Phillip Lord's publications

Following is a largely complete list of my paper and conference publications. There is also a list of my appearances in the popular press, my programme committees, invited talks and so on. These lists are also available as part of a [pdf] file, or as a [bib] file.

From 2012, all papers here will be published in my Journal and arXiv. These should be considered to be the canonical versions, as these versions are produced and checked by the authors; versions published elsewhere are secondary, and only for advertising and research assessment.

These pages are produced with Emacs Muse and a hacky Makefile.

Journal Papers

[1] M. J. Bell, M. Collison, and P. Lord. Can inferred provenance and its visualisation be used to detect erroneous annotation? a case study using UniProtKB. PLoS ONE, 8(10):e75541, 10 2013. [ bib | DOI | arXiv | http ]
[2] 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. [ bib | DOI | blog | http ]
[3] M. Bell, C. Gillespie, D. Swan, and P. Lord. An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB. Bioinformatics, 28(18):i562-i568, 2012. [ bib | DOI | arXiv | http ]
[4] T. Quinn, S. Granite, M. Allessie, C. Antzelevitch, C. Bollensdorff, G. Bub, R. Burton, E. Cerbai, P. Chen, M. Delmar, D. DiFrancesco, Y. Earm, I. Efimov, M. Egger, E. Entcheva, M. Fink, R. Fischmeister, M. Franz, A. Garny, W. Giles, T. Hannes, S. Harding, P. Hunter, G. Iribe, J. Jalife, C. Johnson, R. Kass, I. Kodama, G. Koren, P. Lord, V. Markhasin, S. Matsuoka, A. McCulloch, G. Mirams, G. Morley, S. Nattel, D. Noble, S. Olesen, A. Panfilov, N. Trayanova, U. Ravens, S. Richard, D. Rosenbaum, Y. Rudy, F. Sachs, F. Sachse, D. Saint, U. Schotten, O. Solovyova, P. Taggart, L. Tung, A. Varro, P. Volders, K. Wang, J. Weiss, E. Wettwer, E. White, R. Wilders, R. Winslow, and P. Kohl. Minimum information about a cardiac electrophysiology experiment (micee): Standardised reporting for model reproducibility, interoperability, and data sharing. Progress in Biophysics and Molecular Biology, 107(1):4 - 10, 2011. [ bib | DOI | http | .pdf ]
[5] J. Weile, M. Pocock, S. J. Cockell, P. Lord, J. M. Dewar, E.-M. Holstein, D. Wilkinson, D. Lydall, J. Hallinan, and A. Wipat. Customizable views on semantically integrated networks for systems biology. Bioinformatics, 27(9):1299-1306, 2011. [ bib | DOI | arXiv | http ]
[6] R. Brinkman, M. Courtot, D. Derom, J. Fostel, Y. He, P. Lord, J. Malone, H. Parkinson, B. Peters, P. Rocca-Serra, A. Ruttenberg, S.-A. Sansone, L. Soldatova, C. Stoeckert, J. Turner, J. Zheng, and the OBI consortium. Modeling biomedical experimental processes with obi. Journal of Biomedical Semantics, 1(Suppl 1):S7, 2010. [ bib | DOI | http ]
[7] A. Lister, P. Lord, M. Pocock, and A. Wipat. Annotation of SBML models through rule-based semantic integration. Journal of Biomedical Semantics, 1(Suppl 1):S3, 2010. [ bib | DOI | http ]
[8] P. Lord. An evolutionary approach to Function. Journal of Biomedical Semantics, 1(Suppl 1):S4, 2010. [ bib | DOI | arXiv | http ]
[9] P. Lord and R. Stevens. Adding a little reality to building ontologies for biology. PLoS One, 2010. [ bib | DOI | blog | http | .pdf ]
[10] A. R. Jones, A. L. Lister, L. Hermida, P. Wilkinson, M. Eisenacher, K. Belhajjame, F. Gibson, P. Lord, M. Pocock, H. Rosenfelder, J. Santoyo-Lopez, A. Wipat, and N. W. Paton. Modeling and managing experimental data using FuGE. OMICS: A Journal of Integrative Biology, 13(3):239-251, 2009. PMID: 19441879. [ bib | DOI | arXiv | http ]
[11] C. Pesquita, D. Faria, A. O. Falcão, P. Lord, and F. M. Couto. Semantic similarity in biomedical ontologies. PLoS Comput Biol, 5(7):e1000443, 2009. [ bib | DOI | http ]
[12] F. Dawn, G. Garrity, T. Gray, N. Morrison, J. Selengut, P. Sterk, T. Tatusova, N. Thomson, M. Allen, S. Angiuoli, M. Ashburner, N. Axelrod, S. Baldauf, S. Ballard, J. Boore, G. Cochrane, J. Cole, P. Dawyndt, P. De Vos, C. dePamphilis, R. Edwards, N. Faruque, R. Feldman, J. Gilbert, P. Gilna, F. O. Glockner, P. Goldstein, R. Guralnick, D. Haft, D. Hancock, H. Hermjakob, C. Hertz-Fowler, P. Hugenholtz, I. Joint, L. Kagan, M. Kane, J. Kennedy, G. Kowalchuk, R. Kottmann, E. Kolker, S. Kravitz, N. Kyrpides, J. Leebens-Mack, S. Lewis, K. Li, A. Lister, P. Lord, N. Maltsev, V. Markowitz, J. Martiny, B. Methe, I. Mizrachi, R. Moxon, K. Nelson, J. Parkhill, L. Proctor, O. White, S.-A. Sansone, A. Spiers, R. Stevens, P. Swift, C. Taylor, Y. Tateno, A. Tett, S. Turner, D. Ussery, B. Vaughan, N. Ward, T. Whetzel, I. San Gil, G. Wilson, and A. Wipat. The minimum information about a genome sequence (MIGS) specification. Nat Biotech, 26:541-547, May 2008. 10.1038/nbt1360. [ bib | DOI | http ]
[13] C. F. Taylor, D. Field, S.-A. Sansone, J. Aerts, R. Apweiler, M. Ashburner, C. A. Ball, P.-A. Binz, M. Bogue, T. Booth, A. Brazma, R. R. Brinkman, A. M. Clark, E. W. Deutsch, O. Fiehn, J. Fostel, P. Ghazal, F. Gibson, T. Gray, G. Grimes, J. M. Hancock, N. W. Hardy, H. Hermjakob, R. K. Julian, M. Kane, C. Kettner, C. Kinsinger, E. Kolker, M. Kuiper, N. L. Novere, J. Leebens-Mack, S. E. Lewis, P. Lord, A.-M. Mallon, N. Marthandan, H. Masuya, R. McNally, A. Mehrle, N. Morrison, S. Orchard, J. Quackenbush, J. M. Reecy, D. G. Robertson, P. Rocca-Serra, H. Rodriguez, H. Rosenfelder, J. Santoyo-Lopez, R. H. Scheuermann, D. Schober, B. Smith, J. Snape, C. J. Stoeckert, K. Tipton, P. Sterk, A. Untergasser, J. Vandesompele, and S. Wiemann. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol, 26(8):889-896, 2008. [ bib | DOI | http ]
[14] M. Aranguren, S. Bechhofer, P. Lord, U. Sattler, and R. Stevens. Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL. BMC Bioinformatics, 8(1):57, 2007. [ bib | DOI | http ]
[15] S. Bechhofer, R. Stevens, and P. Lord. GOHSE: Ontology Driven Dynamic Linking of Biology Resources. Journal of Web Semantics, 4(3):155-63, 2006. [ bib | DOI | link ]
[16] E. Merelli, G. Armano, N. Cannata, F. Corradini, M. d'Inverno, A. Domse, P. Lord, A. Martin, L. Milanesi, S. Moeller, M. Schroeder, , and M. Luck. Agents in bioinformatics, computational and systems biology. Briefings in Bioinformatics, 2006. [ bib | DOI ]
[17] K. Wolstencroft, P. Lord, L. Tabernero, A. Brass, and R. Stevens. Protein classification using ontology classification. Bioinformatics, 22(14):e530-538, 2006. [ bib | DOI | arXiv | http ]
[18] T. Oinn, M. Greenwood, M. Addis, M. N. Alpdemir, J. Ferris, K. Glover, C. Goble, A. Goderis, D. Hull, D. Marvin, P. Li, P. Lord, M. R. Pocock, M. Senger, R. Stevens, A. Wipat, and C. Wroe. Taverna: Lessons in creating a workflow environment for the life sciences. Concurrency and Computation: Practice and Experience Grid Workflow, 18(10):1067 - 1100, 2005. [ bib | DOI ]
[19] C. Wroe, C. Goble, M. Greenwood, P. Lord, S. Miles, J. Papay, T. Payne, and L. Moreau. Automating experiments using semantic data on a bioinformatics grid. IEEE Intelligent Systems, 19(1):48-55, 2004. [ bib | DOI | link ]
[20] P. W. Lord, R. D. Stevens, A. Brass, and C. A. Goble. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics, 19(10):1275-83, 2003. [ bib | DOI | Faculty of 1000 | link ]
[21] R. Stevens, C. Wroe, S. Bechhofer, P. Lord, A. Rector, and C. Goble. Building ontologies in DAML + OIL. Comparative and Functional Genomics, 4(1), 2003. [ bib | link ]
[22] P.W. Lord, J.N.Selley, and T.K.Attwood. CINEMA-MX: A modular multiple alignment editor. Bioinformatics, 18(10):1402-03, 2002. [ bib ]

Books

[1] A. Garcia, K. O'Neill, L. J. Garcia, P. Lord, R. Stevens, O. Corcho, and F. Gibson. Developing ontologies within decentralised settings. In H. Chen, Y. Wang, and K.-H. Cheung, editors, Semantic e-Science, pages 99-140. Springer, 2010. [ bib | http ]
[2] R. Stevens and P. Lord. Application of ontologies in bioinformatics. In S. Staab and R. Studer, editors, Handbook on Ontologies in Information Systems. Springer, second edition, 2008. [ bib | .pdf ]
[3] R. Stevens, P. Lord, and D. Hull. Using distributed data and tools in bioinformatics applications. In Bioinformatics From Genomes to Therapies. Wiley, VCH, 2007. [ bib | DOI ]
[4] C. Goble, K. Wolstencroft, A. Goderis, D. Hull, J. Zhao, P. Alper, P. Lord, C. Wroe, K. Belhajjame, D. Turi, R. Stevens, T. Oinn, and D. D. Roure. Knowledge discovery for biology with taverna: Producing and consuming semantics in the web of science. In C. J. Baker and K.-H. Cheung, editors, Revolutionizing Knowledge Discovery in the Life Sciences. Springer-Verlag, 2007. [ bib | link ]
[5] P. Lord, R. D. Stevens, C. A. Goble, and I. Horrocks. Description Logics: OWL and DAML+OIL. In Genetics, Genomics, Proteomics, and Bioinformatics. Wiley, 2004. Invited Article In Press. [ bib | link | .pdf ]
[6] R. Stevens, C. Wroe, P. Lord, and C. Goble. Ontologies in bioinformatics. In S. Staab and R. Studer, editors, Handbook on Ontologies, pages 635-657. Springer, 2003. [ bib ]

Conference Papers

[1] P. Lord. The Semantic Web takes Wing: Programming Ontologies with Tawny-OWL. Mar. 2013. [ bib | arXiv | http ]
[2] J. D. Warrender and P. Lord. The Karyotype Ontology: a computational representation for human cytogenetic patterns. 2013. [ bib | arXiv ]
[3] P. Lord and L. Marshall. Twenty five shades of greycite: Semantics for referencing and preservation. 2013. [ bib | arXiv | .pdf ]
[4] P. Lord, S. Cockell, and R. Stevens. Three steps to heaven. 2012. [ bib | arXiv | slides | script | http ]
[5] A. Splendiani, C. J. Rawlings, S. Kuo, R. Stevens, and P. Lord. Lost in translation: data integration tools meet the Semantic Web (experiences from the Ondex project). Mar. 2011. [ bib | arXiv | http ]
[6] P. Lord, S. Cockell, D. C. Swan, and R. Stevens. The ontogenesis knowledgeblog: Lightweight publishing about semantics, with lightweight semantic publishing. In Semantic Web Technologies for Libraries and Readers, 2011. [ bib | http | .pdf ]
[7] S. J. Cockell, J. Weile, P. Lord, C. Wipat, D. Andriychenko, M. Pocock, D. Wilkinson, M. Young, and A. Wipat. An integrated dataset for in silico drug discovery. In International Symposium on Integrative Bioinformatics, 2010. [ bib | DOI ]
[8] The OBI consortium. Modeling biomedical experimental processes with OBI. In Bio-Ontologies 2009: Knowledge in Biology, 2009. [ bib ]
[9] A. Lister, P. Lord, M. Pocock, and A. Wipat. Annotation of SBML Models through Rule-Based Semantic Integration. In Bio-Ontologies 2009: Knowledge in Biology, 2009. [ bib ]
[10] P. Lord. An Evolutionary Approach to Function. In Bio-Ontologies 2009: Knowledge in Biology, 2009. [ bib | http ]
[11] P. Watson, P. Lord, F. Gibson, P. Periorellis, and G. Pitsilis. Cloud Computing for e-Science with CARMEN. In 2nd Iberian Grid Infrastructure Conference Proceedings, 2008. [ bib ]
[12] K. Wolstencroft, P. Alper, D. Hull, C. Wroe, P. W. Lord, R. D. Stevens, and C. A. Goble. The mygrid ontology: bioinformatics service discovery. International journal of bioinformatics research and applications, 3:303-325, 2007. [ bib | http ]
[13] P. Watson, T. Jackson, G. Pitsilis, F. Gibson, J. Austin, M. Fletcher, B. Liang, and P. Lord. The CARMEN Neuroscience Server. In Proceedings of the UK e-Science All Hands Meeting 2007. National e-Science Centre, 2007. ISBN 978-0-9553988-3-4. [ bib ]
[14] T. Craddock, P. Lord, C. Harwood, and A. Wipat. e-science tools for the genomic scale characterisation of bacterial secreted proteins. In S. J. Cox, editor, Proceedings of the UK e-Science All Hands Meeting 2006. National e-Science Centre, 2006. [ bib | link | slides | .pdf ]
[15] K. Wolstencroft, T. Oinn, C. Goble, J. Ferris, C. Wroe, P. Lord, K. Glover, and R. Stevens. Panoply of Utilities in Taverna. In 1st IEEE Intl Conf on e-Science and Grid Technologies, 2005. [ bib ]
[16] J. Zhao, P. Lord, P. Alper, C. Wroe, , and C. Goble. The implications of semantic web technologies for support of the escience process. In Proc UK e-Science All Hands Meeting 2005. EPSRC, 2005. [ bib | link ]
[17] A. Goderis, U. Sattler, P. Lord, and C. Goble. Seven bottlenecks to workflow reuse and repurposing. In Fourth International Semantic Web Conference (ISWC 2005), volume 3792, Galway, Ireland, 2005. [ bib | DOI | link | .pdf ]
[18] K. Wolstencroft, A. Brass, I. Horrocks, P. Lord, U. Sattler, R. Stevens, and D. Turi. A Little Semantic Web Goes a Long Way in Biology. In 4th International Semantic Web Conference, volume 3792, Galway, Ireland, 2005. [ bib | DOI | link | .pdf ]
[19] K. Garwood, P. Lord, H. Parkinson, N. W. Paton, and C. Goble. Pedro ontology services: A framework for rapid ontology markup. In A. Gómez-Pérez and J. Euzenat, editors, European Semantic Web Conference. Springer-Verlag, 2005. [ bib | link | .pdf ]
[20] P. Lord, P. Alper, C. Wroe, and C. Goble. Feta: A light-weight architecture for user oriented semantic service discovery. In A. Gómez-Pérez and J. Euzenat, editors, European Semantic Web Conference. Springer-Verlag, 2005. [ bib | DOI | .pdf ]
[21] S. Bechhofer, R. Stevens, and P. 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, Pacific Symposium on Biocomputing (PSB) 2005. World Scientific, 2005. [ bib | link ]
[22] R. Stevens, H. Tipney, C. Wroe, T. Oinn, M. Senger, P. Lord, C. Goble, A. Brass, and M. Tassabehji. Genome science performed with e-science tools. In Proceedings of the All Hands Meeting, 2004. [ bib | .pdf ]
[23] P. Lord, S. Bechhofer, M. D. Wilkinson, G. Schiltz, D. Gessler, D. Hull, C. Goble, and L. Stein. Applying semantic web services to bioinformatics: Experiences gained, lessons learnt. In International Semantic Web Conference, 2004. [ bib | DOI | .pdf ]
[24] R. Stevens, H. Tipney, C. Wroe, T. Oinn, M. Senger, P. Lord, C. Goble, A. Brass, and M. Tassabehji. Exploring Williams Beuren Syndrome Using myGrid. In Bioinformatics, volume 20, 2004. Intelligent Systems for Molecular Biology (ISMB) 2004. [ bib | link | .pdf ]
[25] C. Wroe, P. Lord, S. Miles, J. Papay, L. Moreau, and C. Goble. Recycling services and workflows through discovery and reuse. In Proc UK e-Science All Hands Meeting 2004. EPSRC, 2004. [ bib | link | .pdf ]
[26] P. Lord, C. Wroe, R. Stevens, C. Goble, S. Miles, L. Moreau, K. Decker, T. Payne, and J. Papay. Semantic and personalised service discovery. In Proc UK e-Science All Hands Meeting 2003. EPSRC, 2003. ISBN 1-904425-11-9. [ bib | .pdf ]
[27] S. Bechhofer, R. Volz, and P. Lord. Cooking the semantic web with the OWL API. In Internaional Semantic Web Conference, 2003. [ bib | DOI | link | .pdf ]
[28] P. Lord, R. Stevens, A. Brass, and C. Goble. Semantic similarity measures as tools for exploring the Gene Ontology. In Pacific Symposium on Biocomputing, 2003. [ bib | slides | script | .pdf ]
[29] P. Lord, J. Reich, A. Mitchell, R. Stevens, T. Attwood, and C. Goble. PRECIS: An automated pipeline for producing concise reports about proteins. In IEEE International Symposium on Bio-informatics and Biomedical engineering, pages 59-64. IEEE press, November 2001. [ bib | slides | script | .pdf ]

Grants

[1] Data linking with knowledge-blogging. JISC, 2010-2011. [ bib | http ]
[2] The ONDEX System for integrating Life Sciences data source. BBSRC, 2008-2011. BB/F006039/1. [ bib | http ]
[3] CARMEN: Code analysis, repository, and modelling for e-Neuroscience. EPSRC, 2006-2011. EP/E002331/1. [ bib | http ]

Disclaimer: This is my personal website, and represents my opinion. My formal pages and those of the school and university are linked above.