Search results for " Ontologies"
showing 10 items of 28 documents
Reactome diagram viewer: data structures and strategies to boost performance
2017
Abstract Motivation Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. Here, we present comprehensive enhancements in usability and performance based on extensive usability testing sessions and technology developments, aiming to optimize the viewer towards the needs of the community. Results The pathway diagram viewer version 3 achieves consistently better performance, loading and rendering of 97% of the diagrams in Reactome in less than 1 s. Combining the multi-layer html5 canvas strategy with a space partit…
Semantic technologies for industry: From knowledge modeling and integration to intelligent applications
2013
Artificial Intelligence technologies are growingly used within several software systems ranging from Web services to mobile applications. It is by no doubt true that the more AI algorithms and methods are used the more they tend to depart from a pure "AI" spirit and end to refer to the sphere of standard software. In a sense, AI seems strongly connected with ideas, methods and tools that are not (yet) used by the general public. On the contrary, a more realistic view of it would be a rich and pervading set of successful paradigms and approaches. Industry is currently perceiving semantic technologies as a key contribution of AI to innovation. In this paper a survey of current industrial expe…
Domain-Specific OWL Ontology Visualization with OWLGrEd
2015
The OWLGrEd ontology editor allows graphical visualization and authoring of OWL 2.0 ontologies using a compact yet intuitive presentation that combines UML class diagram notation with textual Manchester syntax for expressions. We present an extension mechanism for OWLGrEd that allows adding custom information areas, rules and visual effects to the ontology presentation thus enabling domain specific OWL ontology visualizations. The usage of OWLGrEd and its extensions is demonstrated on ontology engineering examples involving custom annotation visualizations, advanced UML class dia-gram constructs and integrity constraints in semantic database schema design.
Database to Ontology Mapping Patterns in RDB2OWL Lite
2016
We describe the RDB2OWL Lite language for relational database to RDF/OWL mapping specification and discuss the architectural and content specification patterns arising in mapping definition. RDB2OWL Lite is a simplification of original RDB2OWL with aggregation possibilities and order-based filters removed, while providing in-mapping SQL view definition possibilities. The mapping constructs and their usage patterns are illustrated on mapping examples from medical domain: medicine registries and hospital information system. The RDB2OWL Lite mapping implementation is offered both via translation into D2RQ and into standard R2RML mapping notations.
Swarming : An Investigation Practice Supporting a Bottom-up Ecological Transition
2022
Dans cet article, nous rendons compte des pratiques d’essaimage d’initiatives locales de transition portées par des collectifs citoyens et associatifs en région Bourgogne Franche-Comté. L’essaimage, défini comme une façon d’enquêter pour agir, caractérise un « activisme environnemental du faire » qui se structure de manière réticulaire et translocale. Ces multiples initiatives qui font des gestes du quotidien un levier de transformation écologique s’activent avec ou sans les institutions territoriales. Celles-ci, indépendamment de l’écho qu’elles renvoient à ces expérimentations, sont interpellées dans leur manière de concevoir l’action publique sous contrainte écologique forte.
DeepSRE: Identification of sterol responsive elements and nuclear transcription factors Y proximity in human DNA by Convolutional Neural Network anal…
2021
SREBP1 and 2, are cholesterol sensors able to modulate cholesterol-related gene expression responses. SREBPs binding sites are characterized by the presence of multiple target sequences as SRE, NFY and SP1, that can be arranged differently in different genes, so that it is not easy to identify the binding site on the basis of direct DNA sequence analysis. This paper presents a complete workflow based on a one-dimensional Convolutional Neural Network (CNN) model able to detect putative SREBPs binding sites irrespective of target elements arrangements. The strategy is based on the recognition of SRE linked (less than 250 bp) to NFY sequences according to chromosomal localization derived from …
Ontology mapping specification in description logics for cooperative systems
2006
Le developpement rapide du Web semantique est lie a la specification de plus en plus d'ontologies. Celles-ci permettent de modeliser des connaissances agreees par des communautes de personnes concernant des domaines ou des tâches specifiques. Le meme domaine decrit par deux communautes distinctes sera modelise de facon differente. Les systemes cooperatifs visent a rendre les informations provenant de differentes sources disponibles au-dela de leurs divergences. Pour cela, ils doivent aligner, fusionner ou integrer ces ontologies. La decouverte de mappings est un point cle dans la resolution efficace des heterogeneites entre ontologies. Nous developpons une architecture qui connecte des syst…
Ontology Views for Ontology Change Management
2014
International audience; In the literature, ontology change management systems (OCMS) are direct implementation of the concept of “change management” stated by reference (Klein, 2004). Ontology change management combines ontol- ogy evolution and versioning features to manage ontol- ogy changes and their impacts. Since 2007, many works have combined ontology evolution and versioning into ontology change management systems (OCMS). The evolution subject has been massively studied in these works. They especially addressed the consistence issue for the application of changes on the ontology. These proposals constituted a consequent background for ontology change management but they did not take i…
Data Mining of Specific-Domain Ontology Components
2008
This paper describes an approach for eliciting ontology components by using knowledge maps. The knowledge contained in a particular domain, any kind of text digital archive, is portrayed by assembling and displaying its ontology components.
Semi-automatic Derivation of Specific-Domain Ontologies for the Semantic Web
2006
This paper describes an approach for helping in the semi-automatic construction of specific-domain ontology components contained in a digital archive. This proposal for extracting knowledge from digital sources allows users to have a view of this knowledge and visualize specific-domain ontology components that with further processing can be shared with software agents by embedding it into digital archives themselves in the context of the Semantic Web. In particular, we deal with the issue of not constructing the ontology from scratch, our approach helps us to speed up the ontology creation process.