Helen E. Parkinson

发表

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation

Robert Stevens, Andy Brown, James Malone, 2014, J. Biomed. Semant..

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

Helen E. Parkinson, Jacqueline A. L. MacArthur, Emily Bowler, 2016, Nucleic Acids Res..

ArrayExpress update—simplifying data submissions

Robert Petryszak, Maria Keays, Marco Brandizi, 2014, Nucleic Acids Res..

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data

Gang Fu, Evan Bolton, Chris Mungall, 2014, Nucleic Acids Res..

ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments

Ibrahim Emam, Marco Brandizi, James Malone, 2010, Nucleic Acids Res..

Putting OWL into Production at the European Bioinformatics Institute

Simon Jupp, James Malone, Jon C. Ison, 2013, OWLED.

Use of Text Mining for Experimental Factor Ontology Coverage Expansion in the Scope of Target Validation

Helen E. Parkinson, Senay Kafkas, Johanna R. McEntyre, 2016, ICBO/BioCreative.

Diachronic linked data: towards long-term preservation of structured interrelated information

Dimitris Sacharidis, Yannis Stavrakas, George Papastefanatos, 2012, WOD.

Ten Simple Rules for Selecting a Bio-ontology

Robert Stevens, Catherine Brooksbank, Simon Jupp, 2016, PLoS Comput. Biol..

EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database

Vincent Lombard, Helen E. Parkinson, Nicole Redaschi, 2002, Bioinform..

Using OWL reasoning to support the generation of novel gene sets for enrichment analysis

Helen E. Parkinson, David Osumi-Sutherland, Mélanie Courtot, 2018, J. Biomed. Semant..

OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript

Morris A. Swertz, Helen E. Parkinson, Tony Burdett, 2011, BMC Bioinformatics.

Reporting phenotypes in mouse models when considering body size as a potential confounder

Helen E. Parkinson, Sirarat Sarntivijai, Anika Oellrich, 2016, J. Biomed. Semant..

An open letter to the scientific journals

Catherine Brooksbank, Duccio Cavalieri, Paul T. Spellman, 2002, Bioinform..

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

Morris A. Swertz, Anthony J. Brookes, Helen E. Parkinson, 2010, BMC Bioinformatics.

Gene Expression Atlas at the European Bioinformatics Institute

Ibrahim Emam, James Malone, Helen E. Parkinson, 2009, Nucleic Acids Res..

Semantic Web Atlas: Putting Gene Expression Data into Biological Context

Simon Jupp, James Malone, Helen E. Parkinson, 2012, SWAT4LS.

The BioSample Database (BioSD) at the European Bioinformatics Institute

Marco Brandizi, Helen E. Parkinson, Alvis Brazma, 2011, Nucleic Acids Res..

PhenoImageShare: an image annotation and query infrastructure

Helen E. Parkinson, David Osumi-Sutherland, Tony Burdett, 2016, J. Biomed. Semant..

The cellular microscopy phenotype ontology

Simon Jupp, James Malone, Helen E. Parkinson, 2016, Journal of Biomedical Semantics.

Gramene 2016: comparative plant genomics and pathway resources

Lincoln Stein, Nuno A. Fonseca, Robert Petryszak, 2015, Nucleic Acids Res..

Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

Nuno A. Fonseca, Robert Petryszak, Maria Keays, 2013, Nucleic Acids Res..

ArrayExpress—a public database of microarray experiments and gene expression profiles

Helen E. Parkinson, Alvis Brazma, Ugis Sarkans, 2006, Nucleic Acids Res..

Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation

Gautier Koscielny, Samiul Hasan, Simon Jupp, 2016, J. Biomed. Semant..

Modeling sample variables with an Experimental Factor Ontology

Anna Zhukova, James Malone, Helen E. Parkinson, 2010, Bioinform..

Slim-o-matic: a Semi-Automated Way to Generate Gene Ontology Slims

Robert D. Finn, Laura I. Furlong, Helen E. Parkinson, 2016, SWAT4LS.

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

Helen E. Parkinson, Jacqueline A. L. MacArthur, Maria Cerezo, 2018, Nucleic Acids Res..

The EMBL Nucleotide Sequence Database

Vincent Lombard, Rodrigo Lopez, Helen E. Parkinson, 2002, Nucleic Acids Res..

ArrayExpress—a public repository for microarray gene expression data at the EBI

Sergio Contrino, Helen E. Parkinson, Susanna-Assunta Sansone, 2004, Nucleic Acids Res..

Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates

Simon Jupp, James Malone, Helen E. Parkinson, 2016, J. Biomed. Semant..

The human-induced pluripotent stem cell initiative—data resources for cellular genetics

Helen E. Parkinson, Paul Flicek, Laura Clarke, 2016, Nucleic Acids Res..

Developing an Ontology from the Application Up

James Malone, Helen E. Parkinson, Tomasz Adamusiak, 2009, OWLED.

Modeling biomedical experimental processes with OBI

Jessica A. Turner, et al., Alan Ruttenberg, 2010, J. Biomed. Semant..

Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics

Alexander D. Diehl, James Malone, Helen E. Parkinson, 2011, ICBO.

Pedro Ontology Services: A Framework for Rapid Ontology Markup

Carole A. Goble, Norman W. Paton, Helen E. Parkinson, 2005, ESWC.

Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

Nuno A. Fonseca, Elisabet Barrera, Robert Petryszak, 2015, Nucleic Acids Res..

CLO: The cell line ontology

Yue Liu, David J. States, Yu Lin, 2014, J. Biomed. Semant..

Biomedical Ontology Evolution in the EMBL-EBI Ontology Lookup Service

Simon Jupp, Helen E. Parkinson, Tony Burdett, 2016, EDBT/ICDT Workshops.

The European Bioinformatics Institute's data resources

Maria Jesus Martin, Claire O'Donovan, Rolf Apweiler, 2003, Nucleic Acids Res..

BioSamples database: an updated sample metadata hub

Helen E. Parkinson, Tony Burdett, Patricia L. Whetzel, 2018, Nucleic Acids Res..

The ArrayExpress gene expression database: a software engineering and implementation perspective

Sergio Contrino, Helen E. Parkinson, Susanna-Assunta Sansone, 2005, Bioinform..

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

Paul T. Spellman, Rafael A. Irizarry, John Quackenbush, 2006, BMC Bioinformatics.

Anatomy ontologies and potential users: bridging the gap

Michael Gruenberger, John M. Hancock, Paul N. Schofield, 2011, J. Biomed. Semant..

OxO - A Gravy of Ontology Mapping Extracts

Simon Jupp, Helen E. Parkinson, Tony Burdett, 2017, ICBO.

MageComet—web application for harmonizing existing large-scale experiment descriptions

Helen E. Parkinson, Tony Burdett, Alvis Brazma, 2012, Bioinform..

Open Targets: a platform for therapeutic target identification and validation

Gautier Koscielny, Robert Petryszak, Maria Keays, 2016, Nucleic Acids Res..

The SWO Project: A Case Study for Applying Agile Ontology Engineering Methods for Community Driven Ontologies

Robert Stevens, Andy Brown, James Malone, 2012, ICBO.

Comparison, alignment, and synchronization of cell line information between CLO and EFO

Simon Jupp, Helen E. Parkinson, Yongqun He, 2017, BMC Bioinformatics.

PDX Finder: A portal for patient-derived tumor xenograft model discovery

Helen E. Parkinson, Debra M. Krupke, Dale A. Begley, 2018, bioRxiv.

Annotare—a tool for annotating high-throughput biomedical investigations and resulting data

Ravi Shankar, Michael Miller, Helen E. Parkinson, 2010, Bioinform..

GOCI: An Ontology-Driven Search and Curation Infrastructure for the NHGRI GWAS Catalog

Helen E. Parkinson, Heather Junkins, Danielle Welter, 2012, ICBO.

ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression

Ibrahim Emam, Marco Brandizi, Faisal Ibne Rezwan, 2008, Nucleic Acids Res..

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data

Gautier Koscielny, Henrik Westerberg, Damian Smedley, 2013, Nucleic Acids Res..

The MGED Ontology: a resource for semantics-based description of microarray experiments

Chris F. Taylor, Norman Morrison, Helen E. Parkinson, 2006, Bioinform..

Collaborative Ontology Development Using the Webulous Architecture and Google App

Simon Jupp, James Malone, Helen E. Parkinson, 2015, SWAT4LS.

Importing ArrayExpress datasets into R/Bioconductor

Audrey Kauffmann, Helen E. Parkinson, Wolfgang Huber, 2009, Bioinform..

Gene Expression Atlas update—a value-added database of microarray and sequencing-based functional genomics experiments

Aedín C. Culhane, Robert Petryszak, James Malone, 2011, Nucleic Acids Res..

Cell, Chemical and Anatomical Views of the Gene Ontology: Mapping to a Roche Controlled Vocabulary

Helen E. Parkinson, David Osumi-Sutherland, Mélanie Courtot, 2015, SWAT4LS.

Updates to BioSamples database at European Bioinformatics Institute

Marco Brandizi, Helen E. Parkinson, Tony Burdett, 2014, Nucleic Acids Res..

ArrayExpress - a public repository for microarray gene expression data at the EBI

Helen E. Parkinson, Susanna-Assunta Sansone, Philippe Rocca-Serra, 2003, Nucleic Acids Res..

The EBI RDF platform: linked open data for the life sciences

Andrew M. Jenkinson, Maria Jesus Martin, Nicolas Le Novère, 2014, Bioinform..

Tools and data services registry: a community effort to document bioinformatics resources

Silvio C. E. Tosatto, Anthony Bretaudeau, Burkhard Rost, 2015, Nucleic Acids Res..

MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB

Faisal Ibne Rezwan, James Malone, Helen E. Parkinson, 2009, Bioinform..

The Vertebrate Bridging Ontology (VBO)

John M. Hancock, Paul N. Schofield, James Malone, 2011, ICBO.

ArrayExpress update—trends in database growth and links to data analysis tools

Maria Keays, Ibrahim Emam, Marco Brandizi, 2012, Nucleic Acids Res..

Soft windowing application to improve analysis of high-throughput phenotyping data

Damian Smedley, Mary E. Dickinson, Helen E. Parkinson, 2019, bioRxiv.

A new Ontology Lookup Service at EMBL-EBI

Simon Jupp, Helen E. Parkinson, Tony Burdett, 2015, SWAT4LS.

Rapid Development of an Ontology of Coriell Cell Lines

James Malone, Helen E. Parkinson, Chao Pang, 2011, ICBO.