Search results for "Graph database"
showing 10 items of 11 documents
Reactome graph database: Efficient access to complex pathway data
2018
Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its qu…
Performance optimisation of biological pathway data storage, retrieval, analysis and its interactive visualisation
2018
The aim of this research was to optimise the performance of the storage, retrieval, analysis and interactive visualisation of biomolecular pathways data. This was achieved by the adoption of new technologies and a variety of highly optimised data structures, algorithms and strategies across the different layers of the software. The first challenge to overcome was the creation of a long-lasting, large-scale web application to enable pathways navigation; the Pathway Browser. This tool had to aggregate different modules to allow users to browse pathway content and use their own data to perform pathway analysis. Another challenge was the development of a high-performance pathway analysis tool t…
Efficient Graph Models for Retrieving Top-k News Feeds from Ego Networks
2012
A key challenge of web platforms like social networking sites and services for news feed aggregation is the efficient and targeted distribution of new content items to users. This can be formulated as the problem of retrieving the top-k news items out of the d-degree ego network of each given user, where the set of all users producing feeds is of size n, with n >> d >> k and typically k
Estimation des performances, test et contrôle des systèmes cyber-physiques employant des réseaux de communication non idéaux
2020
Wireless technology is a key enabler of the promises of Industry 4.0 (Smart Manufacturing). As such, wireless technology will be adopted as a principal mode of communication within the factory beginning with the factory enterprise and eventually being adopted for use within the factory workcell. Factory workcell communication has particular requirements on latency, reliability, scale, and security that must first be met by the wireless communication technology used. Wireless is considered a non-ideal form of communication in that when compared to its wired counterparts, it is considered less reliable (lossy) and less secure. These possible impairments lead to delay and loss of data in indus…
A Graph Database Approach to Wireless IIoT Workcell Performance Evaluation
2020
The workcell is considered a main building block of various industrial settings. Hence, it is examined as a primary testing environment for studying wireless communication techniques in factory automation processes. A new testbed was recently designed and developed to facilitate such studies in workcells by replicating various data flows in an emulated production environment. In this paper, an approach to storing and analyzing network performance data from a manufacturing factory workcell is introduced. A robotic testbed was constructed using two collaborative grade robot arms, machine emulators, and wireless communication devices. A graph database approach was implemented to capture networ…
RDF* Graph Database as Interlingua for the TextWorld Challenge
2019
This paper briefly describes the top-scoring submission to the First TextWorld Problems: A Reinforcement and Language Learning Challenge. To alleviate the partial observability problem, characteristic to the TextWorld games, we split the Agent into two independent components: Observer and Actor, communicating only via the Interlingua of the RDF* graph database. The RDF* graph database serves as the “world model” memory incrementally updated by the Observer via FrameNet informed Natural Language Understanding techniques and is used by the Actor for the efficient exploration and planning of the game Action sequences. We find that the deep-learning approach works best for the Observer componen…
Approximate Matching over Biological RDF Graphs
2012
In the last few years, the amount of biological interaction data discovered and stored in public databases (e.g., KEGG [2]) considerably increased. To this aim, RDF is a powerful representation for interactions (or pathways), since they can be modeled as directed graphs, often referred to as biological networks, where nodes represent cellular components and the (labeled or unlabeled) edges correspond to interactions among components. Often for a given organism some components are known to be linked by well studied interactions. Such groups of components are called modules and they can be represented by sub-graphs in the corresponding biological network model. At today, one of the most impor…
A new approach based on NμSMV Model to query semantic graph
2011
International audience; The language most frequently used to represent the semantic graphs is the RDF (W3C standard for meta-modeling). The construction of semantic graphs is a source of numerous errors of interpretation. Processing of large semantic graphs can be a limit to use semantics in modern information systems. The work presented in this paper is part of a new research at the border between two areas: the semantic web and the model checking. For this, we developed a tool, RDF2NμSMV, which converts RDF graphs into NμSMV language. This conversion aims checking the semantic graphs with the model checker NμSMV in order to verify the consistency of the data. The data integration and shar…
Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes
2023
Legumes, and especially pulses, are an important source of protein for food and feed, and are appreciated for their positive impact on the “one health”. However, their unstable yields and their susceptibility to biotic and abiotic stresses highlight the need for varietal improvement in order to increase the cultivated areas and productivity. With the advent of sequencing technologies, a large pool of genetic and -omics resources, heterogeneous at the inter- and intra-species scale, is emerging. Thus, it is important to capitalize on these scattered heterogeneous data to develop translational research to boost breeding projects and crop diversification. To meet this need, we undertook the de…
A modelling framework for social media monitoring
2013
This paper describes a hierarchical, three-level modelling framework for monitoring social media. Immediate social reality is modelled through the first level of the models. They represent various virtual communities at social media sites and adhere to the social world models of the sites, i.e., the "site ontologies". The second-level model is a temporal multirelational graph that captures the static and dynamic properties of the first-level models from the perspective of the monitoring site. The third-level model consists of a temporal relational database scheme that models the temporal multirelational graph within the database. The models are specified and instantiated at the monitoring s…