A5089900113- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- Semantic Web and Ontologies
- Genomics and Rare Diseases
- Inflammatory Bowel Disease
- Atrial Fibrillation Management and Outcomes
- Topic Modeling
- Gene expression and cancer classification
- Emergency and Acute Care Studies
- Cardiovascular Function and Risk Factors
- Disaster Response and Management
- Scientific Computing and Data Management
- Trauma and Emergency Care Studies
- Microscopic Colitis
- Metabolomics and Mass Spectrometry Studies
- Natural Language Processing Techniques
- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Helicobacter pylori-related gastroenterology studies
- Machine Learning in Healthcare
- Cardiomyopathy and Myosin Studies
- Colorectal Cancer Screening and Detection
- Computational Drug Discovery Methods
- Genetics, Bioinformatics, and Biomedical Research
- Diabetes Management and Research
University of Birmingham
2016-2025
Health Data Research UK
2018-2025
University Hospitals Birmingham NHS Foundation Trust
2016-2025
NIHR CRUK Experimental Cancer Medicine Centre
2018-2024
NIHR Birmingham Biomedical Research Centre
2018-2024
Genomics (United Kingdom)
2019-2024
Turing Institute
2020-2024
University Medical Center Hamburg-Eppendorf
2024
Universität Hamburg
2024
Sorbonne Université
2024
The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% all using terms from ontologies anatomy, cell types, function, embryology, pathology other domains. This allows interoperability with several resources, especially...
Abstract Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is associated with a range of persistent symptoms impacting everyday functioning, known as post-COVID-19 condition or long COVID. We undertook retrospective matched cohort study using UK-based primary care database, Clinical Practice Research Datalink Aurum, to determine that are confirmed SARS-CoV-2 beyond 12 weeks in non-hospitalized adults and the risk factors developing symptoms. selected 486,149 1,944,580...
Abstract We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety anatomical entities, organized according to traditional classification criteria. The represents structures in species-neutral way and includes extensive associations existing species-centric ontologies, allowing integration model organism human data. Uberon provides necessary bridge between different taxa for inference. It uses novel methods taxonomic variation, has proved...
Phenotype ontologies are typically constructed to serve the needs of a particular community, such as annotation genotype-phenotype associations in mouse or human. Here we demonstrate how these can be improved through assignment logical definitions using core ontology phenotypic qualities and multiple additional from Open Biological Ontologies library. We also show used for data integration when combined with unified multi-species anatomy ontology.
Ontologies are widely used in biological and biomedical research. Their success lies their combination of four main features present almost all ontologies: provision standard identifiers for classes relations that represent the phenomena within a domain; vocabulary metadata describes intended meaning ontologies; machine-readable axioms definitions enable computational access to some aspects relations. While each these enables applications facilitate data integration, analysis, great...
Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack community-wide, consensus-based, human- machine-interpretable language for describing phenotypes genomic environmental contexts is perhaps most pressing scientific bottleneck integration across many key fields in biology, including genomics, systems development, medicine, evolution, ecology, systematics. Here we survey phenomics...
<h3>Importance</h3> Previous in vitro and postmortem research suggests that inflammation may lead to structural brain changes via activation of microglia and/or astrocytic dysfunction a range neuropsychiatric disorders. <h3>Objective</h3> To investigate the relationship between structures vivo explore transcriptome-driven functional basis with relevance mental illness. <h3>Design, Setting, Participants</h3> This study used multistage linked analyses, including mendelian randomization (MR),...
Abstract Background The National Early Warning Score (NEWS2) is currently recommended in the UK for risk stratification of COVID-19 patients, but little known about its ability to detect severe cases. We aimed evaluate NEWS2 prediction outcome and identify validate a set blood physiological parameters routinely collected at hospital admission improve upon use alone medium-term stratification. Methods Training cohorts comprised 1276 patients admitted King’s College Hospital Health Service...
BACKGROUND: In patients with hypertrophic cardiomyopathy, the prognostic value of myocardial T1 and extracellular volume fraction for adverse cardiovascular events has not been well defined. METHODS: A total 663 consecutive participants cardiomyopathy who underwent 3T magnetic resonance were recruited. The follow-up end points included heart failure (HF)-related death, HF hospitalization, sudden cardiac death or aborted death. RESULTS: On Cox proportional hazards regression multivariable...
Abstract The mouse is an important model of human genetic disease. Describing phenotypes mutant mice in a standard, structured manner that will facilitate data mining major challenge for bioinformatics. Here we describe novel, compositional approach to this problem which combines core ontologies from variety sources. This produces framework with greater flexibility, power and economy than previous approaches. We discuss some the issues raises.
Phenotypes are investigated in model organisms to understand and reveal the molecular mechanisms underlying disease. Phenotype ontologies were developed capture compare phenotypes within context of a single species. Recently, these augmented with formal class definitions that may be utilized integrate phenotypic data enable direct comparison between different We have method transform phenotype into representation, combine anatomy ontologies, apply measure semantic similarity construct...
The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants annotations to genes phenotypes. Ontologies serve as common standards semantic integration large growing corpus plant genomics, phenomics genetics data. include the Plant Ontology, Trait Ontology Experimental Conditions developed by project, along with Gene Chemical Entities Biological Interest, Phenotype Attribute others. also access Crop various breeding research...
Undetected atrial fibrillation (AF) is a major health concern. Blood biomarkers associated with AF could simplify patient selection for screening and further inform ongoing research towards stratified prevention treatment of AF. Forty common cardiovascular were quantified in 638 consecutive patients referred to hospital [mean ± standard deviation age 70 12 years, 398 (62%) male, 294 (46%) AF] known or ≥2 CHA2DS2-VASc risk factors. Paroxysmal silent was ruled out by 7-day ECG monitoring....
Abstract Background Although a majority of patients with PSC have colitis [PSC-IBD; primary sclerosing cholangitis-inflammatory bowel disease], this is phenotypically different from ulcerative [UC]. We sought to define further the pathophysiological differences between PSC-IBD and UC, by applying comparative integrative approach colonic gene expression, gut microbiota immune infiltration data. Methods Colonic biopsies were collected [n = 10], UC healthy controls [HC; n 10]. Shotgun...
Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These meant replace biocurators, instead assist them in one or more curation steps. To do so, the user interface is an important aspect that needs be considered for tool adoption. The BioCreative Interactive task (IAT) a track designed exploring user-system interactions, promoting development of useful TM tools, providing...
Abstract Phenotypes are the observable characteristics of an organism arising from its response to environment. associated with engineered and natural genetic variation widely recorded using phenotype ontologies in model organisms, as signs symptoms human Mendelian diseases databases such OMIM Orphanet. Exploiting these resources, several computational methods have been developed for integration analysis data identify etiology or suggest plausible interventions. A similar resource would be...
The past decade has seen an explosion in the collection of genotype data domains as diverse medicine, ecology, livestock and plant breeding. Along with this comes challenge dealing related phenotype data, which is not only large but also highly multidimensional. Computational analysis phenotypes therefore become critical for our ability to understand biological meaning genomic sciences. At heart computational are ontologies. A number these ontologies have been developed across many domains,...
Introduction The association between allergic diseases and autoimmune disorders is not well established. Our objective was to determine incidence rates of in rhinitis/conjunctivitis (ARC), atopic eczema asthma, investigate for co-occurring patterns. Methods This a retrospective cohort study (1990–2018) employing data extracted from Health Improvement Network (UK primary care database). exposure group comprised ARC, asthma (all ages). For each exposed patient, up two randomly selected age-...
Abstract Background Biomarker identification is one of the major and important goal functional genomics translational medicine studies. Large scale –omics data are increasingly being accumulated can provide vital means for biomarkers early diagnosis complex disease and/or advanced patient/diseases stratification. These tasks clearly interlinked, it essential that an unbiased stable methodology applied in order to address them. Although, recently, many, primarily machine learning based,...
Abstract The use of primary care electronic health records for research is abundant. benefits gained from utilising such lies in their size, longitudinal data collection and quality. However, the to undertake high quality epidemiological studies, can lead significant challenges particularly dealing with misclassification, variation coding effort required pre-process a meaningful format statistical analysis. In this paper, we describe methodology aid extraction processing databases, delivered...