David Shotton

Research Interests

I lead the Image Bioinformatics Research Group (IBRG) within the Department of Zoology, which is dedicated to research and the development of best practice for the sharing and reuse of biological research data, particularly images. My present interests and R&D activities include developing services for managing research data such as those of the DataFlow Project, and work in semantic publishing, developing exemplar articles and the SPAR Ontologies for describing all aspects of publishing, bibliographic entities and citations. Recent developments include creation of the Open Citation Corpus, containing the bibliographic citations from the reference lists in all the Open Access articles within PubMed Central, and MIIDI, a Minimal Information standard for reporting an Infectious Disease Investigation. The intent is to use MIIDI, together with the MIIDI Editor that facilitates entry of MIIDI-compliant rich metadata, to create Open Research Reports, structured digital summaries of infectious disease datasets or research articles that can be published in an open access data journal. My other interests include using semantic technologies to assist data integration in the humanities, as exemplified by CLAROS, "The World of Art on the Semantic Web".  More details are given in recent conference presentations, and in blog posts in his Open Citations and Semantic Publishing Blog.  Other interests include issues of semantic interoperability between the sciences, arts and humanities, 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 maintain interests in these areas, have published extensively on these techniques, and have taught on many international microscopy courses.

Other Interests

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.

Contacts

Selected Publications

• 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). doi:10.1045/january2012-shotton. (Preprint, giving original text prior to revision and expansion following post-publication peer review, available in Nature Proceedings at http://precedings.nature.com/documents/6542/version/1).
• Peroni S and Shotton D (2011). FaBiO and CiTO: ontologies for describing bibliographic resources and citations. (Submitted for publication, under review). Preprint available at http://imageweb.zoo.ox.ac.uk/pub/2011/publications/fabiocito_ontology_paper_PREPRINT.pdf.
• Bourne P, Clark T, Dale R, de Waard A, Herman I, Hovy E and Shotton D (2011). Force11 White Paper: Improving Future Research Communication and e-Scholarship. Publication resulting from Schloss Dagstuhl Perspectives Workshop: The Future of Research Communication, 15-18 Aug 2011. http://www.force11.org/node/1688. (Submitted to The Open Data Consultation, UK Cabinet Office, 27 Oct 2011.)
• 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.
• Shotton D, Caton C, Klyne G (2010). Ontologies for sharing, ontologies for use. In The Ontogenesis Knowledge Blog: Paper 3. http://ontogenesis.knowledgeblog.org/2010/01/22/ontologies-for-sharing/.
• 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.
• Shotton D (2009). FlyTED: the Drosophila Testis Gene Expression Database. Nucleic Acids Research 38, Supplement 1 - Database Issue, pp D710-D715. http://dx.doi.org/10.1093/nar/gkp1006.
• 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.
• 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.
• 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). Semantic Publishing: The coming revolution in scientific journal publishing. Learned Publishing 22: 85-94. http://dx.doi.org/10.1087/2009202. Preprint available at http://purl.org/net/semanticpublication/Shotton_Semantic_publishing_evaluation.pdf.
• 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.
• Brewster, C., Jupp, S., Luciano, J., Shotton, D., Stevens, R. and Zhang, Z. (2009). Issues in learning an ontology from text. BMC Bioinformatics 10: S1. http://dx.doi.org/10.1186/1471-2105-10-S5-S1.