E
Ele Holloway
Researcher at European Bioinformatics Institute
Publications - 16
Citations - 3901
Ele Holloway is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: Ontology (information science) & Process ontology. The author has an hindex of 12, co-authored 16 publications receiving 3687 citations. Previous affiliations of Ele Holloway include Harvard University & University of Hertfordshire.
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Journal ArticleDOI
ArrayExpress—a public repository for microarray gene expression data at the EBI
Helen Parkinson,Ugis Sarkans,Mohammadreza Shojatalab,Niran Abeygunawardena,Sergio Contrino,Richard M.R. Coulson,Anna Farne,Gonzalo Garcia Lara,Ele Holloway,Misha Kapushesky,P. Lilja,Gaurab Mukherjee,Ahmet Oezcimen,Tim F. Rayner,Philippe Rocca-Serra,Anjan Sharma,Susanna-Assunta Sansone,Alvis Brazma +17 more
TL;DR: ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Informa-tion About a Microarray Experiment) requirements and stores well-annotated raw and normalized data.
Journal ArticleDOI
ArrayExpress—a public database of microarray experiments and gene expression profiles
Helen Parkinson,Misha Kapushesky,Mohammadreza Shojatalab,Niran Abeygunawardena,Richard M.R. Coulson,Anna Farne,Ele Holloway,Nikolay Kolesnykov,P. Lilja,Margus Lukk,Roby Mani,Tim F. Rayner,Anjan Sharma,E. William,Ugis Sarkans,Alvis Brazma +15 more
TL;DR: The ArrayExpress Repository and Data Warehouse is a database of gene expression profiles selected from the repository and consistently re-annotated, which contains data from >50 000 hybridizations and >1 500000 individual expression profiles.
Journal ArticleDOI
Modeling sample variables with an Experimental Factor Ontology
James Malone,Ele Holloway,Tomasz Adamusiak,Misha Kapushesky,Jie Zheng,Nikolay Kolesnikov,Anna Zhukova,Alvis Brazma,Helen Parkinson +8 more
TL;DR: The application of reference ontologies to data is a key problem, and this work presents guidelines on how community ontologies can be presented in an application ontology in a data-driven way.
Journal ArticleDOI
ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression
Helen Parkinson,Misha Kapushesky,Nikolay Kolesnikov,Gabriella Rustici,Mohammadreza Shojatalab,Niran Abeygunawardena,Hugo Bérubé,Miroslaw Dylag,Ibrahim Emam,Anna Farne,Ele Holloway,Margus Lukk,James Malone,Roby Mani,Ekaterina Pilicheva,Tim F. Rayner,Faisal I. Rezwan,Anjan Sharma,Eleanor Williams,Xiangqun Zheng Bradley,Tomasz Adamusiak,Marco Brandizi,Tony Burdett,Richard M.R. Coulson,Maria Krestyaninova,Pavel Kurnosov,Eamonn Maguire,Sudeshna Guha Neogi,Philippe Rocca-Serra,Susanna-Assunta Sansone,Nataliya Sklyar,Mengyao Zhao,Ugis Sarkans,Alvis Brazma +33 more
TL;DR: This update describes the ArrayExpress developments over the last two years and describes the new summary database and meta-analytical tool of ranked gene expression across multiple experiments and different biological conditions.
Journal ArticleDOI
ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments
Helen Parkinson,Ugis Sarkans,Nikolay Kolesnikov,Niran Abeygunawardena,Tony Burdett,Miroslaw Dylag,Ibrahim Emam,Anna Farne,Emma Hastings,Ele Holloway,Natalja Kurbatova,Margus Lukk,James Malone,Roby Mani,Ekaterina Pilicheva,Gabriella Rustici,Anjan Sharma,Eleanor Williams,Tomasz Adamusiak,Marco Brandizi,Nataliya Sklyar,Alvis Brazma +21 more
TL;DR: The ArrayExpress Archive is one of the three international public repositories of functional genomics data supporting publications and provides queries based on technology and sample attributes such as disease, cell types and anatomy.