Search results for "Knowledge base"
showing 10 items of 142 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…
Taxonomy 2.0: computer-aided identification tools to assist Antarctic biologists in the field and in the laboratory
2020
Species inventories are essential to the implementation of conservation policies to mitigate biodiversity loss and maintain ecosystem services and their value to the society. This is particularly topical with respect to climate change and direct anthropogenic effects on Antarctic biodiversity, with the identification of the most at-risk taxa and geographical areas becoming a priority. Identification tools are often neglected and considered helpful only for taxonomists. However, the development of new online information technologies and computer-aided identification tools provides an opportunity to promote them to a wider audience, especially considering the emerging generation of scientists…
A Hierarchical Learning Scheme for Solving the Stochastic Point Location Problem
2012
Published version of a chapter in the book: Advanced Research in Applied Artificial Intelligence. Also available from the publisher at: http://dx.doi.org/10.1007/978-3-642-31087-4_78 This paper deals with the Stochastic-Point Location (SPL) problem. It presents a solution which is novel in both philosophy and strategy to all the reported related learning algorithms. The SPL problem concerns the task of a Learning Mechanism attempting to locate a point on a line. The mechanism interacts with a random environment which essentially informs it, possibly erroneously, if the unknown parameter is on the left or the right of a given point which also is the current guess. The first pioneering work […
Interoperable real-time symbolic programming for smart environments
2019
Smart environments demand novel paradigms offering easy configuration, programming and deployment of pervasive applications. To this purpose, different solutions have been proposed ranging from visual paradigms based on mashups to formal languages. However, most of the paradigms proposed in the literature require further external tools to turn application description code into an executable program before the deployment on target devices. Source code generation, runtime upgrades and recovery, and online debugging and inspection are often cumbersome in these programming environments. In this work we describe a methodology for real-time and on-line programming in smart environments that is co…
New approach to generating insights for aging research based on literature mining and knowledge integration.
2017
The proportion of the elderly population in most countries worldwide is increasing dramatically. Therefore, social interest in the fields of health, longevity, and anti-aging has been increasing as well. However, the basic research results obtained from a reductionist approach in biology and a bioinformatic approach in genome science have limited usefulness for generating insights on future health, longevity, and anti-aging-related research on a case by case basis. We propose a new approach that uses our literature mining technique and bioinformatics, which lead to a better perspective on research trends by providing an expanded knowledge base to work from. We demonstrate that our approach …
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…
Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition) 1
2021
Contains fulltext : 232759.pdf (Publisher’s version ) (Closed access) In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to…
Innovative Strategies to Develop Chemical Categories Using a Combination of Structural and Toxicological Properties.
2016
Interest is increasing in the development of non-animal methods for toxicological evaluations. These methods are however, particularly challenging for complex toxicological endpoints such as repeated dose toxicity. European Legislation, e.g., the European Union's Cosmetic Directive and REACH, demands the use of alternative methods. Frameworks, such as the Read-across Assessment Framework or the Adverse Outcome Pathway Knowledge Base, support the development of these methods. The aim of the project presented in this publication was to develop substance categories for a read-across with complex endpoints of toxicity based on existing databases. The basic conceptual approach was to combine str…
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…
Evaluation of scientific output in Dentistry in Spanish Universities
2016
Background: The aim of this study was to assess the scientific output of Spanish universities that offer a bachelor’s degree in dentistry through the use of various bibliometric indicators. Material and Methods: A total of 21 universities offered a bachelor’s degree in dentistry in academic year 2016- 2017. The search for papers published by authors associated with these institutions was carried out using the selection of journals listed in the Journal Citation Reports (JCR) and the Web of Knowledge database for the period 1986-2017. On the basis of these data, we determined the output, the h-, g- and hg-indexes, the most productive authors, international collaborations, and the most releva…