Allyson Lister › Comments

Annals of Biomedical Engineering, Vol. 28, No. 8. (21 August 2000), pp. 1043-1058., doi:10.1114/1.1313771 The physiome is the quantitative description of the functioning organism in normal and pathophysiological states. The human physiome can be regarded as the virtual human. It is built upon the morphome, the quantitative description of anatomical structure, chemical and biochemical composition, and material properties of an intact organism, including its genome, proteome, cell, tissue, and organ structures up to those of the whole intact being. The Physiome Project is a multicentric integrated program to design, develop, implement, test and document, archive and disseminate quantitative information, and integrative models of the functional behavior of molecules, organelles, cells, tissues, organs, and intact organisms from bacteria to man. A fundamental and major feature of the project is the databasing of experimental observations for retrieval and evaluation. Technologies allowing... - Allyson Lister

FEBS Journal, Vol. 274, No. 21. (November 2007), pp. 5576-5585., doi:10.1111/j.1742-4658.2007.06076.x Two divergent modelling methodologies have been adopted to increase our understanding of metabolism and its regulation. Constraint-based modelling highlights the optimal path through a stoichiometric network within certain physicochemical constraints. Such an approach requires minimal biological data to make quantitative inferences about network behaviour; however, constraint-based modelling is unable to give an insight into cellular substrate concentrations. In contrast, kinetic modelling aims to characterize fully the mechanics of each enzymatic reaction. This approach suffers because parameterizing mechanistic models is both costly and time-consuming. In this paper, we outline a method for developing a kinetic model for a metabolic network, based solely on the knowledge of reaction stoichiometries. Fluxes through the system, estimated by flux balance analysis, are allowed to vary... - Allyson Lister

BMC Systems Biology, Vol. 4, No. 1. (28 January 2010), 6., doi:10.1186/1752-0509-4-6 BACKGROUND:Advances in bioinformatic techniques and analyses have led to the availability of genome-scale metabolic reconstructions. The size and complexity of such networks often means that their potential behaviour can only be analysed with constraint-based methods. Whilst requiring minimal experimental data, such methods are unable to give insight into cellular substrate concentrations. Instead, the long-term goal of systems biology is to use kinetic modelling to characterize fully the mechanics of each enzymatic reaction, and to combine such knowledge to predict system behaviour.RESULTS:We describe a method for building a parameterized genome-scale kinetic model of a metabolic network. Simplified linlog kinetics are used and the parameters are extracted from a kinetic model repository. We demonstrate our methodology by applying it to yeast metabolism. The resultant model has 956 metabolic... - Allyson Lister

[...] What RE Investors Should Know in 2011The Hip Hop DemocratYour Questions About Lab Pitbull MixThe more things change, the more they stay the same body { background: #FFFFFF; color: #666666; } a { color: #0000FF; } #header_wrapper, [...] - Allyson Lister

(October 2009) Matthew Horridge, Peter Patel-Schneider - Allyson Lister

(July 2006) Tim Berners-Lee - Allyson Lister

Nucleic Acids Research, Vol. 37, No. suppl 1. (01 January 2009), pp. D19-D25. Dramatic increases in the throughput of nucleotide sequencing machines, and the promise of ever greater performance, have thrust bioinformatics into the era of petabyte-scale data sets. Sequence repositories, which provide the feed for these data sets into the worldwide computational infrastructure, are challenged by the impact of these data volumes. The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/embl), comprising the EMBL Nucleotide Sequence Database and the Ensembl Trace Archive, has identified challenges in the storage, movement, analysis, interpretation and visualization of petabyte-scale data sets. We present here our new repository for next generation sequence data, a brief summary of contents of the ENA and provide details of major developments to submission pipelines, high-throughput rule-based validation infrastructure and data integration approaches. Guy Cochrane, Ruth Akhtar, James... - Allyson Lister

(June 2008) Philippe Rocca-Serra, Susanna Sansone, Andy Jones, Allyson Lister, Frank Gibson, Ryan Brinkman, Josef Spindlen, Michael Miller - Allyson Lister

BMC Bioinformatics, Vol. 12, No. 1. (2011), 456. BACKGROUND:The Open Biomedical Ontologies (OBO) Foundry is a collection of freely available ontologically structured controlled vocabularies in the biomedical domain. Most of them are disseminated via both the OBO Flatfile Format and the semantic web format Web Ontology Language (OWL), which draws upon formal logic. Based on the interpretations underlying OWL description logics (OWL-DL) semantics, we scrutinize the OWL-DL releases of OBO ontologies to assess whether their logical axioms correspond to the meaning intended by their authors.RESULTS:We analyzed ontologies and ontology cross products available via the OBO Foundry site www.obofoundry.org for existential restrictions (someValuesFrom), from which we examined a random sample of 2,836 clauses. According to a rating done by four experts, 23% of all existential restrictions in OBO Foundry candidate ontologies are suspicious (Cohens' kappa=0.78). We found a smaller proportion of... - Allyson Lister

Nucleic Acids Research, Vol. 39, No. suppl 1. (01 January 2011), pp. D685-D690. Pathway Commons (http://www.pathwaycommons.org) is a collection of publicly available pathway data from multiple organisms. Pathway Commons provides a web-based interface that enables biologists to browse and search a comprehensive collection of pathways from multiple sources represented in a common language, a download site that provides integrated bulk sets of pathway information in standard or convenient formats and a web service that software developers can use to conveniently query and access all data. Database providers can share their pathway data via a common repository. Pathways include biochemical reactions, complex assembly, transport and catalysis events and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. Pathway Commons currently contains data from nine... - Allyson Lister

The Semantic Web – ISWC 2005 (2005), pp. 974-986. Rule languages and rule systems are widely used in business applications including computer-aided training, diagnostic fact finding, compliance monitoring, and process control. However, there is little interoperability between current rule-based systems. Interoperation is one of the main goals of the Semantic Web, and developing a language for sharing rules is often seen as a key step in reaching this goal. The Semantic Web Rule Language (SWRL) is an important first step in defining such a rule language. This paper describes the development of a configurable interoperation environment for SWRL built in Protégé-OWL, the most widely-used OWL development platform. This environment supports both a highly-interactive, full-featured editor for SWRL and a plugin mechanism for integrating third party rule engines. We have integrated the popular Jess rule engine into this environment, thus providing one of the first steps on the path to rule... - Allyson Lister

Genes & Development, Vol. 21, No. 9. (1 May 2007), pp. 1010-1024. The execution of complex biological processes requires the precise interaction and regulation of thousands of molecules. Systematic approaches to study large numbers of proteins, metabolites, and their modification have revealed complex molecular networks. These biological networks are significantly different from random networks and often exhibit ubiquitous properties in terms of their structure and organization. Analyzing these networks provides novel insights in understanding basic mechanisms controlling normal cellular processes and disease pathologies. Xiaowei Zhu, Mark Gerstein, Michael Snyder - Allyson Lister

PLoS Comput Biol, Vol. 7, No. 9. (29 September 2011), e1002191. The use of structured knowledge representations—ontologies and terminologies—has become standard in biomedicine. Definitions of ontologies vary widely, as do the values and philosophies that underlie them. In seeking to make these views explicit, we conducted and summarized interviews with a dozen leading ontologists. Their views clustered into three broad perspectives that we summarize as mathematics, computer code, and Esperanto. Ontology as mathematics puts the ultimate premium on rigor and logic, symmetry and consistency of representation across scientific subfields, and the inclusion of only established, non-contradictory knowledge. Ontology as computer code focuses on utility and cultivates diversity, fitting ontologies to their purpose. Like computer languages C++, Prolog, and HTML, the code perspective holds that diverse applications warrant custom designed ontologies. Ontology as Esperanto focuses on facilitating... - Allyson Lister

Bioinformatics, Vol. 24, No. 11. (1 June 2008), pp. 1381-1385. Motivation: Internet-based electronic resources, as given by Uniform Resource Locators (URLs), are being increasingly used in scientific publications but are also becoming inaccessible in a time-dependant manner, a phenomenon documented across disciplines. Initial reports brought attention to the problem, spawning methods of effectively preserving URL content while some journals adopted policies regarding URL publication and begun storing supplementary information on journal websites. Thus, a reexamination of URL growth and decay in the literature is merited to see if the problem has grown or been mitigated by any of these changes.Results: After the 2003 study, three follow-up studies were conducted in 2004, 2005 and 2007. Unfortunately, no significant change was found in the rate of URL decay among any of the studies. However, only 5% of URLs cited more than twice have decayed versus 20% of URLs cited once or twice. The... - Allyson Lister

Bioinformatics, Vol. 24, No. 19. (1 October 2008), pp. 2127-2128. Contact: jdwren@gmail.comAs biomedical data accumulates, the need to store, share and organize it grows. Consequently, the number of Internet-accessible databases has been rapidly growing on an annual basis. Bioinformatics regularly publishes descriptions of biomedically relevant databases, Nucleic Acids Research has published an annual database issue since 1996 and now a new open-access journal, Database: The Journal of Biological Databases and Curation, will soon be launched by Oxford University Press in 2009 (http://www.oxfordjournals.org/our_jou...). Since databases can be made publicly available on the Internet without publication, it is worth considering what factors prioritize publication of database descriptions in a peer-reviewed journal. In general, publication of a database description in a journal advertises it as a valuable resource for scientific research. Implicitly, it is assumed that this... - Allyson Lister

PLoS Comput Biol, Vol. 4, No. 7. (18 July 2008), e1000136. Stella Veretnik, Lynn Fink, Philip Bourne - Allyson Lister

Genome biology, Vol. 6, No. 2. (2005), R21. We describe an ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds. It includes over 680 cell types. These cell types are classified under several generic categories and are organized as a directed acyclic graph. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. The ontology is freely available at http://obo.sourceforge.net/ and can be viewed using standard ontology visualization tools such as OBO-Edit and COBrA. Jonathan Bard, Seung Rhee, Michael Ashburner - Allyson Lister

Drug discovery today, Vol. 16, No. 21-22. (23 September 2011), pp. 940-947. The life science industries (including pharmaceuticals, agrochemicals and consumer goods) are exploring new business models for research and development that focus on external partnerships. In parallel, there is a desire to make better use of data obtained from sources such as human clinical samples to inform and support early research programmes. Success in both areas depends upon the successful integration of heterogeneous data from multiple providers and scientific domains, something that is already a major challenge within the industry. This issue is exacerbated by the absence of agreed standards that unambiguously identify the entities, processes and observations within experimental results. In this article we highlight the risks to future productivity that are associated with incomplete biological and chemical vocabularies and suggest a new model to address this long-standing issue. Lee Harland,... - Allyson Lister

(February 2004) Web Ontology Working Group - Allyson Lister

Journal of Biomedical Semantics, Vol. 2, No. Suppl 2. (2011), S6. BACKGROUND:The realm of pathological entities can be subdivided into pathological dispositions, pathological processes, and pathological structures. The latter are the bearer of dispositions, which can then be realized by their manifestations -- pathologic processes. Despite its ontological soundness, implementing this model via purpose-oriented domain ontologies will likely require considerable effort, both in ontology construction and maintenance, which constitutes a considerable problem for SNOMED CT, presently the largest biomedical ontology.RESULTS:We describe an ontology design pattern which allows ontologists to make assertions that blur the distinctions between dispositions, processes, and structures until necessary. Based on the domain upper-level ontology BioTop, it permits ascriptions of location and participation in the definition of pathological phenomena even without an ontological commitment to a... - Allyson Lister

Molecular Systems Biology, Vol. 7, No. 1. (25 October 2011) 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)... - Allyson Lister

[...] as part of doing science itself; take Allyson Lister’s excellent and extensive meeting or seminar notes. Or Simon Cockell’s experience sharing. Or my own move to just blogging my own papers [...] - Allyson Lister

(August 2007) Bijan Parsia - Allyson Lister

In Genomes to Systems (2008) Nicolas Le Novere - Allyson Lister

In Data Integration in the Life Sciences, Proceedings; Lecture Notes in Computer Science; 6th International Workshop on Data Integration in the Life Sciences, Vol. 5647 (JUL 2009), pp. 5-15. V Chelliah, L Endler, N Juty, C Laibe, C Li, N Rodriguez, Le Novere - Allyson Lister

In OWLED 2011 (June 2011) Pascal Hitzler - Allyson Lister

Bioinformatics, Vol. 26, No. 18. (15 September 2010), pp. 2354-2356. Summary: The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination of omics and other technologies; (ii) empowers users to uptake community-defined checklists and ontologies; and (iii) facilitates submission to international public repositories.Availability and Implementation: Software, documentation, case studies and implementations at http://www.isa-tools.orgContact: isatools@googlegroups.com Philippe Rocca-Serra, Marco Brandizi, Eamonn Maguire, Nataliya Sklyar, Chris Taylor, Kimberly Begley, Dawn Field, Stephen Harris, Winston Hide, Oliver Hofmann, Steffen Neumann, Peter Sterk, Weida Tong, Susanna-Assunta Sansone - Allyson Lister

FEBS Journal, Vol. 278, No. 16. (25 August 2011), pp. 2767-2857. Systems biology has received an ever increasing interest during the last decade. A large amount of third-party funding is spent on this topic, which involves quantitative experimentation integrated with computational modeling. Industrial companies are also starting to use this approach more and more often, especially in pharmaceutical research and biotechnology. This leads to the question of whether such interest is wisely invested and whether there are success stories to be told for basic science and/or technology/biomedicine. In this review, we focus on the application of systems biology approaches that have been employed to shed light on both biochemical functions and previously unknown mechanisms. We point out which computational and experimental methods are employed most frequently and which trends in systems biology research can be observed. Finally, we discuss some problems that we have encountered in publications... - Allyson Lister

Nature, Vol. 455, No. 7209. (03 September 2008), pp. 1-1. Researchers need to adapt their institutions and practices in response to torrents of new data — and need to complement smart science with smart searching. - Allyson Lister

Journal of biomedical informatics In Biomedical Ontologies, Vol. 39, No. 3. (June 2006), pp. 314-320. Biomedical research is increasingly a data-driven science. New technologies support the generation of genome-scale data sets of sequences, sequence variants, transcripts, and proteins; genetic elements underpinning understanding of biomedicine and disease. Information systems designed to manage these data, and the functional insights (biological knowledge) that come from the analysis of these data, are critical to mining large, heterogeneous data sets for new biologically relevant patterns, to generating hypotheses for experimental validation, and ultimately, to building models of how biological systems work. Bio-ontologies have an essential role in supporting two key approaches to effective interpretation of genome-scale data sets: data integration and comparative genomics. To date, bio-ontologies such as the Gene Ontology have been used primarily in community genome databases as... - Allyson Lister