scholarly journals COVID-19 knowledge graph from semantic integration of biomedical literature and databases

2021 ◽  
Author(s):  
Chuming Chen ◽  
Karen E Ross ◽  
Sachin Gavali ◽  
Julie E Cowart ◽  
Cathy H Wu
Keyword(s):  
Semantic Web ◽  
Relevant Information ◽  
Semantic Integration ◽  
Biomedical Literature ◽  
Knowledge Graph ◽  
Biological Databases ◽  
Global Response ◽  
Semantic Web Technology ◽  
Federated Queries ◽  
Insight Into

Abstract Summary The global response to the COVID-19 pandemic has led to a rapid increase of scientific literature on this deadly disease. Extracting knowledge from biomedical literature and integrating it with relevant information from curated biological databases is essential to gain insight into COVID-19 etiology, diagnosis, and treatment. We used Semantic Web technology RDF to integrate COVID-19 knowledge mined from literature by iTextMine, PubTator, and SemRep with relevant biological databases and formalized the knowledge in a standardized and computable COVID-19 Knowledge Graph (KG). We published the COVID-19 KG via a SPARQL endpoint to support federated queries on the Semantic Web and developed a knowledge portal with browsing and searching interfaces. We also developed a RESTful API to support programmatic access and provided RDF dumps for download. Availability and implementation The COVID-19 Knowledge Graph is publicly available under CC-BY 4.0 license at https://research.bioinformatics.udel.edu/covid19kg/.

State-of-the-Art Information Retrieval Tools for Biological Resources

2018 ◽  
pp. 77-96
Author(s):  
Shashi Bhushan Lal ◽  
Anu Sharma ◽  
Krishna Kumar Chaturvedi ◽  
Mohammad Samir Farooqi ◽  
Sanjeev Kumar ◽  
...  
Keyword(s):  
Information Retrieval ◽  
Statistical Analysis ◽  
Relevant Information ◽  
Ease Of Use ◽  
Video Data ◽  
Biological Databases ◽  
Biological Resources ◽  
Sequencing Technologies ◽  
Scientific Experiments ◽  
Insight Into

With the advancements in sequencing technologies, there is an exponential growth in the availability of the biological databases. Biological databases consist of information and knowledge collected from scientific experiments, published literature and statistical analysis of text, numerical, image and video data. These databases are widely spread across the globe and are being maintained by many organizations. A number of tools have been developed to retrieve the information from these databases. Most of these tools are available on web but are scattered. So, finding a relevant information is a very difficult, and tedious task for the researchers. Moreover, many of these databases use disparate storage formats but are linked to each other. So, an important issue concerning present biological resources is their availability and integration at single platform. This chapter provides an insight into existing biological resources with an aim to provide consolidated information at one place for ease of use and access by researchers, academicians and students.

scholarly journals CRITICAL REVIEW OF THE INTEGRATION OF BIM TO SEMANTIC WEB TECHNOLOGY

2018 ◽  
Vol XLII-4 ◽  
pp. 233-240 ◽  
Author(s):  
B. Godager
Keyword(s):  
Semantic Web ◽  
Relevant Information ◽  
Web Technology ◽  
Information Modeling ◽  
Facilities Management ◽  
Literature Study ◽  
Strategic Research ◽  
Semantic Web Technology ◽  
Starting Point ◽  
Building Information

<p><strong>Abstract.</strong> The AEC–FM industry (Architecture/Engineering/Construction and Facilities Management) is increasingly using different building information modeling (BIM) methodology to solve complex challenges. With help of Semantic WEB technology, product data models and other relevant information are increasingly linked to BIM models. The article discusses the challenges of existing BIM standards to meet future requirements, to fully utilize semantic technology. The article provides suggestions for further research, and it specifically calls for a more strategic research that can look a bit longer than just the challenges associated with various limited case projects. The article discusses whether existing BIM formats are able to meet future requirements, where the potential in the construction industry to fully utilize semantic web technology is difficult with today's BIM standards. Furthermore, it is suggested that previously developed SW resources should be gathered, then earlier initiatives are easier to find, use and build upon. The literature study shows many initiatives spread across many domains in the AEC-FM area. Most studied articles have a high degree of technological focus, where the semantic web opportunities are tested in a chosen case.The findings of this study can be used as a starting point for further strategic research and development.</p>

State-of-the-Art Information Retrieval Tools for Biological Resources

2017 ◽  
pp. 203-226
Author(s):  
Shashi Bhushan Lal ◽  
Anu Sharma ◽  
Krishna Kumar Chaturvedi ◽  
Mohammad Samir Farooqi ◽  
Sanjeev Kumar ◽  
...  
Keyword(s):  
Information Retrieval ◽  
Statistical Analysis ◽  
Relevant Information ◽  
Ease Of Use ◽  
Video Data ◽  
Biological Databases ◽  
Biological Resources ◽  
Sequencing Technologies ◽  
Scientific Experiments ◽  
Insight Into

With the advancements in sequencing technologies, there is an exponential growth in the availability of the biological databases. Biological databases consist of information and knowledge collected from scientific experiments, published literature and statistical analysis of text, numerical, image and video data. These databases are widely spread across the globe and are being maintained by many organizations. A number of tools have been developed to retrieve the information from these databases. Most of these tools are available on web but are scattered. So, finding a relevant information is a very difficult, and tedious task for the researchers. Moreover, many of these databases use disparate storage formats but are linked to each other. So, an important issue concerning present biological resources is their availability and integration at single platform. This chapter provides an insight into existing biological resources with an aim to provide consolidated information at one place for ease of use and access by researchers, academicians and students.

scholarly journals Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature

Database ◽  
2021 ◽  
Vol 2021 ◽  
Author(s):  
Valerio Arnaboldi ◽  
Jaehyoung Cho ◽  
Paul W Sternberg
Keyword(s):  
Search Engines ◽  
Complex Structure ◽  
Model Organism ◽  
Gene Interaction ◽  
Relevant Information ◽  
Biomedical Literature ◽  
C Elegans ◽  
Word Clouds ◽  
Scientific Papers ◽  
Model Organism Databases

Abstract Finding relevant information from newly published scientific papers is becoming increasingly difficult due to the pace at which articles are published every year as well as the increasing amount of information per paper. Biocuration and model organism databases provide a map for researchers to navigate through the complex structure of the biomedical literature by distilling knowledge into curated and standardized information. In addition, scientific search engines such as PubMed and text-mining tools such as Textpresso allow researchers to easily search for specific biological aspects from newly published papers, facilitating knowledge transfer. However, digesting the information returned by these systems—often a large number of documents—still requires considerable effort. In this paper, we present Wormicloud, a new tool that summarizes scientific articles in a graphical way through word clouds. This tool is aimed at facilitating the discovery of new experimental results not yet curated by model organism databases and is designed for both researchers and biocurators. Wormicloud is customized for the Caenorhabditis  elegans literature and provides several advantages over existing solutions, including being able to perform full-text searches through Textpresso, which provides more accurate results than other existing literature search engines. Wormicloud is integrated through direct links from gene interaction pages in WormBase. Additionally, it allows analysis on the gene sets obtained from literature searches with other WormBase tools such as SimpleMine and Gene Set Enrichment. Database URL: https://wormicloud.textpressolab.com

Dynamic faceted navigation in decision making using Semantic Web technology

2014 ◽  
Vol 61 ◽  
pp. 59-68 ◽  
Author(s):  
Hak-Jin Kim ◽  
Yongjun Zhu ◽  
Wooju Kim ◽  
Taimao Sun
Keyword(s):  
Decision Making ◽  
Semantic Web ◽  
Web Technology ◽  
Semantic Web Technology ◽  
Faceted Navigation

Using Semantic Web Technology for Ubiquitous Location and Situation Modeling

Annals of GIS ◽  
2004 ◽  
Vol 10 (2) ◽  
pp. 157-165 ◽  
Author(s):  
Stahl Christoph ◽  
Heckmann Dominik
Keyword(s):  
Semantic Web ◽  
Web Technology ◽  
Semantic Web Technology

scholarly journals Proposing an Ontology Model for Planning Photovoltaic Systems

2021 ◽  
Vol 3 (3) ◽  
pp. 582-600
Author(s):  
Farhad Khosrojerdi ◽  
Stéphane Gagnon ◽  
Raul Valverde
Keyword(s):  
Solar Energy ◽  
Semantic Web ◽  
Relevant Information ◽  
Pv System ◽  
Semantic Web Technologies ◽  
Pv Systems ◽  
Knowledge Based ◽  
Point Tracking ◽  
Power Point ◽  
Energy Community

The performance of a photovoltaic (PV) system is negatively affected when operating under shading conditions. Maximum power point tracking (MPPT) systems are used to overcome this hurdle. Designing an efficient MPPT-based controller requires knowledge about power conversion in PV systems. However, it is difficult for nontechnical solar energy consumers to define different parameters of the controller and deal with distinct sources of data related to the planning. Semantic Web technologies enable us to improve knowledge representation, sharing, and reusing of relevant information generated by various sources. In this work, we propose a knowledge-based model representing key concepts associated with an MPPT-based controller. The model is featured with Semantic Web Rule Language (SWRL), allowing the system planner to extract information about power reductions caused by snow and several airborne particles. The proposed ontology, named MPPT-On, is validated through a case study designed by the System Advisor Model (SAM). It acts as a decision support system and facilitate the process of planning PV projects for non-technical practitioners. Moreover, the presented rule-based system can be reused and shared among the solar energy community to adjust the power estimations reported by PV planning tools especially for snowy months and polluted environments.

scholarly journals Facilitating Dialogue - Using Semantic Web Technology for eParticipation

2010 ◽  
pp. 258-272 ◽  
Author(s):  
George Anadiotis ◽  
Panos Alexopoulos ◽  
Konstantinos Mpaslis ◽  
Aristotelis Zosakis ◽  
Konstantinos Kafentzis ◽  
...  
Keyword(s):  
Semantic Web ◽  
Web Technology ◽  
Semantic Web Technology
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