A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

<p>Abstract</p> <p>Background</p> <p>Metabolic reconstructions (MRs) are common denominators in systems biology and represent biochemical, genetic, and genomic (BiGG) knowledge-bases for target organisms by capturing currently available information in a consistent, structured manner. <it>Salmonella enterica </it>subspecies I serovar Typhimurium is a human pathogen, causes various diseases and its increasing antibiotic resistance poses a public health problem.</p> <p>Results</p> <p>Here, we describe a community-driven effort, in which more than 20 experts in <it>S</it>. Typhimurium biology and systems biology collaborated to reconcile and expand the <it>S</it>. Typhimurium BiGG knowledge-base. The consensus MR was obtained starting from two independently developed MRs for <it>S</it>. Typhimurium. Key results of this reconstruction jamboree include i) development and implementation of a community-based workflow for MR annotation and reconciliation; ii) incorporation of thermodynamic information; and iii) use of the consensus MR to identify potential multi-target drug therapy approaches.</p> <p>Conclusion</p> <p>Taken together, with the growing number of parallel MRs a structured, community-driven approach will be necessary to maximize quality while increasing adoption of MRs in experimental design and interpretation.</p

OntoDB2 (un système flexible et efficient de base de données à base ontologique pour le web sémantique et les données techniques)

Le besoin d'expliciter la sémantique des données dans différents domaines scientifiques (biologie, médecine, géographie, ingénierie, etc.) s'est traduit par la définition de données faisant référence à des ontologies, encore appelées données à base ontologique. Avec la multiplication des ontologies de domaine, et le volume important de données à manipuler, est apparu le besoin de systèmes susceptibles de gérer des données à base ontologique de grande taille. De tels systèmes sont appelés des systèmes de gestion de Bases de Données à Base Ontologique (BDBO). Les principales limitations des systèmes de gestion de BDBO existants sont (1) leur rigidité, due à la prise en compte des constructions d'un unique formalisme d'expression d'ontologies, (2) l'absence de support pour les données non standard (spatiales, temporelles, etc.) et, (3) leur manque d'efficacité pour gérer efficacement les données de grande taille. Nous proposons dans cette thèse un nouveau système de gestion de BDBO permettant (1) de supporter des ontologies basées sur différents formalismes d'ontologies, (2) l'extension de son formalisme d'ontologie pour répondre aux besoins spécifiques des applications, et (3) une gestion originale des données facilitant le passage à grande échelle. Le système que nous proposons dans cette thèse, ontodb2, se fonde sur l'existence d'un ensemble de constructions communes aux différents formalismes d'expression d'ontologies, susceptible de constituer une ontologie noyau, et sur les techniques de gestion des modèles pour permettre l'extension flexible de ce noyau. Nous proposons également une approche originale de gestion des données à base ontologique. Cette approche part du fait que les données à base ontologique peuvent se classifier en données canoniques (instances de classes primitives) et noncanoniques (instances de classes définies). Les instances de classes définies peuvent, sous certaines hypothèses, s'exprimer en termes d'instances de classes primitives. Nous proposons donc de ne représenter que les données canoniques, en transformant sous certaines conditions, toute donnée non-canonique en donnée canonique. Enfin, nous proposons d'exploiter l'interpréteur de requêtes ontologiques pour permettre (1) l'accès aux données non-canoniques ainsi transformées et, (2) d'indexer et pré-calculer les raisonnements en se basant sur les mécanismes du SGBD support. L'ensemble de ces propositions est validé (1) à travers une implémentation sur le SGBD PostgreSQL basée sur les formalismes d'ontologies PLIB, RDFS et OWL Lite, (2) des tests de performances sur des ensembles de données issus de la géographie et du Web.The need to represent the semantics of data in various scientific fields (medicine, geography, engineering, etc ) has resulted in the definition of data referring to ontologies, also called ontology-based data. With the proliferation of domain ontologies, and the increasing volume of data to handle, has emerge the need to define systems capable of managing large size of ontology-based data. Such systems are called Ontology Based DataBase (OBDB) Management Systems. The main limitations of existing OBDB systems are (1) their rigidity, (2) lack of support for non standard data (spatial, temporal, etc ) and (3) their lack of effectiveness to manage large size data. In this thesis, we propose a new OBDB called OntoDB2, allowing (1) the support of ontologies based on different ontology models, (2) the extension of its model to meet specific applications requirements, and (3) an original management of ontology-based data facilitating scalability. Onto DB2 is based on the existence of a kernel ontology, and model-based techniques to enable a flexible extension of this kernel. We propose to represent only canonical data by transforming, under certain conditions, any given non-canonical data to its canonical representation. We propose to use the ontology query language to (1) to access non-canonical data thereby transform and, (2) index and pre-calculate the reasoning operations by using the mechanisms of the underlying DBMS.POITIERS-BU Sciences (861942102) / SudocSudocFranceF

Contaminants in Foods of Animal Origin in Cameroon: A One Health Vision for Risk Management “from Farm to Fork”

Foods of animal origin represent an important share in the diet of Cameroonian populations. Cameroon is known to be a food basket in the west and central Africa sub-region, and an important supplier of foods on the international markets. In the meantime, food importation is continuously increasing to meet the high demand of a more westernized segment of the population. Cereals, fish, sea products, eggs, honey, shrimps, chicken, and feed ingredients are important share in the international trade of agricultural products. Few controls are made on the quality and safety of these products. Certain safety standards do exist but are still yet to be enforced. Inspections done so far by regulatory authorities are partial and do not cover important hazards that require laboratory analysis. The increasing awareness of population, the burden of new types of disease, as well as the recurrence of food scandals have recently launched a scientific and population debate on the contribution of foods items, especially those of animal origin, to the toxic exposure of food producing animals and humans. This paper critically reviews the occurrence of toxicants in most consumed foods of animal origin in Cameroon. This study included the most consumed food of animal origin, identified during the national household budget survey and contributing to 8.1% of the total diet of an individual. Data evaluated suggest an important contamination by toxic metals, mycotoxins, veterinary drugs’ residues, and pesticides. The current national legal framework is briefly analyzed to explore possible intervention measures in the frame of the One Health approach

Semantic Hubs for Geological Projects

International audienceThis paper describes a service-oriented architecture for accessing resources through semantically designed portals called hubs. The services are dedicated to: (a) ontology management, (b) annotation generation from texts based on linguistic or machine learning techniques, (c) persistent storage ofontologies and metadata, and (d) semantic search in annotation bases or ontological databases. These services are, themselves, semantically annotated in order to facilitate their identification and composition. The application of our methodology is carried out within the e-WOK_HUB project in the geological domain

Semantic Hubs for Geological Projects

International audienceThis paper describes a service-oriented architecture for accessing resources through semantically designed portals called hubs. The services are dedicated to: (a) ontology management, (b) annotation generation from texts based on linguistic or machine learning techniques, (c) persistent storage ofontologies and metadata, and (d) semantic search in annotation bases or ontological databases. These services are, themselves, semantically annotated in order to facilitate their identification and composition. The application of our methodology is carried out within the e-WOK_HUB project in the geological domain