Helen E. Parkinson

Orcid: 0000-0003-3035-4195

According to our database1, Helen E. Parkinson authored at least 78 papers between 2001 and 2023.

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Bibliography

2023
Features of a FAIR vocabulary.
J. Biomed. Semant., December, 2023

The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource.
Nucleic Acids Res., January, 2023

PDCM Finder: an open global research platform for patient-derived cancer models.
Nucleic Acids Res., January, 2023

The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease.
Nucleic Acids Res., January, 2023

COVoc and COVTriage: novel resources to support literature triage.
Bioinform., January, 2023

2022
The European Genome-phenome Archive in 2021.
Nucleic Acids Res., 2022

The European Variation Archive: a FAIR resource of genomic variation for all species.
Nucleic Acids Res., 2022

2021
Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics.
Nucleic Acids Res., 2021

2020
Soft windowing application to improve analysis of high-throughput phenotyping data.
Bioinform., 2020

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences.
Bioinform., 2020

2019
BioSamples database: an updated sample metadata hub.
Nucleic Acids Res., 2019

PDX Finder: A portal for patient-derived tumor xenograft model discovery.
Nucleic Acids Res., 2019

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

2018
Using OWL reasoning to support the generation of novel gene sets for enrichment analysis.
J. Biomed. Semant., 2018

2017
The human-induced pluripotent stem cell initiative - data resources for cellular genetics.
Nucleic Acids Res., 2017

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog).
Nucleic Acids Res., 2017

Open Targets: a platform for therapeutic target identification and validation.
Nucleic Acids Res., 2017

Comparison, alignment, and synchronization of cell line information between CLO and EFO.
BMC Bioinform., 2017

OxO - A Gravy of Ontology Mapping Extracts.
Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th, 2017

2016
Ten Simple Rules for Selecting a Bio-ontology.
PLoS Comput. Biol., 2016

Gramene 2016: comparative plant genomics and pathway resources.
Nucleic Acids Res., 2016

Expression Atlas update - an integrated database of gene and protein expression in humans, animals and plants.
Nucleic Acids Res., 2016

Tools and data services registry: a community effort to document bioinformatics resources.
Nucleic Acids Res., 2016

Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation.
J. Biomed. Semant., 2016

Reporting phenotypes in mouse models when considering body size as a potential confounder.
J. Biomed. Semant., 2016

The cellular microscopy phenotype ontology.
J. Biomed. Semant., 2016

Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates.
J. Biomed. Semant., 2016

PhenoImageShare: an image annotation and query infrastructure.
J. Biomed. Semant., 2016

Slim-o-matic: a Semi-Automated Way to Generate Gene Ontology Slims.
Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences, 2016

Use of Text Mining for Experimental Factor Ontology Coverage Expansion in the Scope of Target Validation.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

Biomedical Ontology Evolution in the EMBL-EBI Ontology Lookup Service.
Proceedings of the Workshops of the EDBT/ICDT 2016 Joint Conference, 2016

2015
ArrayExpress update - simplifying data submissions.
Nucleic Acids Res., 2015

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

Cell, Chemical and Anatomical Views of the Gene Ontology: Mapping to a Roche Controlled Vocabulary.
Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

Collaborative Ontology Development Using the Webulous Architecture and Google App.
Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

A new Ontology Lookup Service at EMBL-EBI.
Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

2014
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations.
Nucleic Acids Res., 2014

Expression Atlas update - a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.
Nucleic Acids Res., 2014

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.
Nucleic Acids Res., 2014

Updates to BioSamples database at European Bioinformatics Institute.
Nucleic Acids Res., 2014

CLO: The cell line ontology.
J. Biomed. Semant., 2014

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.
J. Biomed. Semant., 2014

The EBI RDF platform: linked open data for the life sciences.
Bioinform., 2014

2013
ArrayExpress update - trends in database growth and links to data analysis tools.
Nucleic Acids Res., 2013

Putting OWL into Production at the European Bioinformatics Institute.
Proceedings of the 10th International Workshop on OWL: Experiences and Directions (OWLED 2013) co-located with 10th Extended Semantic Web Conference (ESWC 2013), 2013

2012
Gene Expression Atlas update - a value-added database of microarray and sequencing-based functional genomics experiments.
Nucleic Acids Res., 2012

The BioSample Database (BioSD) at the European Bioinformatics Institute.
Nucleic Acids Res., 2012

MageComet - web application for harmonizing existing large-scale experiment descriptions.
Bioinform., 2012

Diachronic linked data: towards long-term preservation of structured interrelated information.
Proceedings of the International Workshop on Open Data, 2012

Semantic Web Atlas: Putting Gene Expression Data into Biological Context.
Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2012

GOCI: An Ontology-Driven Search and Curation Infrastructure for the NHGRI GWAS Catalog.
Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

The SWO Project: A Case Study for Applying Agile Ontology Engineering Methods for Community Driven Ontologies.
Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

2011
ArrayExpress update - an archive of microarray and high-throughput sequencing-based functional genomics experiments.
Nucleic Acids Res., 2011

OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript.
BMC Bioinform., 2011

Anatomy ontologies and potential users: bridging the gap.
J. Biomed. Semant., 2011

The Vertebrate Bridging Ontology (VBO).
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Rapid Development of an Ontology of Coriell Cell Lines.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

2010
Gene Expression Atlas at the European Bioinformatics Institute.
Nucleic Acids Res., 2010

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.
BMC Bioinform., 2010

Modeling biomedical experimental processes with OBI.
J. Biomed. Semant., 2010

Annotare - a tool for annotating high-throughput biomedical investigations and resulting data.
Bioinform., 2010

Modeling sample variables with an Experimental Factor Ontology.
Bioinform., 2010

2009
ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression.
Nucleic Acids Res., 2009

MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB.
Bioinform., 2009

Importing ArrayExpress datasets into R/Bioconductor.
Bioinform., 2009

Developing an Ontology from the Application Up.
Proceedings of the 5th International Workshop on OWL: Experiences and Directions (OWLED 2009), 2009

2007
ArrayExpress - a public database of microarray experiments and gene expression profiles.
Nucleic Acids Res., 2007

2006
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
BMC Bioinform., 2006

The MGED Ontology: a resource for semantics-based description of microarray experiments.
Bioinform., 2006

2005
ArrayExpress - a public repository for microarray gene expression data at the EBI.
Nucleic Acids Res., 2005

The ArrayExpress gene expression database: a software engineering and implementation perspective.
Bioinform., 2005

Pedro Ontology Services: A Framework for Rapid Ontology Markup.
Proceedings of the Semantic Web: Research and Applications, 2005

2003
The European Bioinformatics Institute's data resources.
Nucleic Acids Res., 2003

ArrayExpress - a public repository for microarray gene expression data at the EBI.
Nucleic Acids Res., 2003

2002
EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database.
Bioinform., 2002

An open letter to the scientific journals.
Bioinform., 2002

2001
The EMBL nucleotide sequence database.
Nucleic Acids Res., 2001


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