James Malone, Tomasz Adamusiak, Ele Holloway, Helen Parkinson
The Experimental Factor Ontology ("www.ebi.ac.uk/efo":http://www.ebi.ac.uk/efo) is an application focused ontology modelling the experimental factors in ArrayExpress. The ontology has been...
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...
Importing ArrayExpress datasets into R/Bioconductor (2009)
Kauffmann, Audrey, Rayner, Tim F., Parkinson, Helen, Kapushesky, Misha, Lukk, Margus, Brazma, Alvis, ...
Summary:ArrayExpress is one of the largest public repositories of microarray datasets. R/Bioconductor provides a comprehensive suite of microarray analysis and integrative bioinformatics software....
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB (2009)
Rayner, Tim F., Rezwan, Faisal Ibne, Lukk, Margus, Bradley, Xiangqun Zheng, Farne, Anna, Holloway, Ele, ...
Summary: The MAGE-TAB format for microarray data representation and exchange has been proposed by the microarray community to replace the more complex MAGE-ML format. We present a suite of tools to...
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...
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...
MIAME/Plant – adding value to plant microarrray experiments (2006)
Zimmermann, Philip, Schildknecht, Beatrice, Craigon, David, Garcia-Hernandez, Margarita, Gruissem, Wilhelm, May, Sean, ...
Abstract Appropriate biological interpretation of microarray data calls for relevant experimental annotation. The widely accepted MIAME guidelines provide a generic, organism-independant standard for...
Cancer Informatics in the U.K.: The NCRI Informatics Initiative (2006)
Fiona Reddington, J. Max Wilkinson, Robin Clark, Helen Parkinson, Peter Kerr, Richard Begent
The arrival of high-throughput technologies in cancer science and medicine has made the possibility for knowledge generation greater than ever before. However, this has brought with it real...
The SOFG Anatomy Entry List (SAEL): An Annotation Tool for Functional Genomics Data (2006)
Helen Parkinson, Stuart Aitken, Richard A. Baldock, Albert Burger, Terry F. Hayamizu, ...
A great deal of data in functional genomics studies needs to be annotated with low-resolution anatomical terms. For example, gene expression assays based on manually dissected samples (microarray,...
The MGED Ontology: A Framework for Describing Functional Genomics Experiments (2006)
Christian J. Stoeckert, Helen Parkinson
The Microarray Gene Expression Data (MGED) society was formed with an initial focus on experiments involving microarray technology. Despite the diversity of applications, there are common concepts...
A simple spreadsheet-based, MIAME-supportive format for microarray data (2006)
Tim Rayner, Paul Spellman, Helen C. Causton, Anna Farne, Ele Holloway, Jumin Liu, ...
{Note- this author list is not final; authors may still be added, and the list order has yet to be finalised.}
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
Vito Perrone, Anthony Finkelstein, Leah Goldin, Jeff Kramer, Helen Parkinson, Fiona Reddington
The NCRI Informatics Initiative has been established with the goal of using informatics to maximise the impact of cancer research. A clear foundation to achieving this goal is to enable the...
* Corresponding authors (2006)
Tim F Rayner, Paul T Spellman, Helen C Causton, Anna Farne, Ele Holloway, Rafael A Irizarry, ...
A simple spreadsheet-based, MIAME-supportive format for
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...
Cowley, Natalie, Nicholls, Mark, Parkinson, Helen, Swain, David
This research was a three-fold investigation into the viability of previous recommendations for vehicle-related child driveway accident safety . Firstly, the groups most at risk of these types of...
Cowley, Natalie, Nicholls, Mark, Parkinson, Helen, Swain, David
This research was a three-fold investigation into the viability of previous recommendations for vehicle-related child driveway accident safety . Firstly, the groups most at risk of these types of...
Pedro ontology services: A framework for rapid ontology markup (2005)
Kevin Garwood, Phillip Lord, Helen Parkinson, Norman W. Paton, Carole Goble
Abstract. Semantic Web technologies offer the possibility of increased accuracy and completeness in search and retrieval operations. In recent years, curators of data resources have begun favouring...
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, ...
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...
The SOFG Anatomy Entry List (SAEL): An Annotation Tool for Functional Genomics Data (2004)
Helen Parkinson, Stuart Aitken, Richard A. Baldock, Albert Burger, Terry F. Hayamizu, ...
A great deal of data in functional genomics studies needs to be annotated with low-resolution anatomical terms. For example, gene expression assays based on manually dissected samples (microarray,...
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...
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...
The MGED Ontology: A Framework for Describing Functional Genomics Experiments (2003)
The Microarray Gene Expression Data (MGED) society was formed with an initial focus on experiments involving microarray technology. Despite the diversity of applications, there are common concepts...
The European Bioinformatics Institute's data resources (2003)
Brooksbank, Catherine, Camon, Evelyn, Harris, Midori A., Magrane, Michele, Martin, Maria Jesus, Mulder, Nicola, ...
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics...
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...
DOI: 10.1093/nar/gkg066 The European Bioinformatics Institute’s data resources (2002)
Catherine Brooksbank, Evelyn Camon, Midori A. Harris, Michele Magrane, Maria Jesus Martin, Nicola Mulder, ...
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics...
An open letter to the scientific journals (2002)
Ball, Catherine A., Sherlock, Gavin, Parkinson, Helen, Rocca-Sera, Philippe, Brooksbank, Catherine, Causton, Helen C., ...
The EMBL nucleotide sequence database (2001)
Stoesser, Guenter, Baker, Wendy, Van Den Broek, Alexandra, Camon, Evelyn, Garcia-Pastor, Maria, Kanz, Carola, ...
The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data...
The EMBL nucleotide sequence database
Stoesser, Guenter, Baker, Wendy, Van Den Broek, Alexandra, Camon, Evelyn, Garcia-Pastor, Maria, Kanz, Carola, ...
The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan...
The European Bioinformatics Institute's data resources
Brooksbank, Catherine, Camon, Evelyn, Harris, Midori A., Magrane, Michele, Martin, Maria Jesus, Mulder, Nicola, ...
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics...
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
Microarray Data Standards: An Open Letter
Ball, Catherine, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
MIAME/Plant – adding value to plant microarrray experiments
Zimmermann, Philip, Schildknecht, Beatrice, Craigon, David, Garcia-Hernandez, Margarita, Gruissem, Wilhelm, May, Sean, ...
Appropriate biological interpretation of microarray data calls for relevant experimental annotation. The widely accepted MIAME guidelines provide a generic, organism-independant standard for minimal...
Mukherjee, Gaurab, Abeygunawardena, Niran, Parkinson, Helen, Contrino, Sergio, Durinck, Steffen, Farne, Anna, ...
ArrayExpress is a public microarray repository founded on the Minimum Information About a Microarray Experiment (MIAME) principles that stores MIAME-compliant gene expression data. Plant-based data...
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, ...
The EMBL nucleotide sequence database
Stoesser, Guenter, Baker, Wendy, Van Den Broek, Alexandra, Camon, Evelyn, Garcia-Pastor, Maria, Kanz, Carola, ...
The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan...
The European Bioinformatics Institute's data resources
Brooksbank, Catherine, Camon, Evelyn, Harris, Midori A., Magrane, Michele, Martin, Maria Jesus, Mulder, Nicola, ...
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics...
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
Mukherjee, Gaurab, Abeygunawardena, Niran, Parkinson, Helen, Contrino, Sergio, Durinck, Steffen, Farne, Anna, ...
ArrayExpress is a public microarray repository founded on the Minimum Information About a Microarray Experiment (MIAME) principles that stores MIAME-compliant gene expression data. Plant-based data...
Microarray Data Standards: An Open Letter
Ball, Catherine, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
MIAME/Plant – adding value to plant microarrray experiments
Zimmermann, Philip, Schildknecht, Beatrice, Craigon, David, Garcia-Hernandez, Margarita, Gruissem, Wilhelm, May, Sean, ...
Appropriate biological interpretation of microarray data calls for relevant experimental annotation. The widely accepted MIAME guidelines provide a generic, organism-independant standard for minimal...
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, ...
The MGED Ontology: A Framework for Describing Functional Genomics Experiments
Stoeckert, Christian J., Parkinson, Helen
The Microarray Gene Expression Data (MGED) society was formed with an initial focus on experiments involving microarray technology. Despite the diversity of applications, there are common concepts...
The SOFG Anatomy Entry List (SAEL): An Annotation Tool for Functional Genomics Data
Parkinson, Helen, Aitken, Stuart, Baldock, Richard A., Bard, Jonathan B. L., Burger, Albert, Hayamizu, Terry F., ...
A great deal of data in functional genomics studies needs to be annotated with low-resolution anatomical terms. For example, gene expression assays based on manually dissected samples (microarray,...
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB
Rayner, Tim F., Rezwan, Faisal Ibne, Lukk, Margus, Bradley, Xiangqun Zheng, Farne, Anna, Holloway, Ele, ...
Summary: The MAGE-TAB format for microarray data representation and exchange has been proposed by the microarray community to replace the more complex MAGE-ML format. We present a suite of tools to...
Cancer Informatics in the U.K.: The NCRI Informatics Initiative
Reddington, Fiona, Wilkinson, J. Max, Clark, Robin, Parkinson, Helen, Kerr, Peter, Begent, Richard
The arrival of high-throughput technologies in cancer science and medicine has made the possibility for knowledge generation greater than ever before. However, this has brought with it real...
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...
Importing ArrayExpress datasets into R/Bioconductor
Kauffmann, Audrey, Rayner, Tim F., Parkinson, Helen, Kapushesky, Misha, Lukk, Margus, Brazma, Alvis, ...
Summary:ArrayExpress is one of the largest public repositories of microarray datasets. R/Bioconductor provides a comprehensive suite of microarray analysis and integrative bioinformatics software....