Search results for "Knowledge bases"
showing 10 items of 16 documents
Transcriptomic responses to biotic stresses in Malus x domestica: a meta-analysis study.
2017
AbstractRNA-Seq analysis is a strong tool to gain insight into the molecular responses to biotic stresses in plants. The objective of this work is to identify specific and common molecular responses between different transcriptomic data related to fungi, virus and bacteria attacks in Malus x domestica. We analyzed seven transcriptomic datasets in Malus x domestica divided in responses to fungal pathogens, virus (Apple Stem Grooving Virus) and bacteria (Erwinia amylovora). Data were dissected using an integrated approach of pathway- and gene- set enrichment analysis, Mapman visualization tool, gene ontology analysis and inferred protein-protein interaction network. Our meta-analysis revealed…
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…
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…
WES/WGS Reporting of Mutations from Cardiovascular "Actionable" Genes in Clinical Practice: A Key Role for UMD Knowledgebases in the Era of Big Datab…
2016
International audience; High-throughput next-generation sequencing such as whole-exome and whole-genome sequencing are being rapidly integrated into clinical practice. The use of these techniques leads to the identification of secondary variants for which decisions about the reporting or not to the patient need to be made. The American College of Medical Genetics and Genomics recently published recommendations for the reporting of these variants in clinical practice for 56 "actionable" genes. Among these, seven are involved in Marfan Syndrome And Related Disorders (MSARD) resulting from mutations of the FBN1, TGFBR1 and 2, ACTA2, SMAD3, MYH11 and MYLK genes. Here, we show that mutations col…
Implementation of a knowledge-based methodology in a decision support system for the design of suitable wastewater treatment process flow diagrams.
2011
In light of rapid global change, the demand for wastewater treatment is increasing rapidly and will continue to do so in the near future. Wastewater management is a complex puzzle for which the proper pieces must be combined to achieve the desired solution, requiring the simultaneous consideration of technical, economic, social and environmental issues. In this context, a knowledge-based methodology (KBM) for the conceptual design of wastewater treatment plant (WWTP) process flow diagrams (PFDs) and its application for two scenarios is presented in this paper. The core of the KBM is composed of two knowledge bases (KBs). The first, a specification knowledge base (S-KB), summarizes the main …
A knowledge-based decision support system in bioinformatics: An application to protein complex extraction
2013
Abstract Background We introduce a Knowledge-based Decision Support System (KDSS) in order to face the Protein Complex Extraction issue. Using a Knowledge Base (KB) coding the expertise about the proposed scenario, our KDSS is able to suggest both strategies and tools, according to the features of input dataset. Our system provides a navigable workflow for the current experiment and furthermore it offers support in the configuration and running of every processing component of that workflow. This last feature makes our system a crossover between classical DSS and Workflow Management Systems. Results We briefly present the KDSS' architecture and basic concepts used in the design of the knowl…
Probabilistic Logic under Coherence‚ Model−Theoretic Probabilistic Logic‚ and Default Reasoning in System P
2016
We study probabilistic logic under the viewpoint of the coherence principle of de Finetti. In detail, we explore how probabilistic reasoning under coherence is related to model-theoretic probabilistic reasoning and to default reasoning in System P. In particular, we show that the notions of g-coherence and of g-coherent entailment can be expressed by combining notions in model-theoretic probabilistic logic with concepts from default reasoning. Moreover, we show that probabilistic reasoning under coherence is a generalization of default reasoning in System P. That is, we provide a new probabilistic semantics for System P, which neither uses infinitesimal probabilities nor atomic bound (or bi…
Probabilistic Logic under Coherence, Model-Theoretic Probabilistic Logic, and Default Reasoning
2001
We study probabilistic logic under the viewpoint of the coherence principle of de Finetti. In detail, we explore the relationship between coherence-based and model-theoretic probabilistic logic. Interestingly, we show that the notions of g-coherence and of g-coherent entailment can be expressed by combining notions in model-theoretic probabilistic logic with concepts from default reasoning. Crucially, we even show that probabilistic reasoning under coherence is a probabilistic generalization of default reasoning in system P. That is, we provide a new probabilistic semantics for system P, which is neither based on infinitesimal probabilities nor on atomic-bound (or also big-stepped) probabil…
Quasi Conjunction and Inclusion Relation in Probabilistic Default Reasoning
2011
We study the quasi conjunction and the Goodman & Nguyen inclusion relation for conditional events, in the setting of probabilistic default reasoning under coherence. We deepen two recent results given in (Gilio and Sanfilippo, 2010): the first result concerns p-entailment from a family F of conditional events to the quasi conjunction C(S) associated with each nonempty subset S of F; the second result, among other aspects, analyzes the equivalence between p-entailment from F and p-entailment from C(S), where S is some nonempty subset of F. We also characterize p-entailment by some alternative theorems. Finally, we deepen the connections between p-entailment and the Goodman & Nguyen inclusion…
Heyting-valued interpretations for Constructive Set Theory
2006
AbstractWe define and investigate Heyting-valued interpretations for Constructive Zermelo–Frankel set theory (CZF). These interpretations provide models for CZF that are analogous to Boolean-valued models for ZF and to Heyting-valued models for IZF. Heyting-valued interpretations are defined here using set-generated frames and formal topologies. As applications of Heyting-valued interpretations, we present a relative consistency result and an independence proof.