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…
Ontology languages for the semantic web: A never completely updated review
2006
This paper gives a never completely account of approaches that have been used for the research community for representing knowledge. After underlining the importance of a layered approach and the use of standards, it starts with early efforts used for artificial intelligence researchers. Then recent approaches, aimed mainly at the semantic web, are described. Coding examples from the literature are presented in both sections. Finally, the semantic web ontology creation process, as we envision it, is introduced.
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.
Traitpedia: a collaborative effort to gather species traits
2018
Abstract Summary Traitpedia is a collaborative database aimed to collect binary traits in a tabular form for a growing number of species. Availability and implementation Traitpedia can be accessed from http://cbdm-01.zdv.uni-mainz.de/~munoz/traitpedia. Supplementary information Supplementary data are available at Bioinformatics online.
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.
Ontology-based Integration of Web Navigation for Dynamic User Profiling
2015
The development of technology for handling information on a Big Data-scale is a buzzing topic of current research. Indeed, improved techniques for knowledge discovery are crucial for scientific and economic exploitation of large-scale raw data. In research collaboration with an industrial actor, we explore the applicability of ontology-based knowledge extraction and representation for today's biggest source of large-scale data, the Web. The goal is to develop a profiling application, based on the implicit information that every user leaves while navigating the online, with the goal to identify and model preferences and interests in a detailed user profile. This includes the identification o…
An Innovative Statistical Tool for Automatic OWL-ERD Alignment
2016
Aligning two representations of the same domain with different expressiveness is a crucial topic in nowadays semantic web and big data research. OWL ontologies and Entity Relation Diagrams are the most widespread representations whose alignment allows for semantic data access via ontology interface, and ontology storing techniques. The term ""alignment" encompasses three different processes: OWL-to-ERD and ERD-to-OWL transformation, and OWL-ERD mapping. In this paper an innovative statistical tool is presented to accomplish all the three aspects of the alignment. The main idea relies on the use of a HMM to estimate the most likely ERD sentence that is stated in a suitable grammar, and corre…
Knowledge Discovery and Digital Cartography for the ALS (Linguistic Atlas of Sicily) Project
2009
In this paper the latest developments of the ALS (Linguistic Atlas of Sicily) project are presented. The ALS project has the purpose to define methodologies and tools to allow researches in the socio-linguistic field. Different types of variables (both quantitative and qualitative) are involved. The whole framework is based on the definition of ontology-based applications for the creation, retrieval, manipulation and browsing of related data. To this aim, some mapping processes have been defined. The framework eventually shows the result in many ways including spatial maps. The on-going collaboration process is a perfect example a domain hybridizing process, enabling the training on-the-fie…
Multi-Domain Retrieval of Geospatial Data Sources Implementing a Semantic Catalogue
2015
International audience; Nowadays, the expertise of a user plays an important role in the search and retrieval in the information systems that usually combines general and specialized knowledge in the construction of queries. In addition, most of the queries systems are currently restricted on specific domains. Tackling these issues, we propose a methodology that implements a semantic catalogue in order to provide a smart queries system for retrieving data sources on the web by means of the extension of the user expertise. We propose the combination of a query expansion method, and the use of similarity measures and controlled vocabularies. Thus, it allows the system to recommend data source…