Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates (2009)
Bjoern Peters, Alan Ruttenberg, Jason Greenbaum, Melanie Courtot, Ryan Brinkman, Patricia Whetzel, ...
The developers of the Ontology of Biomedical Investigations (OBI) primarily use Protégé for editing. However, adding many classes with similar patterns of logical definition is time...
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...
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...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB (2006)
Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, ...
Abstract Background Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the...
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...
Standardization Initiatives in the (eco)toxicogenomics Domain: A Review (2006)
Susanna Assunta Sansone, Norman Morrison, Philippe Rocca-Serra, Jennifer Fostel
The purpose of this document is to provide readers with a resource of different ongoing standardization efforts within the ‘omics’ (genomic, proteomics, metabolomics) and...
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...
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...
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...
Fostel, Jennifer, Choi, Danielle, Zwickl, Craig, Morrison, Norman, Rashid, Asif, Hasan, Atif, ...
A critical component in the design of the Chemical Effects in Biological Systems (CEBS) Knowledgebase is a strategy to capture toxicogenomics study protocols and the toxicity endpoint data (clinical...
Fostel, Jennifer, Choi, Danielle, Zwickl, Craig, Morrison, Norman, Rashid, Asif, Hasan, Atif, ...
A critical component in the design of the Chemical Effects in Biological Systems (CEBS) Knowledgebase is a strategy to capture toxicogenomics study protocols and the toxicity endpoint data (clinical...
Standardization Initiatives in the (eco)toxicogenomics Domain: A Review (2004)
Susanna Assunta Sansone, Norman Morrison, Philippe Rocca-Serra, Jennifer Fostel
The purpose of this document is to provide readers with a resource of different ongoing standardization efforts within the ‘omics’ (genomic, proteomics, metabolomics) and related communities,...
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...
EnsMart: A Generic System for Fast and Flexible Access to Biological Data (2004)
Kasprzyk, Arek, Keefe, Damian, Smedley, Damian, London, Darin, Spooner, William, Melsopp, Craig, ...
The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools....
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...
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...
EnsMart: A Generic System for Fast and Flexible Access to Biological Data
Kasprzyk, Arek, Keefe, Damian, Smedley, Damian, London, Darin, Spooner, William, Melsopp, Craig, ...
The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools....
Castro, Alexander Garcia, Rocca-Serra, Philippe, Stevens, Robert, Taylor, Chris, Nashar, Karim, Ragan, Mark A, ...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, ...
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...
EnsMart: A Generic System for Fast and Flexible Access to Biological Data
Kasprzyk, Arek, Keefe, Damian, Smedley, Damian, London, Darin, Spooner, William, Melsopp, Craig, ...
The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools....
Castro, Alexander Garcia, Rocca-Serra, Philippe, Stevens, Robert, Taylor, Chris, Nashar, Karim, Ragan, Mark A, ...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, ...
Standardization Initiatives in the (eco)toxicogenomics Domain: A Review
Sansone, Susanna Assunta, Morrison, Norman, Rocca-Serra, Philippe, Fostel, Jennifer
The purpose of this document is to provide readers with a resource of different ongoing standardization efforts within the ‘omics’ (genomic, proteomics, metabolomics) and related communities,...
Using Pathway Signatures as Means of Identifying Similarities among Microarray Experiments
Beltrame, Luca, Rizzetto, Lisa, Paola, Raffaele, Rocca-Serra, Philippe, Gambineri, Luca, Battaglia, Cristina, ...
Widespread use of microarrays has generated large amounts of data, the interrogation of the public microarray repositories, identifying similarities between microarray experiments is now one of the...
Survey-based naming conventions for use in OBO Foundry ontology development
Schober, Daniel, Smith, Barry, Lewis, Suzanna E, Kusnierczyk, Waclaw, Lomax, Jane, Mungall, Chris, ...
Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network
Harttig, Ulrich, Travis, Anthony J., Rocca-Serra, Philippe, Renkema, Marten, Van Ommen, Ben, Boeing, Heiner
New ‘omics’ technologies are changing nutritional sciences research. They enable to tackle increasingly complex questions but also increase the need for collaboration between research groups. An...
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...