scholarly journals RDFizing the biosynthetic pathway of E.coli O-antigen to enable semantic sharing of microbiology data

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Sunmyoung Lee ◽  
Tamiko Ono ◽  
Kiyoko Aoki-Kinoshita
Keyword(s):  
Experimental Data ◽  
Semantic Web ◽  
Data Sharing ◽  
Data Exchange ◽  
Knowledge Integration ◽  
Ontology Development ◽  
Biological Databases ◽  
Data Types ◽  
Technical Barrier ◽  
O Antigen

Abstract Background The abundance of glycomics data that have accumulated has led to the development of many useful databases to aid in the understanding of the function of the glycans and their impact on cellular activity. At the same time, the endeavor for data sharing between glycomics databases with other biological databases have contributed to the creation of new knowledgebases. However, different data types in data description have impeded the data sharing for knowledge integration. To solve this matter, Semantic Web techniques including Resource Description Framework (RDF) and ontology development have been adopted by various groups to standardize the format for data exchange. These semantic data have contributed to the expansion of knowledgebases and hold promises of providing data that can be intelligently processed. On the other hand, bench biologists who are experts in experimental finding are end users and data producers. Therefore, it is indispensable to reduce the technical barrier required for bench biologists to manipulate their experimental data to be compatible with standard formats for data sharing. Results There are many essential concepts and practical techniques for data integration but there is no method to enable researchers to easily apply Semantic Web techniques to their experimental data. We implemented our procedure on unformatted information of E.coli O-antigen structures collected from the web and show how this information can be expressed as formatted data applicable to Semantic Web standards. In particular, we described the E-coli O-antigen biosynthesis pathway using the BioPAX ontology developed to support data exchange between pathway databases. Conclusions The method we implemented to semantically describe O-antigen biosynthesis should be helpful for biologists to understand how glycan information, including relevant pathway reaction data, can be easily shared. We hope this method can contribute to lower the technical barrier that is required when experimental findings are formulated into formal representations and can lead bench scientists to readily participate in the construction of new knowledgebases that are integrated with existing ones. Such integration over the Semantic Web will enable future work in artificial intelligence and machine learning to enable computers to infer new relationships and hypotheses in the life sciences.

Semantic Representation of Balinese Traditional Dance

2020 ◽  
Vol 8 (4) ◽  
pp. 411
Author(s):  
Irianto Liko Koten ◽  
Cokorda Rai Adi Pramartha
Keyword(s):  
Semantic Web ◽  
Semantic Representation ◽  
Ontology Development ◽  
Digital Form ◽  
Dance Performance ◽  
Development Method ◽  
Development Tool ◽  
Traditional Dance ◽  
The World ◽  
Representation Technique

Bali is an island in Indonesia that is rich in culture, for example, is a traditional dance. The traditional dance performance is diverse from one village to another village in Bali. The traditional Balinese dance knowledge should be captured dan documented well in a digital form so that it can be shared easily to different people and generation across the world. The use of ontology as an information representation technique is the preferred solution in this matter because ontology can be used to enhance the development of semantic applications, especially when dealing with semantic webs. In this project, the ontology was built using Protege ontology development tool.  We follow the methontology ontology development method where this methodology clearly describes each of its activity. In this study, we focus to describe two variants of Balinese traditional dance (Barong dance and Pendet dance). In the future, we expect that more type of dance can be documented using our proposed ontology. Keywords: Balinese Dance, Ontology,Semantic Web

scholarly journals ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 146 ◽  
Author(s):  
Guanming Wu ◽  
Eric Dawson ◽  
Adrian Duong ◽  
Robin Haw ◽  
Lincoln Stein
Keyword(s):  
Experimental Data ◽  
Data Analysis ◽  
Graphical Models ◽  
High Throughput ◽  
Interaction Network ◽  
Large Data ◽  
Relevant Information ◽  
Data Sets ◽  
Data Types ◽  
Biological Studies

High-throughput experiments are routinely performed in modern biological studies. However, extracting meaningful results from massive experimental data sets is a challenging task for biologists. Projecting data onto pathway and network contexts is a powerful way to unravel patterns embedded in seemingly scattered large data sets and assist knowledge discovery related to cancer and other complex diseases. We have developed a Cytoscape app called “ReactomeFIViz”, which utilizes a highly reliable gene functional interaction network and human curated pathways from Reactome and other pathway databases. This app provides a suite of features to assist biologists in performing pathway- and network-based data analysis in a biologically intuitive and user-friendly way. Biologists can use this app to uncover network and pathway patterns related to their studies, search for gene signatures from gene expression data sets, reveal pathways significantly enriched by genes in a list, and integrate multiple genomic data types into a pathway context using probabilistic graphical models. We believe our app will give researchers substantial power to analyze intrinsically noisy high-throughput experimental data to find biologically relevant information.

scholarly journals How mHealth can facilitate collaboration in diabetes care: qualitative analysis of co-design workshops

2020 ◽  
Author(s):  
Meghan Bradway ◽  
Rebecca L Morris ◽  
Alain Giordanengo ◽  
Eirik Årsand
Keyword(s):  
Data Sharing ◽  
Healthcare Providers ◽  
End Users ◽  
Self Management ◽  
Afternoon Session ◽  
Data Types ◽  
Full Effect ◽  
Joint Workshop ◽  
Management Recommendations

Abstract Background: Individuals with diabetes are using mobile health (mHealth) to make and track their decisions regarding self-management. However, individuals can understand even more about their diabetes by sharing these patient-gathered data (PGD) with health professionals. We conducted experience-based co-design (EBCD) workshops, with the aim of gathering end-users’ needs and expectations for a PGD-sharing system. Methods: The first workshop (2017) included patients with Type 2 Diabetes (T2D) (n=4) and general practitioners (GPs) (n=3). The second workshop (2018) included patients with Type 1 Diabetes (T1D) (n=5), diabetes specialists (n=2) and a nurse. The workshops involved two sessions: separate morning sessions for patients and healthcare providers (HCPs), followed by a joint lunch and afternoon session for all participants together. A discussion guide was used to gather input regarding end-users’ expectations for the system. Participants then created and explained their own ideas for a data-sharing system, using paper-prototypes. Workshops were audio recorded, transcribed and translated from Norwegian to English. Inductive thematic analysis was performed. Results: The main emergent themes were mHealth technologies’ impacts on end-users, and functionalities of a data-sharing system. Patients and providers agreed that PGD could be used by HCPs to provide more concrete self-management recommendations. Participants made paper-prototypes to explain which data types to gather and display, and how the systems could be used to facilitate shared-decision making. However, all also agreed that a data-sharing system alone was not enough to achieve the full effect of mHealth. Conclusion: Participants’ feedback revealed that both patients and HCPs alike acknowledge that for mHealth integration to be successful, not only must the technology be validated but feasible changes throughout the healthcare education and practice must be addressed. Only then can both sides be adequately prepared for mHealth data-sharing in diabetes consultations. Subsequently, the design of the joint workshop sessions demonstrated that involving both participant groups in the same sessions led to efficient and concrete discussions about realistic solutions and limitations of sharing mHealth data in consultations.

scholarly journals DataStaR: Using the Semantic Web approach for Data Curation

2011 ◽  
Vol 6 (2) ◽  
pp. 209-221 ◽  
Author(s):  
Huda Khan ◽  
Brian Caruso ◽  
Jon Corson-Rikert ◽  
Dianne Dietrich ◽  
Brian Lowe ◽  
...  
Keyword(s):  
Social Sciences ◽  
Semantic Web ◽  
Data Sharing ◽  
Research Data ◽  
Data Curation ◽  
Data Staging ◽  
Domain Specific ◽  
Digital Infrastructure

In disciplines as varied as medicine, social sciences, and economics, data and their analyses are essential parts of researchers’ contributions to their respective fields. While sharing research data for review and analysis presents new opportunities for furthering research, capturing these data in digital forms and providing the digital infrastructure for sharing data and metadata pose several challenges. This paper reviews the motivations behind and design of the Data Staging Repository (DataStaR) platform that targets specific portions of the research data curation lifecycle: data and metadata capture and sharing prior to publication, and publication to permanent archival repositories. The goal of DataStaR is to support both the sharing and publishing of data while at the same time enabling metadata creation without imposing additional overheads for researchers and librarians. Furthermore, DataStaR is intended to provide cross-disciplinary support by being able to integrate different domain-specific metadata schemas according to researchers’ needs. DataStaR’s strategy of a usable interface coupled with metadata flexibility allows for a more scaleable solution for data sharing, publication, and metadata reuse.

scholarly journals An Analysis of a Web Service based Approach for Experimental Data Sharing

2018 ◽  
Vol 14 (09) ◽  
pp. 19
Author(s):  
Velin Spasov Kralev ◽  
Radoslava Stankova Kraleva ◽  
Ninа Sinyagina ◽  
Petia Koprinkova-Hristova ◽  
Nadejda Bocheva
Keyword(s):  
Experimental Data ◽  
Comparative Analysis ◽  
Web Service ◽  
Data Sharing ◽  
Behavioral Experiments ◽  
Specific Data ◽  
Database Server ◽  
Processing Data ◽  
The One ◽  
The Web

<span lang="EN-US">This paper presents the results obtained from a comparative analysis of two methods for experimental data sharing. </span><span>Several </span><span lang="EN-US">works</span><span> related to the </span><span lang="EN-US">topic</span><span> and some </span><span lang="EN-US">approaches</span><span> for </span><span lang="EN-US">processing data</span><span> have been discussed. Different </span><span lang="EN-US">technolgoies related to the web services</span><span>, ways of using them and the areas of their application are analyzed. For the purposes of the study, a </span><span lang="EN-US">web service</span><span> for </span><span lang="EN-US">retrieving </span><span>specific data</span><span lang="EN-US"> from a behavioral experiments database</span><span> was de</span><span lang="EN-US">veloped</span><span>.</span><span>The methodology and conditions for conducting </span><span lang="EN-US">the </span><span>experiments are described. T</span><span lang="EN-US">wo</span><span> different indicators </span><span lang="EN-US">a</span><span>re analyzed, respectively: </span><span lang="EN-US">time to retrieve the data from a database </span><span>and iteration time across all records through one </span><span lang="EN-US">loop</span><span>. The results show that when </span><span lang="EN-US">retrieving</span><span> thousands of records both </span><span lang="EN-US">web service based approach</span><span> and an approach based on a remote database</span><span lang="EN-US"> server can be used. However, when retrieving millions of records</span><span>, </span><span lang="EN-US">the fastest approach was the one that uses remote database server</span><span>.</span><span> <span lang="EN-US">T</span></span><span>he obtained</span><span>results</span><span>show that </span><span lang="EN-US">the </span><span>dynamic arrays</span><span lang="EN-US"> (containing strings) </span><span>iterated much faster </span><span lang="EN-US">across all data records </span><span>than </span><span lang="EN-US">the dataset </span><span>approach.</span>

scholarly journals Data Governance and Sovereignty in Urban Data Spaces Based on Standardized ICT Reference Architectures

Data ◽  
2019 ◽  
Vol 4 (1) ◽  
pp. 16 ◽  
Author(s):  
Silke Cuno ◽  
Lina Bruns ◽  
Nikolay Tcholtchev ◽  
Philipp Lämmel ◽  
Ina Schieferdecker
Keyword(s):  
Data Exchange ◽  
Smart Cities ◽  
Legal Aspects ◽  
Urban Environments ◽  
Added Value ◽  
Data Types ◽  
Data Governance ◽  
European Cities ◽  
Data Space ◽  
Urban Data

European cities and communities (and beyond) require a structured overview and a set of tools as to achieve a sustainable transformation towards smarter cities/municipalities, thereby leveraging on the enormous potential of the emerging data driven economy. This paper presents the results of a recent study that was conducted with a number of German municipalities/cities. Based on the obtained and briefly presented recommendations emerging from the study, the authors propose the concept of an Urban Data Space (UDS), which facilitates an eco-system for data exchange and added value creation thereby utilizing the various types of data within a smart city/municipality. Looking at an Urban Data Space from within a German context and considering the current situation and developments in German municipalities, this paper proposes a reasonable classification of urban data that allows the relation of various data types to legal aspects, and to conduct solid considerations regarding technical implementation designs and decisions. Furthermore, the Urban Data Space is described/analyzed in detail, and relevant stakeholders are identified, as well as corresponding technical artifacts are introduced. The authors propose to setup Urban Data Spaces based on emerging standards from the area of ICT reference architectures for Smart Cities, such as DIN SPEC 91357 “Open Urban Platform” and EIP SCC. In the course of this, the paper walks the reader through the construction of a UDS based on the above-mentioned architectures and outlines all the goals, recommendations and potentials, which an Urban Data Space can reveal to a municipality/city. Finally, we aim at deriving the proposed concepts in a way that they have the potential to be part of the required set of tools towards the sustainable transformation of German and European cities in the direction of smarter urban environments, based on utilizing the hidden potential of digitalization and efficient interoperable data exchange.

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