scholarly journals A SEMANTIC GRAPH DATABASE FOR BIM-GIS INTEGRATED INFORMATION MODEL FOR AN INTELLIGENT URBAN MOBILITY WEB APPLICATION

2018 ◽  
Vol IV-4 ◽  
pp. 89-96 ◽  
Author(s):  
A.-H. Hor ◽  
G. Sohn ◽  
P. Claudio ◽  
M. Jadidi ◽  
A. Afnan
Keyword(s):  
Web Application ◽  
Architectural Design ◽  
Data Extraction ◽  
Semantic Integration ◽  
Graph Database ◽  
Graph Databases ◽  
Urban Mobility ◽  
Real World Data ◽  
Semantic Web Technologies ◽  
Rdf Data

<p><strong>Abstract.</strong> Over the recent years, the usage of semantic web technologies and Resources Description Framework (RDF) data models have been notably increased in many fields. Multiple systems are using RDF data to describe information resources and semantic associations. RDF data plays a very important role in advanced information retrieval, and graphs are efficient ways to visualize and represent real world data by providing solutions to many real-time scenarios that can be simulated and implemented using graph databases, and efficiently query graphs with multiple attributes representing different domains of knowledge. Given that graph databases are schema less with efficient storage for semi-structured data, they can provide fast and deep traversals instead of slow RDBMS SQL based joins allowing Atomicity, Consistency, Isolation and durability (ACID) transactions with rollback support, and by utilizing mathematics of graph they can enormous potential for fast data extraction and storage of information in the form of nodes and relationships. In this paper, we are presenting an architectural design with complete implementation of BIM-GIS integrated RDF graph database. The proposed integration approach is composed of four main phases: ontological BIM and GIS model’s construction, mapping and semantic integration using interoperable data formats, then an import into a graph database with querying and filtering capabilities. The workflows and transformations of IFC and CityGML schemas into object graph databases model are developed and applied to an intelligent urban mobility web application on a game engine platform validate the integration methodology.</p>

scholarly journals Advantages of using graph databases to explore chromatin conformation capture experiments

2021 ◽  
Vol 22 (S2) ◽  
Author(s):  
Daniele D’Agostino ◽  
Pietro Liò ◽  
Marco Aldinucci ◽  
Ivan Merelli
Keyword(s):  
Web Application ◽  
High Throughput Sequencing ◽  
Cell Types ◽  
Graph Database ◽  
Graph Databases ◽  
Sources Of Information ◽  
Chromosome Conformation ◽  
Wide Scale ◽  
User Friendly ◽  
Different Cell Types

Abstract Background High-throughput sequencing Chromosome Conformation Capture (Hi-C) allows the study of DNA interactions and 3D chromosome folding at the genome-wide scale. Usually, these data are represented as matrices describing the binary contacts among the different chromosome regions. On the other hand, a graph-based representation can be advantageous to describe the complex topology achieved by the DNA in the nucleus of eukaryotic cells. Methods Here we discuss the use of a graph database for storing and analysing data achieved by performing Hi-C experiments. The main issue is the size of the produced data and, working with a graph-based representation, the consequent necessity of adequately managing a large number of edges (contacts) connecting nodes (genes), which represents the sources of information. For this, currently available graph visualisation tools and libraries fall short with Hi-C data. The use of graph databases, instead, supports both the analysis and the visualisation of the spatial pattern present in Hi-C data, in particular for comparing different experiments or for re-mapping omics data in a space-aware context efficiently. In particular, the possibility of describing graphs through statistical indicators and, even more, the capability of correlating them through statistical distributions allows highlighting similarities and differences among different Hi-C experiments, in different cell conditions or different cell types. Results These concepts have been implemented in NeoHiC, an open-source and user-friendly web application for the progressive visualisation and analysis of Hi-C networks based on the use of the Neo4j graph database (version 3.5). Conclusion With the accumulation of more experiments, the tool will provide invaluable support to compare neighbours of genes across experiments and conditions, helping in highlighting changes in functional domains and identifying new co-organised genomic compartments.

scholarly journals Blockchain-Authenticated Sharing of Genomic and Clinical Outcomes Data of Patients With Cancer: A Prospective Cohort Study

10.2196/16810 ◽  
2020 ◽  
Vol 22 (3) ◽  
pp. e16810 ◽  
Author(s):  
Benjamin Scott Glicksberg ◽  
Shohei Burns ◽  
Rob Currie ◽  
Ann Griffin ◽  
Zhen Jane Wang ◽  
...  
Keyword(s):  
Real World ◽  
Web Application ◽  
Data Extraction ◽  
Data Representation ◽  
Health Data ◽  
Common Data Model ◽  
Patient Privacy ◽  
Real World Data ◽  
World Data ◽  
Patients With Cancer

Background Efficiently sharing health data produced during standard care could dramatically accelerate progress in cancer treatments, but various barriers make this difficult. Not sharing these data to ensure patient privacy is at the cost of little to no learning from real-world data produced during cancer care. Furthermore, recent research has demonstrated a willingness of patients with cancer to share their treatment experiences to fuel research, despite potential risks to privacy. Objective The objective of this study was to design, pilot, and release a decentralized, scalable, efficient, economical, and secure strategy for the dissemination of deidentified clinical and genomic data with a focus on late-stage cancer. Methods We created and piloted a blockchain-authenticated system to enable secure sharing of deidentified patient data derived from standard of care imaging, genomic testing, and electronic health records (EHRs), called the Cancer Gene Trust (CGT). We prospectively consented and collected data for a pilot cohort (N=18), which we uploaded to the CGT. EHR data were extracted from both a hospital cancer registry and a common data model (CDM) format to identify optimal data extraction and dissemination practices. Specifically, we scored and compared the level of completeness between two EHR data extraction formats against the gold standard source documentation for patients with available data (n=17). Results Although the total completeness scores were greater for the registry reports than those for the CDM, this difference was not statistically significant. We did find that some specific data fields, such as histology site, were better captured using the registry reports, which can be used to improve the continually adapting CDM. In terms of the overall pilot study, we found that CGT enables rapid integration of real-world data of patients with cancer in a more clinically useful time frame. We also developed an open-source Web application to allow users to seamlessly search, browse, explore, and download CGT data. Conclusions Our pilot demonstrates the willingness of patients with cancer to participate in data sharing and how blockchain-enabled structures can maintain relationships between individual data elements while preserving patient privacy, empowering findings by third-party researchers and clinicians. We demonstrate the feasibility of CGT as a framework to share health data trapped in silos to further cancer research. Further studies to optimize data representation, stream, and integrity are required.

scholarly journals Blockchain-Authenticated Sharing of Genomic and Clinical Outcomes Data of Patients With Cancer: A Prospective Cohort Study (Preprint)

2019 ◽  
Author(s):  
Benjamin Scott Glicksberg ◽  
Shohei Burns ◽  
Rob Currie ◽  
Ann Griffin ◽  
Zhen Jane Wang ◽  
...  
Keyword(s):  
Real World ◽  
Web Application ◽  
Data Extraction ◽  
Data Representation ◽  
Health Data ◽  
Common Data Model ◽  
Patient Privacy ◽  
Real World Data ◽  
World Data ◽  
Patients With Cancer

BACKGROUND Efficiently sharing health data produced during standard care could dramatically accelerate progress in cancer treatments, but various barriers make this difficult. Not sharing these data to ensure patient privacy is at the cost of little to no learning from real-world data produced during cancer care. Furthermore, recent research has demonstrated a willingness of patients with cancer to share their treatment experiences to fuel research, despite potential risks to privacy. OBJECTIVE The objective of this study was to design, pilot, and release a decentralized, scalable, efficient, economical, and secure strategy for the dissemination of deidentified clinical and genomic data with a focus on late-stage cancer. METHODS We created and piloted a blockchain-authenticated system to enable secure sharing of deidentified patient data derived from standard of care imaging, genomic testing, and electronic health records (EHRs), called the Cancer Gene Trust (CGT). We prospectively consented and collected data for a pilot cohort (N=18), which we uploaded to the CGT. EHR data were extracted from both a hospital cancer registry and a common data model (CDM) format to identify optimal data extraction and dissemination practices. Specifically, we scored and compared the level of completeness between two EHR data extraction formats against the gold standard source documentation for patients with available data (n=17). RESULTS Although the total completeness scores were greater for the registry reports than those for the CDM, this difference was not statistically significant. We did find that some specific data fields, such as histology site, were better captured using the registry reports, which can be used to improve the continually adapting CDM. In terms of the overall pilot study, we found that CGT enables rapid integration of real-world data of patients with cancer in a more clinically useful time frame. We also developed an open-source Web application to allow users to seamlessly search, browse, explore, and download CGT data. CONCLUSIONS Our pilot demonstrates the willingness of patients with cancer to participate in data sharing and how blockchain-enabled structures can maintain relationships between individual data elements while preserving patient privacy, empowering findings by third-party researchers and clinicians. We demonstrate the feasibility of CGT as a framework to share health data trapped in silos to further cancer research. Further studies to optimize data representation, stream, and integrity are required.

scholarly journals DESIGN AND EVALUATION OF A BIM-GIS INTEGRATED INFORMATION MODEL USING RDF GRAPH DATABASE

2021 ◽  
Vol VIII-4/W2-2021 ◽  
pp. 175-182
Author(s):  
A.-H. Hor ◽  
G. Sohn
Keyword(s):  
Performance Metrics ◽  
Graph Model ◽  
Information Model ◽  
Query Languages ◽  
Semantic Integration ◽  
Graph Database ◽  
Graph Databases ◽  
Rdf Graph ◽  
Functional Components ◽  
Integrated Information

Abstract. The semantic integration modeling of BIM industry foundations classes and GIS City-geographic markup language are a milestone for many applications that involve both domains of knowledge. In this paper, we propose a system design architecture, and implementation of Extraction, Transformation and Loading (ETL) workflows of BIM and GIS model into RDF graph database model, these workflows were created from functional components and ontological frameworks supporting RDF SPARQL and graph databases Cypher query languages. This paper is about full understanding of whether RDF graph database is suitable for a BIM-GIS integrated information model, and it looks deeper into the assessment of translation workflows and evaluating performance metrics of a BIM-GIS integrated data model managed in an RDF graph database, the process requires designing and developing various pipelines of workflows with semantic tools in order to get the data and its structure into an appropriate format and demonstrate the potential of using RDF graph databases to integrate, manage and analyze information and relationships from both GIS and BIM models, the study also has introduced the concepts of Graph-Model occupancy indexes of nodes, attributes and relationships to measure queries outputs and giving insights on data richness and performance of the resulting BIM-GIS semantically integrated model.

scholarly journals Applying graph database technology for analyzing perturbed co-expression networks in cancer

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Claire M Simpson ◽  
Florian Gnad
Keyword(s):  
Relational Databases ◽  
Molecular Mechanisms ◽  
Biological Data ◽  
Database Management System ◽  
Graph Database ◽  
Graph Databases ◽  
Graph Representations ◽  
Rnaseq Data ◽  
Database Technology ◽  
Speed Accuracy

Abstract Graph representations provide an elegant solution to capture and analyze complex molecular mechanisms in the cell. Co-expression networks are undirected graph representations of transcriptional co-behavior indicating (co-)regulations, functional modules or even physical interactions between the corresponding gene products. The growing avalanche of available RNA sequencing (RNAseq) data fuels the construction of such networks, which are usually stored in relational databases like most other biological data. Inferring linkage by recursive multiple-join statements, however, is computationally expensive and complex to design in relational databases. In contrast, graph databases store and represent complex interconnected data as nodes, edges and properties, making it fast and intuitive to query and analyze relationships. While graph-based database technologies are on their way from a fringe domain to going mainstream, there are only a few studies reporting their application to biological data. We used the graph database management system Neo4j to store and analyze co-expression networks derived from RNAseq data from The Cancer Genome Atlas. Comparing co-expression in tumors versus healthy tissues in six cancer types revealed significant perturbation tracing back to erroneous or rewired gene regulation. Applying centrality, community detection and pathfinding graph algorithms uncovered the destruction or creation of central nodes, modules and relationships in co-expression networks of tumors. Given the speed, accuracy and straightforwardness of managing these densely connected networks, we conclude that graph databases are ready for entering the arena of biological data.

Implementation of Web Application for Disease Prediction Using AI

2020 ◽  
pp. 5-9
Author(s):  
Manasvi Srivastava ◽  
◽  
Vikas Yadav ◽  
Swati Singh ◽  
◽  
...  
Keyword(s):  
Web Application ◽  
Ad Hoc ◽  
Data Extraction ◽  
Extraction Methods ◽  
Web Page ◽  
Web Based ◽  
Web Extraction ◽  
Web Scraping ◽  
Audio Video ◽  
Manual Extraction

The Internet is the largest source of information created by humanity. It contains a variety of materials available in various formats such as text, audio, video and much more. In all web scraping is one way. It is a set of strategies here in which we get information from the website instead of copying the data manually. Many Web-based data extraction methods are designed to solve specific problems and work on ad-hoc domains. Various tools and technologies have been developed to facilitate Web Scraping. Unfortunately, the appropriateness and ethics of using these Web Scraping tools are often overlooked. There are hundreds of web scraping software available today, most of them designed for Java, Python and Ruby. There is also open source software and commercial software. Web-based software such as YahooPipes, Google Web Scrapers and Firefox extensions for Outwit are the best tools for beginners in web cutting. Web extraction is basically used to cut this manual extraction and editing process and provide an easy and better way to collect data from a web page and convert it into the desired format and save it to a local or archive directory. In this paper, among others the kind of scrub, we focus on those techniques that extract the content of a Web page. In particular, we use scrubbing techniques for a variety of diseases with their own symptoms and precautions.

scholarly journals BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources

2018 ◽  
Vol 12 (S5) ◽  
Author(s):  
Antonio Messina ◽  
Antonino Fiannaca ◽  
Laura La Paglia ◽  
Massimo La Rosa ◽  
Alfonso Urso
Keyword(s):  
Web Application ◽  
Graph Database

scholarly journals A Rule-based Conversion of an EER Schema to Neo4j Schema Constraints

2021 ◽  
Author(s):  
Telmo Henrique Valverde da Silva ◽  
Ronaldo dos Santos Mello
Keyword(s):  
Data Model ◽  
Design Methodology ◽  
A Priori ◽  
Database Management System ◽  
Conversion Process ◽  
Graph Database ◽  
Graph Databases ◽  
Rule Based ◽  
Promising Solution ◽  
Entity Relationship

Several application domains hold highly connected data, like supply chain and social network. In this context, NoSQL graph databases raise as a promising solution since relationships are first class citizens in their data model. Nevertheless, a traditional database design methodology initially defines a conceptual schema of the domain data, and the Enhanced Entity-Relationship (EER) model is a common tool. This paper presents a rule-based conversion process from an EER schema to Neo4j schema constraints, as Neo4j is the most representative NoSQL graph database management system with an expressive data model. Different from related work, our conversion process deals with all EER model concepts and generates rules for ensuring schema constraints through a set of Cypher instructions ready to run into a Neo4j database instance, as Neo4J is a schemaless system, and it is not possible to create a schema a priori. We also present an experimental evaluation that demonstrates the viability of our process in terms of performance.

scholarly journals IDSM ChemWebRDF: SPARQLing small-molecule datasets

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Jakub Galgonek ◽  
Jiří Vondrášek
Keyword(s):  
Data Storage ◽  
Small Molecule ◽  
Web Application ◽  
Query Language ◽  
Data Interoperability ◽  
Sparql Endpoint ◽  
Data Source ◽  
Rdf Data ◽  
Relational Form ◽  
Federated Queries

AbstractThe Resource Description Framework (RDF), together with well-defined ontologies, significantly increases data interoperability and usability. The SPARQL query language was introduced to retrieve requested RDF data and to explore links between them. Among other useful features, SPARQL supports federated queries that combine multiple independent data source endpoints. This allows users to obtain insights that are not possible using only a single data source. Owing to all of these useful features, many biological and chemical databases present their data in RDF, and support SPARQL querying. In our project, we primary focused on PubChem, ChEMBL and ChEBI small-molecule datasets. These datasets are already being exported to RDF by their creators. However, none of them has an official and currently supported SPARQL endpoint. This omission makes it difficult to construct complex or federated queries that could access all of the datasets, thus underutilising the main advantage of the availability of RDF data. Our goal is to address this gap by integrating the datasets into one database called the Integrated Database of Small Molecules (IDSM) that will be accessible through a SPARQL endpoint. Beyond that, we will also focus on increasing mutual interoperability of the datasets. To realise the endpoint, we decided to implement an in-house developed SPARQL engine based on the PostgreSQL relational database for data storage. In our approach, data are stored in the traditional relational form, and the SPARQL engine translates incoming SPARQL queries into equivalent SQL queries. An important feature of the engine is that it optimises the resulting SQL queries. Together with optimisations performed by PostgreSQL, this allows efficient evaluations of SPARQL queries. The endpoint provides not only querying in the dataset, but also the compound substructure and similarity search supported by our Sachem project. Although the endpoint is accessible from an internet browser, it is mainly intended to be used for programmatic access by other services, for example as a part of federated queries. For regular users, we offer a rich web application called ChemWebRDF using the endpoint. The application is publicly available at https://idsm.elixir-czech.cz/chemweb/.

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