Towards a Biographical Ontology: The OntoBio Framework and Its Applications

In the Semantic Web, items are represented by uniform resource identifiers (URIs) on the Web in order to describe relationships between things in resource description framework (RDF) graphs. Large scale open RDF data (linked data) describing information about various things are available. Hence, relational discovery research has been conducted using RDF data to explore relationships between things. The SPARQL protocol and RDF query language (SPARQL) is usually employed to process RDF data; however, SPARQL is not suitable for relational discovery using linked data because it is difficult to describe unknown vocabularies and relationships in SPARQL queries. In this paper, we propose an aggregation path search for RDF graphs as an extension of shortest path keyword search. The aggregation path search is devised to find RDF paths by merging multiple resource URIs into commonly reachable nodes in an RDF graph. This search method can discover new relationships between items that are connected by a common node. We present a method for treating equivalent resource URIs as a single resource URI; these equivalent URIs essentially represent the same thing based on equivalence relations in different RDF datasets. In our experiments, we show in the integration of multiple large scale RDF datasets that the integration of equivalent resources enables richer retrieval of aggregated paths.

The Internet of Things is a vast and growing virtual universe that includes medical devices, automobiles, industrial systems and a variable number of consumer electronics devices. With some 100 billion devices expected to be connected to the Internet by 2025, providing interoperability among the things on the IoT is one of the most fundamental requirements to support tracking, object addressing and discovery as well as information representation, storage, and exchange. Applying semantic techniques to IoT can support Interoperability, effective data access, integration resource discovery reasoning and processing of data knowledge extraction. In this paper, we present an overview of semantic technologies such as Semantic Web of Things (SWoT), Ontologies, Resource Description Framework (RDF), RDF Schema, Web Ontology Language (OWL), SPARQL Protocol And RDF Query Language (SPARQL), Semantic annotation and reasoning widely deployed in IoT.

BackgroundGenome and proteome annotation pipelines are generally custom built and not easily reusable by other groups. This leads to duplication of effort, increased costs, and suboptimal annotation quality. One way to address these issues is to encourage the adoption of annotation standards and technological solutions that enable the sharing of biological knowledge and tools for genome and proteome annotation.ResultsHere we demonstrate one approach to generate portable genome and proteome annotation pipelines that users can run without recourse to custom software. This proof of concept uses our own rule-based annotation pipeline HAMAP, which provides functional annotation for protein sequences to the same depth and quality as UniProtKB/Swiss-Prot, and the World Wide Web Consortium (W3C) standards Resource Description Framework (RDF) and SPARQL (a recursive acronym for the SPARQL Protocol and RDF Query Language). We translate complex HAMAP rules into the W3C standard SPARQL 1.1 syntax, and then apply them to protein sequences in RDF format using freely available SPARQL engines. This approach supports the generation of annotation that is identical to that generated by our own in-house pipeline, using standard, off-the-shelf solutions, and is applicable to any genome or proteome annotation pipeline.ConclusionsHAMAP SPARQL rules are freely available for download from the HAMAP FTP site, ftp://ftp.expasy.org/databases/hamap/sparql/, under the CC-BY-ND 4.0 license. The annotations generated by the rules are under the CC-BY 4.0 license. A tutorial and supplementary code to use HAMAP as SPARQL are available on GitHub at https://github.com/sib-swiss/HAMAP-SPARQL, and general documentation about HAMAP can be found on the HAMAP website at https://hamap.expasy.org.

BackgroundHealth level seven version 2.5 (HL7 v2.5) is a widespread messaging standard for information exchange between clinical information systems. By applying Semantic Web technologies for handling HL7 v2.5 messages, it is possible to integrate large-scale clinical data with life science knowledge resources.ObjectiveShowing feasibility of a querying method over large-scale resource description framework (RDF)-ized HL7 v2.5 messages using publicly available drug databases.MethodsWe developed a method to convert HL7 v2.5 messages into the RDF. We also converted five kinds of drug databases into RDF and provided explicit links between the corresponding items among them. With those linked drug data, we then developed a method for query expansion to search the clinical data using semantic information on drug classes along with four types of temporal patterns. For evaluation purpose, medication orders and laboratory test results for a 3-year period at the University of Tokyo Hospital were used, and the query execution times were measured.ResultsApproximately 650 million RDF triples for medication orders and 790 million RDF triples for laboratory test results were converted. Taking three types of query in use cases for detecting adverse events of drugs as an example, we confirmed these queries were represented in SPARQL Protocol and RDF Query Language (SPARQL) using our methods and comparison with conventional query expressions were performed. The measurement results confirm that the query time is feasible and increases logarithmically or linearly with the amount of data and without diverging.ConclusionsThe proposed methods enabled query expressions that separate knowledge resources and clinical data, thereby suggesting the feasibility for improving the usability of clinical data by enhancing the knowledge resources. We also demonstrate that when HL7 v2.5 messages are automatically converted into RDF, searches are still possible through SPARQL without modifying the structure. As such, the proposed method benefits not only our hospitals, but also numerous hospitals that handle HL7 v2.5 messages. Our approach highlights a potential of large-scale data federation techniques to retrieve clinical information, which could be applied as applications of clinical intelligence to improve clinical practices, such as adverse drug event monitoring and cohort selection for a clinical study as well as discovering new knowledge from clinical information.

"The purpose of the present paper is to research a rule-based approach for transforming X3D (eXtensible 3D) models to RDF (Resource Description Framework). The transformation is performed by using the RDF Mapping Language (RML). Its advantages are summarized, which are mainly due to the fact that the rules created build a knowledge base. By applying SPARQL (SPARQL Protocol and RDF Query Language) queries to it, the possibility of explore in order to validate and improve the defined RML rules themselves, is pointed out. An approach for reversing from the RDF triples to the original X3D in a unique way is considered, and the types of SPARQL queries needed for its implementation are systematized. Rules are formulated for all elements defined in the X3D schema, their attributes and properties are described. Their accessibility is ensured. The conversion of X3D models to RDF is confirmed to be consistent with guidelines and best practices for creating accessible, understandable, and reusable ontologies on the Web. The systematized SPARQL query types for reversing from RDF triples to the original X3D are checked for specific elements and sample data, and the obtained results establish their correctness. The prerequisites and limitations of the represented approach are explained. The proposed approach allows building a comprehensive knowledge base that includes the RML rules, the transformed X3D models and the domain-specific ontology and its use to analyzing data and semantic reasoning. The electronic libraries that include 3D content could take advantage from the benefits and possible future applications of the solutions discussed in this study."

Interoperability within different healthcare systems (clinics/hospitals/pharmacies) remains an issue of further research due to a barrier in sharing of the patient’s Electronic Health Record (EHR) information. To solve this problem, cross healthcare system collaboration is required. This paper proposes an interoperability framework that enables a pharmacist to access an electronic version of the patient’s prescription from the doctor using a RESTFul API with ease. Semantic technology standards like Web Ontology Language (OWL), RDF (Resource Description Framework) and SPARQL (SPARQL Protocol and RDF Query Language) were used to implement the framework using JENA semantic framework tool to demonstrate how interoperability is achieved between a pharmacy and a clinic JENA was used to generate the ontology models for the pharmacy called pharmacy.rdf and clinic called clinic.rdf. The two models contain all the information from the two isolated systems. The JENA reasoner was used to merge the two ontology models into a single model.rdf file for easy querying with SPARQL. The model.rdf file was uploaded into a triple store database created using FUSEKI server. SPARQL Endpoint generated from FUSEKI was used to query the triple store database using a RESTFul API. The system was able to query the triple store database and output the results containing the prescription name and its details in JSON and XML formats which can be read by both machines and humans.

BackgroundAutomatic e-coaching may motivate individuals to lead a healthy lifestyle with early health risk prediction, personalized recommendation generation, and goal evaluation. Multiple studies have reported on uninterrupted and automatic monitoring of behavioral aspects (such as sedentary time, amount, and type of physical activity); however, e-coaching and personalized feedback techniques are still in a nascent stage. Current intelligent coaching strategies are mostly based on the handcrafted string messages that rarely individualize to each user’s needs, context, and preferences. Therefore, more realistic, flexible, practical, sophisticated, and engaging strategies are needed to model personalized recommendations.ObjectiveThis study aims to design and develop an ontology to model personalized recommendation message intent, components (such as suggestion, feedback, argument, and follow-ups), and contents (such as spatial and temporal content and objects relevant to perform the recommended activities). A reasoning technique will help to discover implied knowledge from the proposed ontology. Furthermore, recommendation messages can be classified into different categories in the proposed ontology.MethodsThe ontology was created using Protégé (version 5.5.0) open-source software. We used the Java-based Jena Framework (version 3.16) to build a semantic web application as a proof of concept, which included Resource Description Framework application programming interface, World Wide Web Consortium Web Ontology Language application programming interface, native tuple database, and SPARQL Protocol and Resource Description Framework Query Language query engine. The HermiT (version 1.4.3.x) ontology reasoner available in Protégé 5.x implemented the logical and structural consistency of the proposed ontology. To verify the proposed ontology model, we simulated data for 8 test cases. The personalized recommendation messages were generated based on the processing of personal activity data in combination with contextual weather data and personal preference data. The developed ontology was processed using a query engine against a rule base to generate personalized recommendations.ResultsThe proposed ontology was implemented in automatic activity coaching to generate and deliver meaningful, personalized lifestyle recommendations. The ontology can be visualized using OWLViz and OntoGraf. In addition, we developed an ontology verification module that behaves similar to a rule-based decision support system to analyze the generation and delivery of personalized recommendation messages following a logical structure.ConclusionsThis study led to the creation of a meaningful ontology to generate and model personalized recommendation messages for physical activity coaching.

An inconsistent and ambiguous Software Requirement Specification (SRS) document results in an erroneous/failed software project. Hence, it is a serious challenge to handle and process complex and ambiguous requirements. Most of the literature work focuses on detection and resolution of ambiguity in software requirements. Also, there is no standardized way to write unambiguous and consistent requirements. The goal of this research was to generate an ambiguity-less SRS document. This paper presents a new approach to write ambiguity-less requirements. Furthermore, we design a framework for Natural Language (NL) to Controlled Natural Language (CNL) (such as Semantic Business Vocabulary and Rules (SBVR)) transition and develop a prototype. The prototype also generates Resource Description Framework (RDF) representation. The SBVR has a shared meaning concept that minimizes ambiguity, and RDF representation is supported by query language such as SPARQL Protocol and RDF Query Language (SPARQL). The proposed approach can help software engineers to translate NL requirements into a format that is understandable by all stakeholders and also is machine processable. The results of our prototype are encouraging, exhibiting the efficient performance of our developed prototype in terms of usability and correctness.

Computational epidemiology seeks to develop computational methods to study the distribution and determinants of health-related states or events (including disease), and the application of this study to the control of diseases and other health problems. Recent advances in computing and data sciences have led to the development of innovative modeling environments to support this important goal. The datasets used to drive the dynamic models as well as the data produced by these models presents unique challenges owing to their size, heterogeneity and diversity. These datasets form the basis of effective and easy to use decision support and analytical environments. As a result, it is important to develop scalable data management systems to store, manage and integrate these datasets. In this paper, we develop EpiK-a knowledge base that facilitates the development of decision support and analytical environments to support epidemic science. An important goal is to develop a framework that links the input as well as output datasets to facilitate effective spatio-temporal and social reasoning that is critical in planning and intervention analysis before and during an epidemic. The data management framework links modeling workflow data and its metadata using a controlled vocabulary. The metadata captures information about storage, the mapping between the linked model and the physical layout, and relationships to support services. EpiK is designed to support agent-based modeling and analytics frameworks-aggregate models can be seen as special cases and are thus supported. We use semantic web technologies to create a representation of the datasets that encapsulates both the location and the schema heterogeneity. The choice of RDF as a representation language is motivated by the diversity and growth of the datasets that need to be integrated. A query bank is developed-the queries capture a broad range of questions that can be posed and answered during a typical case study pertaining to disease outbreaks. The queries are constructed using SPARQL Protocol and RDF Query Language (SPARQL) over the EpiK. EpiK can hide schema and location heterogeneity while efficiently supporting queries that span the computational epidemiology modeling pipeline: from model construction to simulation output. We show that the performance of benchmark queries varies significantly with respect to the choice of hardware underlying the database and resource description framework (RDF) engine.

<span lang="EN-US">Data integration enables combining data from various data sources in a standard format. Internet of things (IoT) applications use ontology approaches to provide a machine-understandable conceptualization of a domain. We propose a unified ontology schema approach to solve all IoT integration problems at once. The data unification layer maps data from different formats to data patterns based on the unified ontology model. This paper proposes a middleware consisting of an ontology-based approach that collects data from different devices. IoT middleware requires an additional semantic layer for cloud-based IoT platforms to build a schema for data generated from diverse sources. We tested the proposed model on real data consisting of approximately 160,000 readings from various sources in different formats like CSV, JSON, raw data, and XML. The data were collected through the file transfer protocol (FTP) and generated 960,000 resource description framework (RDF) triples. We evaluated the proposed approach by running different queries on different machines on SPARQL protocol and RDF query language (SPARQL) endpoints to check query processing time, validation of integration, and performance of the unified ontology model. The average response time for query execution on generated RDF triples on the three servers were approximately 0.144 seconds, 0.070 seconds, 0.062 seconds, respectively.</span>

ABSTRACTGeoLink has leveraged linked data principles to create a dataset that allows users to seamlessly query and reason over some of the most prominent geoscience metadata repositories in the United States. The GeoLink dataset includes such diverse information as port calls made by oceanographic cruises, physical sample metadata, research project funding and staffing, and authorship of technical reports. The data has been published according to best practices for linked data and is publicly available via a SPARQL Protocol and RDF Query Language (SPARQL) end point that at present contains more than 45 million Resource Description Framework (RDF) triples together with a collection of ontologies and geo-visualization tools. This article describes the geoscience datasets, the modeling and publication process, and current uses of the dataset. The focus is on providing enough detail to enable researchers, application developers and others who wish to leverage the GeoLink data in their own work to do so. The dataset is available at http://hdl.handle.net/1912/9524.

PG-explorer: Resource Description Framework data exploration with property graphs

Following an investigation undertaken by the publisher, we have determined that this paper was accepted on the basis of a compromised peer review process. We hereby retract the paper. The corresponding author has been notified of the retraction. The retraction statement can be found here: https://doi.org/10.1520/JTE20269996. Aiming at the problems of poor effect, low precision, and a long time frame in the current data mining analysis algorithm of the network information resource description framework (RDF), a data mining analysis algorithm of the network information RDF based on fuzzy association rules is proposed. Using association rule mining technology combined with fuzzy set theory, a fuzzy association rule algorithm is obtained to deal with quantitative data. Fuzzy c-means (FCM) is used to discretize continuous attributes, and the fuzzy concept pattern and its support and credibility are defined. Add a Mining Query flag to extend the SPARQL Protocol and RDF Query Language (SPARQL) syntax, define the user specified mining model, generate the corresponding project set and transaction, adopt the fuzzy association rule algorithm to generate fuzzy association rules, and realize the RDF data mining analysis of network information. The experimental results show that the network RDF data mining analysis effect of the proposed algorithm is good, which can effectively improve the network RDF data mining analysis accuracy and shorten the mining analysis time.

With the growing importance of the fuzzy spatiotemporal data in information application, there is an increasing need for researching on the integration method of multi-source heterogeneous fuzzy spatiotemporal data. In this paper, we first propose a fuzzy spatiotemporal RDF graph model based on RDF (Resource Description Framework) that proposed by the World Wide Web Consortium (W3C) to represent data in triples (subject, predicate, object). Secondly, we analyze and classify the related heterogeneous problems of multi-source heterogeneous fuzzy spatiotemporal data, and use the fuzzy spatiotemporal RDF graph model to define the corresponding rules to solve these heterogeneous problems. In addition, based on the characteristics of RDF triples, we analyze the heterogeneous problem of multi-source heterogeneous fuzzy spatiotemporal data integration in RDF triples, and provide the integration methods FRDFG in this paper. Finally, we report our experiments results to validate our approach and show its significant superiority.

The Resource Description Framework (RDF) is a popular data model for representing linked data sets arising from the web, as well as large scientific data repositories such as UniProt. RDF data intrinsically represents a labeled and directed multi-graph. SPARQL is a query language for RDF that expresses subgraph pattern-finding queries on this implicit multigraph in a SQL-like syntax. SPARQL queries generate complex intermediate join queries; to compute these joins efficiently, this paper presents a new strategy based on bitmap indexes. We store the RDF data in column-oriented compressed bitmap structures, along with two dictionaries. We find that our bitmap index-based query evaluation approach is up to an order of magnitude faster the state-of-the-art system RDF-3X, for a variety of SPARQL queries on gigascale RDF data sets.