Knowledge4COVID-19: A semantic-based approach for constructing a COVID-19 related knowledge graph from various sources and analyzing treatments’ toxicities
IF 2.1 3区 计算机科学Q3 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE
{"title":"Knowledge4COVID-19: A semantic-based approach for constructing a COVID-19 related knowledge graph from various sources and analyzing treatments’ toxicities","authors":"Ahmad Sakor , Samaneh Jozashoori , Emetis Niazmand , Ariam Rivas , Konstantinos Bougiatiotis , Fotis Aisopos , Enrique Iglesias , Philipp D. Rohde , Trupti Padiya , Anastasia Krithara , Georgios Paliouras , Maria-Esther Vidal","doi":"10.1016/j.websem.2022.100760","DOIUrl":null,"url":null,"abstract":"<div><p>In this paper, we present Knowledge4COVID-19, a framework that aims to showcase the power of integrating disparate sources of knowledge to discover adverse drug effects caused by drug–drug interactions among COVID-19 treatments and pre-existing condition drugs. Initially, we focus on constructing the Knowledge4COVID-19 knowledge graph (KG) from the declarative definition of mapping rules using the RDF Mapping Language. Since valuable information about drug treatments, drug–drug interactions, and side effects is present in textual descriptions in scientific databases (e.g., DrugBank) or in scientific literature (e.g., the CORD-19, the Covid-19 Open Research Dataset), the Knowledge4COVID-19 framework implements Natural Language Processing. The Knowledge4COVID-19 framework extracts relevant entities and predicates that enable the fine-grained description of COVID-19 treatments and the potential adverse events that may occur when these treatments are combined with treatments of common comorbidities, e.g., hypertension, diabetes, or asthma. Moreover, on top of the KG, several techniques for the discovery and prediction of interactions and potential adverse effects of drugs have been developed with the aim of suggesting more accurate treatments for treating the virus. We provide services to traverse the KG and visualize the effects that a group of drugs may have on a treatment outcome. Knowledge4COVID-19 was part of the Pan-European <em>hackathon#EUvsVirus</em> in April 2020 and is publicly available as a resource through a <span>GitHub repository</span><svg><path></path></svg> and a <span>DOI</span><svg><path></path></svg>.</p></div>","PeriodicalId":49951,"journal":{"name":"Journal of Web Semantics","volume":null,"pages":null},"PeriodicalIF":2.1000,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9558693/pdf/","citationCount":"12","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Web Semantics","FirstCategoryId":"94","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1570826822000440","RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE","Score":null,"Total":0}
引用次数: 12
Abstract
In this paper, we present Knowledge4COVID-19, a framework that aims to showcase the power of integrating disparate sources of knowledge to discover adverse drug effects caused by drug–drug interactions among COVID-19 treatments and pre-existing condition drugs. Initially, we focus on constructing the Knowledge4COVID-19 knowledge graph (KG) from the declarative definition of mapping rules using the RDF Mapping Language. Since valuable information about drug treatments, drug–drug interactions, and side effects is present in textual descriptions in scientific databases (e.g., DrugBank) or in scientific literature (e.g., the CORD-19, the Covid-19 Open Research Dataset), the Knowledge4COVID-19 framework implements Natural Language Processing. The Knowledge4COVID-19 framework extracts relevant entities and predicates that enable the fine-grained description of COVID-19 treatments and the potential adverse events that may occur when these treatments are combined with treatments of common comorbidities, e.g., hypertension, diabetes, or asthma. Moreover, on top of the KG, several techniques for the discovery and prediction of interactions and potential adverse effects of drugs have been developed with the aim of suggesting more accurate treatments for treating the virus. We provide services to traverse the KG and visualize the effects that a group of drugs may have on a treatment outcome. Knowledge4COVID-19 was part of the Pan-European hackathon#EUvsVirus in April 2020 and is publicly available as a resource through a GitHub repository and a DOI.
期刊介绍:
The Journal of Web Semantics is an interdisciplinary journal based on research and applications of various subject areas that contribute to the development of a knowledge-intensive and intelligent service Web. These areas include: knowledge technologies, ontology, agents, databases and the semantic grid, obviously disciplines like information retrieval, language technology, human-computer interaction and knowledge discovery are of major relevance as well. All aspects of the Semantic Web development are covered. The publication of large-scale experiments and their analysis is also encouraged to clearly illustrate scenarios and methods that introduce semantics into existing Web interfaces, contents and services. The journal emphasizes the publication of papers that combine theories, methods and experiments from different subject areas in order to deliver innovative semantic methods and applications.