Helen Parkinson
A5020620537- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Scientific Computing and Data Management
- Cancer Genomics and Diagnostics
- Semantic Web and Ontologies
- Research Data Management Practices
- Genomics and Rare Diseases
- Genetics, Bioinformatics, and Biomedical Research
- Cell Image Analysis Techniques
- Single-cell and spatial transcriptomics
- Genetic Associations and Epidemiology
- Genomics and Phylogenetic Studies
- Radiomics and Machine Learning in Medical Imaging
- Molecular Biology Techniques and Applications
- CRISPR and Genetic Engineering
- Genomic variations and chromosomal abnormalities
- Genetic and phenotypic traits in livestock
- Cancer Immunotherapy and Biomarkers
- Health, Environment, Cognitive Aging
- Ruminant Nutrition and Digestive Physiology
- Reproductive Physiology in Livestock
- Lung Cancer Treatments and Mutations
- Service-Oriented Architecture and Web Services
- Genetic Mapping and Diversity in Plants and Animals
European Bioinformatics Institute
2016-2025
Wellcome Trust
2014-2024
Open Targets
2016-2023
King's College Hospital NHS Foundation Trust
2021-2023
European Molecular Biology Organization
2023
Oxford University Hospitals NHS Trust
2023
Health Data Research UK
2020-2021
University of Cambridge
2021
King's College Hospital
2020
Indian Institute of Science Education and Research Pune
2020
The GWAS Catalog delivers a high-quality curated collection of all published genome-wide association studies enabling investigations to identify causal variants, understand disease mechanisms, and establish targets for novel therapies. scope the has also expanded targeted exome arrays with 1000 new associations added these technologies. As September 2018, contains 5687 comprising 71673 variant-trait from 3567 publications. New content includes 284 full P-value summary statistics datasets...
The National Human Genome Research Institute (NHGRI) Catalog of Published Genome-Wide Association Studies (GWAS) provides a publicly available manually curated collection published GWAS assaying at least 100 000 single-nucleotide polymorphisms (SNPs) and all SNP-trait associations with P <1 × 10−5. includes 1751 publications 11 912 SNPs. In addition to the association data, also publishes quarterly diagram mapped SNPs’ chromosomal locations. can be accessed via tabular web interface, dynamic...
The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. new infrastructure includes a graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality an improved curation interface. These developments have release frequency by increasing automation of providing scaling improvements. range available also been extended with structured ancestry recruitment...
ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Informa-tion About Microarray Experiment) requirements and stores well-annotated raw normalized data. As of November 2004, contains from ∼12 000 hybridizations covering 35 species. Data can be submitted online or directly local databases LIMS in standard format, password-protected access to prepublication provided reviewers authors. The retrieved by accession number queried vari-ous parameters such as...
Abstract The NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to &gt;200 000 users per year from academic research, healthcare industry. contains variant-trait associations supporting metadata for &gt;45 published across &gt;5000 human traits, &gt;40 full P-value summary statistics datasets. Content curated publications or acquired via author submission...
ArrayExpress is a public database for high throughput functional genomics data. consists of two parts--the Repository, which MIAME supportive archive microarray data, and the Data Warehouse, gene expression profiles selected from repository consistently re-annotated. Archived experiments can be queried by experiment attributes, such as keywords, species, array platform, authors, journals or accession numbers. Gene names properties, Ontology terms visualized. rapidly growing database,...
The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is an international functional genomics database at the European Bioinformatics Institute (EMBL-EBI) recommended by most journals as a repository for data supporting peer-reviewed publications. It contains from over 7000 public sequencing and 42 000 array-based studies comprising 1.5 million assays in total. proportion sequencing-based submissions has grown significantly last few years doubled 18 months,...
The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands utility ontology for examination and comparison genetic variation, phenotype, protein, drug epitope data through lens human disease. DO is a biomedical resource standardized common rare disease concepts with stable identifiers organized by etiology. content has had 192 revisions since 2012, including addition 760 terms. Thirty-two percent all terms now include definitions. expanded...
Abstract Motivation: Describing biological sample variables with ontologies is complex due to the cross-domain nature of experiments. Ontologies provide annotation solutions; however, for investigations, multiple are needed represent data. These subject rapid change, often not interoperable and present complexities that a barrier resource users. Results: We Experimental Factor Ontology, designed meet cross-domain, application focused use cases gene expression describe our methodology open...
Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal plant samples of different cell types, organism parts, developmental stages, diseases other conditions. It consists selected microarray RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality processed using standardised analysis methods. Since the last update, has grown seven-fold (1572 as August 2015),...
Open Targets Genetics (https://genetics.opentargets.org) is an open-access integrative resource that aggregates human GWAS and functional genomics data including gene expression, protein abundance, chromatin interaction conformation from a wide range of cell types tissues to make robust connections between GWAS-associated loci, variants likely causal genes. This enables systematic identification prioritisation genes across all published trait-associated loci. In this paper, we describe the...
We have designed and developed a data integration visualization platform that provides evidence about the association of known potential drug targets with diseases. The is to support identification prioritization biological for follow-up. Each target linked disease using integrated genome-wide from broad range sources. either target-centric workflow identify diseases may be associated specific target, or disease-centric disease. Users can easily transition between these target- workflows....
ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the Repository—a public archive functional genomics experiments and supporting data, Warehouse—a database gene expression profiles other bio-measurements Atlas—a new summary meta-analytical tool ranked across multiple different biological conditions. The Repository contains data from over 6000 comprising approximately 200 000 assays, doubles in size every 15 months. majority are array based, but types included, most...
The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is one three international functional genomics public data repositories, alongside the Gene Expression Omnibus at NCBI and DDBJ Omics Archive, supporting peer-reviewed publications. It accepts generated by sequencing or array-based technologies currently contains from almost a million assays, over 30 000 experiments. proportion sequencing-based submissions has grown significantly last 2 years reached, in...
The ArrayExpress Archive ( http://www.ebi.ac.uk/arrayexpress ) is one of the three international public repositories functional genomics data supporting publications. It includes generated by sequencing or array-based technologies. Data are submitted users and imported directly from NCBI Gene Expression Omnibus. closely integrated with Atlas sequence databases at European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include based on technology sample...
Expression Atlas (http://www.ebi.ac.uk/gxa) is a value-added database providing information about gene, protein and splice variant expression in different cell types, organism parts, developmental stages, diseases other biological experimental conditions. The consists of selected high-quality microarray RNA-sequencing experiments from ArrayExpress that have been manually curated, annotated with Experimental Factor Ontology terms processed using standardized analysis methods. new version...
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies provide a representation biomedical knowledge from Open Biological Ontologies (OBO) project adds ability this was derived. We here state several applications using it, such as adding semantic expressivity existing databases, building data entry forms,...
Abstract Many gene expression quantitative trait locus (eQTL) studies have published their summary statistics, which can be used to gain insight into complex human traits by downstream analyses, such as fine mapping and co-localization. However, technical differences between these datasets are a barrier widespread use. Consequently, target genes for most genome-wide association study (GWAS) signals still not been identified. In the present study, we eQTL Catalogue (...
In a large-scale double-blind controlled trial of practolol (200 mg twice daily) in the long-term prophylactic treatment 3038 patients recovering from acute myocardial infarction was started one to four weeks after attack. The originally planned include 4000 treated for at least year but had be terminated prematurely because serious oculocutaneous and peritoneal reactions reported elsewhere. Nevertheless, important findings, probably applicable other beta-adrenoreceptor antagonists, have...
Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange information retrieval.