Survey-based naming conventions for use in OBO Foundry ontology development (2009)
Schober, Daniel, Smith, Barry, Lewis, Suzanna E, Kusnierczyk, Waclaw, Lomax, Jane, Mungall, Chris, ...
Abstract Background A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these...
Standards and infrastructure for managing experimental metadata (2009)
Philippe Rocca-Serra, Marco Brandizi, Eamonn Maguire, Nataliya Sklyar, Chris Taylor, Manon Delahaye, ...
*See also the "related presentation":http://precedings.nature.com/documents/3145/version/1* We present an infrastructure that leverages synergistic reporting standards...
Standards and infrastructure for managing experimental metadata (2009)
Susanna-Assunta Sansone, Philippe Rocca-Serra
*See also "related poster":http://precedings.nature.com/documents/3144/version/1* Today’s researchers can perform biological and biomedical studies where the same...
Parkinson, Helen, Kapushesky, Misha, Kolesnikov, Nikolay, Rustici, Gabriella, Shojatalab, Mohammad, Abeygunawardena, Niran, ...
ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository—a public archive of functional genomics experiments and supporting data, the ArrayExpress...
ARC Centre in Bioinformatics (2008)
Er Garcia, Susanna-assunta Sansone, Chris Taylor, Mark A, Embl Outstation Hinxton
Abstract. We briefly describe the methodology we have adopted in order to develop ontologies. Because our scenarios involved domain experts distributed geographically, the domain analysis and...
William B. Mattes, Syril D. Pettit, Susanna-assunta Sansone, Pierre R. Bushel, Michael D. Waters
Toxicology, the study of poisons, focuses on substances and treatments that cause adverse effects in living things. A critical part of this study is the characterization of the adverse effects at the...
Taylor, Chris, Field, Dawn, Sansone, Susanna-Assunta, Apweiler, Rolf, Ashburner, Michael, Ball, Cathy, ...
The Minimum Information for Biological and Biomedical Investigations (MIBBI) project aims to foster the coordinated development of minimum-information checklists and provide a resource for those...
Taylor, Chris F., Field, Dawn, Sansone, Susanna-Assunta, Aerts, Jan, Apweiler, Rolf, Asburner, Michael, ...
The Minimum Information for Biological and Biomedical Investigations (MIBBI) project provides a resource for those exploring the range of extant minimum information checklists and fosters coordinated...
The First RSBI (ISA-TAB) Workshop: "Can a Simple Format Work for Complex Studies?" (2008)
Sansone, Susanna-Assunta, Rocca-Serra, Philippe, Brandizi, Marco, Brazma, Alvis, Field, Dawn, Fostel, Jennifer, ...
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...
Spasić, Irena, Schober, Daniel, Sansone, Susanna-Assunta, Rebholz-Schuhmann, Dietrich, Kell, Douglas B, Paton, Norman W
Abstract Background Many bioinformatics applications rely on controlled vocabularies or ontologies to consistently interpret and seamlessly integrate information scattered across public resources....
Ugis Sarkans, Helen Parkinson, Gonzalo Garcia Lara, Ahmet Oezcimen, Anjan Sharma, Niran Abeygunawardena, ...
Motivation: The lack of microarray data management systems and databases is still one of the major problems faced by many life sciences laboratories. While developing the public repository for...
ArrayExpress: A standards-based public repository for microarray data (2008)
Niran Abeygunawardena, Sergio Contrino, Anna Farne, Gonzalo Garcia Lara, Ele Holloway, Gaurab Mukherjee, ...
ArrayExpress[1] is a public repository based at EBI that provides archive and query functions for well-annotated microarray data. As of August 2004, the data available in ArrayExpress represents...
Deutsch, Eric W, Ball, Catherine A, Berman, Jules J, Bova, G Steven, Brazma, Alvis, Bumgarner, Roger E, ...
One purpose of the biomedical literature is to report results in sufficient detail that the methods of data collection and analysis can be independently replicated and verified. Here we present...
Spasic, Irena, Schober, Daniel, Sansone, Susanna-Assunta, Rebholz-Schuhmann, Dietrich, Kell, Douglas B., Paton, Norman W.
Background. Many bioinformatics applications rely on controlled vocabularies or ontologies to consistently interpret and seamlessly integrate information scattered across public resources....
Jones, Andrew R, Miller, Michael, Aebersold, Ruedi, Apweiler, Rolf, Ball, Catherine A, Brazma, Alvis, ...
The Functional Genomics Experiment data model (FuGE) has been developed to facilitate convergence of data standards for high-throughput, comprehensive analyses in biology. FuGE models the components...
The Metabolomics Standards Initiative (MSI) (2007)
Fiehn, Oliver, Robertson, Donald, Griffin, Julian L., Nikolau, Basil, Morrison, N., ...
In 2005, the Metabolomics Standards Initiative has been formed. An outline and general introduction is provided to inform about the history, structure, working plan and intentions of this initiative....
The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration (2007)
Smith, Barry, Ashburner, Michael, Rosse, Cornelius, Bard, Jonathan, Bug, William, Ceusters, Werner, ...
The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of...
Fiehn, Oliver, Kristal, Bruce, Ommen, Ben Van, Sumner, Lloyd W, Sansone, Susanna-Assunta, Taylor, Chris F, ...
Metabolite concentrations in cellular systems are very much dependent on the physiological, environmental, and genetic status of an organism and are regarded as the ultimate result of cellular...
Castro, Alexander, Rocca-Serra, Philippe, Stevens, Robert, Taylor, Chris, Nashar, Karim, Ragan, Mark A, ...
Abstract Background Incorporation of ontologies into annotations has enabled 'semantic integration' of complex data, making explicit the knowledge within a certain field. One of the major bottlenecks...
Fiehn, Oliver, Kristal, Bruce, Van Ommen, Ben, Sumner, Lloyd W., Sansone, Susanna-Assunta, Taylor, Chris, ...
Metabolite concentrations in cellular systems are very much dependent on the physiological, environmental, and genetic status of an organism and are regarded as the ultimate result of cellular...
The MGED Ontology: a resource for semantics-based description of microarray experiments (2006)
Patricia L. Whetzel, Helen Parkinson, Helen C. Causton, Liju Fan, Fostel Gilberto, Fragoso Laurence Game, ...
* Corresponding authors
The MGED Ontology: a resource for semantics-based description of microarray experiments (2006)
Whetzel, Patricia L., Parkinson, Helen, Causton, Helen C., Fan, Liju, Fostel, Jennifer, Fragoso, Gilberto, ...
Motivation: The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME...
Summary recommendations for standardization and reporting of metabolic analyses (2005)
Lindon, John C., Nicholson, Jeremy, Holmes, Elaine, Keun, Hector, Craig, Andrew, Pearce, Jake, ...
The report of which this paper is a summary can be found at http://www.smrsgroup.org/documents/SMRS_policy_draft_v2.3.pdf
A proposed semantic framework for reporting omics investigations (2005)
Garcia, Alexander, Fostel, Jennifer, Morrison, Norman, Rocca-Serra, Philippe, Sansone, Susanna-Assunta
The current science landscape is rapidly evolving and it is increasingly driven by computational tasks. The deluge of data unleashed by omics-technologies, such as transcriptomics, proteomics and...
Section Coordinators, Glenn H. Cantor, Mark Earll, Nigel Hardy, Michael D. Reily, ...
(Affiliations and e-mail addresses for all contributors can be found in Appendix 1) Version 2.3
BMC Bioinformatics BioMed Central Methodology article (2005)
Er Garcia Castro, Robert Stevens, Chris Taylor, Karim Nashar, Mark A Ragan, Assunta Sansone, ...
The use of concept maps during knowledge elicitation in ontology development processes – the nutrigenomics use case
Garcia, Alexander, Sansone, Susanna-Assunta, Rocca-Serra, Philippe, Taylor, Chris, Ragan, Mark A.
We briefly describe the methodology we have adopted in order to develop ontologies. Because our scenarios involved domain experts distributed geographically, the domain analysis and knowledge...
Sarkans, Ugis, Parkinson, Helen, Lara, Gonzalo Garcia, Oezcimen, Ahmet, Sharma, Anjan, Abeygunawardena, Niran, ...
Motivation: The lack of microarray data management systems and databases is still one of the major problems faced by many life sciences laboratories. While developing the public repository for...
Submission of Microarray Data to Public Repositories (2004)
Catherine A. Ball, Alvis Brazma, Helen Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, ...
The Microarray Gene Expression Data Society believe that the time is right for journals to require that microarray data be deposited in public repositories, as a condition for publication.
Submission of Microarray Data to Public Repositories (2004)
Catherine A. Ball, Alvis Brazma, Helen Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, ...
Running Title: Toxicogenomic Database Review (2003)
William B. Mattes, Syril D. Pettit, Pierre R. Bushel, Michael D. Waters, William B. Mattes, Syril D. Pettit, ...
Address correspondence to:
ArrayExpress--a public repository for microarray gene expression data at the EBI (2003)
Brazma, Alvis, Parkinson, Helen, Sarkans, Ugis, Shojatalab, Mohammadreza, Vilo, Jaak, Abeygunawardena, Niran, ...
ArrayExpress is a new public database of microarray gene expression data at the EBI, which is a generic gene expression database designed to hold data from all microarray platforms. ArrayExpress uses...
ArrayExpress—a public repository for microarray gene expression data at the EBI
Brazma, Alvis, Parkinson, Helen, Sarkans, Ugis, Shojatalab, Mohammadreza, Vilo, Jaak, Abeygunawardena, Niran, ...
ArrayExpress is a new public database of microarray gene expression data at the EBI, which is a generic gene expression database designed to hold data from all microarray platforms. ArrayExpress uses...
Submission of Microarray Data to Public Repositories
Ball, Catherine A, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
The Microarray Gene Expression Data Society believe that the time is right for journals to require that microarray data be deposited in public repositories, as a condition for publication
Database development in toxicogenomics: issues and efforts.
Mattes, William B, Pettit, Syril D, Sansone, Susanna-Assunta, Bushel, Pierre R, Waters, Michael D
The marriage of toxicology and genomics has created not only opportunities but also novel informatics challenges. As with the larger field of gene expression analysis, toxicogenomics faces the...
Microarray Data Standards: An Open Letter
Ball, Catherine, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
Corvi, Raffaella, Ahr, Hans-Jürgen, Albertini, Silvio, Blakey, David H., Clerici, Libero, Coecke, Sandra, ...
This is the report of the first workshop “Validation of Toxicogenomics-Based Test Systems” held 11–12 December 2003 in Ispra, Italy. The workshop was hosted by the European Centre for the...
Castro, Alexander Garcia, Rocca-Serra, Philippe, Stevens, Robert, Taylor, Chris, Nashar, Karim, Ragan, Mark A, ...
ArrayExpress—a public repository for microarray gene expression data at the EBI
Brazma, Alvis, Parkinson, Helen, Sarkans, Ugis, Shojatalab, Mohammadreza, Vilo, Jaak, Abeygunawardena, Niran, ...
ArrayExpress is a new public database of microarray gene expression data at the EBI, which is a generic gene expression database designed to hold data from all microarray platforms. ArrayExpress uses...
Submission of Microarray Data to Public Repositories
Ball, Catherine A, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
The Microarray Gene Expression Data Society believe that the time is right for journals to require that microarray data be deposited in public repositories, as a condition for publication
Database development in toxicogenomics: issues and efforts.
Mattes, William B, Pettit, Syril D, Sansone, Susanna-Assunta, Bushel, Pierre R, Waters, Michael D
The marriage of toxicology and genomics has created not only opportunities but also novel informatics challenges. As with the larger field of gene expression analysis, toxicogenomics faces the...
Microarray Data Standards: An Open Letter
Ball, Catherine, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
Corvi, Raffaella, Ahr, Hans-Jürgen, Albertini, Silvio, Blakey, David H., Clerici, Libero, Coecke, Sandra, ...
This is the report of the first workshop “Validation of Toxicogenomics-Based Test Systems” held 11–12 December 2003 in Ispra, Italy. The workshop was hosted by the European Centre for the...
Castro, Alexander Garcia, Rocca-Serra, Philippe, Stevens, Robert, Taylor, Chris, Nashar, Karim, Ragan, Mark A, ...
Spasić, Irena, Schober, Daniel, Sansone, Susanna-Assunta, Rebholz-Schuhmann, Dietrich, Kell, Douglas B, Paton, Norman W
Survey-based naming conventions for use in OBO Foundry ontology development
Schober, Daniel, Smith, Barry, Lewis, Suzanna E, Kusnierczyk, Waclaw, Lomax, Jane, Mungall, Chris, ...
Parkinson, Helen, Kapushesky, Misha, Kolesnikov, Nikolay, Rustici, Gabriella, Shojatalab, Mohammad, Abeygunawardena, Niran, ...
ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository—a public archive of functional genomics experiments and supporting data, the ArrayExpress...