A5044072805- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- Health Policy Implementation Science
- Behavioral Health and Interventions
- Advanced Text Analysis Techniques
- Scientific Computing and Data Management
- Metabolomics and Mass Spectrometry Studies
- Artificial Intelligence in Healthcare and Education
- Mental Health Research Topics
- Microbial Metabolic Engineering and Bioproduction
- Ethics in Clinical Research
- Genetics, Bioinformatics, and Biomedical Research
- Electronic Health Records Systems
- Topic Modeling
- Mental Health and Psychiatry
- Natural Language Processing Techniques
- Research Data Management Practices
- Smoking Behavior and Cessation
- Digital Mental Health Interventions
- History and advancements in chemistry
- Genetics, Aging, and Longevity in Model Organisms
- Radiomics and Machine Learning in Medical Imaging
- Machine Learning in Materials Science
University of St. Gallen
2022-2025
University of Zurich
2022-2025
SIB Swiss Institute of Bioinformatics
2013-2025
University College London
2019-2023
Otto-von-Guericke University Magdeburg
2020-2023
University of New Brunswick
2023
New York University
2023
Universidad de Londres
2019-2022
University of London
2019-2022
École Polytechnique Fédérale de Lausanne
2020-2021
Scientists have long been driven by the desire to describe, organize, classify, and compare objects using taxonomies and/or ontologies. In contrast biology, geology, many other scientific disciplines, world of chemistry still lacks a standardized chemical ontology or taxonomy. Several attempts at classification made; but they mostly limited either manual, semi-automated proof-of-principle applications. This is regrettable as comprehensive description tools could not only improve our...
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary molecular entities focused on 'small' chemical compounds. The in question are either natural products or synthetic used to intervene the processes living organisms. Genome-encoded macromolecules (nucleic acids, proteins and peptides derived from by cleavage) not as rule included ChEBI. In addition entities, ChEBI contains groups (parts entities) classes entities. includes an ontological classification, whereby...
ChEBI is a database and ontology containing information about chemical entities of biological interest. It currently includes over 46 000 entries, each which classified within the assigned multiple annotations including (where relevant) structure, cross-references, synonyms literature citations. All content freely available can be accessed online at http://www.ebi.ac.uk/chebi. In this update paper, we describe recent improvements additions to offering. We have substantially extended our...
MetaboLights (http://www.ebi.ac.uk/metabolights) is the first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained by one of major providers in molecular biology. Metabolomic profiling an important tool research into biological functioning systemic perturbations caused diseases, diet environment. The effectiveness such methods depends on availability public open across a broad range conditions. repository, powered...
ChEBI (http://www.ebi.ac.uk/chebi) is a database and ontology of chemical entities biological interest. Over the past few years, has continued to grow steadily in content, added several new features. In addition incorporating all user-requested compounds, our annotation efforts have emphasized immunology, natural products metabolites many species. All entries are now 'is_a' classified within ontology, meaning that chemicals available semantic reasoning tools harness classification hierarchy....
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary molecular entities focused on ‘small’ chemical compounds. The in question are either natural products or synthetic used to intervene the processes living organisms. Genome-encoded macromolecules (nucleic acids, proteins and peptides derived from by cleavage) not as rule included ChEBI. In addition entities, ChEBI contains groups (parts entities) classes entities. includes an ontological classification, whereby...
The Behaviour Change Technique Taxonomy v1 (BCTTv1) specifies the potentially active content of behaviour change interventions. Evaluation BCTTv1 showed need to extend it into a formal ontology, improve its labels and definitions, add BCTs subdivide existing BCTs. We aimed develop Ontology (BCTO) that would meet these needs.
UniChem is a freely available compound identifier mapping service on the internet, designed to optimize efficiency with which structure-based hyperlinks may be built and maintained between chemistry-based resources. In past, creation maintenance of such links at EMBL-EBI, where several resources exist, has required independent efforts by each separate teams. These were complicated different data models, release schedules, differing business rules for normalization nomenclature that exist...
PubChem is an open repository for chemical structures, biological activities and biomedical annotations. Semantic Web technologies are emerging as increasingly important approach to distribute integrate scientific data. Exposing data services may help enable automated integration management, well facilitate interoperable web applications.This work, one of a series covering the PubChemRDF project, describes translate Substance Compound information into Resource Description Framework (RDF)...
Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others back Uniform Identifiers (URIs). makes the machine-readable uses extensible vocabularies for additional information, making it easier scale up inference analysis.This paper describes recent developments in an ongoing project converting from ChEMBL database into triples. Relative earlier versions, this...
Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas biology where cheminformatics plays an important role computational research, including metabolism, proteomics, and systems biology. One critical aspect these fields accurate exchange data, which increasingly accomplished through use ontologies. Ontologies formal representations objects their properties using a logic-based ontology language. Many such ontologies currently...
In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such depends on the discipline science humble bricks mortar that make integration possible; identifiers a core component this infrastructure. Drawing our experience work by other groups, we outline 10 lessons have learned about identifier qualities best practices facilitate large-scale integration. Specifically, propose actions...
Background: The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified need for computational infrastructure toxicological data management engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower harmonized approach research in nanotechnology. This setting provides number opportunities challenges representation integration ENM information originating from diverse systems. Within this cluster, eNanoMapper...
<ns4:p><ns4:bold>Background: </ns4:bold>Behaviour change interventions (BCI), their contexts and evaluation methods are heterogeneous, making it difficult to synthesise evidence make recommendations for real-world policy practice. Ontologies provide a means addressing this. They represent knowledge formally as entities relationships using common language able cross disciplinary boundaries topic domains. This paper reports the development of upper level Behaviour Change Intervention Ontology...
Abstract Despite the strong evidence linking aggregation of Huntingtin protein (Htt) to pathogenesis Huntington’s disease (HD), mechanisms underlying Htt and neurodegeneration remain poorly understood. Herein, we investigated ultrastructural properties composition cytoplasmic nuclear inclusions in mammalian cells primary neurons overexpressing mutant exon1 protein. Our findings provide unique insight into their formation. We show that inclusion formation maturation are complex processes...
<ns3:p><ns3:bold>Background: </ns3:bold>Behaviour change interventions (BCI), their contexts and evaluation methods are heterogeneous, making it difficult to synthesise evidence make recommendations for real-world policy practice. Ontologies provide a means addressing this. They represent knowledge formally as entities relationships using common language able cross disciplinary boundaries topic domains. This paper reports the development of upper level Behaviour Change Intervention Ontology...
<ns4:p><ns4:bold>Background:</ns4:bold> Investigating and improving the effects of behaviour change interventions requires detailed consistent specification all aspects interventions. An important feature is way in which these are delivered, i.e. their mode delivery. This paper describes an ontology for specifying delivery interventions, forms part Behaviour Change Intervention Ontology, currently being developed Wellcome Trust funded Human Behaviour-Change Project.</ns4:p><ns4:p>...
Heterogeneous data, different definitions and incompatible models are a huge problem in many domains, with no exception for the field of energy systems analysis. Hence, it is hard to re-use results, compare model results or couple at all. Ontologies provide precisely defined vocabulary build common shared conceptualisation domain. Here, we present Open Energy Ontology (OEO) developed domain Using OEO provides several benefits community. First, enables consistent annotation large amounts data...
<ns4:p>Background The Behaviour Change Technique Taxonomy v1 (BCTTv1) specifies the potentially active content of behaviour change interventions. Evaluation BCTTv1 showed need to extend it into a formal ontology, improve its labels and definitions, add BCTs subdivide existing BCTs. We aimed develop Ontology (BCTO) that would meet these needs. Methods BCTO was developed by: (1) collating synthesising feedback from multiple sources; (2) extracting information published studies classification...
Trace amine-associated receptor 1 (TAAR1) agonism shows promise for treating psychosis, prompting us to synthesise data from human and non-human studies.