Publications from the Ontogenesis Network
Papers arising directly from the work of the Ontogenesis Network
Phillip Lord, James Malone, Robert Stevens and David Shotton. Blogging the Word about Ontologies. Bio-Ontologies 2010, a Special Interest Group meeting at ISMB 2010. Boston, MA. Available at http://www.cs.man.ac.uk/~stevensr/papers/knowledgeblog.pdf
Malone, J. Badarinarayan, N. Ison, J. Stevens, R. and Parkinson, H. An Ontology of Bioinformatics Software. Bio-Ontologies 2010, a Special Interest Group meeting at ISMB 2010. Boston, MA. Available at http://www.cs.man.ac.uk/~stevensr/papers/softwareontologyismb2010.pdf
Dave Randall, Wes Sharrock, Rob Procter, Yuwei Lin, Meik Poschen and Robert Stevens (2010). Distributed Ontology Building as Practical Work: Lessons from CSCW. Intl Journal of Human-Machine Studies. Accepted for publication.
Randall, D., Sharrock, W., Procter, R., Lin, Y., Poschen, M., Griefenhagen, C., and Stevens, R. (2009) What about Sea Urchins?: Collaborative Ontology Building among Bioinformaticians. Fifth International eSocial Science Conference Proceedings 2009. Available at http://www.ncess.ac.uk/resources/content/papers/Randall.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.
Shotton, D. (2010). CiTO, the Citation Typing Ontology. J. Biomedical Semantics, 1:S6. http://www.jbiomedsem.com/content/1/S1/S6.
Schober D, Malone J, Stevens R, Practical Experiences in Concurrent, Collaborative Ontology Building Using Collaborative Protégé, Proceedings of the ICBO 2009, p.147-150, International Conference on Biomedical Ontology, July 24-26, 2009 , Buffalo, New York, USA. Available at, http://icbo.buffalo.edu/Proceedings.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://www.biomedcentral.com/1471-2105/10/S5/S1.
Related papers
Shotton D, Portwin K, Klyne G, Miles A (2009) Adventures in semantic publishing: exemplar semantic enhancement of a research article PLoS Computational Biology 5: e1000361. http://dx.doi.org/10.1371/journal.pcbi.1000361. (Contains first description of CiTO, the Citation Typing Ontology.)
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 Coference, Oxford, 9-11 December 2009. Available at http://imageweb.zoo.ox.ac.uk/pub/2009/publications/Kurtz_Parker_Shotton_et_al-IEEE_CLAROS_paper.pdf. (Involved ontology extensions to CIDOC CRM.)
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 (Database Issue). http://dx.doi.org/10.1093/nar/gkp1006. (Involved enhancements to and use of the Drosophila Anatomy Ontology.)
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. Journal of Biomedical Informatics. Preprint and supplementary files available at http://imageweb.zoo.ox.ac.uk/pub/2009/publications/Miles_et_al_OpenFlyData_paper/. (Involved the development of several ontologies based on the data models of the underlying databases.)
Papers in preparation
Simon Jupp, Robert Stevens, Johanna Völker and David Shotton. Evaluating an Ontology Learning Tool in Biology.
David Shotton, Doug Altman, Nigel Collier, Lindsay Cowell, Mark Forster, Lynn Schriml, Chris Taylor, David Tovey and the MIIDI Standardization Consortium. MIIDI: a Minimal Information Standard for reporting an Infectious Disease Investigations.
This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. These works may not be reposted without the explicit permission of the copyright holder.