journal_papers.out.bib
@article{Quinn20114,
title = {Minimum Information about a Cardiac Electrophysiology
Experiment (MICEE): Standardised reporting for model
reproducibility, interoperability, and data sharing},
journal = {Progress in Biophysics and Molecular Biology},
volume = 107,
number = 1,
pages = {4 - 10},
year = 2011,
issn = {0079-6107},
doi = {10.1016/j.pbiomolbio.2011.07.001},
url = {http://www.sciencedirect.com/science/article/pii/S0079610711000642},
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},
keywords = {Minimum Information Standard},
keywords = {Cardiac electrophysiology},
keywords = {Data sharing},
keywords = {Reproducibility},
keywords = {Integration},
keywords = {Computational modelling},
pdf = {MICEE_manuscript.pdf}
}
@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},
volume = 27,
number = 9,
pages = {1299-1306},
year = 2011,
doi = {10.1093/bioinformatics/btr134},
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.},
url = {http://bioinformatics.oxfordjournals.org/content/27/9/1299.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/27/9/1299.full.pdf+html},
journal = {Bioinformatics}
}
@article{reality_in_biology_2010,
author = {Phillip Lord and Robert Stevens},
title = {Adding a little reality to building ontologies for biology},
journal = {PLoS One},
year = 2010,
annote = {In Press},
pdf = {download/publications/realism_and_science.pdf},
doi = {10.1371/journal.pone.0012258},
url = {http://dx.plos.org/10.1371/journal.pone.0012258},
blog = {http://www.russet.org.uk/blog/2010/07/realism-and-science/}
}
@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},
journal = {Journal of Biomedical Semantics},
volume = 1,
year = 2010,
number = {Suppl 1},
pages = {S3},
url = {http://www.jbiomedsem.com/content/1/S1/S3},
doi = {10.1186/2041-1480-1-S1-S3},
issn = {2041-1480}
}
@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},
journal = {Journal of Biomedical Semantics},
volume = 1,
year = 2010,
number = {Suppl 1},
pages = {S7},
url = {http://www.jbiomedsem.com/content/1/S1/S7},
doi = {10.1186/2041-1480-1-S1-S7},
issn = {2041-1480}
}
@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},
journal = {OMICS: A Journal of Integrative Biology},
volume = 13,
number = 3,
pages = {239-251},
year = 2009,
doi = {10.1089/omi.2008.0080},
note = {PMID: 19441879},
url = {http://www.liebertonline.com/doi/abs/10.1089/omi.2008.0080},
eprint = {http://www.liebertonline.com/doi/pdf/10.1089/omi.2008.0080}
}
@article{evolfunjbs,
author = {Lord, Phillip},
title = {{An evolutionary approach to Function}},
journal = {Journal of Biomedical Semantics},
volume = 1,
year = 2010,
number = {Suppl 1},
pages = {S4},
url = {http://www.jbiomedsem.com/content/1/S1/S4},
doi = {10.1186/2041-1480-1-S1-S4},
issn = {2041-1480}
}
@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}},
journal = {BMC Bioinformatics},
year = {2007},
volume = {8},
pages = {57},
number = {1},
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}},
journal = {Journal of Web Semantics},
year = {2006},
volume = {4},
pages = {155-63},
number = {3},
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{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}},
journal = {Nat Biotech},
year = {2008},
volume = {26},
pages = {541--547},
month = {May},
note = {10.1038/nbt1360},
day = {xx},
issn = {1087-0156},
issue = {5},
keywords = {genome},
doi = {10.1038/nbt1360},
url = {http://dx.doi.org/10.1038/nbt1360}
}
@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.},
journal = {Bioinformatics},
year = {2003},
volume = {19},
pages = {1275-83},
number = {10},
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},
journal = {Briefings in Bioinformatics},
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},
journal = {Concurrency and Computation: Practice and Experience Grid Workflow},
year = {2005},
volume = {18},
pages = {1067 - 1100},
number = {10},
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},
journal = {Bioinformatics},
year = {2002},
volume = {18},
pages = {1402-03},
number = {10},
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},
journal = {PLoS Comput Biol},
year = {2009},
volume = {5},
pages = {e1000443},
number = {7},
month = {07},
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{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}},
journal = {Comparative and Functional Genomics},
year = {2003},
volume = {4},
number = {1},
link = {http://www3.interscience.wiley.com/cgi-bin/issuetoc?ID=102531153}
}
@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.}},
journal = {Nat Biotechnol},
year = {2008},
volume = {26},
pages = {889--896},
number = {8},
month = {Aug},
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{wolstencroftetal2006,
author = {Wolstencroft, K. and Lord, P. and Tabernero, L. and Brass, A. and
Stevens, R.},
title = {{Protein classification using ontology classification}},
journal = {Bioinformatics},
year = {2006},
volume = {22},
pages = {e530-538},
number = {14},
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.},
journal = {IEEE Intelligent Systems},
year = {2004},
volume = {19},
pages = {48-55},
number = {1},
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},
pages = {99-140},
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},
url = {http://www.cs.man.ac.uk/~stevensr/papers/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,
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}
}
@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},
title = {Ontologies in Bioinformatics},
publisher = {Springer},
year = 2003,
pages = {635-657}
}
conference_papers.out.bib
@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)}},
journal = {ArXiv e-prints},
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
}
@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},
pages = {3--14},
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},
pages = {135-141},
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},
pages = {788-795},
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},
pages = {768-775},
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,
pages = {323-337},
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},
pages = {786-800},
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,
pages = {578-591},
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,
pages = {17-31},
link = {http://dx.doi.org/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.},
pages = {79--90},
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,
pages = {350-364},
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},
pages = {i303-310},
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}},
pages = {787-794},
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 = {Internaional Semantic Web Conference},
year = 2003,
pdf = {download/publications/cooking03.pdf},
pages = {659 - 675},
link = {http://www.springerlink.com/app/home/contribution.asp?wasp=acecbdavyg2rwj96ekdw&referrer=parent&backto=issue,42,58;journal,48,1408;linkingpublicationresults,id:105633,1}
}
@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},
pages = {601-612},
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,
pages = {622-629},
publisher = {EPSRC},
pdf = {download/publications/workflow_recycle_all_hands_2005.pdf},
link = {http://www.allhands.org.uk/2004/proceedings/papers/218.pdf}
}
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@misc{dl-kblog,
title = {Data Linking with Knowledge-Blogging},
howpublished = {JISC},
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}
@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}
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@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
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@inproceedings{multiple2011,
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title = {OWLED 2011 OWL: Experiences and Directions},
year = 2011,
link = {http://www.webont.org/owled/2011/}
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title = {International Conference on Biomedical Ontology: ICBO 2011},
year = 2011,
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title = {The Future of the Web for Collaborative Science, 2010},
year = 2010,
link = {http://esw.w3.org/topic/HCLS/WWW2010/Workshop}
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title = {First Workshop on the Semantics of Visual Objects},
year = 2010,
link = {http://semanticscience.org/workshop/semvo2010/}
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@proceedings{ismb2007,
title = {Intelligent Systems for Molecular Biology (ISMB)},
year = 2007,
link = {http://bioinformatics.oxfordjournals.org/content/vol23/issue13/}
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@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}
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@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{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{webdim4ls,
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{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}},
journal = {Nature Precedings},
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}},
journal = {Comparative and Functional Genomics},
year = {2004},
volume = {5},
pages = {498-500},
number = {6},
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}},
journal = {Comparative and Functional Genomics},
year = {2003},
volume = {4},
pages = {663-666},
number = {6},
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}},
journal = {{PLoS} Computational Biology},
year = {2005},
volume = {1},
pages = {e77},
number = {7},
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},
pages = {100--107},
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}
}
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