A5058806280- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- Cell Image Analysis Techniques
- Computational Drug Discovery Methods
- Semantic Web and Ontologies
- Genomics and Rare Diseases
- HER2/EGFR in Cancer Research
- Genetics, Bioinformatics, and Biomedical Research
- Health, Environment, Cognitive Aging
- Advanced Proteomics Techniques and Applications
- Research Data Management Practices
- Pharmacovigilance and Adverse Drug Reactions
- Metabolomics and Mass Spectrometry Studies
- Scientific Computing and Data Management
- Nutrition, Genetics, and Disease
- Animal and Plant Science Education
- Pharmacogenetics and Drug Metabolism
- Neural Networks and Applications
- Enzyme Structure and Function
- Service-Oriented Architecture and Web Services
- Science Education and Pedagogy
- Genetics and Physical Performance
- Evolution and Science Education
- Gene expression and cancer classification
- Protein Structure and Dynamics
Wellcome Trust
2016-2017
European Bioinformatics Institute
2016-2017
University of Michigan
2008-2016
Center for Drug Evaluation and Research
2016
Wellcome Sanger Institute
2015
United States Food and Drug Administration
2014
Michigan United
2012
The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, CL has undergone multiple rounds revision and expansion, most notably representation hematopoietic cells. For vivo cells, focuses on vertebrates but provides general classes that can be used for other metazoans, which subtyped species-specific ontologies. Recent work focused extending various types, developing new modules itself, related...
A medical intervention is a procedure or application intended to relieve prevent illness injury. Examples of interventions include vaccination and drug administration. After intervention, adverse events (AEs) may occur which lie outside the consequences intervention. The representation analysis AEs are critical improvement public health. Ontology Adverse Events (OAE), previously named Event (AEO), community-driven ontology developed standardize integrate data relating arising subsequent...
Cell lines have been widely used in biomedical research. The community-based Line Ontology (CLO) is a member of the OBO Foundry library that covers domain cell lines. Since its publication two years ago, significant updates made, including new groups joining CLO consortium, line cells, upper level alignment with (CL) and for Biomedical Investigation, logical extensions. Collaboration among CLO, CL, OBI has established consensus definitions line-specific terms such as ‘cell line’, cell’,...
The integration of cellular and molecular structural data is key to understanding the function macromolecular assemblies complexes in their vivo context. Here we report on outcomes a workshop that discussed how integrate from range public archives. identified two main priorities: development tools file formats support segmentation (that is, decomposition three-dimensional volume into regions can be associated with defined objects), annotation biological structures.
Vaccine adverse events (VAEs) are bodily changes occurring after vaccination. Understanding the event (AE) profiles is a crucial step to identify serious AEs. Two different types of seasonal influenza vaccines have been used on market: trivalent (killed) inactivated vaccine (TIV) and live attenuated (LAIV). Different induced by these two groups were studied based data drawn from CDC Adverse Event Report System (VAERS). Extracted VAERS 37,621 AE reports for four TIVs (Afluria, Fluarix,...
The Centre for Therapeutic Target Validation (CTTV - https://www.targetvalidation.org/ ) was established to generate therapeutic target evidence from genome-scale experiments and analyses. CTTV aims support the validity of targets by integrating existing newly-generated data. Data integration has been achieved in some resources mapping metadata such as disease phenotypes Experimental Factor Ontology (EFO). Additionally, relationship between ontology descriptions rare common diseases their...
A new inter-governmental research infrastructure, ELIXIR, aims to unify bioinformatics resources and life science data across Europe, thereby facilitating their mining (re-)use.
Abstract Motivation: Cell lines are used extensively in biomedical research, but the nomenclature describing cell has not been standardized. The problems both linguistic and experimental. Many ambiguous line names appear published literature. Users of same may refer to it different ways, mutate or become contaminated without knowledge user. As a first step towards rationalizing this nomenclature, we created knowledgebase (CLKB) with well-structured collection descriptive data for cultured...
Intrinsically disordered proteins (IDPs) and intrinsically regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments the field of IDP research within ELIXIR framework. The goal these is to drive creation high-quality tools resources support identification, analysis functional characterisation IDPs. result workshop titled "An protein user community proposal ELIXIR" held at University Padua....
Authoring bio-ontologies is a task that has traditionally been undertaken by skilled experts trained in understanding complex languages such as the Web Ontology Language (OWL), tools designed for experts. As requests new terms are made, need expert ontologists represents bottleneck development process. Furthermore, ability to rigorously enforce ontology design patterns large, collaboratively developed ontologies difficult with existing authoring software. We present Webulous, an application...
Aiming to understand cellular responses different perturbations, the NIH Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program involves many institutes and laboratories working on over a thousand cell lines. The community-based Cell Line Ontology (CLO) is selected as default ontology for LINCS line representation integration. CLO has consistently represented all 1097 lines included information extracted from Data Portal ChEMBL. Using MCF 10A cells an example, we...
<ns4:p>Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology strong links other fields such as biology, chemistry, pharmacology, medicine. With rise of synthetic new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment...
The Experimental Factor Ontology (EFO) is an application ontology driven by experimental variables including cell lines to organize and describe the diverse data resided in EMBL-EBI resources. Cell Line (CLO) OBO community-based that contains information of immortalized relevant components. EFO integrates extends ontologies from bio-ontology community drive a number practical applications. It desirable shares design patterns therefore reuses line representation (CLO). There are, however,...
Stem cells and stem cell lines are widely used in biomedical research. The Cell Ontology (CL) Line (CLO) two community-based OBO Foundry ontologies the domains of vivo vitro line cells, respectively. To support standardized investigations, we have developed an for Investigations (OSCI). OSCI imports terms from CL CLO, investigation-related existing ontologies. A novel focus is its application representing metadata types associated with various investigations. We also applied to...
<ns3:p>Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology strong links other fields such as biology, chemistry, pharmacology medicine. With rise of synthetic new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment...
Cell lines and cell types are extensively studied in biomedical research yielding to a significant amount of publications each year. Identifying precisely is crucial for science reproducibility knowledge integration. There efforts standardisation the nomenclature based on ontology development support FAIR principles knowledge. However, it important analyse usage at large scale understanding level uptake literature by scientists. In this study, we nomenclature, both Vivo, Vitro using text...
<ns5:p>Integrative drug safety research in translational health informatics has rapidly evolved and included data that are drawn from many resources, combining diverse either reused (curated) repositories, or newly generated at source. Each resource is mandated by different sets of metadata rules imposed on the incoming data. Combination cannot be readily achieved without interference stewardship top-down policy guidelines supervise inform process for combination to aid meaningful...