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. I have removed most of the venue of publication from these pages; if you want to know how good the papers are, I would suggest that you read them. 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] G. Mısırlı, R. Taylor, A. Goñi-Moreno, J. A. McLaughlin, C. Myers, J. H. Gennari, P. Lord, and A. Wipat. Sbol-owl: An ontological approach for formal and semantic representation of synthetic biology information. 8(7), 2019. PMID: 31059645. [ bib | DOI | arXiv | http ]
[2] R. Stevens, P. Lord, J. Malone, and N. Matentzoglu. Measuring expert performance at manually classifying domain entities under upper ontology classes. Journal of Web Semantics, 2018. [ bib | DOI | arXiv | http ]
[3] H. O'Keefe, R. A. Queen, S. Meldau, P. Lord, and J. L. Elson. Haplogroup context is less important in the penetrance of mitochondrial dna complex i mutations compared to mt-trna mutations. Journal of Molecular Evolution, Jul 2018. [ bib | DOI | http ]
[4] M. J. Bell and P. Lord. On patterns and re-use in bioinformatics databases. 2017. [ bib | DOI | arXiv | http ]
[5] P. Lord, R. Spiering, J. C. Aguillon, A. E. Anderson, S. Appel, D. Benitez-Ribas, A. ten Brinke, F. Broere, N. Cools, M. C. Cuturi, J. Diboll, E. K. Geissler, N. Giannoukakis, S. Gregori, S. M. van Ham, S. Lattimer, L. Marshall, R. A. Harry, J. A. Hutchinson, J. D. Isaacs, I. Joosten, C. van Kooten, A. Lopez Diaz de Cerio, T. Nikolic, H. B. Oral, L. Sofronic-Milosavljevic, T. Ritter, P. Riquelme, A. W. Thomson, M. Trucco, M. Vives-Pi, E. M. Martinez-Caceres, and C. M. Hilkens. Minimum information about tolerogenic antigen-presenting cells (MITAP): a first step towards reproducibility and standardisation of cellular therapies. 4, Aug. 2016. [ bib | DOI | http ]
[6] G. Misirli, J. Hallinan, M. Pocock, P. Lord, J. A. McLaughlin, H. Sauro, and A. Wipat. Data integration and mining for synthetic biology design. 2016. PMID: 27110921. [ bib | DOI | arXiv | http ]
[7] A. Ten Brinke, C. M. U. Hilkens, N. Cools, E. K. Geissler, J. A. Hutchinson, G. Lombardi, P. Lord, B. Sawitzki, P. Trzonkowski, S. M. Van Ham, and et al. Clinical Use of Tolerogenic Dendritic Cells-Harmonization Approach in European Collaborative Effort. 2015:18, 2015. [ bib | DOI | http ]
[8] 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. 8(10), 10 2013. [ bib | DOI | arXiv | http ]
[9] J. Weile, K. James, J. Hallinan, S. J. Cockell, P. Lord, A. Wipat, and D. J. Wilkinson. Bayesian integration of networks without gold standards. 28(11):1495--1500, Apr 2012. [ bib | DOI | http ]
[10] P. Lord, S. Cockell, and R. Stevens. Three steps to heaven: Semantic publishing in a real world workflow. 4(4), 2012. [ bib | DOI | blog | http ]
[11] M. Bell, C. Gillespie, D. Swan, and P. Lord. An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB. 2012. [ bib | DOI | arXiv | http ]
[12] 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. 2011. [ bib | DOI | http | .pdf ]
[13] 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. 2011. [ bib | DOI | arXiv | http ]
[14] 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. 2010. [ bib | DOI | http ]
[15] A. Lister, P. Lord, M. Pocock, and A. Wipat. Annotation of SBML models through rule-based semantic integration. 2010. [ bib | DOI | http ]
[16] P. Lord. An evolutionary approach to Function. 2010. [ bib | DOI | arXiv | http ]
[17] P. Lord and R. Stevens. Adding a little reality to building ontologies for biology. 2010. [ bib | DOI | blog | http | .pdf ]
[18] 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. 2009. PMID: 19441879. [ bib | DOI | arXiv | http ]
[19] C. Pesquita, D. Faria, A. O. Falcão, P. Lord, and F. M. Couto. Semantic similarity in biomedical ontologies. 2009. [ bib | DOI | http ]
[20] 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. May 2008. 10.1038/nbt1360. [ bib | DOI | http ]
[21] 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. 2008. [ bib | DOI | http ]
[22] 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. 2007. [ bib | DOI | http ]
[23] S. Bechhofer, R. Stevens, and P. Lord. GOHSE: Ontology Driven Dynamic Linking of Biology Resources. 2006. [ bib | DOI | link ]
[24] 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. 2006. [ bib | DOI ]
[25] K. Wolstencroft, P. Lord, L. Tabernero, A. Brass, and R. Stevens. Protein classification using ontology classification. 2006. [ bib | DOI | arXiv | http ]
[26] 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. 2005. [ bib | DOI ]
[27] 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. 2004. [ bib | DOI | link ]
[28] 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. 2003. [ bib | DOI | Faculty of 1000 | link ]
[29] R. Stevens, C. Wroe, S. Bechhofer, P. Lord, A. Rector, and C. Goble. Building ontologies in DAML + OIL. 2003. [ bib | link ]
[30] P.W. Lord, J.N.Selley, and T.K.Attwood. CINEMA-MX: A modular multiple alignment editor. 2002. [ bib ]
[31] H. O'Keefe, R. Queen, P. Lord, and J. L. Elson. What can a comparative genomics approach tell us about the pathogenicity of mtdna mutations in human populations? [ bib | DOI | arXiv | http ]


[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. 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. Springer, 2003. [ bib ]

Conference Papers

[1] P. Lord and R. Stevens. Facets, tiers and gems: Ontology patterns for hypernormalisation. In International Conference on Biomedical Ontologies, 2017. [ bib | http ]
[2] M. K. Halawani, R. Forsyth, and P. Lord. A literature based approach to define the scope of biomedical ontologies: A case study on a rehabilitation therapy ontology. In International Conference on Biomedical Ontologies, 2017. [ bib | http ]
[3] A. Blfgeh and P. Lord. User and developer interaction with editable and readable ontologies. , 2017. [ bib | link | http ]
[4] A. Blfgeh, J. D. Warrender, C. M. U. Hilkens, and P. Lord. A document-centric approach for developing the tolapc ontology. In F. Loebe, M. Boeker, H. Herre, L. Jansen, and D. Schober, editors, Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences, ODLS 2016, organized by the GI Workgroup Ontologies in Biomedicine and Life Sciences (OBML), Halle (Saale), Germany, September 29-30, 2016., CEUR Workshop Proceedings., 2016. [ bib | .pdf ]
[5] P. Lord and J. Warrender. A highly literate approach to ontology building. 2015. [ bib | arXiv | slides | script ]
[6] J. Warrender and P. Lord. Scaffolding the mitochondrial disease ontology from extant knowledge sources. 2015. [ bib | arXiv ]
[7] J. D. Warrender and P. Lord. How, What and Why to test an ontology, 2015. [ bib | arXiv | blog | slides | script ]
[8] P. Lord. The Semantic Web takes Wing: Programming Ontologies with Tawny-OWL. Mar. 2013. [ bib | arXiv | http ]
[9] J. Warrender and P. Lord. A pattern-driven approach to biomedical ontology engineering. SWAT4LS 2013, 2013. [ bib | arXiv ]
[10] J. D. Warrender and P. Lord. The Karyotype Ontology: a computational representation for human cytogenetic patterns. 2013. [ bib | arXiv ]
[11] P. Lord and L. Marshall. Twenty five shades of greycite: Semantics for referencing and preservation. 2013. [ bib | arXiv | .pdf ]
[12] R. Stevens and P. Lord. Semantic publishing of knowledge about amino acids., 2012. [ bib | .pdf ]
[13] P. Lord, S. Cockell, and R. Stevens. Three steps to heaven. 2012. [ bib | arXiv | slides | script | http ]
[14] 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 ]
[15] 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 ]
[16] 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 ]
[17] The OBI consortium. Modeling biomedical experimental processes with OBI. In Bio-Ontologies 2009: Knowledge in Biology, 2009. [ bib ]
[18] 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 ]
[19] P. Lord. An Evolutionary Approach to Function. In Bio-Ontologies 2009: Knowledge in Biology, 2009. [ bib | http ]
[20] 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 ]
[21] 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 ]
[22] 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 ]
[23] 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 ]
[24] 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 ]
[25] 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 ]
[26] 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 ]
[27] 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 ]
[28] 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 ]
[29] 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 ]
[30] 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 ]
[31] 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 ]
[32] 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 ]
[33] 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 ]
[34] 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 ]
[35] 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 ]
[36] S. Bechhofer, R. Volz, and P. Lord. Cooking the semantic web with the OWL API. In International Semantic Web Conference, 2003. [ bib | DOI | link | .pdf ]
[37] 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 ]
[38] 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 ]


[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.