David Shotton

University Emeritus Reader

Emeritus Fellow of Wolfson College


Research Interests

A cell biologist by background, I currently lead the Research Data Management and Semantic Publishing Research Group (formerly called the Image Bioinformatics Research Group) within the Department of Zoology, which is dedicated to using web and semantic web/linked data technologies to undertake research data management, data integration, data publication, metadata creation and semantic publishing activities, particularly in the biological sciences, and to improve scholarly communication, particularly by means of the semantic enhancement of journal articles and providing free access to bibliographic citations. 

My recent activities have included the development of biological image databases, particularly FlyTED for Drosophila testis gene expression data, and OpenFlyData, a data webs to enable integration of heterogeneous information from distributed Drosophila genomics resources, the development of services to assist the local management and publication of life sciences research data, including the prototype developed during the ADMIRAL Project, the publication of biological datasets linked to peer-reviewed journal articles to the Dryad Data Repository, and exemplar prototypes of semantically enriched on-line research articles.  

Current work for data management focuses on two integrated open-source services - DataStage for local file management at a research group level and DataBank for use as an institution-level data repository.  Data management planning is facilitated by a simple data entry system, DMP20 – Twenty Data Management Planning Questions, and by local customization of the DCC DMPonline tool.   To support our semantic publishing work, we have developed the SPAR (Semantic Publishing and Referencing) Ontologies that permit RDF descriptions of bibliographic entities, citations, reference collections and library catalogues, the structural and rhetorical components of documents, and roles, statuses and workflows in publishing, and FRAPO (the Funders, Research Administration and Projects Ontology) and SCoRO (the Scholarly Communications and Roles Ontology) to permit description of research information about research projects and their administration, and the contributions and roles people and organizations have in producing research outputs such as journal articles. 

We have then used these ontologies to develop easy-to-use tools to assign scholarly contributions and roles, to permit creation of research data management plans, to describe datasets that have been given DataCite DOIs (Digital Object Identifiers), and to describe research investigations, the projects that support them and the research outputs that arise from them, in the form of datasets, journal articles, software, protocols, workflows and models.  For this latter purpose, we have developed MIIRO (Minimal Information about an Investigation and Research Outputs) and its specialization MIIDI (Minimal Information for reporting an Infectious Disease Investigation).

We are currently expanding the Open Citations Corpus,  an open linked data repository of bibliographic citations populated from the reference lists of articles in PubMed Central and arXiv, and soon also to have reference data from subscription access journals, and we have recently developed CiTO Tools to characterize bibliographic citations.  

Other interests include issues of semantic interoperability between the sciences, arts and humanities – we have applied our biological data integration technologies to aggregation of heterogeneous data from distributed Classical Arts databases in the CLAROS Project ("The World of art on the Semantic Web") - and the preservation of our analogue scientific cultural heritage in the digital age.

My past research has included molecular and cell biological investigations of protein and membrane structure in health and disease, investigations that have employed advanced light and electron microscopy techniques, particularly video and confocal light microscopy and freeze fracture electron microscopy. I have published extensively on these techniques, and have taught on many international microscopy courses.

I publish three blogs, on Semantic Publishing, on Open Citations and Related Work, and on Data Management Planning.

Additional Information

I have recently retired from university teaching. From 1981 to 2011 I taught cell biology for the undergraduate Biological Sciences degree, for the EPSRC Life Science Interface Doctoral Training Centre, and for the M. Sc. in Biology, for which I was the Degree Director from its inception in 1995 to its termination in 2011.  I remain a College Lecturer in Biology at Christ Church and a Research Associate of the Oxford e-Research Centre.   I served on the Life Science and Medicine Consultative Group of the Research Information Network (http://www.rin.ac.uk) until its suspension in 2011.



Email: david.shotton@zoo.ox.ac.uk

Selected Publications

  • Peroni S, Lapeyre DA and Shotton D (2012)  From Markup to Linked Data: Mapping NISO JATS v1.0 to RDF using the SPAR (Semantic Publishing and Referencing) Ontologies.   Proc. 2012 JATS Conference, National Library of Medicine, Bethesda, Maryland, USA, 16-17 October 2012.  http://www.ncbi.nlm.nih.gov/books/NBK100491/.

  • Peroni S and Shotton D (2012). FaBiO and CiTO: ontologies for describing bibliographic resources and citations. Web Semantics: Science, Services and Agents on the World Wide Web. 17: 33-34. doi:10.1016/j.websem.2012.08.001

  • Shotton D (2012).  The Five Stars of Online Journal Articles — a Framework for Article Evaluation. D-Lib Magazine 18 (1/2) (January/February 2012 issue).  http://dx.doi.org/10.1045/january2012-shotton.

  • Peroni S, Shotton D and Vitali F (2012). Scholarly publishing and the Linked Data: describing roles, statuses, temporal and contextual extents. In Proceedings of the 8th International Conference on Semantic Systems (i-Semantics 2012): 9-16. New York, New York, USA: ACM. doi:10.1145/2362499.2362502.

  • Peroni S, Shotton D and Vitali F (2012). The Live OWL Documentation Environment: a tool for the automatic generation of ontology documentation. In Proceedings of the 18th International Conference on Knowledge Engineering and Knowledge Management (EKAW 2012) (ten Teije A, Völker J, Handschuh S, Stuckenschmidt H, d'Aquin M, Nikolov A, Aussenac-Gilles N and Hernandez N: Eds.): 398-412. Heidelberg, Germany: Springer. doi:10.1007/978-3-642-33876-2_35.

  • Ciccarese P, Shotton D, Peroni S and Clark T (2011).  CiTO + SWAN: The Web Semantics of Bibliographic Records, Citations, Evidence and Discourse Relationships.  Semantic Web Journal, http://www.semantic-web-journal.net/sites/default/files/swj175.pdf.

  • Bourne P, Clark T, Dale R, de Waard A, Herman I, Hovy E and Shotton D (eds.) (2011).  The Force11 White Paper: Improving Future Research Communication and e-Scholarship.  A publication resulting from the Schloss Dagstuhl Perspectives Workshop: The Future of Research Communication, 15-18 Aug 2011.   http://www.force11.org/white_paper.

  • Shotton D (2011). Data webs for image repositories. In: Dutton W, Jeffreys P, editors. World Wide Research: Reshaping the Sciences and Humanities. Cambridge, Massachusetts: MIT Press.

  • Shotton D (2010). CiTO, the Citation Typing Ontology. J. Biomedical Semantics 1 (Suppl. 1): S6. doi: http://dx.doi.org/10.1186/2041-1480-1-S1-S6.

  • Miles A, Zhao J, Klyne G, White-Cooper H, Shotton D (2010). OpenFlyData: An exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster. J. Biomedical Informatics 43 (5), 752-761. http://dx.doi.org/10.1016/j.jbi.2010.04.004.

  • Kurtz D, Parker G, Shotton D, Klyne G, Schroff F, Zisserman A and Wilks Y (2009). CLAROS – bringing classical art to a global public. Proc. IEEE e-Science Conference, Oxford, 9-11 December 2009, pp20-27. http://doi.ieeecomputersociety.org/10.1109/e-Science.2009.11.

  • Zhao J, Klyne G, Miles A, Benson E, Gudmannsdottir E, White-Cooper H, Shotton D (2009).  FlyTED: the Drosophila Testis Gene Expression Database. Nucleic Acids Research 38, Supplement 1 - Database Issue: D710-D715. http://dx.doi.org/10.1093/nar/gkp1006.

  • Shotton, D., Portwin, K., Klyne, G. and Miles, A. (2009). Adventures in semantic publishing: exemplar semantic enhancement of a research article. PLoS Computational Biology 5 (4): e1000361.http://www.ploscompbiol.org/doi/pcbi.1000361

  • Our semantically enhanced version of Reis et al. (2008) Impact of Environment and Social Gradient on Leptospira Infection in Urban Slums  PLoS Neglected Tropical Diseases 2: e228, is available at http://dx.doi.org/10.1371/journal.pntd.0000228.x001

  • Shotton, D. (2009). CiTO, the Citation Typing Ontology, and its use for annotation of reference lists and visualization of citation networks. Bio-Ontologies 2009, a Special Interest Group meeting at ISMB 2009. Stockholm. Preprint available at http://imageweb.zoo.ox.ac.uk/pub/2008/publications/Shotton_ISMB_BioOntology_CiTO_final_postprint.pdf.
  • Zhao J, Miles A, Klyne G, Shotton D (2009).  Linked data and provenance in biological data webs. Briefings in Bioinformatics 10: 139-152. http://dx.doi.org/10.1093/bib/bbn044.