-Human Interaction, 14(3), 2007. Article Number 14. [ DOI | http ]
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      R. Stevens. A Day in the Life of A Disabled Scientist - Sightless in Science. The Biochemist, 29(3), 2007. [ .pdf ]
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      K. Wolstencroft, R. Stevens, and V. Haarslev. Applying OWL Reasoning to Genomic Data. In C. J.O. Baker and K. Cheung, editors, Semantic Web : Revolutionizing Knowledge Discovery in the Life Sciences, pages 225-248. Springer, 2007. [ DOI | http ]
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      R. Brenchley, H. Tariq, H. McElhinney, B. Szoor, J. Huxley-Jones, R. Stevens, K. Matthews, and L. Tabernero. The TriTryp Phosphatome: Analysis of the Protein Phosphatase Catalytic Domains. BMC Genomics, 8(1):434, 2007. [ DOI | http ]
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      J. Luciano and R. Stevens. e-Science and Biological Pathway Semantics. BMC Bioinformatics, 8(Suppl. 3):S3, 2007. This article is part of the supplement: Semantic e-Science in Biomedicine. [ DOI | http ]
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      R. Stevens, J. Zhao, and C. Goble. Using Provenance to Manage Knowledge of In Silico Experiments. Briefings in Bioinformatics, 8(3):183-194, 2007. This article appears in:Special Issue: Knowledge Integration and Web Communities. [ DOI | http | .pdf ]
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      A. Brown, R.D. Stevens, and S. Pettifer. Audio Representation of Graphs: A Quick Look. In Proceedings of the 12th International Conference on Auditory Displays 2006, 2006. [ .pdf ]
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      C. Jay, R. Stevens, M. Glencross, and A. Chalmers. How people use presentation to search for a link: expanding the understanding of accessibility on the web. In S. Harper, Y. Yesilada, and C. A. Goble, editors, Proceedings of the 2006 International Cross-Disciplinary Workshop on Web Accessibility (W4A'06): Building The Mobile Web: Rediscovering Accessibility?, volume 134 of ACM International Conference Proceeding Series, pages 113-120. ACM, 2006. [ DOI | http ]
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      A. Castro, P. Rocca-Serra, R. Stevens, C. Taylor, K. Nashar, M. Ragan, and S. Sansone. The Use of Concept Maps during Knowledge Elicitation in Ontology Development Processes - The Nutrigenomics Use Case. BMC Bioinformatics, 7(1):267, 2006. [ DOI | http ]
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      S. Harper, G. Khan, and R. Stevens. Design checks for java accessibility. In Accessible Design in the Digital World. British Computer Society, 2005. Winner of the IBM Research Best Paper Prize. [ http ]
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      P. W. Lord, R. Stevens, J. A. Butler, and R. McEntire. The Eighth Annual Bio-Ontologies Meeting. PLOS Computational Biology, 1(7):e77, 2005. [ DOI | http ]
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      S. Harper, C. A. Goble, and R. Stevens. Augmenting the Mobility of Profoundly Blind Web Travellers. Augmenting the mobility of profoundly blind Web travellers- Special Issue : Scholarly Hypermedia, 11(1):103-128, 2005. [ DOI | http | .pdf ]
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      Zoë Lacroix, Bertram Ludaescher, and Robert Stevens. Integrating Biological Databases. In Thomas Lengauer, editor, Bioinformatics - From Genomes to Therapies, pages 1525-1572. Wiley-VCH, 2005.
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      Chris Wroe and Robert Stevens. Ontologies for molecular biology. In Thomas Lengauer, editor, Bioinformatics - From Genomes to Therapies, pages 1061-1085. Wiley-VCH, 2005.
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      Robert Stevens, Phil Lord, and Duncan Hull. Using Distributed Data and Tools in bioinformatics Applications. In Thomas Lengauer, editor, Bioinformatics - From Genomes to Therapies; Volume 3, pages 1627-1649. Wiley-VCH, 2005.
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      K. Wolstencroft, T. Oinn, C. A. Goble, J. Ferris, C. Wroe, P. Lord, K. Glover, and R. Stevens. Panoply of Utilities in Taverna. In Proceedings of the 1st International Conference on e-Science and Grid Technologies (e-Science'05), pages 156-162. IEEE Computer Society, 2005. [ DOI | http ]
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      K. Wolstencroft, A. Brass, I. Horrocks, P. Lord, U. Sattler, D. Turi, and R. Stevens. A Little Semantic Web Goes a Long Way in Biology. In Y. Gil, E. Motta, V. R. Benjamins, and M. A. Musen, editors, Proceedings of the Fourth International Semantic Web Conference : The Semantic Web (ISWC 2005), volume 3729 of Lecture Notes in Computer Science (LNCS), pages 786-800. Springer, 2005. [ DOI | http ]
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      S. K. Bechhofer, R. Stevens, and P. W. Lord. Ontology Driven Dynamic Linking of Biology Resources. In R. B. Altman, A. K. Dunker, L. Hunter, T. A. Jung, and T. E. Klein, editors, Proceedings of the Pacific Symposium on Biocomputing (PSB'05, pages 93-103. World Scientific, 2005. [ .pdf ]
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      C. Goble, S Bechhofer, and R. Stevens. The Semantic Web and Knowledge Grids. Drug Discovery Today: Technologies, 2(3):225-233, 2005. [ DOI | http ]
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      K. Flanagan, R. Stevens, M. Pocock, P. Lee, and A. Wipat. Ontology for Genome Comparison and Genomic Rearrangements. Comparative and Functional Genomics, 5(6-7):537-544, 2005. [ DOI | http ]
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      K. J. Wolstencroft, R. Stevens, L. Tabernero, and A. Brass. PhosphaBase: An Ontology Driven Database Resource for Protein Phosphatases. Proteins, 58(2):290-294, 2005. [ DOI | http ]
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      A. D. N. Edwards and R. D. Stevens. Une interface multimodale pour l'accèss aux formules mathématiques par des élèves ou étudiants aveugles. In Comme les Autres: Interfaces multimodales pour handicapés visuels, Special number 1, pages 97-104. INSERM, 1995.
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      T. Wesley, R. Stevens, and J. Engelen. Overview of the european research work in relation to information access for visually impaired persons. In Proceedings of the 2nd International Maths Workshop. by Recordings for the Blind and Dyslexic, 1995. [ .txt ]
      [296]
      R. Stevens, P. Wright, and A. D. N. Edwards. Strategy and prosody in listening to algebra. In G. Allen, J. Wilkinson, and P. Wright, editors, Adjunct Proceedings of HCI'95: People and Computers, pages 160-166. British Computer Society, 1995.
      [297]
      R. D. Stevens and A. D. N. Edwards. Mathtalk: Usable access to mathematics. Information Technology and Disabilities, 1(4 Article 5), 1994. [ .html ]
      [298]
      R. D. Stevens, P. C. Wright, and A. D. N. Edwards. Prosody improves a speech based interface. In D. England, editor, Ancillary Proceedings of HCI'94. British Computer Society, 1994.
      [299]
      R. D. Stevens, S. A. Brewster, P. C. Wright, and A. D. N. Edwards. Design and evaluation of an auditory glance at algebra for blind readers. In G. Kramer, editor, Auditory Display: The Proceedings of the Second International Conference on Auditory Display. Addison-Wesley, 1994.
      [300]
      R. D. Stevens and A. D. N. Edwards. Mathtalk: The Design of an Interface for Reading Algebra Using Speech. In W. L. Zagler, G. Busby, and R. L. Wagner, editors, Computers for Handicapped Persons: Proceedings of ICCHP '94, Lecture Notes in Computer Science 860, pages 313-320. Springer, 1994.
      [301]
      R. D. Stevens and A. D. N. Edwards. A Sound Interface to Algebra. In Proceedings of the IEE Colloquium on Special Needs and the Interface, pages 511-513. IET, 1993. IEE Digest no. 1993/005. [ http ]
      [302]
      A D N Edwards and R. D. Stevens. Mathematical Representations: Graphs, Curves and Formulas. In D. Burger and J. Sperandio, editors, Proceedings of the INSERM Seminar Non-Visual Presentations of Data in Human-Computer Interactions: Prospects for the Visually Handicapped, pages 181-194. John Libbey Eurotext, 1993.
      [303]
      R. D. Stevens. Spoken mathematics. Master's thesis, Department of Biology, Department of Computer Science, University of York, UK, 1991. Masters dissertation: Internal publication.
      [304]
      Y.B. Meng, R.D. Stevens, W. China, S. McGill, and M. Ashburner. Five glycyl trna genes within the noc gene complex of drosophila melanogaster. Nucleic Acids Research, 16(14):7189, 1988. [ DOI | arXiv | http ]

      Best paper and prize winning Publications

      [1]
      Markel Vigo, Caroline Jay, and Robert Stevens. Protéǵe4us: Harvesting ontology authoring data with protégé. In Heiko Paulheim, Martin Voigt, Annett Mitschick, and Roberto Garcia, editors, 2nd Workshop on Human-Semantic Web Interaction Workshop (HSWI14), 2014. [ http ]
      [2]
      Maria Copeland, Rafael S Gonçalves, Bijan Parsia, Uli Sattler, and Robert Stevens. Finding fault: Detecting issues in a versioned ontology. In Patrick Lambrix, Guilin Qi, Matthew Horridge, and Bijan Parsia, editors, Proceedings of the Second International Workshop on Debugging Ontologies and Ontology Mappings (WoDOOM 2013), 2013. [ http ]
      [3]
      Phillip Lord, Simon Cockell, and Robert Stevens. Three Steps to Heaven: Semantic Publishing in a Real World Workflow. In C. Lange, editor, Workshop on the Semantic Publishing (SePublica 2012), held in conjunction with ESWC 2012, Hersonissos, Crete, Greece, 2012. [ http ]
      [4]
      Alan L. Rector, Luigi Iannone, and Robert Stevens. Quality assurance of the content of a large dl-based terminology using mixed lexical and semantic criteria: experience with snomed ct. In Mark A. Musen and Óscar Corcho, editors, Proceedings of the 6th International Conference on Knowledge Capture (K-CAP 2011), June 26-29, 2011, Banff, Alberta, Canada, pages 57-64. ACM, 2011.
      [5]
      Simon Jupp, Julie Klein, Panagiotis Moulos, Joost Schanstra, and Robert Stevens. Ontologies come of age with the iKUP browser. In Alexander García Castro, Ken Baclawski, John Bateman, Kim Viljanen, and Christoph Lange, editors, Proceedings of the Workshop Ontologies Come of Age in the Semantic Web, International Semantic Web Conference, number 809 in CEUR Workshop Proceedings, pages 25-28, Aachen, 2011. [ .pdf ]
      [6]
      Jesualdo Tomás Fernández-Breis, Luigi Iannone, Ignazio Palmisano, Alan L. Rector, and Robert Stevens. Enriching the gene ontology via the dissection of labels using the ontology pre-processor language. In Philipp Cimiano and Helena Sofia Pinto, editors, Knowledge Engineering and Management by the Masses - 17th International Conference, EKAW 2010, Lisbon, Portugal, October 11-15, 2010. Proceedings, volume 6317 of Lecture Notes in Computer Science, pages 59-73. Springer, 2010. [ .pdf ]
      [7]
      Simon Harper, Ghazalah Khan, and Robert Stevens. Design checks for java accessibility. In Accessible Design in the Digital World, UK, 2005. British Computer Society.
      [8]
      Goble C.A., S. Harper, and R.D. Stevens. The Travails of Visually Impaired Web Travellers. In ACM 2000 Hypertext (Proceedings of the Eleventh ACM Conference on Hypertext and Hypermedia), pages 1-10. ACM Press, 2000. [ .pdf ]

      Articles from the Ontogenesis knowledgeblog

      [1]
      Uli Sattler, Robert Stevens, and Phillip Lord. How does a reasoner work? http://ontogenesis.knowledgeblog.org/1486, 2014. [ http ]
      [2]
      Robert Stevens and Phillip Lord. Ontological commitment: Committing to what an ontology claims. http://ontogenesis.knowledgeblog.org/1468, 2014. [ http ]
      [3]
      Robert Stevens and Uli Sattler. Walking your fingers through the trees in owl: why there are things you want to say but can’t. http://ontogenesis.knowledgeblog.org/1446, 2014. [ http ]
      [4]
      Uli Sattler and Robert Stevens. Nine variations on two pictures: What’s in an arrow between two nodes. http://ontogenesis.knowledgeblog.org/1423, 2013. [ http ]
      [5]
      Robert Stevens and Uli Sattler. An object lesson in choosing between a class and an object. http://ontogenesis.knowledgeblog.org/1418, 2013. [ http ]
      [6]
      Uli Sattler and Robert Stevens. Modelling in multiple dimensions is great in so many ways. http://ontogenesis.knowledgeblog.org/1401, 2013. [ http ]
      [7]
      Robert Stevens. Trivially satisfiable classes. http://ontogenesis.knowledgeblog.org/1335, 2013. [ http ]
      [8]
      Uli Sattler, Robert Stevens, and Phillip Lord. (i can’t get no) satisfiability. http://ontogenesis.knowledgeblog.org/1329, 2013. [ http ]
      [9]
      Robert Stevens and Uli Sattler. Post-coordination: Making things up as you go along. http://ontogenesis.knowledgeblog.org/1305, 2013. [ http ]
      [10]
      Robert Stevens. Why use an ontology? http://ontogenesis.knowledgeblog.org/1296, 2013. [ http ]
      [11]
      Uli Sattler and Robert Stevens. Being complex on the left-hand-side: General concept inclusions. http://ontogenesis.knowledgeblog.org/1288, 2012. [ http ]
      [12]
      Robert Stevens and Uli Sattler. Disjointness between classes in an ontology. http://ontogenesis.knowledgeblog.org/1260, 2012. [ http ]
      [13]
      Robert Stevens and Phillip Lord. Managing synonomy in owl. http://ontogenesis.knowledgeblog.org/1236, 2012. [ http ]
      [14]
      Robert Stevens and Alan Rector. Higher order knowledge in ontologies. http://ontogenesis.knowledgeblog.org/1080, 2011. [ http ]
      [15]
      Robert Stevens and Alan Rector. generalisation statements in ontologies. http://ontogenesis.knowledgeblog.org/1078, 2011. [ http ]
      [16]
      Robert Stevens and Alan Rector. Metadata in ontologies. http://ontogenesis.knowledgeblog.org/1076, 2011. [ http ]
      [17]
      Robert Stevens and Alan Rector. Types of statement in an ontology. http://ontogenesis.knowledgeblog.org/1074, 2011. [ http ]
      [18]
      Robert Stevens. Closing down the open world: Covering axioms and closure axioms. http://ontogenesis.knowledgeblog.org/1001, 2011. [ http ]
      [19]
      Robert Stevens and Phillip Lord. Reification of properties in an ontology. http://ontogenesis.knowledgeblog.org/993, 2010. [ http ]
      [20]
      Robert Stevens and Duncan Hull. There is no other category: When to avoid miscellaneous. http://ontogenesis.knowledgeblog.org/829, 2010. [ http ]
      [21]
      Robert Stevens and Duncan Hull. Defining definitions. http://ontogenesis.knowledgeblog.org/824, 2010. [ http ]
      [22]
      Robert Stevens and Duncan Hull. Separating concepts from labels. http://ontogenesis.knowledgeblog.org/818, 2010. [ http ]
      [23]
      Robert Stevens, Alan Rector, and Duncan Hull. What is an ontology? http://ontogenesis.knowledgeblog.org/66, 2010. [ http ]