scholarly journals NETME: on-the-fly knowledge network construction from biomedical literature

2022 ◽  
Vol 7 (1) ◽  
Author(s):  
Alessandro Muscolino ◽  
Antonio Di Maria ◽  
Rosaria Valentina Rapicavoli ◽  
Salvatore Alaimo ◽  
Lorenzo Bellomo ◽  
...  

Abstract Background The rapidly increasing biological literature is a key resource to automatically extract and gain knowledge concerning biological elements and their relations. Knowledge Networks are helpful tools in the context of biological knowledge discovery and modeling. Results We introduce a novel system called NETME, which, starting from a set of full-texts obtained from PubMed, through an easy-to-use web interface, interactively extracts biological elements from ontological databases and then synthesizes a network inferring relations among such elements. The results clearly show that our tool is capable of inferring comprehensive and reliable biological networks.

PLoS ONE ◽  
2012 ◽  
Vol 7 (11) ◽  
pp. e50411 ◽  
Author(s):  
Sapna Kumari ◽  
Jeff Nie ◽  
Huann-Sheng Chen ◽  
Hao Ma ◽  
Ron Stewart ◽  
...  

Author(s):  
Alessandro Muscolino ◽  
Antonio Di Maria ◽  
Salvatore Alaimo ◽  
Stefano Borzì ◽  
Paolo Ferragina ◽  
...  

2021 ◽  
Vol 13 (3) ◽  
pp. 1124
Author(s):  
Freddy Marín-González ◽  
Alexa Senior-Naveda ◽  
Mercy Narváez Castro ◽  
Alicia Inciarte González ◽  
Ana Judith Paredes Chacín

This article aims to build a network for the exchange of knowledge between the government and production, community and university sectors for sustainable local development. To achieve this, the authors relied on the concepts of sustainable local development, social capital, the relationship between sectors or intersectorality, networks and interdisciplinary and transdisciplinary knowledge. Regarding the methodology, the abductive method was used. Under a documentary design, the research techniques were a content analysis of theoretical documents and the deductive inference technique. The construction of a knowledge exchange network for sustainable local development stands out as the result. It is concluded that knowledge networks for sustainable local development have positive implications in the establishment of alliances and links between the sectors that make up society.


2018 ◽  
Vol 22 (1) ◽  
pp. 1-20 ◽  
Author(s):  
Jose Antonio Belso-Martinez ◽  
Isabel Diez-Vial

Purpose This paper aims to explain how the evolution of knowledge networks and firms’ strategic choices affect innovation. Endogenous factors associated with a path-dependent evolution of the knowledge network are jointly considered with a firm’s development of international relationships and increasing internal absorptive capacity over time. Design/methodology/approach In a biotech cluster, the authors gathered data on the firms’ characteristics and network relationships by asking about the technological knowledge they received in the cluster in 2007 and 2012 – “roster-recall” method. Estimation results were obtained using moderated regression analysis. Findings Firms that increase their involvement in knowledge networks over time also tend to increase their innovative capacity. However, efforts devoted to building international links or absorptive capacity negatively moderate the impact of network growth on innovation. Practical implications Practitioners have two alternative ways of increasing innovation inside knowledge networks: they can increase their centrality by developing their knowledge network interactions or invest in developing their internal absorptive capacity and new international sources of knowledge. Investing in both of these simultaneously does not seem to improve a firm’s innovative capacity. Originality/value Coupling firms’ strategic options with knowledge network dynamics provide a more complete way of explaining how firms can improve their innovative capacity.


2017 ◽  
Vol 9 (4) ◽  
pp. 37-48 ◽  
Author(s):  
Huilan Chen ◽  
Shaofeng Liu ◽  
Festus Oderanti

Making the right decisions for food supply chain is extremely important towards achieving sustainability in agricultural businesses. This paper explores that knowledge sharing to support food supply chain decisions to achieve lean performance (i.e. to reduce/eliminate non-value-adding activities, or “waste” in lean term). The focus of the paper is on defining new knowledge networks and mobilisation approaches to address the network and community nature of current supply chains. Based on critical analysis of the state-of-the-art in the topic area, a knowledge network and mobilisation framework for lean supply chain management has been developed. The framework has then been evaluated using a case study from the food supply chain. Analytic Hierarchy Process (AHP) has been used to incorporate expert's view on the defined knowledge networks and mobilisation approaches with respect to their contribution to achieving various lean performance objectives. The results from the work have a number of implications for current knowledge management and supply chain management in theory and in practice.


BMJ Open ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. e053674
Author(s):  
Enrico Glaab ◽  
Armin Rauschenberger ◽  
Rita Banzi ◽  
Chiara Gerardi ◽  
Paula Garcia ◽  
...  

ObjectiveTo review biomarker discovery studies using omics data for patient stratification which led to clinically validated FDA-cleared tests or laboratory developed tests, in order to identify common characteristics and derive recommendations for future biomarker projects.DesignScoping review.MethodsWe searched PubMed, EMBASE and Web of Science to obtain a comprehensive list of articles from the biomedical literature published between January 2000 and July 2021, describing clinically validated biomarker signatures for patient stratification, derived using statistical learning approaches. All documents were screened to retain only peer-reviewed research articles, review articles or opinion articles, covering supervised and unsupervised machine learning applications for omics-based patient stratification. Two reviewers independently confirmed the eligibility. Disagreements were solved by consensus. We focused the final analysis on omics-based biomarkers which achieved the highest level of validation, that is, clinical approval of the developed molecular signature as a laboratory developed test or FDA approved tests.ResultsOverall, 352 articles fulfilled the eligibility criteria. The analysis of validated biomarker signatures identified multiple common methodological and practical features that may explain the successful test development and guide future biomarker projects. These include study design choices to ensure sufficient statistical power for model building and external testing, suitable combinations of non-targeted and targeted measurement technologies, the integration of prior biological knowledge, strict filtering and inclusion/exclusion criteria, and the adequacy of statistical and machine learning methods for discovery and validation.ConclusionsWhile most clinically validated biomarker models derived from omics data have been developed for personalised oncology, first applications for non-cancer diseases show the potential of multivariate omics biomarker design for other complex disorders. Distinctive characteristics of prior success stories, such as early filtering and robust discovery approaches, continuous improvements in assay design and experimental measurement technology, and rigorous multicohort validation approaches, enable the derivation of specific recommendations for future studies.


F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1651 ◽  
Author(s):  
Ajit Singh ◽  
Christopher J. Rawlings ◽  
Keywan Hassani-Pak

KnetMaps is a BioJS component for the interactive visualization of biological knowledge networks. It is well suited for applications that need to visualise complementary, connected and content-rich data in a single view in order to help users to traverse pathways linking entities of interest, for example to go from genotype to phenotype. KnetMaps loads data in JSON format, visualizes the structure and content of knowledge networks using lightweight JavaScript libraries, and supports interactive touch gestures. KnetMaps uses effective visualization techniques to prevent information overload and to allow researchers to progressively build their knowledge.


2018 ◽  
Vol 15 (3) ◽  
Author(s):  
Marco Brandizi ◽  
Ajit Singh ◽  
Christopher Rawlings ◽  
Keywan Hassani-Pak

Abstract The speed and accuracy of new scientific discoveries – be it by humans or artificial intelligence – depends on the quality of the underlying data and on the technology to connect, search and share the data efficiently. In recent years, we have seen the rise of graph databases and semi-formal data models such as knowledge graphs to facilitate software approaches to scientific discovery. These approaches extend work based on formalised models, such as the Semantic Web. In this paper, we present our developments to connect, search and share data about genome-scale knowledge networks (GSKN). We have developed a simple application ontology based on OWL/RDF with mappings to standard schemas. We are employing the ontology to power data access services like resolvable URIs, SPARQL endpoints, JSON-LD web APIs and Neo4j-based knowledge graphs. We demonstrate how the proposed ontology and graph databases considerably improve search and access to interoperable and reusable biological knowledge (i.e. the FAIRness data principles).


Author(s):  
Christo El Morr ◽  
Mihaela Dinca-Panaitescu ◽  
Marcia Rioux ◽  
Julien Subercaze ◽  
Pierre Maret ◽  
...  

Holistic disability rights monitoring is an imperative approach to permit translation of rights on paper into rights in reality for people with disabilities. However, evidence-based knowledge produced through such a holistic monitoring approach has to be accessible to a broad range of stakeholders, e.g., groups such as: researchers, representatives of disability community, people with disabilities, media, policy makers, and the general public. Besides, the collected evidence should contribute to building capacity within disability community around human rights questions. This article explains the design process of a Virtual Knowledge Network (VKN) as an operational tool to support mobilization and dissemination of evidence-based knowledge produced by the Disability Rights Promotion International Canada (DRPI-Canada) project. This VKN is embedded in the more general framework of DRPI, grounded in a human rights approach to disability that acknowledges the importance of creating knowledgeable communities in order to make the disability rights monitoring efforts sustainable.


2020 ◽  
Vol 166 ◽  
pp. 10022
Author(s):  
Arnold Kiv ◽  
Vladimir Soloviev ◽  
Elena Tarasova ◽  
Tetyana Koycheva ◽  
Katrina Kolesnykova

The article is devoted to the modeling a semantic knowledge networks. The knowledge network is the basic concept of the problem of knowledge management. This is a new discipline that implements the principles of sustainable development of education. The method of constructing a semantic knowledge network allows us to analyze the connections between educational disciplines: “Economic Cybernetics”, “Algorithms and Programming” and “Calculus”. The paper compares the topological characteristics of the concept graphs related to various disciplines. We develop the algorithm to implement the subject area model in the form of a semantic knowledge network. 125 concepts are analyzed that provide optimal mastering disciplines and establish the connection between them.


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