Biotea, semantics for Pubmed Central

A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language. We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at http://biotea.github.io.

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Biotea, semantics for Pubmed Central

10.7287/peerj.preprints.3469v1 ◽

2017 ◽

Cited By ~ 2

Author(s):

Alexander Garcia ◽

Federico Lopez ◽

Leyla Garcia ◽

Olga Giraldo ◽

Victor Bucheli ◽

...

Keyword(s):

Linked Data ◽

Scientific Literature ◽

Query Language ◽

Biomedical Ontology ◽

Sparql Query ◽

Biomedical Literature ◽

Automatic Annotation ◽

Pubmed Central ◽

Web Technologies ◽

Aggregate Content

A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language. We illustrate the utility of our system with several use cases. Availability: Our datasets, methods and techniques are available at http://biotea.github.io

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Creating RESTful APIs over SPARQL endpoints using RAMOSE

Semantic Web ◽

10.3233/sw-210439 ◽

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.

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Question Answering System over Linked Data: A Detailed Survey

ABC Research Alert ◽

10.18034/abcra.v8i1.449 ◽

2020 ◽

Vol 8 (1) ◽

pp. 32-47

Author(s):

G. M. Rasiqul Islam Rasiq ◽

Abdullah Al Sefat ◽

Tanjila Hossain ◽

Md. Israt-E-Hasan Munna ◽

Jubayeath Jahan Jisha ◽

...

Keyword(s):

Semantic Web ◽

Linked Data ◽

Question Answering ◽

Query Language ◽

Sparql Query ◽

Amount Of Information ◽

Advantages And Disadvantages ◽

Detailed Survey ◽

The World ◽

Basic Understanding

As the amount of information in the world is growing very quickly, in the case of the semantic web this increasing amount of information is becoming more difficult to find and manage the exact answers to our various questions. To overcome these difficulties some systems have been developed that make it work for us. But there exists many challenges in developing these systems that require a lot of improvement. In this tutorial, we give a basic understanding of Semantic web, RDF triple, SPARQL query language. Here we will discuss the main obstacles for the QA system in processing the questions and a detailed survey of the existing systems. We also provide some advantages and disadvantages of existing QA systems. We also discuss the evaluation campaigns of the existing models based on their precision, recall and F-1 scores on the QALD dataset.

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LINKDALE: A LIGHTWEIGHT LEARNING ENVIRONMENT FOR (GEOSPATIAL) LINKED DATA

ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences ◽

10.5194/isprs-archives-xlii-4-w8-187-2018 ◽

2018 ◽

Vol XLII-4/W8 ◽

pp. 187-190

Author(s):

S. Ronzhin ◽

G. Bosch ◽

E. Folmer ◽

R. Lemmens

Keyword(s):

Linked Data ◽

Query Language ◽

Process Integration ◽

A Priori ◽

Sparql Query ◽

Design Consideration ◽

Specific Data ◽

Domain Specific ◽

Description Framework ◽

Resource Description

<p><strong>Abstract.</strong> Modern software tools for managing Linked Data are often designed for skilled users. Therefore, they cannot be used for education purposes because they require substantial a priori knowledge about the Resource Description Framework and the SPARQL query language. LinkDaLe is a single page application designed to teach students the concept of Linked Data and work with linked data at the same time. In the paper we showcase the interface and functionality of LinkDaLe by triplifying data on Geo4All member organizations. The application was built and evaluated within The Business Process Integration Lab, a master programme course in 2016 and 2017 years. Positive feedback from both students and teachers proved the relevance of the proposed design consideration. LinkDaLe showed usability working with domain specific data e.g. geospatial and logistic data.</p>

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Theophrastus: On Demand and Real-Time Automatic Annotation and Exploration of (Web) Documents Using Open Linked Data

SSRN Electronic Journal ◽

10.2139/ssrn.3199160 ◽

2014 ◽

Author(s):

Pavlos Fafalios ◽

Panagiotis Papadakos

Keyword(s):

Real Time ◽

Linked Data ◽

Automatic Annotation ◽

Web Documents ◽

On Demand

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Using Semantic Web Technologies to Underpin the SNOMED CT Query Language

Artificial Intelligence XXXIV - Lecture Notes in Computer Science ◽

10.1007/978-3-319-71078-5_20 ◽

2017 ◽

pp. 217-231

Author(s):

Mercedes Arguello Casteleiro ◽

Dmitry Tsarkov ◽

Bijan Parsia ◽

Ulrike Sattler

Keyword(s):

Semantic Web ◽

Query Language ◽

Snomed Ct ◽

Semantic Web Technologies ◽

Web Technologies

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Enabling the Matchmaking of Organizations and Public Procurement Notices by Means of Linked Open Data

Cases on Open-Linked Data and Semantic Web Applications ◽

10.4018/978-1-4666-2827-4.ch006 ◽

2013 ◽

pp. 105-131 ◽

Cited By ~ 3

Author(s):

Jose María Alvarez Rodríguez ◽

José Emilio Labra Gayo ◽

Patricia Ordoñez de Pablos

Keyword(s):

Semantic Web ◽

Linked Data ◽

Public Procurement ◽

Open Data ◽

Specific Information ◽

Semantic Web Technologies ◽

Web Technologies ◽

Domain Specific ◽

The Status ◽

Financial Transactions

The aim of this chapter is to present a proposal and a case study to describe the information about organizations in a standard way using the Linked Data approach. Several models and ontologies have been provided in order to formalize the data, structure and behaviour of organizations. Nevertheless, these tries have not been fully accepted due to some factors: (1) missing pieces to define the status of the organization; (2) tangled parts to specify the structure (concepts and relations) between the elements of the organization; 3) lack of text properties, and other factors. These divergences imply a set of incomplete approaches to formalize data and information about organizations. Taking into account the current trends of applying semantic web technologies and linked data to formalize, aggregate, and share domain specific information, a new model for organizations taking advantage of these initiatives is required in order to overcome existing barriers and exploit the corporate information in a standard way. This work is especially relevant in some senses to: (1) unify existing models to provide a common specification; (2) apply semantic web technologies and the Linked Data approach; (3) provide access to the information via standard protocols, and (4) offer new services that can exploit this information to trace the evolution and behaviour of the organization over time. Finally, this work is interesting to improve the clarity and transparency of some scenarios in which organizations play a key role, like e-procurement, e-health, or financial transactions.

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Semantic Extension of Query for the Linked Data

International Journal on Semantic Web and Information Systems ◽

10.4018/ijswis.2017100106 ◽

2017 ◽

Vol 13 (4) ◽

pp. 109-133 ◽

Cited By ~ 6

Author(s):

Pu Li ◽

Yuncheng Jiang ◽

Ju Wang ◽

Zhilei Yin

Keyword(s):

Similarity Search ◽

Linked Data ◽

Query Language ◽

Semantic Structure ◽

Semantic Extension ◽

Data Querying ◽

Novel Algorithms ◽

Semantic Properties ◽

Query Model ◽

Better Than

With the advent of Big Data Era, users prefer to get knowledge rather than pages from Web. Linked Data, a new form of knowledge representation and publishing described by RDF, can provide a more precise and comprehensible semantic structure to satisfy the aforementioned requirement. Further, the SPARQL query language for RDF is the foundation of many current researches about Linked Data querying. However, these SPARQL-based methods cannot fully express the semantics of the query, so they cannot unleash the potential of Linked Data. To fill this gap, this paper designs a new querying method which extends the SPARQL pattern. Firstly, the authors present some new semantic properties for predicates in RDF triples and design a Semantic Matrix for Predicates (SMP). They then establish a well-defined framework for the notion of Semantically-Extended Query Model for the Linked Data (SEQMLD). Moreover, the authors propose some novel algorithms for executing queries by integrating semantic extension into SPARQL pattern. Lastly, experimental results show that the authors' proposal has a good generality and performs better than some of the most representative similarity search methods.

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Web Data Quality

International Journal on Semantic Web and Information Systems ◽

10.4018/ijswis.2014040101 ◽

2014 ◽

Vol 10 (2) ◽

pp. 1-6 ◽

Cited By ~ 9

Author(s):

Amrapali Zaveri ◽

Andrea Maurino ◽

Laure-Berti Equille

Keyword(s):

Semantic Web ◽

Data Quality ◽

Linked Data ◽

Web Data ◽

Semantic Web Technologies ◽

Future Directions ◽

Web Technologies ◽

Current State ◽

Web Of Data ◽

The Web

The standardization and adoption of Semantic Web technologies has resulted in an unprecedented volume of data being published as Linked Data (LD). However, the “publish first, refine later” philosophy leads to various quality problems arising in the underlying data such as incompleteness, inconsistency and semantic ambiguities. In this article, we describe the current state of Data Quality in the Web of Data along with details of the three papers accepted for the International Journal on Semantic Web and Information Systems' (IJSWIS) Special Issue on Web Data Quality. Additionally, we identify new challenges that are specific to the Web of Data and provide insights into the current progress and future directions for each of those challenges.

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