journal_papers.out.bib

@misc{on_patterns_and_reuse,
  url = {https://arxiv.org/abs/1705.08730},
  title = {On Patterns and Re-Use in Bioinformatics Databases},
  year = 2017,
  howpublished = {\url{https://arxiv.org/abs/1705.08730}},
  author = {Bell, Michael J and Lord, Phillip},
  archived = {http://greycite.knowledgeblog.org/?uri=https%3A%2F%2Farxiv.org%2Fabs%2F1705.08730},
  doi = {10.1093/bioinformatics/btx310}
}
@article{10.7717/peerj.2300,
  title = {Minimum information about tolerogenic antigen-presenting
                  cells {(MITAP)}: a first step towards reproducibility and
                  standardisation of cellular therapies},
  author = {Lord, Phillip and Spiering, Rachel and Aguillon, Juan C. and
                  Anderson, Amy E. and Appel, Silke and Benitez-Ribas, Daniel
                  and ten Brinke, Anja and Broere, Femke and Cools, Nathalie
                  and Cuturi, Maria Cristina and Diboll, Julie and Geissler,
                  Edward K. and Giannoukakis, Nick and Gregori, Silvia and van
                  Ham, S. Marieke and Lattimer, Staci and Marshall, Lindsay
                  and Harry, Rachel A. and Hutchinson, James A. and Isaacs,
                  John D. and Joosten, Irma and van Kooten, Cees and Lopez
                  Diaz de Cerio, Ascension and Nikolic, Tatjana and Oral,
                  Haluk Barbaros and Sofronic-Milosavljevic, Ljiljana and
                  Ritter, Thomas and Riquelme, Paloma and Thomson, Angus W.
                  and Trucco, Massimo and Vives-Pi, Marta and
                  Martinez-Caceres, Eva M. and Hilkens, Catharien M.U.},
  year = 2016,
  month = aug,
  keywords = {Cell therapy, Minimum information model, Antigen-presenting
                  cells, Autoimmune disease, Transplantation, Tolerogenic
                  dendritic cells, Regulatory macrophages, Reporting
                  guidelines},
  abstract = { Cellular therapies with tolerogenic antigen-presenting
                  cells (tolAPC) show great promise for the treatment of
                  autoimmune diseases and for the prevention of destructive
                  immune responses after transplantation. The methodologies
                  for generating tolAPC vary greatly between different
                  laboratories, making it difficult to compare data from
                  different studies; thus constituting a major hurdle for the
                  development of standardised tolAPC therapeutic products.
                  Here we describe an initiative by members of the tolAPC
                  field to generate a minimum information model for tolAPC
                  (MITAP), providing a reporting framework that will make
                  differences and similarities between tolAPC products
                  transparent. In this way, MITAP constitutes a first but
                  important step towards the production of standardised and
                  reproducible tolAPC for clinical application. },
  volume = 4,
  issn = {2167-8359},
  url = {https://doi.org/10.7717/peerj.2300},
  doi = {10.7717/peerj.2300}
}
@article{misirli2015,
  author = {Goksel Misirli and Jennifer Hallinan and Matthew Pocock and
                  Phillip Lord and James Alastair McLaughlin and Herbert Sauro
                  and Anil Wipat},
  title = {Data Integration and Mining for Synthetic Biology Design},
  year = 2016,
  doi = {10.1021/acssynbio.5b00295},
  note = {PMID: 27110921},
  url = {http://dx.doi.org/10.1021/acssynbio.5b00295},
  eprint = {http://dx.doi.org/10.1021/acssynbio.5b00295}
}
@article{Ten_Brinke_2015,
  title = {{Clinical Use of Tolerogenic Dendritic Cells-Harmonization
                  Approach in European Collaborative Effort}},
  volume = 2015,
  issn = {1466-1861},
  url = {http://dx.doi.org/10.1155/2015/471719},
  doi = {10.1155/2015/471719},
  publisher = {Hindawi Publishing Corporation},
  author = {Ten Brinke, Anja and Hilkens, Catharien M. U. and Cools,
                  Nathalie and Geissler, Edward K. and Hutchinson, James A.
                  and Lombardi, Giovanna and Lord, Phillip and Sawitzki,
                  Birgit and Trzonkowski, Piotr and Van Ham, S. Marieke and et
                  al.},
  year = 2015,
  pages = {18}
}
@article{bell_2013_provenance,
  author = {Bell, Michael J. AND Collison, Matthew AND Lord,
                  Phillip},
  arxiv = {http://arxiv.org/abs/1308.4618},
  publisher = {Public Library of Science},
  title = {Can Inferred Provenance and Its Visualisation Be Used to
                  Detect Erroneous Annotation? A Case Study Using {UniProtKB}},
  year = 2013,
  month = 10,
  volume = 8,
  url = {http://dx.doi.org/10.1371%2Fjournal.pone.0075541},
  abstract = {

A constant influx of new data poses a challenge in keeping the annotation in biological databases current. Most biological databases contain significant quantities of textual annotation, which often contains the richest source of knowledge. Many databases reuse existing knowledge; during the curation process annotations are often propagated between entries. However, this is often not made explicit. Therefore, it can be hard, potentially impossible, for a reader to identify where an annotation originated from. Within this work we attempt to identify annotation provenance and track its subsequent propagation. Specifically, we exploit annotation reuse within the UniProt Knowledgebase (UniProtKB), at the level of individual sentences. We describe a visualisation approach for the provenance and propagation of sentences in UniProtKB which enables a large-scale statistical analysis. Initially levels of sentence reuse within UniProtKB were analysed, showing that reuse is heavily prevalent, which enables the tracking of provenance and propagation. By analysing sentences throughout UniProtKB, a number of interesting propagation patterns were identified, covering over sentences. Over sentences remain in the database after they have been removed from the entries where they originally occurred. Analysing a subset of these sentences suggest that approximately are erroneous, whilst appear to be inconsistent. These results suggest that being able to visualise sentence propagation and provenance can aid in the determination of the accuracy and quality of textual annotation.

Source code and supplementary data are available from the authors website at http://homepages.cs.ncl.ac.uk/m.j.bell1/sentence_analysis/.

}, number = 10, doi = {10.1371/journal.pone.0075541} }
@article{Weile_2012,
  title = {Bayesian integration of networks without gold standards},
  volume = 28,
  issn = {1460-2059},
  url = {http://dx.doi.org/10.1093/bioinformatics/bts154},
  doi = {10.1093/bioinformatics/bts154},
  number = 11,
  publisher = {Oxford University Press (OUP)},
  author = {Weile, J. and James, K. and Hallinan, J. and Cockell, S. J.
                  and Lord, P. and Wipat, A. and Wilkinson, D. J.},
  year = 2012,
  month = {Apr},
  pages = {1495-1500}
}
@article{fi4041004,
  author = {Lord, Phillip and Cockell, Simon and Stevens, Robert},
  title = {Three Steps to Heaven: Semantic Publishing in a Real World
                  Workflow},
  volume = 4,
  year = 2012,
  number = 4,
  url = {http://www.mdpi.com/1999-5903/4/4/1004},
  issn = {1999-5903},
  doi = {10.3390/fi4041004},
  blog = {http://www.russet.org.uk/blog/2054}
}
@article{goinowl,
  author = {Aranguren, Mikel and Bechhofer, Sean and Lord, Phillip and Sattler,
	Ulrike and Stevens, Robert},
  title = {{Understanding and using the meaning of statements in a bio-ontology:
	recasting the Gene Ontology in OWL}},
  year = {2007},
  abstract = {:The bio-ontology community falls into two camps: first we have biology
	domain experts, who actually hold the knowledge we wish to capture
	in ontologies; second, we have ontology specialists, who hold knowledge
	about techniques and best practice on ontology development. In the
	bio-ontology domain, these two camps have often come into conflict,
	especially where pragmatism comes into conflict with perceived best
	practice. One of these areas is the insistence of computer scientists
	on a well-defined semantic basis for the Knowledge Representation
	language being used. In this article, we will first describe why
	this community is so insistent. Second, we will illustrate this by
	examining the semantics of the Web Ontology Language and the semantics
	placed on the Directed Acyclic Graph as used by the Gene Ontology.
	Finally we will reconcile the two representations, including the
	broader Open Biomedical Ontologies format. The ability to exchange
	between the two representations means that we can capitalise on the
	features of both languages. Such utility can only arise by the understanding
	of the semantics of the languages being used. By this illustration
	of the usefulness of a clear, well-defined language semantics, we
	wish to promote a wider understanding of the computer science perspective
	amongst potential users within the biological community.},
  doi = {10.1186/1471-2105-8-57},
  issn = {1471-2105},
  pubmedid = {17311682},
  url = {http://www.biomedcentral.com/1471-2105/8/57}
}
@article{bechhofer05:gohse:jws,
  author = {Bechhofer, S.K. and Stevens, R.D and Lord, P.W.},
  title = {{GOHSE: Ontology Driven Dynamic Linking of Biology Resources}},
  year = {2006},
  doi = {10.1016/j.websem.2005.09.003},
  file = {gohse_j_web_semantics.pdf:gohse_j_web_semantics.pdf:PDF},
  link = {http://www.websemanticsjournal.org/ps/pub/2006-9}
}
@article{greycite2243,
  author = {Bell, Michael and Gillespie, Colin and Swan, Daniel and
                  Lord, Phillip},
  title = {An approach to describing and analysing bulk biological
                  annotation quality: a case study using {UniProtKB}},
  year = {2012},
  arxiv = {http://arxiv.org/abs/1208.2175},
  doi = {10.1093/bioinformatics/bts372},
  url = {http://arxiv.org/abs/1208.2175}
}
@article{2041-1480-1-s1-s7,
  author = {Brinkman, Ryan and Courtot, Melanie and Derom, Dirk and Fostel, Jennifer
	and He, Yongqun and Lord, Phillip and Malone, James and Parkinson,
	Helen and Peters, Bjoern and Rocca-Serra, Philippe and Ruttenberg,
	Alan and Sansone, Susanna-Assunta and Soldatova, Larisa and Stoeckert,
	Christian and Turner, Jessica and Zheng, Jie and the OBI consortium},
  title = {Modeling biomedical experimental processes with OBI},
  year = {2010},
  doi = {10.1186/2041-1480-1-S1-S7},
  issn = {2041-1480},
  url = {http://www.jbiomedsem.com/content/1/S1/S7}
}
@article{Field2008,
  author = {Field Dawn and Garrity, George and Gray, Tanya and Morrison, Norman
	and Selengut, Jeremy and Sterk, Peter and Tatusova, Tatiana and Thomson,
	Nicholas and Allen, Michael and Angiuoli, Samuel and Ashburner, Michael
	and Axelrod, Nelson and Baldauf, Sandra and Ballard, Stuart and Boore,
	Jeffrey and Cochrane, Guy and Cole, James and Dawyndt, Peter and
	De Vos, Paul and dePamphilis, Claude and Edwards, Robert and Faruque,
	Nadeem and Feldman, Robert and Gilbert, Jack and Gilna, Paul and
	Glockner, Frank Oliver and Goldstein, Philip and Guralnick, Robert
	and Haft, Dan and Hancock, David and Hermjakob, Henning and Hertz-Fowler,
	Christiane and Hugenholtz, Phil and Joint, Ian and Kagan, Leonid
	and Kane, Matthew and Kennedy, Jessie and Kowalchuk, George and Kottmann,
	Renzo and Kolker, Eugene and Kravitz, Saul and Kyrpides, Nikos and
	Leebens-Mack, Jim and Lewis, Suzanna and Li, Kelvin and Lister, Allyson
	and Lord, Phillip and Maltsev, Natalia and Markowitz, Victor and
	Martiny, Jennifer and Methe, Barbara and Mizrachi, Ilene and Moxon,
	Richard and Nelson, Karen and Parkhill, Julian and Proctor, Lita
	and White, Owen and Sansone, Susanna-Assunta and Spiers, Andrew and
	Stevens, Robert and Swift, Paul and Taylor, Chris and Tateno, Yoshio
	and Tett, Adrian and Turner, Sarah and Ussery, David and Vaughan,
	Bob and Ward, Naomi and Whetzel, Trish and San Gil, Ingio and Wilson,
	Gareth and Wipat, Anil},
  title = {{The minimum information about a genome sequence (MIGS) specification}},
  year = {2008},
  month = {May},
  note = {10.1038/nbt1360},
  day = {xx},
  doi = {10.1038/nbt1360},
  issn = {1087-0156},
  issue = {5},
  keywords = {genome},
  url = {http://dx.doi.org/10.1038/nbt1360}
}
@article{jones2009,
  author = {Jones, Andrew R. and Lister, Allyson L. and Hermida, Leandro and
	Wilkinson, Peter and Eisenacher, Martin and Belhajjame, Khalid and
	Gibson, Frank and Lord, Phil and Pocock, Matthew and Rosenfelder,
	Heiko and Santoyo-Lopez, Javier and Wipat, Anil and Paton, Norman
	W.},
  title = {Modeling and Managing Experimental Data Using {FuGE}},
  year = {2009},
  note = {PMID: 19441879},
  doi = {10.1089/omi.2008.0080},
  eprint = {http://www.liebertonline.com/doi/pdf/10.1089/omi.2008.0080},
  url = {http://www.liebertonline.com/doi/abs/10.1089/omi.2008.0080}
}
@article{2041-1480-1-s1-s3,
  author = {Lister, Allyson and Lord, Phillip and Pocock, Matthew and Wipat,
	Anil},
  title = {Annotation of {SBML} models through rule-based semantic integration},
  year = {2010},
  doi = {10.1186/2041-1480-1-S1-S3},
  issn = {2041-1480},
  url = {http://www.jbiomedsem.com/content/1/S1/S3}
}
@article{evolfunjbs,
  author = {Lord, Phillip},
  title = {{An evolutionary approach to Function}},
  year = {2010},
  arxiv = {http://arxiv.org/abs/1309.5984},
  doi = {10.1186/2041-1480-1-S1-S4},
  issn = {2041-1480},
  url = {http://www.jbiomedsem.com/content/1/S1/S4}
}
@article{reality_in_biology_2010,
  author = {Phillip Lord and Robert Stevens},
  title = {Adding a little reality to building ontologies for biology},
  year = {2010},
  blog = {http://www.russet.org.uk/blog/2010/07/realism-and-science/},
  doi = {10.1371/journal.pone.0012258},
  pdf = {download/publications/realism_and_science.pdf},
  url = {http://dx.plos.org/10.1371/journal.pone.0012258}
}
@article{bioinf-simil,
  author = {P. W. Lord and R. D. Stevens and A. Brass and C. A. Goble},
  title = {Investigating semantic similarity measures across the {Gene Ontology}:
	the relationship between sequence and annotation.},
  year = {2003},
  doi = {10.1093/bioinformatics/btg153},
  f1000 = {http://www.f1000biology.com/article/12835272/evaluation},
  file = {bioinf-sim-2002.pdf:bioinf-sim-2002.pdf:PDF},
  link = {http://bioinformatics.oupjournals.org/cgi/content/abstract/19/10/1275?ijkey=35y5NKFGceWLQ&keytype=ref}
}
@article{agents-bioinformatics,
  author = {Emanuela Merelli and Giuliano Armano and Nicola Cannata and Flavio
	Corradini and Mark d'Inverno and Andrea Domse and Phillip Lord and
	Andrew Martin and Luciano Milanesi and Steffen Moeller and Michael
	Schroeder and and Michael Luck},
  title = {Agents in Bioinformatics, Computational and Systems Biology},
  year = {2006},
  doi = {10.1093/bib/bbl014},
  file = {agents_briefings.pdf:agents_briefings.pdf:PDF}
}
@article{oinn2005,
  author = {Tom Oinn and Mark Greenwood and Matthew Addis and M. Nedim Alpdemir
	and Justin Ferris and Kevin Glover and Carole Goble and Antoon Goderis
	and Duncan Hull and Darren Marvin and Peter Li and Phillip Lord and
	Matthew R. Pocock and Martin Senger and Robert Stevens and Anil Wipat
	and Chris Wroe},
  title = {Taverna: Lessons in creating a workflow environment for the life
	sciences},
  year = {2005},
  doi = {10.1002/cpe.993},
  file = {taverna-ccpe.pdf:taverna-ccpe.pdf:PDF}
}
@article{bioinf-cinema,
  author = {P.W.Lord and J.N.Selley and T.K.Attwood},
  title = {{CINEMA-MX}: A modular multiple alignment editor},
  year = {2002},
  download = {cinema-paper.pdf},
  file = {cinema-paper.pdf:cinema-paper.pdf:PDF}
}
@article{10.1371/journal.pcbi.1000443,
  author = {Pesquita, Catia AND Faria, Daniel AND Falc\~{a}o, André O. AND Lord,
	Phillip AND Couto, Francisco M.},
  title = {Semantic Similarity in Biomedical Ontologies},
  year = {2009},
  abstract = {In recent years, ontologies have become a mainstream topic in biomedical
	research. When biological entities are described using a common schema,
	such as an ontology, they can be compared by means of their annotations.
	This type of comparison is called semantic similarity, since it assesses
	the degree of relatedness between two entities by the similarity
	in meaning of their annotations. The application of semantic similarity
	to biomedical ontologies is recent; nevertheless, several studies
	have been published in the last few years describing and evaluating
	diverse approaches. Semantic similarity has become a valuable tool
	for validating the results drawn from biomedical studies such as
	gene clustering, gene expression data analysis, prediction and validation
	of molecular interactions, and disease gene prioritization.We review
	semantic similarity measures applied to biomedical ontologies and
	propose their classification according to the strategies they employ:
	node-based versus edge-based and pairwise versus groupwise. We also
	present comparative assessment studies and discuss the implications
	of their results. We survey the existing implementations of semantic
	similarity measures, and we describe examples of applications to
	biomedical research. This will clarify how biomedical researchers
	can benefit from semantic similarity measures and help them choose
	the approach most suitable for their studies. Biomedical ontologies
	are evolving toward increased coverage, formality, and integration,
	and their use for annotation is increasingly becoming a focus of
	both effort by biomedical experts and application of automated annotation
	procedures to create corpora of higher quality and completeness than
	are currently available. Given that semantic similarity measures
	are directly dependent on these evolutions, we can expect to see
	them gaining more relevance and even becoming as essential as sequence
	similarity is today in biomedical research.},
  doi = {10.1371/journal.pcbi.1000443},
  publisher = {Public Library of Science},
  url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1000443}
}
@article{Quinn20114,
  author = {T.A. Quinn and S. Granite and M.A. Allessie and C. Antzelevitch and
	C. Bollensdorff and G. Bub and R.A.B. Burton and E. Cerbai and P.S.
	Chen and M. Delmar and D. DiFrancesco and Y.E. Earm and I.R. Efimov
	and M. Egger and E. Entcheva and M. Fink and R. Fischmeister and
	M.R. Franz and A. Garny and W.R. Giles and T. Hannes and S.E. Harding
	and P.J. Hunter and G. Iribe and J. Jalife and C.R. Johnson and R.S.
	Kass and I. Kodama and G. Koren and P. Lord and V.S. Markhasin and
	S. Matsuoka and A.D. McCulloch and G.R. Mirams and G.E. Morley and
	S. Nattel and D. Noble and S.P. Olesen and A.V. Panfilov and N.A.
	Trayanova and U. Ravens and S. Richard and D.S. Rosenbaum and Y.
	Rudy and F. Sachs and F.B. Sachse and D.A. Saint and U. Schotten
	and O. Solovyova and P. Taggart and L. Tung and A. Varro and P.G.
	Volders and K. Wang and J.N. Weiss and E. Wettwer and E. White and
	R. Wilders and R.L. Winslow and P. Kohl},
  title = {Minimum Information about a Cardiac Electrophysiology Experiment
	(MICEE): Standardised reporting for model reproducibility, interoperability,
	and data sharing},
  year = {2011},
  doi = {10.1016/j.pbiomolbio.2011.07.001},
  issn = {0079-6107},
  keywords = {Minimum Information Standard},
  pdf = {download/publications/MICEE_manuscript.pdf},
  url = {http://www.sciencedirect.com/science/article/pii/S0079610711000642}
}
@article{sofg03,
  author = {Robert Stevens and Chris Wroe and Sean Bechhofer and Phillip Lord
	and Alan Rector and Carole Goble},
  title = {Building ontologies in {DAML + OIL}},
  year = {2003},
  link = {http://www.ncbi.nlm.nih.gov/pubmed/18629114}
}
@article{Taylor2008,
  author = {Chris F Taylor and Dawn Field and Susanna-Assunta Sansone and Jan
	Aerts and Rolf Apweiler and Michael Ashburner and Catherine A Ball
	and Pierre-Alain Binz and Molly Bogue and Tim Booth and Alvis Brazma
	and Ryan R Brinkman and Adam Michael Clark and Eric W Deutsch and
	Oliver Fiehn and Jennifer Fostel and Peter Ghazal and Frank Gibson
	and Tanya Gray and Graeme Grimes and John M Hancock and Nigel W Hardy
	and Henning Hermjakob and Randall K Julian and Matthew Kane and Carsten
	Kettner and Christopher Kinsinger and Eugene Kolker and Martin Kuiper
	and Nicolas Le Novere and Jim Leebens-Mack and Suzanna E Lewis and
	Phillip Lord and Ann-Marie Mallon and Nishanth Marthandan and Hiroshi
	Masuya and Ruth McNally and Alexander Mehrle and Norman Morrison
	and Sandra Orchard and John Quackenbush and James M Reecy and Donald
	G Robertson and Philippe Rocca-Serra and Henry Rodriguez and Heiko
	Rosenfelder and Javier Santoyo-Lopez and Richard H Scheuermann and
	Daniel Schober and Barry Smith and Jason Snape and Christian J Stoeckert
	and Keith Tipton and Peter Sterk and Andreas Untergasser and Jo Vandesompele
	and Stefan Wiemann},
  title = {{Promoting coherent minimum reporting guidelines for biological and
	biomedical investigations: the MIBBI project.}},
  year = {2008},
  doi = {10.1038/nbt.1411},
  institution = {European Bioinformatics Institute, Wellcome Trust Genome Campus,
	Hinxton, Cambridgeshire CB10 1SD, UK. chris.taylor@ebi.ac.uk, dfield@ceh.ac.uk},
  owner = {phillord},
  pii = {nbt.1411},
  pmid = {18688244},
  timestamp = {2008.08.11},
  url = {http://dx.doi.org/10.1038/nbt.1411}
}
@article{Weile01052011,
  author = {Weile, Jochen and Pocock, Matthew and Cockell, Simon J. and Lord,
	Phillip and Dewar, James M. and Holstein, Eva-Maria and Wilkinson,
	Darren and Lydall, David and Hallinan, Jennifer and Wipat, Anil},
  title = {Customizable views on semantically integrated networks for systems
	biology},
  year = {2011},
  abstract = {Motivation: The rise of high-throughput technologies in the post-genomic
	era has led to the production of large amounts of biological data.
	Many of these datasets are freely available on the Internet. Making
	optimal use of these data is a significant challenge for bioinformaticians.
	Various strategies for integrating data have been proposed to address
	this challenge. One of the most promising approaches is the development
	of semantically rich integrated datasets. Although well suited to
	computational manipulation, such integrated datasets are typically
	too large and complex for easy visualization and interactive exploration.Results:
	We have created an integrated dataset for Saccharomyces cerevisiae
	using the semantic data integration tool Ondex, and have developed
	a view-based visualization technique that allows for concise graphical
	representations of the integrated data. The technique was implemented
	in a plug-in for Cytoscape, called OndexView. We used OndexView to
	investigate telomere maintenance in S. cerevisiae.Availability: The
	Ondex yeast dataset and the OndexView plug-in for Cytoscape are accessible
	at http://bsu.ncl.ac.uk/ondexview.Contact: anil.wipat@ncl.ac.ukSupplementary
	information: Supplementary data is available at Bioinformatics online.},
  doi = {10.1093/bioinformatics/btr134},
  eprint = {http://bioinformatics.oxfordjournals.org/content/27/9/1299.full.pdf+html},
  url = {http://bioinformatics.oxfordjournals.org/content/27/9/1299.abstract}
}
@article{wolstencroftetal2006,
  author = {Wolstencroft, K. and Lord, P. and Tabernero, L. and Brass, A. and
	Stevens, R.},
  title = {{Protein classification using ontology classification}},
  year = {2006},
  abstract = {Motivation: The classification of proteins expressed by an organism
	is an important step in understanding the molecular biology of that
	organism. Traditionally, this classification has been performed by
	human experts. Human knowledge can recognise the functional properties
	that are sufficient to place an individual gene product into a particular
	protein family group. Automation of this task usually fails to meet
	the gold standard' of the human annotator because of the difficult
	recognition stage. The growing number of genomes, the rapid changes
	in knowledge and the central role of classification in the annotation
	process, however, motivates the need to automate this process. Results:
	We capture human understanding of how to recognise members of the
	protein phosphatases family by domain architecture as an ontology.
	By describing protein instances in terms of the domains they contain,
	it is possible to use description logic reasoners and our ontology
	to assign those proteins to a protein family class. We have tested
	our system on classifying the protein phosphatases of the human and
	Aspergillus fumigatus genomes and found that our knowledge-based,
	automatic classification matches, and sometimes surpasses, that of
	the human annotators. We have made the classification process fast
	and reproducible and, where appropriate knowledge is available, the
	method can potentially be generalised for use with any protein family.
	Availability: All components described in this paper are freely available.
	OWL ontology http://www.bioinf.man.ac.uk/phosphabase myGrid http://www.mygrid.org.uk
	Instance Store http://instancestore.man.ac.uk Contact: KWolstencroft@cs.man.ac.uk
	},
  doi = {10.1093/bioinformatics/btl208},
  eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e530.pdf},
  url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e530}
}
@article{wroe2004a,
  author = {C. Wroe and C. Goble and M. Greenwood and P. Lord and S. Miles and
	J. Papay and T. Payne and L. Moreau},
  title = {Automating Experiments Using Semantic Data on a Bioinformatics Grid.},
  year = {2004},
  doi = {10.1109/MIS.2004.1265885},
  link = {http://eprints.ecs.soton.ac.uk/9482/01/01265885.pdf}
}

books.out.bib

@incollection{semantic_escience,
  author = {Alexander Garcia and Kieran O'Neill and Leyla Jael Garcia
                  and Phillip Lord and Robert Stevens and Oscar Corcho and
                  Frank Gibson},
  editor = {Huajun Chen and Yimin Wang and Kei-Hoi Cheung},
  title = {Developing Ontologies within Decentralised Settings},
  year = 2010,
  booktitle = {Semantic e-Science},
  publisher = {Springer},
  url = {http://precedings.nature.com/documents/3231/version/1/html}
}
@incollection{handbook2,
  author = {Robert Stevens and Phillip Lord},
  editor = {Stefan Staab and Rudi Studer},
  booktitle = {Handbook on Ontologies in Information Systems},
  title = {Application of Ontologies in Bioinformatics},
  year = 2008,
  publisher = {Springer},
  edition = {Second},
  pdf = {download/publications/handbook2.pdf}
}
@incollection{disitributed_technologies_2007,
  author = {Robert Stevens and Phillip Lord and Duncan Hull},
  title = {Using distributed data and tools in Bioinformatics
                  Applications},
  booktitle = {Bioinformatics From Genomes to Therapies},
  publisher = {Wiley, VCH},
  year = 2007,
  doi = {10.1002/9783527619368.ch44},
  annotate = {ISBN-10: 3527312781},
  annotate = {ISBN-13: 978-3527312788}
}
@incollection{knowledge_discovery_2006,
  author = {Carole Goble and Katy Wolstencroft and Antoon
                  Goderis and Duncan Hull and Jun Zhao and Pinar Alper
                  and Phillip Lord and Chris Wroe and Khalid
                  Belhajjame and Daniele Turi and Robert Stevens and
                  Tom Oinn and David De Roure},
  title = {Knowledge Discovery for Biology with Taverna:
                  Producing and Consuming Semantics in the Web of
                  Science},
  booktitle = {Revolutionizing Knowledge Discovery in the Life
                  Sciences},
  publisher = {Springer-Verlag},
  year = 2007,
  editor = {Christopher J.O. Baker and Kei-Hoi Cheung},
  annote = {ISBN-13: 978-0-387-48436-5},
  link = {http://download.springer.com/static/pdf/961/chp%253A10.1007%252F978-0-387-48438-9_17.pdf?auth66=1381051719_2aca90164a1e8378da7a828f5fb43cb8&ext=.pdf}
}
@incollection{ggbp-description-logics-2004,
  author = {Phillip Lord and Robert D. Stevens and Carole A. Goble and Ian Horrocks},
  title = {{Description Logics: OWL and DAML+OIL}},
  booktitle = {Genetics, Genomics, Proteomics, and Bioinformatics},
  link = {http://www.wiley.com/ggpb/},
  publisher = {Wiley},
  year = 2004,
  note = {Invited Article In Press},
  pdf = {download/publications/wiley_gggb_encyc.pdf}
}
@incollection{onto-handbook-chap:03,
  author = {Robert Stevens and Chris Wroe and Phillip Lord and
                  Carole Goble},
  editor = {Stefan Staab and Rudi Studer},
  booktitle = {Handbook on Ontologies},
  download = {handbook.pdf},
  title = {Ontologies in Bioinformatics},
  publisher = {Springer},
  year = 2003
}

conference_papers.out.bib

@misc{greycite92227,
  url = {https://arxiv.org/abs/1709.09450},
  canonicaluri = {\url{https://arxiv.org/abs/1709.09450}},
  title = {A Literature Based Approach to Define the Scope of
                  Biomedical Ontologies: A Case Study on a
                  Rehabilitation Therapy Ontology},
  journal = {International Conference on Biomedical Ontologies,
                  2017},
  year = {2017},
  howpublished = {\url{}},
  author = {Halawani, Mohammad K. and Forsyth, Rob and Lord,
                  Phillip},
  archived = {http://greycite.knowledgeblog.org/?uri=https%3A%2F%2Farxiv.org%2Fabs%2F1709.09450,
                  http://wayback.archive.org/web/https://arxiv.org/abs/1709.09450}
}
@misc{greycite92226,
  url = {https://arxiv.org/abs/1709.08982},
  canonicaluri = {\url{https://arxiv.org/abs/1709.08982}},
  title = {User and Developer Interaction with Editable and
                  Readable Ontologies},
  journal = {International Conference on Biomedical Ontologies,
                  2017},
  year = {2017},
  howpublished = {\url{}},
  author = {Blfgeh, Aisha and Lord, Phillip},
  archived = {http://greycite.knowledgeblog.org/?uri=https%3A%2F%2Farxiv.org%2Fabs%2F1709.08982,
                  http://wayback.archive.org/web/https://arxiv.org/abs/1709.08982}
}
@inproceedings{DBLP:conf/odls/BlfgehWHL16,
  author = {Aisha Blfgeh and
               Jennifer D. Warrender and
               Catharien M. U. Hilkens and
               Phillip Lord},
  editor = {Frank Loebe and
               Martin Boeker and
               Heinrich Herre and
               Ludger Jansen and
               Daniel Schober},
  title = {A document-centric approach for developing the tolAPC Ontology},
  booktitle = {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.},
  series = {{CEUR} Workshop Proceedings},
  publisher = {CEUR-WS.org},
  year = {2016},
  url = {http://ceur-ws.org/Vol-1692/paperB.pdf},
  timestamp = {Tue, 18 Oct 2016 15:00:41 +0200},
  biburl = {http://dblp2.uni-trier.de/rec/bib/conf/odls/BlfgehWHL16},
  bibsource = {dblp computer science bibliography, http://dblp.org}
}
@article{highly_literate,
  author = {Phillip Lord and Jennifer Warrender},
  title = {A Highly Literate Approach to Ontology Building},
  year = 2015,
  slides = {download/publications/2015_12_04_lentic_pwl_jw.html},
  script = {download/publications/2015_12_04_lentic_pwl_jw_script.html},
  arxiv = {http://arxiv.org/abs/1512.04250}
}
@article{scaffolding,
  author = {Jennifer Warrender and Phillip Lord},
  title = {Scaffolding the Mitochondrial Disease Ontology from Extant
                  Knowledge Sources},
  year = 2015,
  arxiv = {http://arxiv.org/abs/1505.04114}
}
@misc{how_what_why_2015,
  author = {{Warrender}, J.~D. and {Lord}, P.},
  title = {{How, What and Why to test an ontology}},
  arxiv = {http://arxiv.org/abs/1505.04112},
  primaryclass = {cs.CE},
  year = 2015,
  blog = {http://www.russet.org.uk/blog/3074},
  slides = {download/publications/2015_bio_ont_testable_jw_pwl_pres.html},
  script = {download/publications/2015_bio_ont_testable_jw_pwl_pres_notes.html}
}
@misc{greycite9379,
  url = {http://ceur-ws.org/Vol-903/paper-06.pdf},
  title = {Semantic Publishing of Knowledge about Amino Acids},
  year = 2012,
  howpublished = {\url{http://ceur-ws.org/Vol-903/paper-06.pdf}},
  author = {Stevens, Robert and Lord, Phillip},
  archived = {http://greycite.knowledgeblog.org/?uri=http%3A%2F%2Fceur-ws.org%2FVol-903%2Fpaper-06.pdf,
                  http://webcitation.org/query.php?url=http%3A%2F%2Fceur-ws.org%2FVol-903%2Fpaper-06.pdf,
                  http://wayback.archive.org/web/http%3A%2F%2Fceur-ws.org%2FVol-903%2Fpaper-06.pdf}
}
@article{pattern_driven_approach_2013,
  author = {Jennifer Warrender and Phillip Lord},
  title = {A pattern-driven approach to biomedical ontology
                  engineering},
  journal = {SWAT4LS 2013},
  year = 2013,
  arxiv = {http://arxiv.org/abs/1312.0465}
}
@article{2013arXiv1305.3758W,
  author = {{Warrender}, J.~D. and {Lord}, P.},
  title = {{The Karyotype Ontology: a computational representation for
                  human cytogenetic patterns}},
  arxiv = {http://arxiv.org/abs/1305.3758},
  primaryclass = {cs.CE},
  keywords = {Computer Science - Computational Engineering, Finance, and
                  Science, Quantitative Biology - Genomics},
  year = 2013
}
@article{lord_semantic_2013,
  title = {{The Semantic Web takes Wing: Programming Ontologies with Tawny-OWL}},
  shorttitle = {The Semantic Web takes Wing},
  arxiv = {http://arxiv.org/abs/1303.0213},
  url = {http://arxiv.org/abs/1303.0213},
  abstract = {The Tawny-{OWL} library provides a fully-programmatic environment for ontology building; it enables the use of a rich set of tools for ontology development, by recasting development as a form of programming. It is built in Clojure - a modern Lisp dialect, and is backed by the {OWL} {API.} Used simply, it has a similar syntax to {OWL} Manchester syntax, but it provides arbitrary extensibility and abstraction. It builds on existing facilities for Clojure, which provides a rich and modern programming tool chain, for versioning, distributed development, build, testing and continuous integration. In this paper, we describe the library, this environment and the its potential implications for the ontology development process.},
  urldate = {2013-03-04},
  author = {Lord, Phillip},
  month = mar,
  year = {2013},
  keywords = {Computer Science - Artificial Intelligence, Computer Science - Digital Libraries},
  file = {1303.0213 PDF:/home/phillord/Dropbox/zotero/storage/MZQBASWR/Lord - 2013 - The Semantic Web takes Wing Programming Ontologie.pdf:application/pdf;arXiv.org Snapshot:/home/phillord/Dropbox/zotero/storage/J94EF2HP/1303.html:text/html}
}
@article{twenty-five,
  title = {Twenty Five Shades of Greycite: Semantics for Referencing and Preservation},
  year = 2013,
  author = {Lord, Phillip and Marshall, Lindsay},
  arxiv = {http://arxiv.org/abs/1304.7151},
  url = {http://ceur-ws.org/Vol-994/paper-01.pdf}
}
@article{three_steps,
  url = {http://www.russet.org.uk/blog/2012/04/three-steps-to-heaven/},
  title = {Three Steps to Heaven},
  year = 2012,
  author = {Lord, Phillip and Cockell, Simon and Stevens, Robert},
  slides = {download/publications/2012_05_24_pwl_sepublica.html},
  script = {download/publications/2012_05_24_pwl_sepublica_web.html},
  arxiv = {http://arxiv.org/abs/1206.5135v1}
}
@inproceedings{stlr_kblog_2011,
  title = {The Ontogenesis Knowledgeblog: Lightweight publishing about
                  semantics, with lightweight semantic publishing},
  year = 2011,
  author = {Phillip Lord and Simon Cockell and Daniel C. Swan and Robert Stevens},
  booktitle = {Semantic Web Technologies for Libraries and Readers},
  url = {http://www.russet.org.uk/blog/2011/06/ontogenesis-knowledgeblog-lightweight-semantic-publishing/},
  pdf = {download/publications/stlr_2011.pdf}
}
@article{2011arXiv1103.4749S,
  author = {{Splendiani}, A. and {Rawlings}, C.~J and {Kuo}, {S.-C.} and
                  {Stevens}, R. and {Lord}, P.},
  title = {{Lost in translation: data integration tools meet the
                  Semantic Web (experiences from the Ondex project)}},
  archiveprefix = {arXiv},
  eprint = {1103.4749},
  primaryclass = {cs.SE},
  keywords = {Computer Science - Software Engineering},
  year = 2011,
  month = mar,
  url = {http://adsabs.harvard.edu/abs/2011arXiv1103.4749S}
}
@inproceedings{cockell2010,
  author = {Simon J. Cockell and Jochen Weile and Phillip Lord and C.E.
                  Wipat and D. Andriychenko and Matthew Pocock and Darren
                  Wilkinson and Malcolm Young and Anil Wipat},
  title = {An integrated dataset for in silico drug discovery},
  booktitle = {International Symposium on Integrative Bioinformatics},
  year = {2010},
  doi = {10.2390/biecoll-jib-2010-116}
}
@inproceedings{soldatova2009,
  author = {{The OBI consortium}},
  title = {{Modeling biomedical experimental processes with OBI}},
  booktitle = {Bio-Ontologies 2009: Knowledge in Biology},
  year = 2009
}
@inproceedings{Lister2009,
  author = {Allyson Lister and Phillip Lord and Matthew Pocock and Anil Wipat},
  title = {{Annotation of SBML Models through Rule-Based Semantic Integration}},
  booktitle = {Bio-Ontologies 2009: Knowledge in Biology},
  year = 2009
}
@inproceedings{Lord2009,
  author = {Phillip Lord},
  title = {{An Evolutionary Approach to Function}},
  booktitle = {Bio-Ontologies 2009: Knowledge in Biology},
  year = 2009,
  url = {http://hdl.handle.net/10101/npre.2009.3228.1}
}
@conference{watson2008cloud,
  title = {{Cloud Computing for e-Science with CARMEN}},
  author = {Watson, P. and Lord, P. and Gibson, F. and Periorellis, P.
                  and Pitsilis, G.},
  booktitle = {2nd Iberian Grid Infrastructure Conference Proceedings},
  year = {2008}
}
@article{Wolstencroft2007,
  author = {K. Wolstencroft and P. Alper and D. Hull and C. Wroe and 
                  P. W. Lord and R. D. Stevens and C. A. Goble},
  title = {The myGrid ontology: bioinformatics service discovery.},
  journal = {International journal of bioinformatics research and
                  applications},
  year = 2007,
  volume = 3,
  issue = 3,
  pages = {303--325},
  issn = {1744-5485},
  url = {http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=18048194&dopt=AbstractPlus}
}
@inproceedings{watson_all_hands_2007,
  author = {Paul Watson and Tom Jackson and Georgios Pitsilis and Frank
                  Gibson and Jim Austin and Martyn Fletcher and Bojian Liang
                  and Phillip Lord},
  title = {{The CARMEN Neuroscience Server}},
  booktitle = {Proceedings of the UK e-Science All Hands Meeting 2007},
  year = 2007,
  publisher = {National e-Science Centre},
  note = {ISBN 978-0-9553988-3-4}
}
@inproceedings{Craddock_all_hands06,
  author = {Tracy Craddock and Phillip Lord and Colin Harwood
                  and Anil Wipat},
  title = {e-Science Tools For The Genomic Scale
                  Characterisation Of Bacterial Secreted Proteins},
  booktitle = {Proceedings of the UK e-Science All Hands Meeting
                  2006},
  year = 2006,
  editor = {Simon J Cox},
  publisher = {National e-Science Centre},
  link = {http://www.allhands.org.uk/2006/proceedings/papers/709.pdf},
  slides = {download/publications/all_hands_06_709_tracy_slides.ppt},
  pdf = {download/publications/all_hands_06_709.pdf}
}
@inproceedings{stevens_all_hands_2004,
  author = {R.D. Stevens and H.J. Tipney and C.J. Wroe and
                  T.M. Oinn and M. Senger and P.W. Lord and C.A. Goble
                  and A. Brass and M. Tassabehji},
  title = {Genome Science performed with e-Science Tools},
  booktitle = {Proceedings of the All Hands Meeting},
  year = 2004,
  pdf = {download/publications/all_hands_2004.pdf}
}
@inproceedings{wolstencroft2005,
  author = {K. Wolstencroft and T. Oinn and C. Goble and
                  J. Ferris and C. Wroe and P. Lord and K. Glover and
                  R. Stevens},
  title = {{Panoply of Utilities in Taverna}},
  booktitle = {1st IEEE Intl Conf on e-Science and Grid
                  Technologies},
  location = {Melbourne, Australia},
  year = 2005
}
@inproceedings{zhao2005,
  title = {The implications of Semantic Web technologies for support of  the eScience process},
  author = {Jun Zhao and Phillip Lord and Pinar Alper and Chris Wroe and and Carole Goble},
  booktitle = {{Proc UK e-Science All Hands Meeting 2005}},
  year = 2005,
  publisher = {EPSRC},
  link = {http://www.allhands.org.uk/2005/proceedings/papers/510.pdf}
}
@inproceedings{goderis+05,
  author = {Antoon Goderis and Ulrike Sattler and Phillip Lord
                  and Carole Goble},
  title = {Seven bottlenecks to workflow reuse and repurposing},
  booktitle = {Fourth International Semantic Web Conference (ISWC
                  2005)},
  isnn = {0302-9743},
  volume = 3792,
  doi = {10.1007/11574620\_25},
  year = 2005,
  link = {http://dx.doi.org/10.1007/11574620_25},
  address = {Galway, Ireland},
  pdf = {download/publications/antoon_repurposing.pdf}
}
@inproceedings{phosphatase-iswc,
  author = {K. Wolstencroft and A. Brass and I. Horrocks and
                  P. Lord and U. Sattler and R. Stevens and D. Turi},
  title = {{A Little Semantic Web Goes a Long Way in Biology}},
  booktitle = {4th International Semantic Web Conference},
  year = 2005,
  volume = 3792,
  isbn = {3-540-29754-5},
  doi = {10.1007/11574620_56},
  pdf = {download/publications/iswc_phosphatase_main.pdf},
  link = {http://dx.doi.org/10.1007/11574620_56},
  address = {Galway, Ireland}
}
@inproceedings{pedro-eswc,
  author = {Kevin Garwood and Phillip Lord and Helen Parkinson
                  and Norman W. Paton and Carole Goble},
  title = {Pedro Ontology Services: A framework for rapid
                  ontology markup},
  booktitle = {European Semantic Web Conference},
  year = 2005,
  link = {http://dx.doi.org/10.1007/11431053_39},
  editor = {A. G\'omez-P\'erez and J. Euzenat},
  publisher = {Springer-Verlag},
  pdf = {download/publications/european_semantic_web2005_pedro.pdf}
}
@inproceedings{feta-eswc,
  author = {Phillip Lord and Pinar Alper and Chris Wroe and
                  Carole Goble},
  title = {Feta: A light-weight architecture for user oriented
                  semantic service discovery},
  booktitle = {European Semantic Web Conference},
  year = 2005,
  doi = {10.1007/11431053_2},
  editor = {A. G\'omez-P\'erez and J. Euzenat},
  publisher = {Springer-Verlag},
  pdf = {download/publications/european_semantic_web2005_feta.pdf}
}
@inproceedings{bechhofer05:gohse,
  author = {Bechhofer, S.K. and Stevens, R.D and Lord, P.W.},
  title = {{Ontology Driven Dynamic Linking of Biology
                  Resources}},
  booktitle = {Pacific Symposium on Biocomputing (PSB) 2005},
  year = {2005},
  editor = {Altman, Russ B. and Dunker, A. Keith and Hunter,
                  Lawrence and Jung, Tiffany A. and Klein, Teri E.},
  publisher = {World Scientific},
  owner = {seanb},
  link = {http://helix-web.stanford.edu/psb05/bechhofer.pdf}
}
@inproceedings{iswc-bio-moby-comparison04,
  author = {Phillip Lord and Sean Bechhofer and Mark
                  D. Wilkinson and Gary Schiltz and Damian Gessler and
                  Duncan Hull and Carole Goble and Lincoln Stein},
  title = {Applying Semantic Web Services to bioinformatics:
                  Experiences gained, lessons learnt},
  booktitle = {International Semantic Web Conference},
  year = 2004,
  doi = {10.1007/b102467},
  pdf = {download/publications/biomoby-comparison-iswc2004.pdf}
}
@inproceedings{mygrid-williams-ismb04,
  title = {{Exploring Williams Beuren Syndrome Using
                  $^{my}$Grid}},
  author = {R.D. Stevens and H.J. Tipney and C.J. Wroe and
                  T.M. Oinn and M. Senger and P.W. Lord and C.A. Goble
                  and A. Brass and M. Tassabehji},
  booktitle = {Bioinformatics},
  link = {http://bioinformatics.oupjournals.org/cgi/content/abstract/20/suppl_1/i303?},
  pdf = {http://bioinformatics.oupjournals.org/cgi/reprint/20/suppl_1/i303.pdf},
  year = 2004,
  note = {Intelligent Systems for Molecular Biology (ISMB)
                  2004},
  volume = 20
}
@inproceedings{all_hands_find03,
  author = {Phillip Lord and Chris Wroe and Robert Stevens and
                  Carole Goble and Simon Miles and Luc Moreau and
                  Keith Decker and Terry Payne and Juri Papay},
  title = {Semantic and Personalised Service Discovery},
  booktitle = {{Proc UK e-Science All Hands Meeting 2003}},
  year = 2003,
  publisher = {EPSRC},
  note = {ISBN 1-904425-11-9},
  pdf = {download/publications/find-all-hands-03-paper.pdf}
}
@inproceedings{bechhofer03:_cookin_owl_api,
  author = {Sean Bechhofer and Raphael Volz and Phillip Lord},
  title = {Cooking the semantic web with the {OWL API}},
  booktitle = {International Semantic Web Conference},
  year = 2003,
  pdf = {download/publications/cooking03.pdf},
  link = {http://www.springerlink.com/app/home/contribution.asp?wasp=acecbdavyg2rwj96ekdw&referrer=parent&backto=issue,42,58;journal,48,1408;linkingpublicationresults,id:105633,1},
  doi = {10.1007/978-3-540-39718-2_42}
}
@inproceedings{psb-simil,
  author = {P.W. Lord and R.D. Stevens and A. Brass and
                  C.A. Goble},
  title = {Semantic similarity measures as tools for exploring
                  the {Gene Ontology}},
  booktitle = {Pacific Symposium on Biocomputing},
  year = 2003,
  pdf = {download/publications/psb-2003-paper.pdf},
  slides = {download/publications/psb-03-talk.pdf},
  script = {download/publications/psb-2003-script.pdf}
}
@inproceedings{prcis01,
  author = {P.W. Lord and J.R. Reich and A. Mitchell and R.D. Stevens and T.K. Attwood and C.A. Goble},
  title = {{PRECIS}: An Automated Pipeline for Producing Concise
                  Reports About Proteins},
  booktitle = {IEEE International Symposium on Bio-informatics and
                  Biomedical engineering},
  location = {Washington DC},
  month = {November},
  year = 2001,
  pages = {59-64},
  publisher = {IEEE press},
  isbn = {0-7695-1423-5},
  pdf = {download/publications/bibe-2001.pdf},
  slides = {download/publications/bibe-slides.pdf},
  script = {download/publications/bibe-commentary.pdf}
}
@inproceedings{wroe2004,
  author = {Chris Wroe and Phillip Lord and Simon Miles and Juri Papay and Luc Moreau and Carole Goble},
  title = {Recycling Services and Workflows through Discovery and Reuse},
  booktitle = {{Proc UK e-Science All Hands Meeting 2004}},
  year = 2004,
  publisher = {EPSRC},
  pdf = {download/publications/workflow_recycle_all_hands_2005.pdf},
  link = {http://www.allhands.org.uk/2004/proceedings/papers/218.pdf}
}

grants.out.bib

@misc{dl-kblog,
  title = {Data Linking with Knowledge-Blogging},
  howpublished = {JISC},
  year = {2010-2011},
  url = {http://www.russet.org.uk/blog/2010/08/a-new-grant-for-knowledgeblog/}
}
@misc{ondex,
  title = {{The ONDEX System for integrating Life Sciences data source}},
  howpublished = {BBSRC},
  year = {2008-2011},
  note = {BB/F006039/1},
  url = {http://www.bbsrc.ac.uk/pa/grants/AwardDetails.aspx?FundingReference=BB%2fF006063%2f1}
}
@misc{carmen,
  title = {{CARMEN: Code analysis, repository, and modelling for e-Neuroscience}},
  howpublished = {{EPSRC}},
  note = {EP/E002331/1},
  url = {http://gow.epsrc.ac.uk/ViewGrant.aspx?GrantRef=EP/E002331/1},
  year = {2006-2011}
}

popular_press.out.bib

@misc{greycite12539,
  url = {http://www.nature.com/nature/journal/v507/n7493/full/nj7493-523a.html},
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  year = 2014,
  howpublished = {\url{http://www.nature.com/nature/journal/v507/n7493/full/nj7493-523a.html}},
  author = {Mascarelli, Amanda},
  archived = {http://greycite.knowledgeblog.org/?uri=http%3A%2F%2Fwww.nature.com%2Fnature%2Fjournal%2Fv507%2Fn7493%2Ffull%2Fnj7493-523a.html,
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@misc{greycite6992,
  url = {\url{http://blogs.lse.ac.uk/impactofsocialsciences/2012/11/08/lord-publishing-coffee-shop/}},
  title = {Why academic publishing is like a coffee shop: An enormous
                  mystique adds relatively little},
  year = 2012,
  howpublished = {\url{http://blogs.lse.ac.uk/impactofsocialsciences/2012/11/08/lord-publishing-coffee-shop/}},
  author = {Phillip Lord}
}
@misc{guardian2010,
  author = {David Dobbs},
  url = {http://www.guardian.co.uk/science/blog/2010/sep/22/science-publishing-peer-review},
  title = {Publishing your science paper is only half the job},
  year = 2010
}
@misc{wired2011,
  author = {David Dobbs},
  url = {http://www.wired.com/wiredscience/2011/05/free-science-one-paper-at-a-time-2},
  title = {Free Science, One Paper at a Time},
  year = 2011
}

programme_committees.out.bib

@proceesings{icbo2015,
  title = {International Conference on Biomedical Ontologies (ICBO)},
  year = 2015
}
@proceedings{Bioont-2015,
  title = {Bio-Ontologies 2015},
  year = 2015
}
@proceedings{swatl4ls-2014,
  title = {Semantic Web Applications and Tools for Life Sciences},
  year = 2014
}
@proceedings{swatl4ls-2013,
  title = {Semantic Web Applications and Tools for Life Sciences},
  year = 2013
}
@proceedings{swatl4ls-2012,
  title = {Semantic Web Applications and Tools for Life Sciences},
  year = 2012
}
@proceedings{swatl4ls-2011,
  title = {Semantic Web Applications and Tools for Life Sciences},
  year = 2011
}
@proceedings{swatl4ls-2010,
  title = {Semantic Web Applications and Tools for Life Sciences},
  year = 2010
}
@proceedings{CSHALS2014,
  title = {Conference on Semantics in Healthcare and Life Sciences},
  year = 2014
}
@proceedings{swatl4ls-2009,
  title = {Semantic Web Applications and Tools for Life Sciences},
  year = 2009
}
@proceedings{swatl4ls-2008,
  title = {Semantic Web Applications and Tools for Life Sciences},
  year = 2008
}
@proceedings{icbo2013,
  title = {International Conference on Biomedical Ontology: ICBO 2013},
  year = 2013
}
@proceedings{eccb12,
  title = {11th European Conference on Computational Biology},
  year = 2012,
  link = {http://www.eccb12.org/home}
}
@inproceedings{multiple2011,
  title = {Working with Multiple Biomedical Ontologies },
  year = 2011,
  link = {http://icbo.buffalo.edu/wombo.htm}
}
@proceedings{owled2011,
  title = {OWLED 2011 OWL: Experiences and Directions},
  year = 2011,
  link = {http://www.webont.org/owled/2011/}
}
@proceedings{icbo2011,
  title = {International Conference on Biomedical Ontology: ICBO 2011},
  year = 2011,
  link = {http://icbo.buffalo.edu/cfp2011.html}
}
@proceedings{fwcs2010,
  title = {The Future of the Web for Collaborative Science, 2010},
  year = 2010,
  link = {http://esw.w3.org/topic/HCLS/WWW2010/Workshop}
}
@proceedings{semvo2010,
  title = {First Workshop on the Semantics of Visual Objects},
  year = 2010,
  link = {http://semanticscience.org/workshop/semvo2010/}
}
@proceedings{ismb2007,
  title = {Intelligent Systems for Molecular Biology (ISMB)},
  year = 2007,
  link = {http://bioinformatics.oxfordjournals.org/content/vol23/issue13/}
}
@proceedings{webdim4ls,
  title = {{Approaches and Architectures for Web Data Integration and
                  Mining in Life Sciences (WebDIM4LS)}},
  year = 2007,
  note = {at The 8th International Conference on Web Information Systems
                  Engineering (WISE2007)},
  link = {http://www.loria.fr/~malika/WebDIM4LS-CFP.html}
}
@proceedings{magsbiomed2007,
  title = {Multi-Agent and Grid Systems for Medicine,
                  Computational Biology and Bioinformatics},
  year = 2006,
  link = {http://www.diee.unica.it/biomed07/}
}
@proceedings{KSInBit,
  title = {Knowledge Systems in Bioinformatics (KSinBit '06)},
  year = 2006,
  link = {http://www.cs.rmit.edu.au/fedconf/index.html?page=ksinbit2006cfp}
}
@proceedings{icde2007,
  title = {IEEE 23rd International Conference on Data
                  Engineering},
  year = 2007,
  link = {http://www.srdc.metu.edu.tr/webpage/icde/}
}
@proceedings{kr-med2006,
  title = {Biomedical Ontology in Action - KR-MED},
  year = 2006,
  link = {http://www.imbi.uni-freiburg.de/medinf/kr-med-2006/}
}
@proceedings{ismb2006,
  title = {Intelligent Systems for Molecular Biology (ISMB)},
  year = 2006,
  link = {http://ismb2006.cbi.cnptia.embrapa.br/committees-2.html}
}
@proceedings{ismb2005,
  title = {Intelligent Systems for Molecular Biology (ISMB)},
  year = 2005,
  link = {http://www.iscb.org/ismb2005/}
}
@proceedings{gada2005,
  title = {Grid Computing and its Application to Data Analysis
                  (GADA'05)},
  year = 2005,
  link = {http://www.cs.rmit.edu.au/fedconf/2005/gada2005cfp.html}
}

invited_presentations.out.bib

@misc{manchester_2015,
  author = {Phillip Lord},
  title = {Programmatic and Literate Ontology Development},
  year = 2015,
  howpublished = {School of Computer Science, University of Manchester},
  slides = {download/publications/2015_06_manchester.html}
}
@misc{who_needs_semantics,
  author = {Phillip Lord},
  title = {Who needs semantics when you have big data?},
  year = 2014,
  note = {Semantic Data Analytics and Bioinformatics},
  link = {http://scm.ulster.ac.uk/~e10267487/SDAB2014/index.html},
  slides = {download/publications/2014_10_29_belfast_who_needs_semantics_phil_lord.html}
}
@misc{euon2014_tawny,
  author = {Phillip Lord},
  title = {Usable Semantic Interoperability: Panel},
  year = 2014,
  howpublished = {European Ontolgy Network, 2014}
}
@misc{is_academ_publis_dutch_tulip_bulb,
  author = {Phillip Lord},
  title = {Is Academic Publishing a Dutch Tulip Bulb?},
  year = 2012,
  note = {Research Seminar, School of Computing Science,Newcastle University},
  slides = {download/publications/2012_06_open_science_srg.html},
  script = {download/publications/2012_06_open_science_srg_web.html}
}
@misc{reality_of_semantic_publishing,
  author = {Phillip Lord},
  title = {The reality of semantic publishing},
  year = 2012,
  note = {UK Ontology Network},
  slides = {download/publications/2012_04_11_pwl_uk_ontology_network.html}
}
@misc{dcc_rin_research_data_management,
  author = {Phillip Lord},
  title = {Reasons why other people should share their data},
  month = {April},
  year = 2009,
  note = {Third DCC/RIN Research Data Management Forum}
}
@misc{webdim4lskeynote,
  author = {Phillip Lord},
  title = {Spreading Semantics over Biology},
  howpublished = {Web Data Integraton and Mining in LIfe Sciences (WebDIM4LS)},
  month = {November},
  year = 2007,
  note = {8th International Conference on Web Information Systems
                  Engineering},
  link = {http://www.loria.fr/~malika/WebDIM4LS-CFP.html},
  ppt = {download/publications/2007_11_nancy_webdim4ls_phil_lord.ppt}
}
@misc{pnnl2007,
  author = {Phillip Lord and Frank Gibson},
  title = {Doing it again. Workflows and Ontologies supporting the
                  scientific process},
  year = 2007,
  note = {Pacific Northwest National Laboratory},
  ppt = {download/publications/pnnl_comparagrid_and_carmen.ppt}
}
@misc{dcc_repeatability,
  author = {Phillip Lord},
  title = {Digital Curation or Digital Data? The impact of Services and
                  Federation},
  year = 2007,
  note = {Digital Curation Centre, UK},
  ppt = {download/publications/07_05_09_carmen_digital_curation_bath.ppt}
}
@misc{ontogenesis2006,
  author = {Phillip Lord},
  title = {The Sociology of Ontologies in Neurosciences},
  year = 2006,
  howpublished = {Ontogenesis Network of Excellence},
  note = {Manchester},
  ppt = {download/publications/ontogenesis_phil_lord.ppt}
}
@misc{knowledge-management2005,
  author = {Phillip Lord},
  title = {{Knowledge Management in Biology}},
  year = 2005,
  howpublished = {Knowledge Management Workshop, at All Hands 2005}
}
@misc{sofg-protege-2004,
  author = {Phillip Lord},
  title = {{The Protege OWL plugin and CO-ODE}},
  link = {http://www.sofg.org/meetings/sofg2004/index.html},
  year = 2004,
  howpublished = {Standards and Ontologies for Functional Genomics,
                  2004}
}
@misc{sem-web-appln-hungary,
  author = {Phillip Lord},
  title = {{Migrating to the Semantic Web: Bioinformatics as a
                  case study}},
  howpublished = {The First European Workshop on Semantic Web
                  Applications in Biomedicine},
  link = {http://www.ida.liu.se/~magba/SemWebWS/SemWebWS.htm},
  note = {Balatonf\"ured, Lake Balaton, Hungary},
  slides = {download/publications/sem_web_applicn_biomedicine_hungary.ppt},
  year = 2004
}
@misc{bio-agents-iii,
  author = {Phillip Lord},
  title = {{Knowledge in Middleware for \textit{in silico} Biology}},
  howpublished = {AgentLink III Technical Forum:- Agents in
                  Bioinformatics.},
  note = {Rome, Italy},
  year = 2004,
  link = {http://www.agentlink.org/activities/al3-tf/tf1/},
  slides = {download/publications/rome_talk_phil_lord.ppt}
}
@misc{go-users-simil,
  author = {P.W. Lord},
  title = {{Semantic Similarity:- Measuring Similarity across
                  the Gene Ontology.}},
  howpublished = {GO Users Meeting},
  note = {Hinxton, UK},
  year = 2002,
  slides = {download/publications/go-users-02-talk.pdf},
  script = {download/publications/go-users-02-script.pdf},
  inmem = {in-memoriam-nw.html}
}

journal_reviewing.out.bib

@misc{nat_biot,
  title = {{Nature Biotech}},
  year = 2004
}
@misc{j_para_dist_comp,
  title = {{Journal of Parallel and Distributed Computing}},
  year = 2003
}
@misc{j_web_sem,
  title = {{Journal of Web Semantics}},
  year = 2006
}
@misc{j_con_com,
  title = {{Journal of Concurrency and Computation, Practice and Experience}},
  year = 2003
}
@misc{bioinf,
  title = {{Bioinformatics}},
  year = {2008, 2007, 2006, 2005}
}
@misc{ploscb,
  title = {{PLoS Computational Biology}},
  year = 2006
}
@misc{tkde,
  title = {{IEEE Transactions on Knowledge and Data
                  Enginneering}},
  year = 2006
}
@misc{07:_bmc_bioin,
  title = {BMC Bioinformatics},
  year = {2007, 2011}
}
@misc{database,
  title = {Database},
  year = 2011
}

others.out.bib

@misc{euon2015_lentic,
  author = {Phillip Lord},
  title = {Highly Literate Ontologies},
  year = 2015,
  howpublished = {European Ontolgy Network, 2015},
  slides = {download/publications/2015_05_ukon_literate_pwl.html}
}
@misc{euon2014_tawny,
  author = {Phillip Lord},
  title = {Semantic Documents and Literate Ontologies: A rose by any other name?},
  year = 2014,
  howpublished = {European Ontolgy Network, 2014},
  slides = {download/publications/2014_09_22_literate_semantic_phil_lord.html}
}
@misc{ebi_ontology_group,
  author = {Phillip Lord},
  title = {Programmatic Development of Ontologies using Tawny-OWL},
  year = 2014,
  howpublished = {EBI Ontology Group Meeting},
  slides = {download/publications/2014_05_phil_lord_tawny_owl_ebi.html}
}
@misc{ukon2014_tawny,
  author = {Phillip Lord},
  title = {{Tawny-OWL: A programmatic, testable and literate
                  environment for Ontology Development}},
  year = 2014,
  howpublished = {UK Ontology Network 2014},
  slides = {download/publications/2014_04_programmatic_testable_literate.html}
}
@misc{flanagan_iswc2005,
  author = {Keith Flanagan and Matthew Pocock and Robert Stevens and Phillip
	Lord and Pete Lee and Anil Wipat},
  title = {Logical and Probabilistic Reasoning for Genomic Rearrangement Detection},
  year = {2005},
  note = {Poster},
  booktitle = {Fourth International Semantic Web Conference (ISWC 2005)},
  file = {iswc2005_bayesian_poster.pdf:iswc2005_bayesian_poster.pdf:PDF}
}
@misc{2009-ontologies-distrib,
  author = {Alexander Garcia and Kieran O'Neill and Leyla Garcia and Phillip
	Lord and Robert Stevens and Oscar Corcho and Frank Gibson},
  title = {Developing ontologies in decentralised settings.},
  howpublished = {Available from Nature Precedings},
  year = {2009},
  url = {http://hdl.handle.net/10101/npre.2009.3231.1}
}
@article{gibson2009minimum,
  author = {Gibson, F. and Overton, P.G. and Smulders, T.V. and Schultz, S.R.
	and Eglen, S.J. and Ingram, C.D. and Panzeri, S. and Bream, P. and
	Whittington, M. and Sernagor, E. and others},
  title = {{Minimum Information about a Neuroscience Investigation (MINI) Electrophysiology}},
  year = {2009},
  hdl = {http://hdl.handle.net/10101/npre.2009.1720.2}
}
@inproceedings{HSL05XDDSyy,
  author = {Duncan Hull and Robert Stevens and Phillip Lord},
  title = {Describing Web Services for user-oriented retrieval},
  booktitle = {{W3C Workshop on Frameworks for Semantics in Web Services, Digital
	Enterprise Research Institute (DERI), Innsbruck, Austria. June 9-10,
	2005}},
  year = {2005},
  note = {see http://www.w3.org/2005/01/ws-swsf-cfp.html, http://www.w3.org/2005/04/FSWS/accepted-papers.html
	and http://www.w3.org/2005/04/FSWS/Submissions/52/DescribingWebServicesForUserOrientedRetrieval.pdf}
}
@inproceedings{HSL+04,
  author = {Duncan Hull and Robert Stevens and Phillip Lord and Chris Wroe and
	Carole Goble},
  title = {Treating shimantic web syndrome with ontologies},
  booktitle = {First AKT workshop on Semantic Web Services (AKT-SWS04) KMi, The
	Open University, Milton Keynes, UK. December 8, 2004},
  year = {2004},
  note = {Workshop proceedings CEUR-WS.org ISSN:1613-0073}
}
@misc{2008-03-riken,
  author = {Phillip Lord},
  title = {{Metadata for CARMEN}},
  howpublished = {RIKEN-CARMEN Joint Workshop on Developing Web Services for Neurophysiological
	data},
  ppt = {download/publications/08_03_phil_lord_riken_metadata_carmen.ppt}
}
@misc{sheffield-nlp-2006,
  author = {Phillip Lord},
  title = {The many uses for information content within bio-ontologies},
  howpublished = {Invited talk, NLP Group, University of Sheffield},
  month = {June},
  year = {2006},
  abstract = {The use of information content based measures have widespread applications
	for the analysis of text, but their use over ontologies or controlled
	vocabularies is less well known. I will describe the application
	of several of these measures, originally developed to enable textual
	analysis using WordNet, to the Gene Ontology -- the largest and most
	widely used ontology in biology. Initally, we have used these measures
	to answer a simple question: how similar is the knowledge about two
	proteins? The use of these measures have now become relatively widespread
	within bioinformatics. So I will finish by describing two new applications
	to biology which, we hope, we can answer with variations on these
	information content measures. },
  ppt = {download/publications/sheffield_2006_06_similarity.ppt}
}
@misc{img-sem-simil,
  author = {P. Lord},
  title = {Semantic Similarity:- Measuring Similarity across the {Gene Ontology}},
  howpublished = {IMG Internal Seminar},
  year = {2002},
  script = {download/publications/img_seminar_02_script.pdf},
  slides = {download/publications/img_seminar_02_talk.pdf}
}
@misc{swls2004,
  author = {Phillip Lord and Pinar Alper and Chris Wroe and Robert Stevens and
	Carole Goble and Jun Zhao and Duncan Hull and Mark Greenwood},
  title = {{The Semantic Web: Service discovery and provenance in myGrid}},
  howpublished = {Semantic Web for Life Sciences Workshop},
  month = {October},
  year = {2004},
  file = {semantic_web_for_life_sciences_position.pdf:semantic_web_for_life_sciences_position.pdf:PDF},
  slides = {download/publications/semantic_web_for_life_sciences_mygrid.ppt}
}
@misc{cns08_interoperability_metadata,
  author = {Phillip Lord and Frank Gibson and {the CARMEN Consortium}},
  title = {Sharing the knowledge of electrophysiology data},
  howpublished = {Workshop on Interoperability at CNS'08},
  month = {July},
  year = {2008},
  ppt = {download/publications/08_07_14_phil_lord_interoperability.ppt}
}
@article{cafg-7-bioont-review,
  author = {Phillip Lord and Robert Stevens},
  title = {{The seventh annual Bio-Ontologies meeting: Moat House Hotel, Glasgow,
	30 July 2004}},
  year = {2004},
  month = {December},
  link = {http://www3.interscience.wiley.com/cgi-bin/abstract/109860921/ABSTRACT}
}
@article{cafg-bioontreview2004,
  author = {Phillip Lord and Robert Stevens},
  title = {{ISMB 2003 bio-ontologies SIG and sixth annual bio-ontologies meeting
	report}},
  year = {2003},
  month = {December},
  link = {http://www3.interscience.wiley.com/cgi-bin/abstract/106569254/ABSTRACT}
}
@article{plos-bio-ont,
  author = {Phillip Lord and Robert Stevens and James A. Baker and Robin McEntire},
  title = {{The Eighth Annual Bio-Ontologies Meeting}},
  year = {2005},
  doi = {10.1371/journal.pcbi.0010077},
  link = {http://dx.doi.org/10.1371/journal.pcbi.0010077}
}
@misc{bio-ont-simil,
  author = {Phillip Lord and Robert Stevens and Andy Brass and Carole Goble},
  title = {{Semantic Similarity:- Measuring Similarity across the Gene Ontology.}},
  howpublished = {Fifth Annual Bio-Ontologies Meeting},
  year = {2002},
  inmem = {in-memoriam.html},
  link = {http://www.cs.man.ac.uk/~stevensr/meeting02/},
  script = {download/publications/bio-ont-02-script.pdf},
  slides = {download/publications/bio-ont-02-talk.pdf}
}
@misc{ismb-simil-poster,
  author = {Phillip Lord and Robert Stevens and Andy Brass and Carole Goble},
  title = {{Semantic Similiarity across the Gene Ontology: Relating Sequence
	to Annotation.}},
  howpublished = {ISMB: Poster},
  year = {2002},
  ppt = {download/publications/similarity-ismb.ms.ppt}
}
@misc{bosc-mygrid,
  author = {P. Lord and {The Mygrid Consortium}},
  title = {$^{my}$Grid:- Personalised biological services on the Grid.},
  howpublished = {BOSC 02},
  year = {2002},
  link = {http://www.open-bio.org/bosc2002/},
  script = {download/publications/bosc-2002-script.pdf},
  slides = {download/publications/bosc-2002-slides.pdf}
}
@inproceedings{kggi03semantic,
  author = {Phillip Lord and Chris Wroe and Robert Stevens and Carole Goble and
	Simon Miles and Luc Moreau and Keith Decker and Terry Payne and Juri
	Papay},
  title = {{Semantic and Personalised Service Discovery}},
  booktitle = {WI/IAT 2003 Workshop on Knowledge Grid and Grid Intelligence},
  year = {2003},
  editor = {W. K. Cheung and Y. Ye},
  address = {Halifax, Canada},
  month = oct,
  file = {WIKGGI03Semantic.pdf:WIKGGI03Semantic.pdf:PDF},
  isbn = {0-9734039-0-X}
}
@inproceedings{Moreau:NETTAB2002,
  author = {Luc Moreau and Simon Miles and Carole Goble and Mark Greenwood and
	Vijay Dialani and Matthew Addis and Nedim Alpdemir and Rich Cawley
	and David De Roure and Justin Ferris and Rob Gaizauskas and Kevin
	Glover and Chris Greenhalgh and Mark Greenwood and Peter Li and Xiaojian
	Liu and Phillip Lord and Michael Luck and Darren Marvin and Tom Oinn
	and Norman Paton and Stephen Pettifer and Milena V Radenkovic and
	Angus Roberts and Alan Robinson and Tom Rodden and Martin Senger
	and Nick Sharman and Robert Stevens and Brian Warboys and Paul Watson
	and Chris Wroe},
  title = {{On the Use of Agents in a BioInformatics Grid}},
  booktitle = {Network Tools and Applications in Biology (NETTAB'2002) --- Agents
	in Bioinformatics},
  year = {2002},
  address = {Bologna, Italy},
  month = jul,
  abstract = {MyGrid is an e-Science Grid project that aims to help biologists and
	bioinformaticians to perform workflow-based {\em in silico\/} experiments,
	and help to automate the management of such workflows through personalisation,
	notification of change and publication of experiments. In this paper,
	we describe the architecture of myGrid and how it will be used by
	the scientist. We then show how myGrid can benefit from agents technologies.
	We have identified three key uses of agent technologies in myGrid:
	{\em user agents\/}, able to customize and personalise data, {\em
	agent communication languages\/} offering a generic and portable
	communication medium, and {\em negotiation\/} allowing multiple distributed
	entities to reach service level agreements.},
  export = {yes},
  mygrid = {yes},
  url = {http://www.ecs.soton.ac.uk/~lavm/papers/nettab.ps}
}
@misc{reconciling-liepzig2004,
  author = {Robert Stevens and Sean Bechhofer and Ulrike Sattler and Phillip
	Lord},
  title = {{Reconciling the Semantics of DAG and OWL ontology representations}},
  howpublished = {The Formal Architecture of the Gene Ontology, Leipzig},
  year = {2004},
  file = {go-semantics5.pdf:go-semantics5.pdf:PDF}
}
@misc{owled26-public-knowledge,
  author = {Robert Stevens and Phillip Lord and Andrew Gibson},
  title = {Something Nasty in the Woodshed: The Public Knowledge Model},
  howpublished = {Proceedings of the OWLED*06 Workshop on OWL: Experiences and Directions},
  year = {2006},
  file = {owled_06_public_knowledge_model.pdf:owled_06_public_knowledge_model.pdf:PDF},
  link = {http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS//Vol-216/}
}
@misc{mygrid-ismb-poster-03,
  author = {Robert Stevens and Phillip Lord and Tom Oinn and Peter Li},
  title = {Performing \textit{in silico} experiments on the {Grid} using $^{my}$Grid},
  howpublished = {ISMB: Poster},
  year = {2003},
  ppt = {download/publications/mygrid-ismb03.ms.ppt}
}
@misc{instance-store-ismb-2004,
  author = {Daniele Turi and Phillip Lord and Michael Bada and Robert Stevens},
  title = {Storing and Retrieving Biological Instances with the Instance Store},
  howpublished = {ISMB: Poster},
  year = {2004},
  ppt = {download/publications/ismb_2004_instance_store_poster.ppt}
}

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