scholarly journals Building an OWL ontology with Xper3

2018 ◽  
Vol 2 ◽  
pp. e25614 ◽  
Author(s):  
Florian Pellen ◽  
Sylvain Bouquin ◽  
Isabelle Mougenot ◽  
Régine Vignes-Lebbe
Keyword(s):  
Semantic Web ◽  
Knowledge Base ◽  
Expressive Power ◽  
Knowledge Bases ◽  
User Friendliness ◽  
Standard Format ◽  
Ontology Language ◽  
Closed World ◽  
Web Standards ◽  
Description Framework

Xper3 (Vignes Lebbe et al. 2016) is a collaborative knowledge base publishing platform that, since its launch in november 2013, has been adopted by over 2 thousand users (Pinel et al. 2017). This is mainly due to its user friendly interface and the simplicity of its data model. The data are stored in MySQL Relational DBs, but the exchange format uses the TDWG standard format SDD (Structured Descriptive DataHagedorn et al. 2005). However, each Xper3 knowledge base is a closed world that the author(s) may or may not share with the scientific community or the public via publishing content and/or identification key (Kopfstein 2016). The explicit taxonomic, geographic and phenotypic limits of a knowledge base are not always well defined in the metadata fields. Conversely terminology vocabularies, such as Phenotype and Trait Ontology PATO and the Plant Ontology PO, and software to edit them, such as Protégé and Phenoscape, are essential in the semantic web, but difficult to handle for biologist without computer skills. These ontologies constitute open worlds, and are expressed themselves by RDF triples (Resource Description Framework). Protégé offers vizualisation and reasoning capabilities for these ontologies (Gennari et al. 2003, Musen 2015). Our challenge is to combine the user friendliness of Xper3 with the expressive power of OWL (Web Ontology Language), the W3C standard for building ontologies. We therefore focused on analyzing the representation of the same taxonomic contents under Xper3 and under different models in OWL. After this critical analysis, we chose a description model that allows automatic export of SDD to OWL and can be easily enriched. We will present the results obtained and their validation on two knowledge bases, one on parasitic crustaceans (Sacculina) and the second on current ferns and fossils (Corvez and Grand 2014). The evolution of the Xper3 platform and the perspectives offered by this link with semantic web standards will be discussed.

Web knowledge

2006 ◽  
Author(s):  
Christopher Walton
Keyword(s):  
Semantic Web ◽  
Knowledge Representation ◽  
Knowledge Base ◽  
Web Applications ◽  
Semantic Network ◽  
Knowledge Bases ◽  
Web Standards ◽  
Description Framework ◽  
The Web

In the introductory chapter of this book, we discussed the means by which knowledge can be made available on the Web. That is, the representation of the knowledge in a form by which it can be automatically processed by a computer. To recap, we identified two essential steps that were deemed necessary to achieve this task: 1. We discussed the need to agree on a suitable structure for the knowledge that we wish to represent. This is achieved through the construction of a semantic network, which defines the main concepts of the knowledge, and the relationships between these concepts. We presented an example network that contained the main concepts to differentiate between kinds of cameras. Our network is a conceptualization, or an abstract view of a small part of the world. A conceptualization is defined formally in an ontology, which is in essence a vocabulary for knowledge representation. 2. We discussed the construction of a knowledge base, which is a store of knowledge about a domain in machine-processable form; essentially a database of knowledge. A knowledge base is constructed through the classification of a body of information according to an ontology. The result will be a store of facts and rules that describe the domain. Our example described the classification of different camera features to form a knowledge base. The knowledge base is expressed formally in the language of the ontology over which it is defined. In this chapter we elaborate on these two steps to show how we can define ontologies and knowledge bases specifically for the Web. This will enable us to construct Semantic Web applications that make use of this knowledge. The chapter is devoted to a detailed explanation of the syntax and pragmatics of the RDF, RDFS, and OWL Semantic Web standards. The resource description framework (RDF) is an established standard for knowledge representation on the Web. Taken together with the associated RDF Schema (RDFS) standard, we have a language for representing simple ontologies and knowledge bases on the Web.

scholarly journals Petri nets on the semantic web guidelines and infrastructure

2004 ◽  
Vol 1 (2) ◽  
pp. 127-151 ◽  
Author(s):  
Dragan Gasevic
Keyword(s):  
Semantic Web ◽  
Petri Net ◽  
Ontology Language ◽  
Uml Profiles ◽  
Community Effort ◽  
Model Sharing ◽  
Petri Net Markup Language ◽  
Description Framework ◽  
Definition Of ◽  
Resource Description

This paper gives the Petri net ontology as the most important element in providing Petri net support for the Semantic Web. Available Petri net formal descriptions are: metamodels, UML profiles, ontologies and syntax. Metamodels are useful, but their main purpose is for Petri net tools. Although the current Petri-net community effort Petri Net Markup Language (PNML) is XML-based, it lacks a precise definition of semantics. Existing Petri net ontologies are partial solutions specialized for a specific problem. In order to show current Petri net model sharing features we use P3 tool that uses PNML/XSLT-based approach for model sharing. This paper suggests developing the Petri net ontology to represent semantics appropriately. This Petri net ontology is described using UML, Resource Description Framework (Schema) RDF(S) and the Web Ontology Language-OWL.

SWRLx

2018 ◽  
pp. 348-367
Author(s):  
Souad Bouaicha ◽  
Zizette Boufaida
Keyword(s):  
Semantic Web ◽  
Knowledge Base ◽  
Object Oriented ◽  
Web Ontology Language ◽  
Rule Engine ◽  
Ontology Language ◽  
New Knowledge ◽  
Semantic Web Rule Language

Although OWL (Web Ontology Language) and SWRL (Semantic Web Rule Language) add considerable expressiveness to the Semantic Web, they do have expressive limitations. For some reasoning problems, it is necessary to modify existing knowledge in an ontology. This kind of problem cannot be fully resolved by OWL and SWRL, as they only support monotonic inference. In this paper, the authors propose SWRLx (Extended Semantic Web Rule Language) as an extension to the SWRL rules. The set of rules obtained with SWRLx are posted to the Jess engine using rewrite meta-rules. The reason for this combination is that it allows the inference of new knowledge and storing it in the knowledge base. The authors propose a formalism for SWRLx along with its implementation through an adaptation of different object-oriented techniques. The Jess rule engine is used to transform these techniques to the Jess model. The authors include a demonstration that demonstrates the importance of this kind of reasoning. In order to verify their proposal, they use a case study inherent to interpretation of a preventive medical check-up.

Data Confidentiality on the Semantic Web

2008 ◽  
pp. 3309-3320
Author(s):  
Csilla Farkas
Keyword(s):  
Semantic Web ◽  
Formal Semantics ◽  
Future Research ◽  
Semantic Web Technologies ◽  
Inference Problem ◽  
Web Technologies ◽  
Ontology Language ◽  
Future Research Directions ◽  
Description Framework ◽  
Resource Description

This chapter investigates the threat of unwanted Semantic Web inferences. We survey the current efforts to detect and remove unwanted inferences, identify research gaps, and recommend future research directions. We begin with a brief overview of Semantic Web technologies and reasoning methods, followed by a description of the inference problem in traditional databases. In the context of the Semantic Web, we study two types of inferences: (1) entailments defined by the formal semantics of the Resource Description Framework (RDF) and the RDF Schema (RDFS) and (2) inferences supported by semantic languages like the Web Ontology Language (OWL). We compare the Semantic Web inferences to the inferences studied in traditional databases. We show that the inference problem exists on the Semantic Web and that existing security methods do not fully prevent indirect data disclosure via inference channels.

Mining information from sentences through Semantic Web data and Information Extraction tasks

2020 ◽  
pp. 016555152093438
Author(s):  
Jose L. Martinez-Rodriguez ◽  
Ivan Lopez-Arevalo ◽  
Ana B. Rios-Alvarado
Keyword(s):  
Semantic Web ◽  
Natural Language ◽  
Information Extraction ◽  
Knowledge Base ◽  
Semantic Similarity ◽  
Similarity Measure ◽  
Real World ◽  
Semantic Similarity Measure ◽  
Web Standards ◽  
Extract Information

The Semantic Web provides guidelines for the representation of information about real-world objects (entities) and their relations (properties). This is helpful for the dissemination and consumption of information by people and applications. However, the information is mainly contained within natural language sentences, which do not have a structure or linguistic descriptions ready to be directly processed by computers. Thus, the challenge is to identify and extract the elements of information that can be represented. Hence, this article presents a strategy to extract information from sentences and its representation with Semantic Web standards. Our strategy involves Information Extraction tasks and a hybrid semantic similarity measure to get entities and relations that are later associated with individuals and properties from a Knowledge Base to create RDF triples (Subject–Predicate–Object structures). The experiments demonstrate the feasibility of our method and that it outperforms the accuracy provided by a pattern-based method from the literature.

scholarly journals Towards closed world reasoning in dynamic open worlds

2010 ◽  
Vol 10 (4-6) ◽  
pp. 547-563 ◽  
Author(s):  
MARTIN SLOTA ◽  
JOÃO LEITE
Keyword(s):  
Semantic Web ◽  
State Of The Art ◽  
Knowledge Bases ◽  
Order Logic ◽  
First Order Logic ◽  
Static Case ◽  
First Order ◽  
Closed World ◽  
Hybrid Knowledge ◽  
First Time

AbstractThe need for integration of ontologies with nonmonotonic rules has been gaining importance in a number of areas, such as the Semantic Web. A number of researchers addressed this problem by proposing a unified semantics forhybrid knowledge basescomposed of both an ontology (expressed in a fragment of first-order logic) and nonmonotonic rules. These semantics have matured over the years, but only provide solutions for the static case when knowledge does not need to evolve.In this paper we take a first step towards addressing the dynamics of hybrid knowledge bases. We focus on knowledge updates and, considering the state of the art of belief update, ontology update and rule update, we show that current solutions are only partial and difficult to combine. Then we extend the existing work on ABox updates with rules, provide a semantics for such evolving hybrid knowledge bases and study its basic properties.To the best of our knowledge, this is the first time that an update operator is proposed for hybrid knowledge bases.

Representing n-ary relations in the Semantic Web

2019 ◽  
Author(s):  
Marco Giunti ◽  
Giuseppe Sergioli ◽  
Giuliano Vivanet ◽  
Simone Pinna
Keyword(s):  
Artificial Intelligence ◽  
Semantic Web ◽  
Expressive Power ◽  
Abstract Model ◽  
Relational Ontology ◽  
Rdf Graph ◽  
Labeled Graphs ◽  
Ontology Language ◽  
Technical Simplicity ◽  
In Virtue Of

Abstract Knowledge representation is a central issue for Artificial Intelligence and the Semantic Web. In particular, the problem of representing n-ary relations in RDF-based languages such as RDFS or OWL by no means is an obvious one. With respect to previous attempts, we show why the solutions proposed by the well known W3C Working Group Note on n-ary relations are not satisfactory on several scores. We then present our abstract model for representing n-ary relations as directed labeled graphs, and we show how this model gives rise to a new ontological pattern (parametric pattern) for the representation of such relations in the Semantic Web. To this end, we define PROL (Parametric Relational Ontology Language). PROL is an ontological language designed to express any n-ary fact as a parametric pattern, which turns out to be a special RDF graph. The vocabulary of PROL is defined by a simple RDFS ontology. We argue that the parametric pattern may be particularly beneficial in the context of the Semantic Web, in virtue of its high expressive power, technical simplicity, and faithful meaning rendition. Examples are also provided.

Function Semantic Representation (FSR): A Rule-Based Ontology for Product Functions

2010 ◽  
Vol 10 (3) ◽  
Author(s):  
Seung-Cheol Yang ◽  
Lalit Patil ◽  
Debasish Dutta
Keyword(s):  
Semantic Web ◽  
Semantic Representation ◽  
Functional Model ◽  
Consistency Checking ◽  
Formal Representation ◽  
Rule Based ◽  
Modeling And Analysis ◽  
Ontology Language ◽  
Web Standards ◽  
Product Function

Defining or understanding a product in terms of its functions facilitates a wide variety of tasks such as design synthesis, modeling, and analysis. However, the lack of a semantically correct formal representation of product functions creates a barrier to their effective capture, exchange, and reuse. This paper presents Function Semantics Representation, a rule-based ontological formalism that is consistent with the Semantic Web standards to capture different components of a product function. In particular, the Semantic Web Rule Language is used to overcome limitations in using the basic Web Ontology Language ontology to explicitly capture advanced semantics essential to completely represent product functions. This enables support for an effective reasoning mechanism to develop and validate the product function (or functional model). We present examples that demonstrate consistency checking and the ability to retrieve functionally similar products from a repository.

scholarly journals Algorithm of Ontology Transformation to Concept Map for Usage in Semantic Web Expert System

2013 ◽  
Vol 14 (1) ◽  
pp. 80-87
Author(s):  
Olegs Verhodubs ◽  
Janis Grundspenkis
Keyword(s):  
Expert System ◽  
Semantic Web ◽  
Knowledge Base ◽  
Concept Map ◽  
Web Ontology Language ◽  
Subsequent Generation ◽  
Ontology Language ◽  
Owl Ontology ◽  
System Knowledge

Abstract The main purpose of this paper is to present an algorithm of OWL (Web Ontology Language) ontology transformation to concept map for subsequent generation of rules and also to evaluate the efficiency of this algorithm. These generated rules are necessary to supplement and even to develop SWES (Semantic Web Expert System) knowledge base. This paper is a continuation of the earlier research of OWL ontology transformation to rules.

Survey of directly mapping SQL databases to the Semantic Web

2011 ◽  
Vol 26 (4) ◽  
pp. 445-486 ◽  
Author(s):  
Juan F. Sequeda ◽  
Syed Hamid Tirmizi ◽  
Oscar Corcho ◽  
Daniel P. Miranker
Keyword(s):  
Semantic Web ◽  
Resource Description Framework ◽  
Information Sources ◽  
The Internet ◽  
Web Ontology Language ◽  
Ontology Language ◽  
Description Framework ◽  
Resource Description ◽  
Semantic Properties ◽  
Rdf Schema

AbstractThe Semantic Web anticipates integrated access to a large number of information sources on the Internet represented as Resource Description Framework (RDF). Given the large number of websites that are backed by SQL databases, methods that automate the translation of those databases to RDF are crucial. One approach, taken by a number of researchers, is to directly map the SQL schema to an equivalent Web Ontology Language (OWL) or RDF Schema representation, which in turn, implies an RDF representation for the relational data. This paper reviews this research, and derives a consolidated, overarching set of translation rules expressible as a stratified Datalog program. We present all the possible key combinations in an SQL schema and consider their implied semantic properties. We review the approaches and characterize them with respect to the scope of their coverage of SQL constructs.

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