Bernard de Bono

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Reactome, located at is a curated, peer-reviewed resource of human biological processes. Given the genetic makeup of an organism, the complete set of possible reactions constitutes its reactome. The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathways. The Reactome data(More)
Reactome ( is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2975 human proteins, 2907 reactions and 4455 literature citations. A new entity-level pathway viewer and improved search and data mining tools(More)
The CD33-related sialic acid binding Ig-like lectins (CD33rSiglecs) are predominantly inhibitory receptors expressed on leukocytes. They are distinguishable from conserved Siglecs, such as Sialoadhesin and MAG, by their rapid evolution. A comparison of the CD33rSiglec gene cluster in different mammalian species showed that it can be divided into(More)
Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an(More)
SUMMARY The article presents an infrastructure for supporting the semantic interoperability of biomedical resources based on the management (storing and inference-based querying) of their ontology-based annotations. This infrastructure consists of: (i) a repository to store and query ontology-based annotations; (ii) a knowledge base server with an inference(More)
The practice and research of biomedicine generates considerable quantities of data and model resources (DMRs). The RICORDO effort works closely with modelling communities in the physiology and pharmacology domains to provide a semantic interoperability framework that addresses obstacles to biomedical DMR sharing. The RICORDO framework adopts a core set of(More)
BACKGROUND Large biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. Hindering these initiatives is a lack of a comprehensive ontology that covers the essential concepts of the simulation domain. RESULTS We(More)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD United Kingdom Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY 11724 USA NYU School of Medicine, 550 First Avenue, New York NY 10016 USA College of Pharmacy and Allied Health Professions, St. John’s University, 8000 Utopia Parkway, Queens NY(More)