Dr. Allyson Lister

Research Associate

I am a Research Associate for the ARIES project at Newcastle University School for Computing Science. I am currently working on the data integration aspect of the project, which aims to integrate datasets from ALSPAC (Avon Longitudinal Study of Parents and Children) with publicly available datasets.

I received my PhD from the School for Computing Science at Newcastle University, my Master’s degree in Bioinformatics from the University of York and my undergraduate degree in Biology and Ancient Mediterranean Civilizations from Rice University.

Prior to the ARIES project, I was a member of the Centre for Integrated Systems Biology of Ageing and Nutrition (CISBAN) at Newcastle. Recently, I have also worked for Robert Stevens at the University of Manchester on the Software Ontology. Before working at Newcastle University, I spent 6 1/2 years as part of the UniProt team at the European Bioinformatics Institute.

Please note that, while all social media links on this page deal primarily with my research areas, they are linked to my personal accounts and do not necessarily reflect the position or opinions of Newcastle University.

Research Interests

  • Ontologies
  • Semantic Data Integration
  • Data visualisation
  • Epigenomics
  • Systems Biology

Publications

  • [DOI] A. Bandrowski, R. Brinkman, M. Brochhausen, M. H. Brush, B. Bug, M. C. Chibucos, K. Clancy, M. Courtot, D. Derom, M. Dumontier, L. Fan, J. Fostel, G. Fragoso, F. Gibson, A. Gonzalez-Beltran, M. A. Haendel, Y. He, M. Heiskanen, T. Hernandez-Boussard, M. Jensen, Y. Lin, A. L. Lister, P. Lord, J. Malone, E. Manduchi, M. McGee, N. Morrison, J. A. Overton, H. Parkinson, B. Peters, P. Rocca-Serra, A. Ruttenberg, S. Sansone, R. H. Scheuermann, D. Schober, B. Smith, L. N. Soldatova, C. J. Stoeckert, C. F. Taylor, C. Torniai, J. A. Turner, R. Vita, P. L. Whetzel, and J. Zheng, “The ontology for biomedical investigations,” Plos one, vol. 11, iss. 4, p. e0154556+, 2016.
    [Bibtex]
    @article{citeulike:14025790,
    abstract = {The Ontology for Biomedical Investigations ({OBI}) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. {OBI} re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies ({OBO}) project and adds the ability to describe how this knowledge was derived. We here describe the state of {OBI} and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. {OBI} covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to {OBI}, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. {OBI} has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as {GO}, Chemical Entities of Biological Interest ({ChEBI}) and Phenotype Attribute and Trait Ontology ({PATO}) without altering their meaning. {OBI} is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. {OBI} has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term ({MIREOT})). The {OBI} project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, {OBI} has created 2366 classes and 40 relations along with textual and formal definitions. The {OBI} Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with {OBI}. The current release of {OBI} is available at http://purl.obolibrary.org/obo/obi.owl.},
    author = {Bandrowski, Anita and Brinkman, Ryan and Brochhausen, Mathias and Brush, Matthew H. and Bug, Bill and Chibucos, Marcus C. and Clancy, Kevin and Courtot, M\'{e}lanie and Derom, Dirk and Dumontier, Michel and Fan, Liju and Fostel, Jennifer and Fragoso, Gilberto and Gibson, Frank and Gonzalez-Beltran, Alejandra and Haendel, Melissa A. and He, Yongqun and Heiskanen, Mervi and Hernandez-Boussard, Tina and Jensen, Mark and Lin, Yu and Lister, Allyson L. and Lord, Phillip and Malone, James and Manduchi, Elisabetta and McGee, Monnie and Morrison, Norman and Overton, James A. and Parkinson, Helen and Peters, Bjoern and Rocca-Serra, Philippe and Ruttenberg, Alan and Sansone, Susanna-Assunta and Scheuermann, Richard H. and Schober, Daniel and Smith, Barry and Soldatova, Larisa N. and Stoeckert, Christian J. and Taylor, Chris F. and Torniai, Carlo and Turner, Jessica A. and Vita, Randi and Whetzel, Patricia L. and Zheng, Jie},
    citeulike-article-id = {14025790},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0154556},
    day = {29},
    doi = {10.1371/journal.pone.0154556},
    issn = {1932-6203},
    journal = {PLOS ONE},
    keywords = {ontologies, owl},
    month = apr,
    number = {4},
    pages = {e0154556+},
    posted-at = {2016-05-11 12:16:29},
    priority = {0},
    publisher = {Public Library of Science},
    title = {The Ontology for Biomedical Investigations},
    url = {http://dx.doi.org/10.1371/journal.pone.0154556},
    volume = {11},
    year = {2016}
    }
  • [DOI] P. McQuilton, A. Gonzalez-Beltran, P. Rocca-Serra, M. Thurston, A. Lister, E. Maguire, and S. Sansone, “BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences,” Database, vol. 2016, p. baw075+, 2016.
    [Bibtex]
    @article{citeulike:14037243,
    abstract = {{BioSharing} (http://www.biosharing.org) is a manually curated, searchable portal of three linked registries. These resources cover standards (terminologies, formats and models, and reporting guidelines), databases, and data policies in the life sciences, broadly encompassing the biological, environmental and biomedical sciences. Launched in 2011 and built by the same core team as the successful {MIBBI} portal, {BioSharing} harnesses community curation to collate and cross-reference resources across the life sciences from around the world. {BioSharing} makes these resources findable and accessible (the core of the {FAIR} principle). Every record is designed to be interlinked, providing a detailed description not only on the resource itself, but also on its relations with other life science infrastructures. Serving a variety of stakeholders, {BioSharing} cultivates a growing community, to which it offers diverse benefits. It is a resource for funding bodies and journal publishers to navigate the metadata landscape of the biological sciences; an educational resource for librarians and information advisors; a publicising platform for standard and database developers/curators; and a research tool for bench and computer scientists to plan their work. {BioSharing} is working with an increasing number of journals and other registries, for example linking standards and databases to training material and tools. Driven by an international Advisory Board, the {BioSharing} user-base has grown by over 40\% (by unique {IP} address), in the last year thanks to successful engagement with researchers, publishers, librarians, developers and other stakeholders via several routes, including a joint {RDA}/Force11 working group and a collaboration with the International Society for Biocuration. In this article, we describe {BioSharing}, with a particular focus on community-led curation.},
    author = {McQuilton, Peter and Gonzalez-Beltran, Alejandra and Rocca-Serra, Philippe and Thurston, Milo and Lister, Allyson and Maguire, Eamonn and Sansone, Susanna-Assunta},
    citeulike-article-id = {14037243},
    citeulike-linkout-0 = {http://dx.doi.org/10.1093/database/baw075},
    citeulike-linkout-1 = {http://database.oxfordjournals.org/content/2016/baw075.abstract},
    citeulike-linkout-2 = {http://database.oxfordjournals.org/content/2016/baw075.full.pdf},
    day = {01},
    doi = {10.1093/database/baw075},
    issn = {1758-0463},
    journal = {Database},
    month = jan,
    pages = {baw075+},
    posted-at = {2016-05-18 10:38:44},
    priority = {0},
    publisher = {Oxford University Press},
    title = {{BioSharing}: curated and crowd-sourced metadata standards, databases and data policies in the life sciences},
    url = {http://dx.doi.org/10.1093/database/baw075},
    volume = {2016},
    year = {2016}
    }
  • [DOI] C. L. Relton, T. Gaunt, W. McArdle, K. Ho, A. Duggirala, H. Shihab, G. Woodward, O. Lyttleton, D. M. Evans, W. Reik, Y. Paul, G. Ficz, S. E. Ozanne, A. Wipat, K. Flanagan, A. Lister, B. T. Heijmans, S. M. Ring, and G. D. Smith, “Data resource profile: accessible resource for integrated epigenomic studies (ARIES),” International journal of epidemiology, vol. 44, iss. 4, pp. 1181-1190, 2015.
    [Bibtex]
    @article{citeulike:13620944,
    author = {Relton, Caroline L. and Gaunt, Tom and McArdle, Wendy and Ho, Karen and Duggirala, Aparna and Shihab, Hashem and Woodward, Geoff and Lyttleton, Oliver and Evans, David M. and Reik, Wolf and Paul, Yu-Lee and Ficz, Gabriella and Ozanne, Susan E. and Wipat, Anil and Flanagan, Keith and Lister, Allyson and Heijmans, Bastiaan T. and Ring, Susan M. and Smith, George D.},
    citeulike-article-id = {13620944},
    citeulike-linkout-0 = {http://dx.doi.org/10.1093/ije/dyv072},
    citeulike-linkout-1 = {http://ije.oxfordjournals.org/content/early/2015/05/22/ije.dyv072.full.abstract},
    citeulike-linkout-2 = {http://ije.oxfordjournals.org/content/early/2015/05/22/ije.dyv072.full.full.pdf},
    citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/25991711},
    citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=25991711},
    day = {01},
    doi = {10.1093/ije/dyv072},
    issn = {1464-3685},
    journal = {International Journal of Epidemiology},
    month = aug,
    number = {4},
    pages = {1181--1190},
    pmid = {25991711},
    posted-at = {2016-05-11 12:18:38},
    priority = {0},
    publisher = {Oxford University Press},
    title = {Data Resource Profile: Accessible Resource for Integrated Epigenomic Studies ({ARIES})},
    url = {http://dx.doi.org/10.1093/ije/dyv072},
    volume = {44},
    year = {2015}
    }
  • [DOI] J. Malone, A. Brown, A. L. Lister, J. Ison, D. Hull, H. Parkinson, and R. Stevens, “The software ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation,” Journal of biomedical semantics, vol. 5, iss. 1, p. 25+, 2014.
    [Bibtex]
    @article{citeulike:13207264,
    abstract = {{MotivationBiomedical} ontologists to date have concentrated on ontological descriptions of biomedical entities such as gene products and their attributes, phenotypes and so on. Recently, effort has diversified to descriptions of the laboratory investigations by which these entities were produced. However, much biological insight is gained from the analysis of the data produced from these investigations, and there is a lack of adequate descriptions of the wide range of software that are central to bioinformatics. We need to describe how data are analyzed for discovery, audit trails, provenance and {reproducibility.RESULTS}:The Software Ontology ({SWO}) is a description of software used to store, manage and analyze data. Input to the {SWO} has come from beyond the life sciences, but its main focus is the life sciences. We used agile techniques to gather input for the {SWO} and keep engagement with our users. The result is an ontology that meets the needs of a broad range of users by describing software, its information processing tasks, data inputs and outputs, data formats versions and so on. Recently, the {SWO} has incorporated {EDAM}, a vocabulary for describing data and related concepts in bioinformatics. The {SWO} is currently being used to describe software used in multiple biomedical {applications.CONCLUSION}:The {SWO} is another element of the biomedical ontology landscape that is necessary for the description of biomedical entities and how they were discovered. An ontology of software used to analyze data produced by investigations in the life sciences can be made in such a way that it covers the important features requested and prioritized by its users. The {SWO} thus fits into the landscape of biomedical ontologies and is produced using techniques designed to keep it in line with user's {needs.AVAILABILITY}:The Software Ontology is available under an Apache 2.0 license at http://theswo.sourceforge.net/; the Software Ontology blog can be read at http://softwareontology.wordpress.com.},
    author = {Malone, James and Brown, Andy and Lister, Allyson L. and Ison, Jon and Hull, Duncan and Parkinson, Helen and Stevens, Robert},
    citeulike-article-id = {13207264},
    citeulike-linkout-0 = {http://dx.doi.org/10.1186/2041-1480-5-25},
    doi = {10.1186/2041-1480-5-25},
    issn = {2041-1480},
    journal = {Journal of Biomedical Semantics},
    number = {1},
    pages = {25+},
    posted-at = {2016-05-11 12:21:22},
    priority = {0},
    title = {The Software Ontology ({SWO}): a resource for reproducibility in biomedical data analysis, curation and digital preservation},
    url = {http://dx.doi.org/10.1186/2041-1480-5-25},
    volume = {5},
    year = {2014}
    }
  • A. L. Lister, “Enhancing systems biology models through semantic data integration,” PhD Thesis, 2012.
    [Bibtex]
    @phdthesis{citeulike:14033181,
    author = {Lister, A. L.},
    citeulike-article-id = {14033181},
    citeulike-linkout-0 = {http://hdl.handle.net/10443/1419},
    posted-at = {2016-05-11 12:24:00},
    priority = {0},
    school = {Newcastle University},
    title = {Enhancing systems biology models through semantic data integration},
    url = {http://hdl.handle.net/10443/1419},
    year = {2012}
    }
  • [DOI] S. G. Addinall, E. Holstein, C. Lawless, M. Yu, K. Chapman, P. A. Banks, H. Ngo, L. Maringele, M. Taschuk, A. Young, A. Ciesiolka, A. L. Lister, A. Wipat, D. J. Wilkinson, and D. Lydall, “Quantitative fitness analysis shows that NMD proteins and many other protein complexes suppress or enhance distinct telomere cap defects,” Plos genet, vol. 7, iss. 4, p. e1001362+, 2011.
    [Bibtex]
    @article{citeulike:9114899,
    abstract = {To better understand telomere biology in budding yeast, we have performed systematic suppressor/enhancer analyses on yeast strains containing a point mutation in the essential telomere capping gene {CDC13} (cdc13-1) or containing a null mutation in the {DNA} damage response and telomere capping gene {YKU70} (yku70Δ). We performed Quantitative Fitness Analysis ({QFA}) on thousands of yeast strains containing mutations affecting telomere-capping proteins in combination with a library of systematic gene deletion mutations. To perform {QFA}, we typically inoculate 384 separate cultures onto solid agar plates and monitor growth of each culture by photography over time. The data are fitted to a logistic population growth model; and growth parameters, such as maximum growth rate and maximum doubling potential, are deduced. {QFA} reveals that as many as 5\% of systematic gene deletions, affecting numerous functional classes, strongly interact with telomere capping defects. We show that, while Cdc13 and Yku70 perform complementary roles in telomere capping, their genetic interaction profiles differ significantly. At least 19 different classes of functionally or physically related proteins can be identified as interacting with cdc13-1, yku70Δ, or both. Each specific genetic interaction informs the roles of individual gene products in telomere biology. One striking example is with genes of the nonsense-mediated {RNA} decay ({NMD}) pathway which, when disabled, suppress the conditional cdc13-1 mutation but enhance the null yku70Δ mutation. We show that the suppressing/enhancing role of the {NMD} pathway at uncapped telomeres is mediated through the levels of Stn1, an essential telomere capping protein, which interacts with Cdc13 and recruitment of telomerase to telomeres. We show that increased Stn1 levels affect growth of cells with telomere capping defects due to cdc13-1 and yku70Δ. {QFA} is a sensitive, high-throughput method that will also be useful to understand other aspects of microbial cell biology. Telomeres, specialized structures at the end of linear chromosomes, ensure that chromosome ends are not mistakenly treated as {DNA} double-strand breaks. Defects in the telomere cap contribute to ageing and cancer. In yeast, defects in telomere capping proteins can cause telomeres to behave like double-strand breaks. To better understand the telomere and responses to capping failure, we have combined a systematic yeast gene deletion library with mutations affecting important yeast telomere capping proteins, Cdc13 or Yku70. Quantitative Fitness Analysis ({QFA}) was used to accurately measure the fitness of thousands of different yeast strains containing telomere capping defects and additional deletion mutations. Interestingly, we find that many gene deletions suppress one type of telomere capping defect while enhancing another. Through {QFA}, we can begin to define the roles of different gene products in contributing to different aspects of the telomere cap. Strikingly, mutations in nonsense-mediated {mRNA} decay pathways, which degrade many {RNA} molecules, suppress the cdc13-1 defect while enhancing the yku70Δ defect. {QFA} is widely applicable and will be useful for understanding other aspects of yeast cell biology.},
    author = {Addinall, Stephen G. and Holstein, Eva-Maria and Lawless, Conor and Yu, Min and Chapman, Kaye and Banks, A. Peter and Ngo, Hien-Ping and Maringele, Laura and Taschuk, Morgan and Young, Alexander and Ciesiolka, Adam and Lister, Allyson L. and Wipat, Anil and Wilkinson, Darren J. and Lydall, David},
    citeulike-article-id = {9114899},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pgen.1001362},
    day = {7},
    doi = {10.1371/journal.pgen.1001362},
    journal = {PLoS Genet},
    keywords = {cdc13, cisban, systems-biology, telomeres, yeast},
    month = apr,
    number = {4},
    pages = {e1001362+},
    posted-at = {2011-04-16 08:11:31},
    priority = {0},
    publisher = {Public Library of Science},
    title = {Quantitative Fitness Analysis Shows That {NMD} Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects},
    url = {http://dx.doi.org/10.1371/journal.pgen.1001362},
    volume = {7},
    year = {2011}
    }
  • [DOI] M. Courtot, N. Juty, C. Knupfer, D. Waltemath, A. Zhukova, A. Drager, M. Dumontier, A. Finney, M. Golebiewski, J. Hastings, S. Hoops, S. Keating, D. B. Kell, S. Kerrien, J. Lawson, A. Lister, J. Lu, R. Machne, P. Mendes, M. Pocock, N. Rodriguez, A. Villeger, D. J. Wilkinson, S. Wimalaratne, C. Laibe, M. Hucka, and N. Le Novere, “Controlled vocabularies and semantics in systems biology,” Molecular systems biology, vol. 7, iss. 1, 2011.
    [Bibtex]
    @article{citeulike:9946377,
    abstract = {The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the tools frequently used for this purpose. We describe here three ontologies created specifically to address the needs of the systems biology community. The Systems Biology Ontology ({SBO}) provides semantic information about the model components. The Kinetic Simulation Algorithm Ontology ({KiSAO}) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. The Terminology for the Description of Dynamics ({TEDDY}) categorizes dynamical features of the simulation results and general systems behavior. The provision of semantic information extends a model's longevity and facilitates its reuse. It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments.},
    author = {Courtot, Melanie and Juty, Nick and Knupfer, Christian and Waltemath, Dagmar and Zhukova, Anna and Drager, Andreas and Dumontier, Michel and Finney, Andrew and Golebiewski, Martin and Hastings, Janna and Hoops, Stefan and Keating, Sarah and Kell, Douglas B. and Kerrien, Samuel and Lawson, James and Lister, Allyson and Lu, James and Machne, Rainer and Mendes, Pedro and Pocock, Matthew and Rodriguez, Nicolas and Villeger, Alice and Wilkinson, Darren J. and Wimalaratne, Sarala and Laibe, Camille and Hucka, Michael and Le Novere, Nicolas},
    citeulike-article-id = {9946377},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/msb.2011.77},
    citeulike-linkout-1 = {http://dx.doi.org/10.1038/msb201177},
    citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261705/},
    citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/22027554},
    citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=22027554},
    day = {25},
    doi = {10.1038/msb.2011.77},
    issn = {1744-4292},
    journal = {Molecular Systems Biology},
    keywords = {ontologies, semantics, systems-biology},
    month = oct,
    number = {1},
    pmcid = {PMC3261705},
    pmid = {22027554},
    posted-at = {2011-10-26 09:42:09},
    priority = {0},
    publisher = {Nature Publishing Group},
    title = {Controlled vocabularies and semantics in systems biology},
    url = {http://dx.doi.org/10.1038/msb.2011.77},
    volume = {7},
    year = {2011}
    }
  • [DOI] D. Waltemath, N. Swainston, A. Lister, F. Bergmann, R. Henkel, S. Hoops, M. Hucka, N. Juty, S. Keating, C. Knuepfer, F. Krause, C. Laibe, W. Liebermeister, C. Lloyd, G. Misirli, M. Schulz, M. Taschuk, and N. Le Novère, “SBML level 3 package proposal: annotation,” Nature precedings, iss. 713, 2011.
    [Bibtex]
    @article{citeulike:9274960,
    abstract = {The annotation of Systems Biology Markup Language ({SBML}) models with semantic terms has been supported for a number of years. The prevalence of such annotated models is growing, with repositories such as Biomodels.net and an increasing number of software tools supporting and encouraging their use and {development.With} the increasing use of semantic annotations in the context of systems biology modeling has come the realization that the current Core {SBML} specification defining their use contains limitations that reduce the scope of metadata that can be captured in such {models.SBML} Level 3 provides the facility to propose and develop optional extensions to the Core specification. One such extension is described here, with an initial proposal of an Annotation {package.This} proposal extends the current Core annotation specification to provide support for a richer set of semantic annotations while adhering more closely to the existing specification of Resource Description Framework ({RDF}).},
    author = {Waltemath, Dagmar and Swainston, Neil and Lister, Allyson and Bergmann, Frank and Henkel, Ron and Hoops, Stefan and Hucka, Michael and Juty, Nick and Keating, Sarah and Knuepfer, Christian and Krause, Falko and Laibe, Camille and Liebermeister, Wolfram and Lloyd, Catherine and Misirli, Goksel and Schulz, Marvin and Taschuk, Morgan and Le Nov\`{e}re, Nicolas},
    citeulike-article-id = {9274960},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/npre.2011.5610.1},
    citeulike-linkout-1 = {http://precedings.nature.com/documents/5610/version/1},
    day = {31},
    doi = {10.1038/npre.2011.5610.1},
    issn = {1756-0357},
    journal = {Nature Precedings},
    keywords = {sbml},
    month = jan,
    number = {713},
    posted-at = {2011-05-11 09:17:37},
    priority = {2},
    publisher = {Nature Publishing Group},
    title = {{SBML} Level 3 Package Proposal: Annotation},
    url = {http://dx.doi.org/10.1038/npre.2011.5610.1},
    year = {2011}
    }
  • [DOI] M. Courtot, F. Gibson, A. L. Lister, J. Malone, D. Schober, R. R. Brinkman, and A. Ruttenberg, “MIREOT: the minimum information to reference an external ontology term,” Applied ontology, vol. 6, iss. 1, pp. 23-33, 2011.
    [Bibtex]
    @article{citeulike:9165963,
    abstract = {While the Web Ontology Language ({OWL}) provides a mechanism to import ontologies, this mechanism is not always suitable. Current editing tools present challenges for working with large ontologies and direct {OWL} imports can prove impractical for day-to-day development. Furthermore, external ontologies often undergo continuous change which can introduce conflicts when integrated with multiple efforts. Finally, importing heterogeneous ontologies in their entirety may lead to inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the methodology, its implementation, present some examples of this application, and outline future work and extensions.},
    author = {Courtot, M\'{e}lanie and Gibson, Frank and Lister, Allyson L. and Malone, James and Schober, Daniel and Brinkman, Ryan R. and Ruttenberg, Alan},
    citeulike-article-id = {9165963},
    citeulike-linkout-0 = {http://dx.doi.org/10.3233/ao-2011-0087},
    citeulike-linkout-1 = {http://iospress.metapress.com/content/h54m2237310v13x1},
    day = {1},
    doi = {10.3233/ao-2011-0087},
    journal = {Applied Ontology},
    keywords = {mireot, obi, ontologies},
    month = jan,
    number = {1},
    pages = {23--33},
    posted-at = {2011-04-16 08:08:13},
    priority = {0},
    title = {{MIREOT}: The minimum information to reference an external ontology term},
    url = {http://dx.doi.org/10.3233/ao-2011-0087},
    volume = {6},
    year = {2011}
    }
  • [DOI] A. L. Lister, R. S. Datta, O. Hofmann, R. Krause, M. Kuhn, B. Roth, and R. Schneider, “Live coverage of intelligent systems for molecular Biology/European conference on computational biology (ISMB/ECCB) 2009.,” Plos computational biology, vol. 6, iss. 1, p. e1000640+, 2010.
    [Bibtex]
    @article{citeulike:6603290,
    author = {Lister, Allyson L. and Datta, Ruchira S. and Hofmann, Oliver and Krause, Roland and Kuhn, Michael and Roth, Bettina and Schneider, Reinhard},
    citeulike-article-id = {6603290},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000640},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20126524},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20126524},
    day = {29},
    doi = {10.1371/journal.pcbi.1000640},
    issn = {1553-7358},
    journal = {PLoS computational biology},
    keywords = {conference-reports, conferences, eccb, friendfeed, ismb, live\_coverage, social-networking},
    month = jan,
    number = {1},
    pages = {e1000640+},
    pmid = {20126524},
    posted-at = {2010-01-29 14:44:12},
    priority = {0},
    publisher = {Public Library of Science},
    title = {Live Coverage of Intelligent Systems for Molecular {Biology/European} Conference on computational biology ({ISMB}/{ECCB}) 2009.},
    url = {http://dx.doi.org/10.1371/journal.pcbi.1000640},
    volume = {6},
    year = {2010}
    }
  • [DOI] A. R. Jones and A. L. Lister, “Managing experimental data using FuGE.,” Methods in molecular biology (clifton, n.j.), vol. 604, pp. 333-343, 2010.
    [Bibtex]
    @article{citeulike:6527866,
    abstract = {
    Data management and sharing in omics science is highly challenging due to the constant evolution of experimental techniques, the range of instrument types and software used for analysis, and the high volumes of data produced. The Functional Genomics Experiment ({FuGE}) Model was created to provide a model for capturing descriptions of sample processing, experimental protocols and multidimensional data for any kind of omics experiment. {FuGE} has two modes of action: (a) as a storage architecture for experimental workflows and (b) as a framework for building new technology-specific data {standards.FuGE} is an object model that is converted into an {XML} implementation for data exchange. Software toolkits have been developed for data handling and for bridging between {XML} data files and relational database implementations. {FuGE} has been adopted by the Proteomics Standards Initiative ({PSI}, http://www.psidev.info ) for building several new data formats, and it is being used in a variety of other experimental contexts, thus allowing data to be integrated across a range of experimental types to support Systems Biology approaches. This chapter provides a practical guide for laboratories or groups wishing to manage their data, and for developers wishing to create new data formats using {FuGE}.
    },
    address = {Totowa, NJ},
    author = {Jones, Andrew R. and Lister, Allyson L.},
    booktitle = {Proteome Bioinformatics },
    chapter = {23},
    citeulike-article-id = {6527866},
    citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-1-60761-444-9\_23},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20013382},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20013382},
    citeulike-linkout-3 = {http://www.springerlink.com/content/r72434t642777862},
    doi = {10.1007/978-1-60761-444-9\_23},
    isbn = {978-1-60761-443-2},
    issn = {1940-6029},
    journal = {Methods in molecular biology (Clifton, N.J.)},
    keywords = {data-exchange, data-integration, fuge},
    pages = {333--343},
    pmid = {20013382},
    posted-at = {2010-01-12 09:40:02},
    priority = {0},
    publisher = {Humana Press},
    title = {Managing experimental data using {FuGE}.},
    url = {http://dx.doi.org/10.1007/978-1-60761-444-9\_23},
    volume = {604},
    year = {2010}
    }
  • [DOI] A. L. Lister, R. S. Datta, O. Hofmann, R. Krause, M. Kuhn, B. Roth, and R. Schneider, “Live coverage of scientific conferences using web technologies,” Plos comput biol, vol. 6, iss. 1, p. e1000563+, 2010.
    [Bibtex]
    @article{Lister2010LiveGeneral,
    author = {Lister, Allyson L. and Datta, Ruchira S. and Hofmann, Oliver and Krause, Roland and Kuhn, Michael and Roth, Bettina and Schneider, Reinhard},
    citeulike-article-id = {6603301},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000563},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20126525},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20126525},
    day = {29},
    doi = {10.1371/journal.pcbi.1000563},
    issn = {1553-7358},
    journal = {PLoS Comput Biol},
    keywords = {conferences, eccb, friendfeed, ismb, live\_coverage, social-networking, web\_technologies},
    month = jan,
    number = {1},
    pages = {e1000563+},
    pmid = {20126525},
    posted-at = {2010-01-29 14:50:32},
    priority = {0},
    publisher = {Public Library of Science},
    title = {Live Coverage of Scientific Conferences Using Web Technologies},
    url = {http://dx.doi.org/10.1371/journal.pcbi.1000563},
    volume = {6},
    year = {2010}
    }
  • [DOI] A. L. Lister, P. Lord, M. Pocock, and A. Wipat, “Annotation of SBML models through rule-based semantic integration,” Journal of biomedical semantics, vol. 1, iss. Suppl 1, p. S3+, 2010.
    [Bibtex]
    @article{citeulike:7351534,
    abstract = {The creation of accurate quantitative Systems Biology Markup Language ({SBML}) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort.},
    author = {Lister, Allyson L. and Lord, Phillip and Pocock, Matthew and Wipat, Anil},
    citeulike-article-id = {7351534},
    citeulike-linkout-0 = {http://dx.doi.org/10.1186/2041-1480-1-s1-s3},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20626923},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20626923},
    day = {22},
    doi = {10.1186/2041-1480-1-s1-s3},
    issn = {2041-1480},
    journal = {Journal of Biomedical Semantics},
    keywords = {ontologies, owl, semantic-data-integration, systems-biology},
    month = jun,
    number = {Suppl 1},
    pages = {S3+},
    pmid = {20626923},
    posted-at = {2010-07-21 13:53:43},
    priority = {0},
    publisher = {BioMed Central Ltd},
    title = {Annotation of {SBML} models through rule-based semantic integration},
    url = {http://dx.doi.org/10.1186/2041-1480-1-s1-s3},
    volume = {1},
    year = {2010}
    }
  • A. L. Lister, “Semantic integration in the life sciences,” Ontogenesis, 2010.
    [Bibtex]
    @article{citeulike:9635823,
    abstract = {There are a number of limitations in data integration: data sets are often noisy, incomplete, of varying levels of granularity and highly changeable. Every time one of the underlying databases changes, the integrated database needs to be updated, and if there are any format changes, the parsers that convert to the unified format need to be modified as well. This ”database churn” was identified by Stein to be a major limiting factor in establishing a successful data warehouse (Stein 2003).
    Ruttenberg et al. see the Semantic Web, of which both {OWL} and {RDF} are components, as having the potential to aid translational and systems biology research; indeed, any life science field where there are large amounts of data in distributed, disparate formats should benefit from Semantic Web technologies (Ruttenberg et al. 2007).},
    author = {Lister, Allyson L.},
    citeulike-article-id = {9635823},
    citeulike-linkout-0 = {http://ontogenesis.knowledgeblog.org/126},
    day = {21},
    journal = {Ontogenesis},
    month = jan,
    posted-at = {2011-08-09 10:52:38},
    priority = {0},
    title = {Semantic Integration in the Life Sciences},
    url = {http://ontogenesis.knowledgeblog.org/126},
    year = {2010}
    }
  • M. Courtot, F. Gibson, A. L. Lister, J. Malone, D. Schober, R. R. Brinkman, and A. Ruttenberg, “MIREOT: the minimum information to reference an external ontology term,” in International conference on biomedical ontology, 2009, pp. 87-90.
    [Bibtex]
    @inproceedings{citeulike:6336875,
    abstract = {While the Web Ontology Language ({OWL}) provides a mechanism to import ontologies, this mechanism is not always suitable. First, given the current state of editing tools and the issues they have working with large ontologies, direct {OWL} imports have sometimes proven impractical for day-to-day development. Second, ontologies chosen for integration may be
    under active development and not aligned with the chosen design principles. Importing heterogeneous
    ontologies in their entirety may lead to
    inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the guidelines, their implementation, present some examples of
    application, and outline future work and extensions.},
    author = {Courtot, M\'{e}lanie and Gibson, Frank and Lister, Allyson L. and Malone, James and Schober, Daniel and Brinkman, Ryan R. and Ruttenberg, Alan},
    booktitle = {International Conference on Biomedical Ontology},
    citeulike-article-id = {6336875},
    citeulike-linkout-0 = {http://purl.obolibrary.org/obo/obi/repository/trunk/docs/papers/MIREOT\_ICBO2009/ICBOCameraReady.pdf},
    editor = {Smith, Barry},
    keywords = {mireot, obi, ontologies},
    location = {Buffalo, New York},
    month = jul,
    organization = {University at Buffalo College of Arts and Sciences, National Center for Ontological Research, National Center for Biomedical Ontology},
    pages = {87--90},
    posted-at = {2009-12-08 10:42:55},
    priority = {0},
    title = {{MIREOT}: the Minimum Information to Reference an External Ontology Term},
    url = {http://purl.obolibrary.org/obo/obi/repository/trunk/docs/papers/MIREOT\_ICBO2009/ICBOCameraReady.pdf},
    year = {2009}
    }
  • A. L. Lister, P. Lord, M. Pocock, and A. Wipat, “Annotation of SBML models through Rule-Based semantic integration,” in The 12th annual bio-ontologies meeting, ismb 2009, 2009, p. 49+.
    [Bibtex]
    @inproceedings{citeulike:5158322,
    abstract = {Motivation: The creation of accurate quantitative Systems Biology Markup Language ({SBML}) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. Here, we present a method using off-the-shelf semantic web technology which enables this process: the heterogeneous data sources are first syntactically converted into ontologies; these are then aligned to a small domain ontology by applying a rule base. Integrating resources in this way can accommodate multiple formats with different semantics; it provides richly modelled biological knowledge suitable for annotation of {SBML} models.
    Results: We demonstrate proof-of-principle for this rule-based mediation with two use cases for {SBML} model annotation. This was implemented with existing tools, decreasing development time and increasing reusability. This initial work establishes the feasibility of this approach as part of an automated {SBML} model annotation system.
    Availability: Detailed information including download and mapping of the ontologies as well as integration results is available from {http://www.cisban.ac.uk/RBM}},
    author = {Lister, Allyson L. and Lord, Phillip and Pocock, Matthew and Wipat, Anil},
    booktitle = {The 12th Annual Bio-Ontologies Meeting, ISMB 2009},
    citeulike-article-id = {5158322},
    citeulike-linkout-0 = {http://precedings.nature.com/documents/3286/version/1},
    day = {28},
    editor = {Lord, Phillip and Sansone, Susanna-Assunta and Shah, Nigam and Stephens, Susie and Soldatova, Larisa},
    keywords = {data-integration, model-annotation, ontologies, ontology-mapping, owl, rule-based-mediation, sbml, semantics, sqwrl, swrl},
    month = jun,
    pages = {49+},
    posted-at = {2009-07-15 13:14:59},
    priority = {0},
    title = {Annotation of {SBML} Models Through {Rule-Based} Semantic Integration},
    url = {http://precedings.nature.com/documents/3286/version/1},
    year = {2009}
    }
  • A. L. Lister, M. Pocock, and A. Wipat, “Saint: a lightweight SBML annotation integration environment,” in Biosysbio 2009, 2009.
    [Bibtex]
    @inproceedings{lister2009SaintBSB,
    author = {Lister, A. L. and Pocock, M. and Wipat, A.},
    booktitle = {BioSysBio 2009},
    citeulike-article-id = {4282062},
    keywords = {data-integration, model-annotation, modelling},
    month = mar,
    organization = {IET},
    posted-at = {2009-04-07 10:53:14},
    priority = {0},
    title = {Saint: a lightweight {SBML} annotation integration environment},
    year = {2009}
    }
  • [DOI] A. L. Lister, M. Pocock, M. Taschuk, and A. Wipat, “Saint: a lightweight integration environment for model annotation,” Bioinformatics, vol. 25, iss. 22, pp. 3026-3027, 2009.
    [Bibtex]
    @article{citeulike:5726758,
    abstract = {10.1093/bioinformatics/btp523 Summary: Saint is a web application which provides a lightweight annotation integration environment for quantitative biological models. The system enables modellers to rapidly mark up models with biological information derived from a range of data {sources.Availability} and Implementation: Saint is freely available for use on the web at http://www.cisban.ac.uk/saint. The web application is implemented in Google Web Toolkit and Tomcat, with all major browsers supported. The Java source code is freely available for download at http://saint-annotate.sourceforge.net. The Saint web server requires an installation of {libSBML} and has been tested on Linux (32-bit Ubuntu 8.10 and {9.04).Contact}: helpdesk@cisban.ac.uk; {a.l.lister@ncl.ac.ukSupplementary} information: Supplementary data are available at Bioinformatics online.},
    author = {Lister, Allyson L. and Pocock, Matthew and Taschuk, Morgan and Wipat, Anil},
    citeulike-article-id = {5726758},
    citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp523},
    citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/25/22/3026.abstract},
    citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/25/22/3026.full.pdf},
    citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/22/3026},
    citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19734151},
    citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19734151},
    day = {15},
    doi = {10.1093/bioinformatics/btp523},
    issn = {1367-4811},
    journal = {Bioinformatics},
    keywords = {data-integration, model-annotation, modelling, sbml, software, systems-biology},
    month = nov,
    number = {22},
    pages = {3026--3027},
    pmid = {19734151},
    posted-at = {2009-09-05 18:31:08},
    priority = {0},
    title = {Saint: a lightweight integration environment for model annotation},
    url = {http://dx.doi.org/10.1093/bioinformatics/btp523},
    volume = {25},
    year = {2009}
    }
  • [DOI] A. Lister, V. Charoensawan, S. De, K. James, S. C. C. Janga, and J. Huppert, “Interfacing systems biology and synthetic biology.,” Genome biology, vol. 10, iss. 6, p. 309+, 2009.
    [Bibtex]
    @article{citeulike:4999887,
    abstract = {A report of {BioSysBio} 2009, the {IET} conference on Synthetic Biology, Systems Biology and Bioinformatics, Cambridge, {UK}, 23-25 March 2009.},
    author = {Lister, Allyson and Charoensawan, Varodom and De, Subhajyoti and James, Katherine and Janga, Sarath Chandra C. and Huppert, Julian},
    citeulike-article-id = {4999887},
    citeulike-linkout-0 = {http://genomebiology.com/2009/10/6/309},
    citeulike-linkout-1 = {http://dx.doi.org/10.1186/gb-2009-10-6-309},
    citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19591648},
    citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19591648},
    doi = {10.1186/gb-2009-10-6-309},
    issn = {1465-6914},
    journal = {Genome biology},
    keywords = {conference-report, systems-biology},
    number = {6},
    pages = {309+},
    pmid = {19591648},
    posted-at = {2009-06-29 10:35:06},
    priority = {0},
    title = {Interfacing systems biology and synthetic biology.},
    url = {http://genomebiology.com/2009/10/6/309},
    volume = {10},
    year = {2009}
    }
  • [DOI] A. R. Jones, A. L. Lister, L. Hermida, P. Wilkinson, M. Eisenacher, K. Belhajjame, F. Gibson, P. Lord, M. Pocock, H. Rosenfelder, J. Santoyo-Lopez, A. Wipat, and N. W. W. Paton, “Modeling and managing experimental data using FuGE.,” Omics : a journal of integrative biology, vol. 13, iss. 3, pp. 239-251, 2009.
    [Bibtex]
    @article{citeulike:4540763,
    abstract = {The Functional Genomics Experiment data model ({FuGE}) has been developed to increase the consistency and efficiency of experimental data modeling in the life sciences, and it has been adopted by a number of high-profile standardization organizations. {FuGE} can be used: (1) directly, whereby generic modeling constructs are used to represent concepts from specific experimental activities; or (2) as a framework within which method-specific models can be developed. {FuGE} is both rich and flexible, providing a considerable number of modeling constructs, which can be used in a range of different ways. However, such richness and flexibility also mean that modelers and application developers have choices to make when applying {FuGE} in a given context. This paper captures emerging best practice in the use of {FuGE} in the light of the experience of several groups by: (1) proposing guidelines for the use and extension of the {FuGE} data model; (2) presenting design patterns that reflect recurring requirements in experimental data modeling; and (3) describing a community software tool kit ({STK}) that supports application development using {FuGE}. We anticipate that these guidelines will encourage consistent usage of {FuGE}, and as such, will contribute to the development of convergent data standards in omics research.},
    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. W.},
    citeulike-article-id = {4540763},
    citeulike-linkout-0 = {http://dx.doi.org/10.1089/omi.2008.0080},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19441879},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19441879},
    day = {14},
    doi = {10.1089/omi.2008.0080},
    issn = {1557-8100},
    journal = {Omics : a journal of integrative biology},
    keywords = {data-integration, data-standards, fuge, xml},
    month = jun,
    number = {3},
    pages = {239--251},
    pmid = {19441879},
    posted-at = {2009-05-18 17:16:34},
    priority = {0},
    title = {Modeling and managing experimental data using {FuGE}.},
    url = {http://dx.doi.org/10.1089/omi.2008.0080},
    volume = {13},
    year = {2009}
    }
  • The OBI Consortium, “Modeling biomedical experimental processes with OBI,” in The 12th annual bio-ontologies meeting, ismb 2009, 2009, p. 41+.
    [Bibtex]
    @inproceedings{citeulike:5158479,
    abstract = {Motivation: Experimental metadata are stored in many different formats and styles, creating challenges in comparison, reproduction and analysis. These difficulties impose severe limitations on the usability of such metadata in a wider context. The Ontology for Biomedical Investigations ({OBI}), developed as part of a global, cross community effort, provides an approach to represent biological and clinical investigations in an explicit and integrative framework which facilitates computational processing and semantic web compatibility. Here we detail two real-world applications of {OBI} and show how {OBI} satisfies such use cases.},
    author = {{The OBI Consortium}},
    booktitle = {The 12th Annual Bio-Ontologies Meeting, ISMB 2009},
    citeulike-article-id = {5158479},
    citeulike-linkout-0 = {http://bio-ontologies.org.uk/download/Bio-Ontologies2009.pdf},
    day = {28},
    editor = {Lord, Phillip and Sansone, Susanna-Assunta and Shah, Nigam and Stephens, Susie and Soldatova, Larisa},
    keywords = {data-integration, obi, ontologies, ontology-mapping, owl, rule-based-mediation, semantics, sqwrl, swrl},
    month = jun,
    pages = {41+},
    posted-at = {2009-07-15 13:36:09},
    priority = {0},
    title = {Modeling biomedical experimental processes with {OBI}},
    url = {http://bio-ontologies.org.uk/download/Bio-Ontologies2009.pdf},
    year = {2009}
    }
  • M. Courtot, W. Bug, F. Gibson, A. L. Lister, J. Malone, D. Schober, R. R. Brinkman, and A. Ruttenberg, “The OWL of biomedical investigations,” in Owled 2008, 2008.
    [Bibtex]
    @inproceedings{citeulike:3457924,
    abstract = {The Ontology for Biomedical Investigations ({OBI}), written in {OWL} {DL}, is being developed by a large consortium seeking to provide a cross-domain,shared framework for representing investigations in the biological andbiomedical sciences. In this paper we report our experiences and describe ourdevelopment process as it pertains to {OWL}, which includes a number ofelements that might inform tool developers as well as suggestgeneral development patterns. Finally, we review where improvements to {OWLand} {OWL} related tools might be beneficial.},
    author = {Courtot, M\'{e}lanie and Bug, William and Gibson, Frank and Lister, Allyson L. and Malone, James and Schober, Daniel and Brinkman, Ryan R. and Ruttenberg, Alan},
    booktitle = {OWLED 2008},
    citeulike-article-id = {3457924},
    citeulike-linkout-0 = {http://www.webont.org/owled/2008/papers/owled2008eu\_submission\_38.pdf},
    keywords = {methodologies, obi, ontologies, owl},
    month = oct,
    posted-at = {2008-12-05 14:27:07},
    priority = {0},
    title = {The {OWL} of Biomedical Investigations},
    url = {http://www.webont.org/owled/2008/papers/owled2008eu\_submission\_38.pdf},
    year = {2008}
    }
  • [DOI] D. Field, G. Garrity, T. Gray, N. Morrison, J. Selengut, P. Sterk, T. Tatusova, N. Thomson, M. J. Allen, S. V. Angiuoli, M. Ashburner, N. Axelrod, S. Baldauf, S. Ballard, J. Boore, G. Cochrane, J. Cole, P. Dawyndt, P. De Vos, C. dePamphilis, R. Edwards, N. Faruque, R. Feldman, J. Gilbert, P. Gilna, F. O. Glockner, P. Goldstein, R. Guralnick, D. Haft, D. Hancock, H. Hermjakob, C. Hertz-Fowler, P. Hugenholtz, I. Joint, L. Kagan, M. Kane, J. Kennedy, G. Kowalchuk, R. Kottmann, E. Kolker, S. Kravitz, N. Kyrpides, J. Leebens-Mack, S. E. Lewis, K. Li, A. L. Lister, P. Lord, N. Maltsev, V. Markowitz, J. Martiny, B. Methe, I. Mizrachi, R. Moxon, K. Nelson, J. Parkhill, L. Proctor, O. White, S. Sansone, A. Spiers, R. Stevens, P. Swift, C. Taylor, Y. Tateno, A. Tett, S. Turner, D. Ussery, B. Vaughan, N. Ward, T. Whetzel, I. San Gil, G. Wilson, and A. Wipat, “The minimum information about a genome sequence (MIGS) specification,” Nature biotechnology, vol. 26, iss. 5, pp. 541-547, 2008.
    [Bibtex]
    @article{citeulike:2773795,
    abstract = {With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium ({GSC}). Here, we introduce the minimum information about a genome sequence ({MIGS}) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the {GSC} also supports improving the 'transparency' of the information contained in existing genomic databases.},
    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 J. and Angiuoli, Samuel V. 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 O. 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 E. and Li, Kelvin and Lister, Allyson L. 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},
    citeulike-article-id = {2773795},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt1360},
    citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt1360},
    citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2409278/},
    citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/18464787},
    citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=18464787},
    day = {08},
    doi = {10.1038/nbt1360},
    issn = {1087-0156},
    journal = {Nature Biotechnology},
    keywords = {data-standards, migs},
    month = may,
    number = {5},
    pages = {541--547},
    pmcid = {PMC2409278},
    pmid = {18464787},
    posted-at = {2008-10-14 11:33:27},
    priority = {0},
    publisher = {Nature Publishing Group},
    title = {The minimum information about a genome sequence ({MIGS}) specification},
    url = {http://dx.doi.org/10.1038/nbt1360},
    volume = {26},
    year = {2008}
    }
  • [DOI] S. Sansone, P. Rocca-Serra, M. Brandizi, A. Brazma, D. Field, J. Fostel, A. G. Garrow, J. Gilbert, F. Goodsaid, N. Hardy, P. Jones, A. Lister, M. Miller, N. Morrison, T. Rayner, N. Sklyar, C. Taylor, W. Tong, G. Warner, and S. Wiemann, “The first RSBI (ISA-TAB) workshop: ” can a simple format work for complex studies?”,” Omics: a journal of integrative biology, vol. 12, iss. 2, pp. 143-149, 2008.
    [Bibtex]
    @article{citeulike:3153404,
    abstract = {Abstract This article summarizes the motivation for, and the proceedings of, the first {ISA}-{TAB} workshop held December 6-8, 2007, at the {EBI}, Cambridge, {UK}. This exploratory workshop, organized by members of the Microarray Gene Expression Data ({MGED}) Society's Reporting Structure for Biological Investigations ({RSBI}) working group, brought together a group of developers of a range of collaborative systems to discuss the use of a common format to address the pressing need of reporting and communicating data and metadata from biological, biomedical, and environmental studies employing combinations of genomics, transcriptomics, proteomics, and metabolomics technologies along with more conventional methodologies. The expertise of the participants comprised database development, data management, and hands-on experience in the development of data communication standards. The workshop's outcomes are set to help formalize the proposed Investigation, Study, Assay ({ISA})-{TAB} tab-delimited format for representing and communicating experimental metadata. This article is part of the special issue of {OMICS} on the activities of the Genomics Standards Consortium ({GSC}).},
    author = {Sansone, Susanna-Assunta and Rocca-Serra, Philippe and Brandizi, Marco and Brazma, Alvis and Field, Dawn and Fostel, Jennifer and Garrow, Andrew G. and Gilbert, Jack and Goodsaid, Federico and Hardy, Nigel and Jones, Phil and Lister, Allyson and Miller, Michael and Morrison, Norman and Rayner, Tim and Sklyar, Nataliya and Taylor, Chris and Tong, Weida and Warner, Guy and Wiemann, Stefan},
    citeulike-article-id = {3153404},
    citeulike-linkout-0 = {http://dx.doi.org/10.1089/omi.2008.0019},
    citeulike-linkout-1 = {http://online.liebertpub.com/doi/abs/10.1089/omi.2008.0019},
    citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18447634},
    citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18447634},
    doi = {10.1089/omi.2008.0019},
    issn = {1536-2310},
    journal = {OMICS: A Journal of Integrative Biology},
    keywords = {data-standards, fuge, isa-tab},
    month = jun,
    number = {2},
    pages = {143--149},
    pmid = {18447634},
    posted-at = {2008-10-15 16:17:15},
    priority = {0},
    title = {The First {RSBI} ({ISA}-{TAB}) Workshop: ” Can a Simple Format Work for Complex Studies?”},
    url = {http://dx.doi.org/10.1089/omi.2008.0019},
    volume = {12},
    year = {2008}
    }
  • P. Rocca-Serra, S. Sansone, A. Jones, A. Lister, F. Gibson, R. Brinkman, J. Spindlen, and M. Miller, XSL transformations for FuGE and FuGE extension documents for HTML and tab-delimited rendering, 2008.
    [Bibtex]
    @misc{citeulike:10114355,
    author = {Rocca-Serra, Philippe and Sansone, Susanna and Jones, Andy and Lister, Allyson and Gibson, Frank and Brinkman, Ryan and Spindlen, Josef and Miller, Michael},
    citeulike-article-id = {10114355},
    howpublished = {\url{http://isatab.sourceforge.net/docs/FUGE-and-XSL-transformations-R1.doc}},
    month = jun,
    posted-at = {2011-12-10 21:50:02},
    priority = {0},
    title = {{XSL} transformations for {FuGE} and {FuGE} extension documents for {HTML} and tab-delimited rendering},
    year = {2008}
    }
  • A. L. Lister, M. Pocock, and A. Wipat, “Integration of constraints documented in SBML, SBO, and the SBML manual facilitates validation of biological models,” Journal of integrative bioinformatics, vol. 4, iss. 3, p. 80+, 2007.
    [Bibtex]
    @article{citeulike:3049915,
    abstract = {The creation of quantitative, simulatable, Systems Biology Markup Language ({SBML}) models that accurately simulate the system under study is a time-intensive manual process that requires careful checking. Currently, the rules and constraints of model creation, curation, and annotation are distributed over at least three separate documents: the {SBML} schema document ({XSD}), the Systems Biology Ontology ({SBO}), and the ?Structures and Facilities for Model Definition? document. The latter document contains the richest set of constraints on models, and yet it is not amenable to computational processing. We have developed a Web Ontology Language ({OWL}) knowledge base that integrates these three structure documents, and that contains a representative sample of the information contained within them. This Model Format {OWL} ({MFO}) performs both structural and constraint integration and can be reasoned over and validated. {SBML} Models are represented as individuals of {OWL} classes, resulting in a single computationally amenable resource for model checking. Knowledge that was only accessible to humans is now explicitly and directly available for computational approaches. The integration of all structural knowledge for {SBML} models into a single resource creates a new style of model development and checking.},
    author = {Lister, A. L. and Pocock, M. and Wipat, A.},
    citeulike-article-id = {3049915},
    citeulike-linkout-0 = {http://journal.imbio.de/index.php?subid=7\&\#38;paper\_id=80},
    journal = {Journal of Integrative Bioinformatics},
    keywords = {data-integration, mfo, model-annotation, model-format-ontology, ontologies, sbml, sbo, semantic-data-integration},
    number = {3},
    pages = {80+},
    posted-at = {2008-10-15 16:44:14},
    priority = {0},
    title = {Integration of constraints documented in {SBML}, {SBO}, and the {SBML} Manual facilitates validation of biological models},
    url = {http://journal.imbio.de/index.php?subid=7\&\#38;paper\_id=80},
    volume = {4},
    year = {2007}
    }
  • A. L. Lister, A. R. Jones, M. Pocock, O. Shaw, and A. Wipat, “CS-TR number 1016: implementing the FuGE object model: a systems biology data portal and integrator,” Newcastle University 2007.
    [Bibtex]
    @techreport{citeulike:9846489,
    author = {Lister, A. L. and Jones, A. R. and Pocock, M. and Shaw, O. and Wipat, A.},
    citeulike-article-id = {9846489},
    citeulike-linkout-0 = {http://www.cs.ncl.ac.uk/publications/trs/papers/1016.pdf},
    institution = {Newcastle University},
    month = apr,
    posted-at = {2011-10-03 10:07:40},
    priority = {2},
    publisher = {School of Computing Science},
    title = {{CS}-{TR} Number 1016: Implementing the {FuGE} Object Model: a Systems Biology Data Portal and Integrator},
    url = {http://www.cs.ncl.ac.uk/publications/trs/papers/1016.pdf},
    year = {2007}
    }
  • [DOI] D. Field, G. Garrity, T. Gray, J. Selengut, P. Sterk, N. Thomson, T. Tatusova, G. Cochrane, F. O. Glöckner, R. Kottmann, A. L. Lister, Y. Tateno, and R. Vaughan, “eGenomics: cataloguing our complete genome collection III,” Comparative and functional genomics, vol. 2007, 2007.
    [Bibtex]
    @article{citeulike:4538088,
    abstract = {This meeting report summarizes the proceedings of the ” {eGenomics}: Cataloguing our Complete Genome Collection {III}” workshop held September 11–13, 2006, at the National Institute for Environmental {eScience} ({NIEeS}), Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised ” Minimum Information about a Genome Sequence” ({MIGS}) specification (v1.1), consensus on a variety of features to be added to the Genome Catalogue ({GCat}), agreement by several researchers to adopt {MIGS} for imminent genome publications, and an agreement by the {EBI} and {NCBI} to input their genome collections into {GCat} for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates) and working towards a single, global list of all public genomes and metagenomes.},
    author = {Field, Dawn and Garrity, George and Gray, Tanya and Selengut, Jeremy and Sterk, Peter and Thomson, Nick and Tatusova, Tatiana and Cochrane, Guy and Gl\"{o}ckner, Frank O. and Kottmann, Renzo and Lister, Allyson L. and Tateno, Yoshio and Vaughan, Robert},
    citeulike-article-id = {4538088},
    citeulike-linkout-0 = {http://dx.doi.org/10.1155/2007/47304},
    citeulike-linkout-1 = {http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2007/47304},
    doi = {10.1155/2007/47304},
    journal = {Comparative and Functional Genomics},
    keywords = {curation, data-standards, standards},
    posted-at = {2009-05-18 12:50:20},
    priority = {0},
    publisher = {Hindawi},
    title = {{eGenomics}: Cataloguing Our Complete Genome Collection {III}},
    url = {http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2007/47304},
    volume = {2007},
    year = {2007}
    }
  • A. L. Williams, P. J. Kersey, M. Pruess, and R. Apweiler, “Biological databases: infrastructure, content, and integration,” in Data analysis and visualization in genomics and proteomics, F. Azuaje and J. Dopazo, Eds., John Wiley & Sons, 2005.
    [Bibtex]
    @inbook{citeulike:4538973,
    author = {Williams, A. L. and Kersey, P. J. and Pruess, M. and Apweiler, R.},
    booktitle = {Data Analysis and Visualization in Genomics and Proteomics},
    chapter = {2},
    citeulike-article-id = {4538973},
    citeulike-linkout-0 = {http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470094397,descCd-tableOfContents.html},
    editor = {Azuaje, F. and Dopazo, J.},
    isbn = {978-0-470-09439-6},
    keywords = {bioinformatics, data-integration, databases},
    month = mar,
    posted-at = {2009-05-18 13:00:49},
    priority = {0},
    publisher = {John Wiley \& Sons},
    title = {Biological Databases: Infrastructure, Content, and Integration},
    url = {http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470094397,descCd-tableOfContents.html},
    year = {2005}
    }
  • [DOI] P. J. Kersey, J. Duarte, A. Williams, Y. Karavidopoulou, E. Birney, and R. Apweiler, “The international protein index: an integrated database for proteomics experiments,” Proteomics, vol. 4, iss. 7, pp. 1985-1988, 2004.
    [Bibtex]
    @article{citeulike:2877002,
    abstract = {Despite the complete determination of the genome sequence of several higher eukaryotes, their proteomes remain relatively poorly defined. Information about proteins identified by different experimental and computational methods is stored in different databases, meaning that no single resource offers full coverage of known and predicted proteins. {IPI} (the International Protein Index) has been developed to address these issues and offers complete nonredundant data sets representing the human, mouse and rat proteomes, built from the {Swiss-Prot}, {TrEMBL}, Ensembl and {RefSeq} databases.},
    address = {EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK. pkersey@ebi.ac.uk},
    author = {Kersey, Paul J. and Duarte, Jorge and Williams, Allyson and Karavidopoulou, Youla and Birney, Ewan and Apweiler, Rolf},
    citeulike-article-id = {2877002},
    citeulike-linkout-0 = {http://dx.doi.org/10.1002/pmic.200300721},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15221759},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15221759},
    citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/108562573/ABSTRACT},
    day = {1},
    doi = {10.1002/pmic.200300721},
    issn = {1615-9853},
    journal = {Proteomics},
    keywords = {ipi, proteomics, uniprot},
    month = jul,
    number = {7},
    pages = {1985--1988},
    pmid = {15221759},
    posted-at = {2008-10-15 16:20:32},
    priority = {0},
    publisher = {WILEY-VCH Verlag},
    title = {The International Protein Index: An integrated database for proteomics experiments},
    url = {http://dx.doi.org/10.1002/pmic.200300721},
    volume = {4},
    year = {2004}
    }
  • The OBI Consortium, OBI ontology.
    [Bibtex]
    @misc{citeulike:9635899,
    author = {{The OBI Consortium}},
    citeulike-article-id = {9635899},
    citeulike-linkout-0 = {http://purl.obolibrary.org/obo/obi},
    keywords = {ontologies},
    posted-at = {2011-08-09 11:45:31},
    priority = {0},
    title = {{OBI} Ontology},
    url = {http://purl.obolibrary.org/obo/obi}
    }

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