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(June 2008)
posted to no-tag
by allysonlister
on 2011-12-10 21:50:02
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by Melanie Courtot, Nick Juty, Christian Knupfer, et al.Dagmar Waltemath, Anna Zhukova, Andreas Drager, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas B. Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer Machne, Pedro Mendes, Matthew Pocock, Nicolas Rodriguez, Alice Villeger, Darren J. Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, Nicolas Le Novere
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 ...
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(April 2007)
posted to no-tag
by allysonlister
on 2011-10-03 10:07:40
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posted to ontologies
by allysonlister
on 2011-08-09 11:45:31
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Ontogenesis (21 January 2010)
posted to no-tag
by allysonlister
on 2011-08-09 10:52:38
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 ...
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by Dagmar Waltemath, Neil Swainston, Allyson Lister, et al.Frank Bergmann, Ron Henkel, Stefan Hoops, Michael Hucka, Nick Juty, Sarah Keating, Christian Knuepfer, Falko Krause, Camille Laibe, Wolfram Liebermeister, Catherine Lloyd, Goksel Misirli, Marvin Schulz, Morgan Taschuk, Nicolas Le Novère
posted to sbml
by allysonlister
on 2011-05-11 09:17:37
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 ...
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by Stephen G. Addinall, Eva-Maria Holstein, Conor Lawless, et al.Min Yu, Kaye Chapman, A. Peter Banks, Hien-Ping Ngo, Laura Maringele, Morgan Taschuk, Alexander Young, Adam Ciesiolka, Allyson L. Lister, Anil Wipat, Darren J. Wilkinson, David Lydall
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 ...
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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 ...
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Abstract
ABSTRACT : BACKGROUND : 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. RESULTS : Here we present rule-based mediation, a method of semantic data integration applied to systems biology model annotation. The ...
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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 ...
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In International Conference on Biomedical Ontology (July 2009), pp. 87-90
posted to mireot obi ontologies
by allysonlister
on 2009-12-08 10:42:55
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 ...
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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 ...
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In The 12th Annual Bio-Ontologies Meeting, ISMB 2009 (28 June 2009), 41
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 ...
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In The 12th Annual Bio-Ontologies Meeting, ISMB 2009 (28 June 2009), 49
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 ...
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Abstract
A report of BioSysBio 2009, the IET conference on Synthetic Biology, Systems Biology and Bioinformatics, Cambridge, UK, 23-25 March 2009. ...
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by Andrew R. Jones, Allyson L. Lister, Leandro Hermida, et al.Peter Wilkinson, Martin Eisenacher, Khalid Belhajjame, Frank Gibson, Phil Lord, Matthew Pocock, Heiko Rosenfelder, Javier Santoyo-Lopez, Anil Wipat, Norman W. W. Paton
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 ...
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In Data Analysis and Visualization in Genomics and Proteomics (March 2005)
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by Dawn Field, George Garrity, Tanya Gray, et al.Jeremy Selengut, Peter Sterk, Nick Thomson, Tatiana Tatusova, Guy Cochrane, Frank O. Glöckner, Renzo Kottmann, Allyson L. Lister, Yoshio Tateno, Robert Vaughan
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 ...
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In BioSysBio 2009 (March 2009)
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In OWLED 2008 (October 2008)
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. ...
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Journal of Integrative Bioinformatics, Vol. 4, No. 3. (2007), 80
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 ...
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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. ...
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by Susanna-Assunta Sansone, Philippe Rocca-Serra, Marco Brandizi, et al.Alvis Brazma, Dawn Field, Jennifer Fostel, Andrew G. Garrow, Jack Gilbert, Federico Goodsaid, Nigel Hardy, Phil Jones, Allyson Lister, Michael Miller, Norman Morrison, Tim Rayner, Nataliya Sklyar, Chris Taylor, Weida Tong, Guy Warner, Stefan Wiemann
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, ...
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by Dawn Field, George Garrity, Tanya Gray, et al.Norman Morrison, Jeremy Selengut, Peter Sterk, Tatiana Tatusova, Nicholas Thomson, Michael J. Allen, Samuel V. Angiuoli, Michael Ashburner, Nelson Axelrod, Sandra Baldauf, Stuart Ballard, Jeffrey Boore, Guy Cochrane, James Cole, Peter Dawyndt, Paul De Vos, Claude DePamphilis, Robert Edwards, Nadeem Faruque, Robert Feldman, Jack Gilbert, Paul Gilna, Frank Oliver O. Glöckner, Philip Goldstein, Robert Guralnick, Dan Haft, David Hancock, Henning Hermjakob, Christiane Hertz-Fowler, Phil Hugenholtz, Ian Joint, Leonid Kagan, Matthew Kane, Jessie Kennedy, George Kowalchuk, Renzo Kottmann, Eugene Kolker, Saul Kravitz, Nikos Kyrpides, Jim Leebens-Mack, Suzanna E. Lewis, Kelvin Li, Allyson L. Lister, Phillip Lord, Natalia Maltsev, Victor Markowitz, Jennifer Martiny, Barbara Methe, Ilene Mizrachi, Richard Moxon, Karen Nelson, Julian Parkhill, Lita Proctor, Owen White, Susanna-Assunta A. Sansone, Andrew Spiers, Robert Stevens, Paul Swift, Chris Taylor, Yoshio Tateno, Adrian Tett, Sarah Turner, David Ussery, Bob Vaughan, Naomi Ward, Trish Whetzel, Ingio San Gil, Gareth Wilson, Anil Wipat
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 ...
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