journal_papers.out.bib
@article{10.1093/bioadv/vbae057,
author = {Ross, Karen E and Bastian, Frederic B and Buys, Matt
and Cook, Charles E and D’Eustachio, Peter and
Harrison, Melissa and Hermjakob, Henning and Li,
Donghui and Lord, Phillip and Natale, Darren A and
Peters, Bjoern and Sternberg, Paul W and Su, Andrew
I and Thakur, Matthew and Thomas, Paul D and
Bateman, Alex and and the UniProt Consortium },
title = {{Perspectives on tracking data reuse across biodata
resources}},
journal = {Bioinformatics Advances},
volume = 4,
number = 1,
pages = {vbae057},
year = 2024,
month = 04,
abstract = {{Data reuse is a common and vital practice in
molecular biology and enables the knowledge gathered
over recent decades to drive discovery and
innovation in the life sciences. Much of this
knowledge has been collated into molecular biology
databases, such as UniProtKB, and these resources
derive enormous value from sharing data among
themselves. However, quantifying and documenting
this kind of data reuse remains a challenge.The
article reports on a one-day virtual workshop hosted
by the UniProt Consortium in March 2023, attended by
representatives from biodata resources, experts in
data management, and NIH program managers. Workshop
discussions focused on strategies for tracking data
reuse, best practices for reusing data, and the
challenges associated with data reuse and
tracking. Surveys and discussions showed that data
reuse is widespread, but critical information for
reproducibility is sometimes lacking. Challenges
include costs of tracking data reuse, tensions
between tracking data and open sharing, restrictive
licenses, and difficulties in tracking commercial
data use. Recommendations that emerged from the
discussion include: development of standardized
formats for documenting data reuse, education about
the obstacles posed by restrictive licenses, and
continued recognition by funding agencies that data
management is a critical activity that requires
dedicated resources.Summaries of survey results are
available at:
https://docs.google.com/forms/d/1j-VU2ifEKb9C-sW6l3ATB79dgHdRk5v\_lESv2hawnso/viewanalytics
(survey of data providers) and
https://docs.google.com/forms/d/18WbJFutUd7qiZoEzbOytFYXSfWFT61hVce0vjvIwIjk/viewanalytics
(survey of users). }},
issn = {2635-0041},
doi = {10.1093/bioadv/vbae057},
url = {https://doi.org/10.1093/bioadv/vbae057},
eprint = {https://academic.oup.com/bioinformaticsadvances/article-pdf/4/1/vbae057/57445755/vbae057.pdf}
}
@article{10.7717/peerj.15352,
title = {Tolerogenic dendritic cell reporting: Has a minimum
information model made a difference?},
author = {Sahar, Ayesha and Nicorescu, Ioana and Barran,
Gabrielle and Paterson, Megan and Hilkens, Catharien
M.U. and Lord, Phillip},
year = 2023,
month = may,
keywords = {Tolerogenic dendritic cell, Cell therapy, Minimum
information model, Reporting guidelines,
Standardised data reporting, Open data sharing,
Metadata sharing, FAIR data},
abstract = { Minimum information models are reporting frameworks
that describe the essential information that needs
to be provided in a publication, so that the work
can be repeated or compared to other work. In 2016,
Minimum Information about Tolerogenic
Antigen-Presenting cells (MITAP) was created to
standardize the reporting on tolerogenic
antigen-presenting cells, including tolerogenic
dendritic cells (tolDCs). tolDCs is a generic term
for dendritic cells that have the ability to
(re-)establish immune tolerance; they have been
developed as a cell therapy for autoimmune diseases
or for the prevention of transplant
rejection. Because protocols to generate these
therapeutic cells vary widely, MITAP was deemed to
be a pivotal reporting tool by and for the tolDC
community. In this paper, we explored the impact
that MITAP has had on the tolDC field. We did this
by examining a subset of the available literature on
tolDCs. Our analysis shows that MITAP is used in
only the minority of relevant papers (14%), but
where it is used the amount of metadata available is
slightly increased over where it is not. From this,
we conclude that MITAP has been a partial success,
but that much more needs to be done if standardized
reporting is to become common within the discipline.
},
volume = 11,
pages = {e15352},
journal = {PeerJ},
issn = {2167-8359},
url = {https://doi.org/10.7717/peerj.15352},
doi = {10.7717/peerj.15352}
}
@article{doi:10.1111/eva.12851,
author = {O'Keefe, Hannah and Queen, Rachel and Lord, Phillip
and Elson, Joanna L.},
title = {What can a comparative genomics approach tell us
about the pathogenicity of mtDNA mutations in human
populations?},
journal = {Evolutionary Applications},
volume = {0},
number = {0},
pages = {},
keywords = {comparative genomics, haplogroup, mitochondrial
disease, mtDNA},
doi = {10.1111/eva.12851},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.12851},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.12851},
abstract = {Abstract Mitochondrial disorders are heterogeneous,
showing variable presentation and penetrance. Over
the last three decades, our ability to recognize
mitochondrial patients and diagnose these mutations,
linking genotype to phenotype, has greatly
improved. However, it has become increasingly clear
that these strides in diagnostics have not benefited
all population groups. Recent studies have
demonstrated that patients from genetically
understudied populations, in particular those of
black African heritage, are less likely to receive a
diagnosis of mtDNA disease. It has been suggested
that haplogroup context might influence the
presentation and penetrance of mtDNA disease; thus,
the spectrum of mutations that are associated with
disease in different populations. However, to date
there is only one well-established example of such
an effect: the increased penetrance of two Leber's
hereditary optic neuropathy mutations on a
haplogroup J background. This paper conducted the
most extensive investigation to date into the
importance of haplogroup context on the
pathogenicity of mtDNA mutations. We searched for
proven human point mutations across 726 multiple
sequence alignments derived from 33 non-human
species absent of disease. A total of 58 pathogenic
point mutations arise in the sequences of these
species. We assessed the sequence context and found
evidence of population variants that could modulate
the phenotypic expression of these point mutations
masking the pathogenic effects seen in humans. This
supports the theory that sequence context is
influential in the presentation of mtDNA disease and
has implications for diagnostic practices. We have
shown that our current understanding of the
pathogenicity of mtDNA point mutations, primarily
built on studies of individuals with haplogroups
HVUKTJ, will not present a complete picture. This
will have the effect of creating a diagnostic
inequality, whereby individuals who do not belong to
these lineages are less likely to receive a genetic
diagnosis.}
}
@article{doi:10.1021/acssynbio.8b00532,
author = {Mısırlı, Göksel and Taylor, Renee and Goñi-Moreno,
Angel and McLaughlin, James Alastair and Myers,
Chris and Gennari, John H. and Lord, Phillip and
Wipat, Anil},
title = {SBOL-OWL: An Ontological Approach for Formal and
Semantic Representation of Synthetic Biology
Information},
journal = {ACS Synthetic Biology},
volume = 8,
number = 7,
pages = {1498-1514},
year = 2019,
doi = {10.1021/acssynbio.8b00532},
note = {PMID: 31059645},
url = {https://doi.org/10.1021/acssynbio.8b00532},
eprint = {https://doi.org/10.1021/acssynbio.8b00532}
}
@article{STEVENS2018,
title = {Measuring expert performance at manually classifying
domain entities under upper ontology classes},
journal = {Journal of Web Semantics},
arxiv = {http://arxiv.org/abs/1810.05093},
year = 2018,
issn = {1570-8268},
doi = {https://doi.org/10.1016/j.websem.2018.08.004},
url = {http://www.sciencedirect.com/science/article/pii/S157082681830043X},
author = {Robert Stevens and Phillip Lord and James Malone and
Nicolas Matentzoglu},
keywords = {OWL, Ontologies, Upper ontologies, Ontology
engineering, Empirical study},
abstract = {Background: Classifying entities in domain
ontologies under upper ontology classes is a
recommended task in ontology engineering to
facilitate semantic interoperability and modelling
consistency. Integrating upper ontologies this way
is difficult and, despite emerging automated
methods, remains a largely manual task. Problem:
Little is known about how well experts perform at
upper ontology integration. To develop
methodological and tool support, we first need to
understand how well experts do this task. We
designed a study to measure the performance of human
experts at manually classifying classes in a general
knowledge domain ontology with entities in the Basic
Formal Ontology (BFO), an upper ontology used widely
in the biomedical domain. Method: We recruited 8
BFO experts and asked them to classify 46 commonly
known entities from the domain of travel with BFO
entities. The tasks were delivered as part of a web
survey. Results: We find that, even for a well
understood general knowledge domain such as travel,
the results of the manual classification tasks are
highly inconsistent: the mean agreement of the
participants with the classification decisions of an
expert panel was only 51\%, and the inter-rater
agreement using Fleiss’ Kappa was merely moderate
(0.52). We further follow up on the conjecture that
the degree of classification consistency is
correlated with the frequency the respective BFO
classes are used in practice and find that this is
only true to a moderate degree (0.52, Pearson).
Conclusions: We conclude that manually classifying
domain entities under upper ontology classes is
indeed very difficult to do correctly. Given the
importance of the task and the high degree of
inconsistent classifications we encountered, we
further conclude that it is necessary to improve the
methodological framework surrounding the manual
integration of domain and upper ontologies.}
}
@article{OKeefe2018,
author = {O'Keefe, Hannah and Queen, Rachel A. and Meldau,
Surita and Lord, Phillip and Elson, Joanna L.},
title = {Haplogroup Context is Less Important in the
Penetrance of Mitochondrial DNA Complex I Mutations
Compared to mt-tRNA Mutations},
journal = {Journal of Molecular Evolution},
year = {2018},
month = {Jul},
day = {09},
abstract = {Mitochondrial diseases are a highly complex,
heterogeneous group of disorders. Mitochondrial DNA
variants that are linked to disease can exhibit
variable expression and penetrance. This has an
implication for mitochondrial diagnostics as
variants that cause disease in one individual may
not in another. It has been suggested that the
sequence context in which a variant arises could
influence the genotype--phenotype
relationship. However, the consequence of sequence
variation between different haplogroups on the
expression of disease is not well
understood. European haplogroups are the most widely
studied. To ensure accurate diagnostics for patients
globally, we first need to understand how, if at
all, the sequence context in which a variant arises
contributes to the manifestion of disease. To help
us understand this, we used 2752 sequences from 33
non-human species that do not have disease. We
searched for variants in the seven complex I genes
that are associated with disease in humans. Our
findings indicate that only three reported
pathogenic complex I variants have arisen in these
species. More importantly, only one of these,
m.3308T>C, has arisen with its associated amino acid
change in the studied non-human species. With the
status of m.3308T>C as a disease causing variant
being a matter of debate. This is a stark contrast
to previous findings in the mitochondrial tRNA genes
and suggests that sequence context may be less
important in the complex I genes. This information
will help us improve the identification and
diagnosis of mitochondrial DNA variants in
non-European populations.},
issn = {1432-1432},
doi = {10.1007/s00239-018-9855-7},
url = {https://doi.org/10.1007/s00239-018-9855-7}
}
@article{on_patterns_and_reuse,
url = {https://arxiv.org/abs/1705.08730},
title = {On Patterns and Re-Use in Bioinformatics Databases},
journal = {Bioinformatics},
volume = {33},
number = {17},
pages = {2731-2736},
year = {2017},
doi = {10.1093/bioinformatics/btx310},
arxiv = {http://arxiv.org/abs/\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}
}
@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,
pages = {e2300},
journal = {PeerJ},
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},
journal = {ACS Synthetic Biology},
number = {ja},
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},
journal = {Mediators of Inflammation},
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},
journal = {PLoS ONE},
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},
pages = {e75541},
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
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,
journal = {Bioinformatics},
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},
journal = {Future Internet},
volume = 4,
year = 2012,
number = 4,
pages = {1004--1015},
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}},
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{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}},
journal = {Bioinformatics},
volume = {28},
number = {18},
pages = {i562-i568},
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},
journal = {Journal of Biomedical Semantics},
year = {2010},
volume = {1},
pages = {S7},
number = {Suppl 1},
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}},
journal = {Nat Biotech},
year = {2008},
volume = {26},
pages = {541--547},
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}},
journal = {OMICS: A Journal of Integrative Biology},
year = {2009},
volume = {13},
pages = {239-251},
number = {3},
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{lister_2010,
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},
year = {2010},
volume = {1},
pages = {S3},
number = {Suppl 1},
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}},
journal = {Journal of Biomedical Semantics},
year = {2010},
volume = {1},
pages = {S4},
number = {Suppl 1},
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},
journal = {PLoS One},
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.},
journal = {Bioinformatics},
year = {2003},
volume = {19},
pages = {1275-83},
number = {10},
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},
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},
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},
journal = {PLoS Comput Biol},
year = {2009},
volume = {5},
pages = {e1000443},
number = {7},
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},
journal = {Progress in Biophysics and Molecular Biology},
year = {2011},
volume = {107},
pages = {4 - 10},
number = {1},
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}},
journal = {Comparative and Functional Genomics},
year = {2003},
volume = {4},
number = {1},
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.}},
journal = {Nat Biotechnol},
year = {2008},
volume = {26},
pages = {889--896},
number = {8},
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},
journal = {Bioinformatics},
year = {2011},
volume = {27},
pages = {1299-1306},
number = {9},
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}},
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},
pdf = {download/publications/handbook2.pdf}
}
@incollection{distributed_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-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,
pages = {635-657}
}
conference_papers.out.bib
@inproceedings{arguello2023,
author = {Casteleiro Arguello and N Joyce and N Maroto and Prieto
Fernandez and T Furmston and Fernandez Maseda and P Lord and C
Wroe and J Keane and Y Cheong and R Stevens},
title = {Text‐based phenotyping with Semantic Deep Learning: setting up experiments for women's health},
booktitle = {14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences 2023},
year = 2023,
url = {https://ceur-ws.org/Vol-3415/paper-39.pdf}
}
@inproceedings{horned-owl-2021,
author = {Phillip Lord and Jennifer Warrender},
title = {Horned-OWL: Building Ontologies at Big Data Scale},
booktitle = {International Conference on Biomedical Ontologies},
year = 2021,
url = {https://ceur-ws.org/Vol-3073/paper20.pdf}
}
@misc{online_conference_2021,
author = {GE de Blaquière and Phillip Lord},
title = {Evidence and reflections on organising a large
online multi-track research student conference
across the science and engineering disciplines},
journal = {UK Council for Graduate Education - Annual
Conference},
year = 2021
}
@inproceedings{10.1145/3372356.3372367,
author = {Barnes, J. and Colquhoun, J. and Devlin, M. and
Heels, L. and Lord, P. and Marshall, L. and Napier,
C. and Solaiman, E. and Speirs, N. and Talbot,
L. and Ushaw, G. and Witty, C.},
title = {Designing a Portfolio-Oriented Curriculum Using
Problem Based Learning},
year = {2020},
isbn = {9781450377294},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
url = {https://doi.org/10.1145/3372356.3372367},
doi = {10.1145/3372356.3372367},
abstract = {With an ever-growing demand on teaching resources,
and with student numbers on the increase, can we
develop a curriculum that is appealing and engaging
to the student? In this paper we present our
experience of creating a new undergraduate CS
programme which focuses on problem-based learning
and formative assessment. We outline our curriculum
design process from the initial stages to
implementation. The new curriculum has a reduced
emphasis on summative assessment and introduces the
use of programming portfolios so students can
graduate with concrete samples of their technical
and reflective work to show employers.We also
present results from a survey conducted with two
cohorts of first year undergraduate students. The
results illustrate the trends and differences
between student perceptions of their skills. We then
discuss how we have designed the new curriculum to
incorporate student feedback and address
concerns.This academic year rolled out the new
curriculum to our Stage 1 students, and are working
on the new Stage 2 and 3 implementation. Results
discussed in this paper include: some tips for best
practice when undertaking a whole curriculum change
and a discussion of the mistakes we made and lessons
learned. We also detail aspects of our new design
and how we support students and allow them to build
on their previous experiences.},
booktitle = {Proceedings of the 4th Conference on Computing
Education Practice},
articleno = {11},
numpages = {4},
keywords = {Portfolio, Assessment, Curriculum Design, Problem
based learning},
location = {Durham, United Kingdom},
series = {CEP '20}
}
@inproceedings{hyper,
url = {https://arxiv.org/abs/1711.07273},
canonicaluri = {\url{https://arxiv.org/abs/1711.07273}},
title = {Facets, Tiers and Gems: Ontology Patterns for Hypernormalisation},
booktitle = {International Conference on Biomedical Ontologies},
year = 2017,
author = {Phillip Lord and Robert Stevens}
}
@inproceedings{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},
booktitle = {International Conference on Biomedical Ontologies},
year = {2017},
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},
link = {http://www.russet.org.uk/blog/3178}
}
@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},
volume = {1692},
pages = {1--6},
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},
journal = {Semantic Web for Life Sciences},
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,
journal = {International Conference on Biomedical Ontology (ICBO)},
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}},
journal = {Bio-Ontologies 2015},
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},
journal = {Proceedings of the 2nd Workshop on Semantic Publishing},
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}},
journal = {Bio-Ontologies 2013},
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},
journal = {{OWLED 2013}},
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},
journal = {SePublica},
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},
journal = {SePublica},
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)}},
journal = {ArXiv e-prints},
archiveprefix = {arXiv},
eprint = {1103.4749},
primaryclass = {cs.SE},
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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.
