scholarly journals Accessing biological data with semantic web technologies

2013 ◽  
Author(s):  
Egon Willighagen
Keyword(s):  
Semantic Web ◽  
Brca1 Gene ◽  
Database Systems ◽  
Biological Data ◽  
Biological Database ◽  
Semantic Web Technologies ◽  
Data Set ◽  
Web Technologies ◽  
Web Standards ◽  
Rdf Data

Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness show advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows. Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be use in the statistical environment R. The code is exposed as two R packages available from the Comprehensive R Archive Network (CRAN). The RJava library and a custom convenience class is used to bridge between R and the Jena library. Results. We here present two examples showing how the Resource Description Framework (RDF) and SPARQL query standards can be employed in R. The first example takes input on BRCA1 SNPs from a BioMart and converts this into a RDF data set. The second example runs a query on an experimental remote SPARQL end point provided by Uniprot, and searches textual annotations of proteins encoded by the BRCA1 gene. Discussion. The two provided library bring basic semantic web technologies to R. While only a subset of Apache Jena is currently exposed, it provides key methods to deal with RDF data and resources. The libraries are freely available from the CRAN under the Affero GNU Public License version 3: http://cran.r-project.org/web/packages/rrdf/.

scholarly journals Accessing biological data in R with semantic web technologies

2014 ◽  
Author(s):  
Egon Willighagen
Keyword(s):  
Semantic Web ◽  
Brca1 Gene ◽  
Database Systems ◽  
Biological Data ◽  
Biological Database ◽  
Semantic Web Technologies ◽  
Data Set ◽  
Web Technologies ◽  
Web Standards ◽  
Rdf Data

Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness show advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows. Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be use in the statistical environment R. The code is exposed as two R packages available from the Comprehensive R Archive Network (CRAN). The RJava library and a custom convenience class is used to bridge between R and the Jena library. Results. We here present two examples showing how the Resource Description Framework (RDF) and SPARQL query standards can be employed in R. The first example takes input on BRCA1 SNPs from a BioMart and converts this into a RDF data set. The second example runs a query on an experimental remote SPARQL end point provided by Uniprot, and searches textual annotations of proteins encoded by the BRCA1 gene. The third example shows how the package can be used to handle RDF returned by OpenTox web services. Discussion. The two provided library bring basic semantic web technologies to R. While only a subset of Apache Jena is currently exposed, it provides key methods to deal with RDF data and resources. The libraries are freely available from the CRAN under the Affero GNU Public License version 3: http://cran.r-project.org/web/packages/rrdf/.

scholarly journals Accessing biological data in R with semantic web technologies

2014 ◽  
Author(s):  
Egon Willighagen
Keyword(s):  
Semantic Web ◽  
Brca1 Gene ◽  
Database Systems ◽  
Biological Data ◽  
Biological Database ◽  
Semantic Web Technologies ◽  
Data Set ◽  
Web Technologies ◽  
Web Standards ◽  
Description Framework

Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness shows advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows. Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be used in the statistical environment R. The code is exposed as two R packages available from the Comprehensive R Archive Network (CRAN). The RJava library and a custom convenience class is used to bridge between R and the Jena library. Results. We here present three examples showing how the Resource Description Framework (RDF) and SPARQL query standards can be employed in R. The first example takes input on BRCA1 SNPs from a BioMart and converts this into a RDF data set. The second example runs a query on an experimental remote SPARQL end point provided by Uniprot, and searches textual annotations of proteins encoded by the BRCA1 gene. The third example shows how the package can be used to handle RDF returned by OpenTox web services. Discussion. The two provided library bring basic semantic web technologies to R. This paper only shows examples from the biology domain, but we believe the approaches are generally applicable. It currently only exposes a subset of key Apache Jena, but the rrdf package makes it easy to make more of the library's functionality, such as the shortest path finding. The rrdf libraries are freely available from the CRAN under the Affero GNU Public License version 3: http://cran.r-project.org/web/packages/rrdf/.

scholarly journals Accessing biological data in R with semantic web technologies

2014 ◽  
Author(s):  
Egon Willighagen
Keyword(s):  
Semantic Web ◽  
Brca1 Gene ◽  
Database Systems ◽  
Biological Data ◽  
Biological Database ◽  
Semantic Web Technologies ◽  
Data Set ◽  
Web Technologies ◽  
Web Standards ◽  
Description Framework

Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness shows advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows. Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be used in the statistical environment R. The code is exposed as two R packages available from the Comprehensive R Archive Network (CRAN). The RJava library and a custom convenience class is used to bridge between R and the Jena library. Results. We here present three examples showing how the Resource Description Framework (RDF) and SPARQL query standards can be employed in R. The first example takes input on BRCA1 SNPs from a BioMart and converts this into a RDF data set. The second example runs a query on an experimental remote SPARQL end point provided by Uniprot, and searches textual annotations of proteins encoded by the BRCA1 gene. The third example shows how the package can be used to handle RDF returned by OpenTox web services. Discussion. The two provided library bring basic semantic web technologies to R. This paper only shows examples from the biology domain, but we believe the approaches are generally applicable. It currently only exposes a subset of key Apache Jena, but the rrdf package makes it easy to make more of the library's functionality, such as the shortest path finding. The rrdf libraries are freely available from the CRAN under the Affero GNU Public License version 3: http://cran.r-project.org/web/packages/rrdf/.

Personalizing News Services Using Semantic Web Technologies

2011 ◽  
pp. 261-289 ◽  
Author(s):  
Flavius Frasincar ◽  
Jethro Borsje ◽  
Frederik Hogenboom
Keyword(s):  
Semantic Web ◽  
Knowledge Base ◽  
Language Processing ◽  
Word Sense Disambiguation ◽  
Word Sense ◽  
Semantic Web Technologies ◽  
Web Technologies ◽  
Web Standards ◽  
Processing Techniques ◽  
News Services

This chapter describes Hermes, a framework for building personalized news services using Semantic Web technologies. The Hermes framework consists of four phases: classification, which categorizes news items with respect to a domain ontology, knowledge base updating, which keeps the knowledge base up-to-date based on the news information, news querying, which allows the user to search the news with concepts of interest, and results presentation, which shows the news results of the search process. Hermes is supported by a framework implementation, the Hermes News Portal, a tool that enables users to have a personalized access to news items. The Hermes framework and its associated implementation aim at advancing the state-of-the-art of semantic approaches for personalized news services by employing Semantic Web standards, exploiting and keeping up-to-date domain information, using advanced natural language processing techniques (e.g., ontology-based gazetteering, word sense disambiguation, etc.), and supporting time-based queries for expressing the desired news items.

Interconnecting music repositories with semantic web technologies—an RDF- and schema.org-based approach

2020 ◽  
Author(s):  
Anna Neovesky ◽  
Frederic von Vlahovits
Keyword(s):  
Semantic Web ◽  
Research Data ◽  
Semantic Web Technologies ◽  
Metadata Standard ◽  
Web Technologies ◽  
Data Standard ◽  
Research Perspectives ◽  
Web Standards ◽  
Research Questions ◽  
New Research

Abstract The growing amount of openly available research data enables various possibilities of reuse. Data can be analyzed, visualized, or even further processed, enriched, and combined with other sources to enable new research questions and a different view on the material. Several catalogues and research tools aggregate collections on specific topics to make them searchable and reusable. To be able to bring together different collections, a common data standard is necessary. This article discusses how semantic web technologies can be used to connect digital as well as analogue music catalogues and music editions. The article first discusses how music can be searched using its characteristic melody and presents the approach of the open-source search engine for music incipits, IncipitSearch. Subsequently, the advantages of semantic web standards for musicology are highlighted. Then, the underlying RDF- and schema.org-based metadata standard, which is used to aggregate and distribute the data, is discussed. The article concludes with an outlook on research perspectives for digital musicology and musicology in general.

scholarly journals Creating RESTful APIs over SPARQL endpoints using RAMOSE

Semantic Web ◽  
2021 ◽  
pp. 1-19
Author(s):  
Marilena Daquino ◽  
Ivan Heibi ◽  
Silvio Peroni ◽  
David Shotton
Keyword(s):  
Semantic Web ◽  
Service Providers ◽  
Query Language ◽  
Sparql Query ◽  
Direct Access ◽  
Technical Solution ◽  
Semantic Web Technologies ◽  
Web Technologies ◽  
Sparql Endpoint ◽  
Rdf Data

Semantic Web technologies are widely used for storing RDF data and making them available on the Web through SPARQL endpoints, queryable using the SPARQL query language. While the use of SPARQL endpoints is strongly supported by Semantic Web experts, it hinders broader use of RDF data by common Web users, engineers and developers unfamiliar with Semantic Web technologies, who normally rely on Web RESTful APIs for querying Web-available data and creating applications over them. To solve this problem, we have developed RAMOSE, a generic tool developed in Python to create REST APIs over SPARQL endpoints. Through the creation of source-specific textual configuration files, RAMOSE enables the querying of SPARQL endpoints via simple Web RESTful API calls that return either JSON or CSV-formatted data, thus hiding all the intrinsic complexities of SPARQL and RDF from common Web users. We provide evidence that the use of RAMOSE to provide REST API access to RDF data within OpenCitations triplestores is beneficial in terms of the number of queries made by external users of such RDF data using the RAMOSE API, compared with the direct access via the SPARQL endpoint. Our findings show the importance for suppliers of RDF data of having an alternative API access service, which enables its use by those with no (or little) experience in Semantic Web technologies and the SPARQL query language. RAMOSE can be used both to query any SPARQL endpoint and to query any other Web API, and thus it represents an easy generic technical solution for service providers who wish to create an API service to access Linked Data stored as RDF in a triplestore.

scholarly journals SEMANTIC WEB TECHNOLOGIES MEET BIM FOR ACCESSING AND UNDERSTANDING CULTURAL HERITAGE

2019 ◽  
Vol XLII-2/W9 ◽  
pp. 381-388 ◽  
Author(s):  
E. Iadanza ◽  
F. Maietti ◽  
A. E. Ziri ◽  
R. Di Giulio ◽  
M. Medici ◽  
...  
Keyword(s):  
Semantic Web ◽  
Cultural Heritage ◽  
3D Models ◽  
Information Modeling ◽  
Semantic Web Technologies ◽  
Web Technologies ◽  
Web Standards ◽  
Semantic Modelling ◽  
Building Information ◽  
Funded Project

<p><strong>Abstract.</strong> Within the EU funded project INCEPTION &amp;ndash; <i>Inclusive Cultural Heritage in Europe through 3D semantic modelling</i>, the key-targeted achievement is the development of a specific cloud based platform, in order to accomplish the main objectives of accessing, understanding and strengthening European Cultural Heritage by means of enriched 3D models. The whole INCEPTION project is based on the close connection between state-of-the-art architectural modeling technologies (BIM, Building Information Modeling) and the latest cutting-edge web technologies. The platform is grounded on semantic web technologies and makes extensive use of WebGL and RESTful APIs, in order to enrich heritage 3D models by using Semantic Web standards. The INCEPTION platform will be a space for interchange of information and for the dialogue among professionals, students, scholars, curators, non-expert users, etc. Furthermore, the Semantic Web structure interlinks the platform with external Cultural Heritage available linked data and makes it gradually enhanced by specific flexible data structures provided as project specific ontologies. The paper will describe solutions based on the match between BIM, Cloud and Semantic Web.</p>

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