Search results for "Ontologies"
showing 10 items of 49 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.
Sub-Symbolic Mapping of Cyc Microtheories in Data-Driven 'Conceptual' Spaces
2007
The presented work aims to combine statistical and cognitive-oriented approaches with symbolic ones so that a conceptual similarity relationship layer can be added to a Cyc KB microtheory. Given a specific microtheory, a LSA-inspired conceptual space is inferred from a corpus of texts created using both ad hoc extracted pages from the Wikipedia repository and the built-in comments about the concepts of the specific Cyc microtheory. Each concept is projected in the conceptual space and the desired layer of sub-symbolic relationships between concepts is created. This procedure can help a user in finding the concepts that are "sub-symbolically conceptually related" to a new concept that he wan…
Defining the genomic signature of totipotency and pluripotency during early human development.
2013
The genetic mechanisms governing human pre-implantation embryo development and the in vitro counterparts, human embryonic stem cells (hESCs), still remain incomplete. Previous global genome studies demonstrated that totipotent blastomeres from day-3 human embryos and pluripotent inner cell masses (ICMs) from blastocysts, display unique and differing transcriptomes. Nevertheless, comparative gene expression analysis has revealed that no significant differences exist between hESCs derived from blastomeres versus those obtained from ICMs, suggesting that pluripotent hESCs involve a new developmental progression. To understand early human stages evolution, we developed an undifferentiation netw…
A Semantic Web Approach for Geodata Discovery
2013
International audience; Currently, vast amounts of geospatial information are o ffered through OGC's services. However this information has limited formal semantics. The most common method to search for a dataset consists in matching keywords to metadata elements. By adding semantics to available descriptions we could use modern inference and reasoning mechanisms currently available in the SemanticWeb. In this paper we present a novel architecture currently in development in which we use state of the art triplestores as the backend of a CSW service. In our approach, each metadata record is considered an instance of a given class in a domain ontology. Our architecture also adds a spatial dat…
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.
Enrichissement sémantique d'un fichier IFC pour une extraction partielle dynamique
2014
International audience; La dématérialisation de l'ensemble des données et des processus dans le domaine du bâtiment est un enjeu mondial depuis ces 10 dernières années. Au-delà de la simple représentation géométrique d'un bâtiment, le BIM s'impose petit à petit comme un système d'information coopératif complexe, intégrant avec difficulté les données et pratiques hétérogènes des différents acteurs du domaine. La restitution intégrée de ces données aux usagers du bâtiment est une opération délicate. Pour répondre à ce verrou, nous utilisons une approche sémantique de représentation du bâtiment et particulièrement de la norme IFC. Cette approche permet d'extraire des fichiers IFC valides, part…
On Using Conceptual Modeling for Ontologies
2004
Are database concepts and techniques suitable for ontology design and management? The question has been on the floor for some time already. It gets a new emphasis today, thanks to the focus on ontologies and ontology services due to the spread of web services as a new paradigm for information management. This paper analyzes some of the arguments that are relevant to the debate, in particular the question whether conceptual data models would adequately support the design and use of ontologies. It concludes suggesting a hybrid approach, combining databases and logic-based services.
DYNAMIC SEMANTIC USER PROFILING FROM IMPLICIT WEB NAVIGATION DATA
2014
International audience; On the Web, pages are often dynamically generated and allow publishers to individually adapt contents to each viewer. Underlying systems must correctly understand the user's context - crucial especially in the case of online advertisement placement. The article at hand describes our proposition of a novel profiling system, adapted to the special needs of digital advertising. Based on Semantic Web Technologies, the MindMinings system relies on an ontology to enable thorough understanding of each user's context and needs. The underlying ontology structure also provides enhanced interoperability with semantically annotated knowledge resources, notably vocabularies from …