scholarly journals ByNowLife: A Novel Framework for OWL and Bayesian Network Integration

Information ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 95
Author(s):  
Foni Setiawan ◽  
Eko Budiardjo ◽  
Wahyu Wibowo
Keyword(s):  
Bayesian Network ◽  
Knowledge Base ◽  
Structural Adjustment ◽  
Description Logic ◽  
Probabilistic Reasoning ◽  
Knowledge Bases ◽  
Third Party ◽  
Probabilistic Information ◽  
Ontology Language ◽  
Novel Approach

An ontology-based system can currently logically reason through the Web Ontology Language Description Logic (OWL DL). To perform probabilistic reasoning, the system must use a separate knowledge base, separate processing, or third-party applications. Previous studies mainly focus on how to represent probabilistic information in ontologies and perform reasoning through them. These approaches are not suitable for systems that already have running ontologies and Bayesian network (BN) knowledge bases because users must rewrite the probabilistic information contained in a BN into an ontology. We present a framework called ByNowLife, which is a novel approach for integrating BN with OWL by providing an interface for retrieving probabilistic information through SPARQL queries. ByNowLife catalyzes the integration process by transforming logical information contained in an ontology into a BN and probabilistic information contained in a BN into an ontology. This produces a system with a complete knowledge base. Using ByNowLife, a system that already has separate ontologies and BN knowledge bases can integrate them into a single knowledge base and perform both logical and probabilistic reasoning through it. The integration not only facilitates the unity of reasoning but also has several other advantages, such as ontology enrichment and BN structural adjustment through structural and parameter learning.

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.

scholarly journals The Complexity of Answering Conjunctive and Navigational Queries over OWL 2 EL Knowledge Bases

2014 ◽  
Vol 51 ◽  
pp. 645-705 ◽  
Author(s):  
G. Stefanoni ◽  
B. Motik ◽  
M. Kroetzsch ◽  
S. Rudolph
Keyword(s):  
Description Logic ◽  
Knowledge Bases ◽  
Complexity Bound ◽  
Total Size ◽  
Worst Case ◽  
Ontology Language ◽  
Lower Complexity ◽  
Bounded Size ◽  
Compositional Properties ◽  
Context Free

OWL 2 EL is a popular ontology language that supports role inclusions---that is, axioms that capture compositional properties of roles. Role inclusions closely correspond to context-free grammars, which was used to show that answering conjunctive queries (CQs) over OWL 2 EL knowledge bases with unrestricted role inclusions is undecidable. However, OWL 2 EL inherits from OWL 2 DL the syntactic regularity restriction on role inclusions, which ensures that role chains implying a particular role can be described using a finite automaton (FA). This is sufficient to ensure decidability of CQ answering; however, the FAs can be worst-case exponential in size so the known approaches do not provide a tight upper complexity bound. In this paper, we solve this open problem and show that answering CQs over OWL 2 EL knowledge bases is PSPACE-complete in combined complexity (i.e., the complexity measured in the total size of the input). To this end, we use a novel encoding of regular role inclusions using bounded-stack pushdown automata---that is, FAs extended with a stack of bounded size. Apart from theoretical interest, our encoding can be used in practical tableau algorithms to avoid the exponential blowup due to role inclusions. In addition, we sharpen the lower complexity bound and show that the problem is PSPACE-hard even if we consider only role inclusions as part of the input (i.e., the query and all other parts of the knowledge base are fixed). Finally, we turn our attention to navigational queries over OWL 2 EL knowledge bases, and we show that answering positive, converse-free conjunctive graph XPath queries is PSPACE-complete as well; this is interesting since allowing the converse operator in queries is known to make the problem EXPTIME-hard. Thus, in this paper we present several important contributions to the landscape of the complexity of answering expressive queries over description logic knowledge bases.

scholarly journals Identifying Principles for the Construction of an Ontology-Based Knowledge Base: A Case Study Approach (Preprint)

2018 ◽  
Author(s):  
Xia Jing ◽  
Nicholas R Hardiker ◽  
Stephen Kay ◽  
Yongsheng Gao
Keyword(s):  
Cystic Fibrosis ◽  
Knowledge Base ◽  
Health Information ◽  
Domain Knowledge ◽  
Information Needs ◽  
Molecular Mechanisms ◽  
Critical Role ◽  
Clinical Information ◽  
Knowledge Bases ◽  
Ontology Language

BACKGROUND Ontologies are key enabling technologies for the Semantic Web. The Web Ontology Language (OWL) is a semantic markup language for publishing and sharing ontologies. OBJECTIVE The supply of customizable, computable, and formally represented molecular genetics information and health information, via electronic health record (EHR) interfaces, can play a critical role in achieving precision medicine. In this study, we used cystic fibrosis as an example to build an Ontology-based Knowledge Base prototype on Cystic Fibrobis (OntoKBCF) to supply such information via an EHR prototype. In addition, we elaborate on the construction and representation principles, approaches, applications, and representation challenges that we faced in the construction of OntoKBCF. The principles and approaches can be referenced and applied in constructing other ontology-based domain knowledge bases. METHODS First, we defined the scope of OntoKBCF according to possible clinical information needs about cystic fibrosis on both a molecular level and a clinical phenotype level. We then selected the knowledge sources to be represented in OntoKBCF. We utilized top-to-bottom content analysis and bottom-up construction to build OntoKBCF. Protégé-OWL was used to construct OntoKBCF. The construction principles included (1) to use existing basic terms as much as possible; (2) to use intersection and combination in representations; (3) to represent as many different types of facts as possible; and (4) to provide 2-5 examples for each type. HermiT 1.3.8.413 within Protégé-5.1.0 was used to check the consistency of OntoKBCF. RESULTS OntoKBCF was constructed successfully, with the inclusion of 408 classes, 35 properties, and 113 equivalent classes. OntoKBCF includes both atomic concepts (such as amino acid) and complex concepts (such as “adolescent female cystic fibrosis patient”) and their descriptions. We demonstrated that OntoKBCF could make customizable molecular and health information available automatically and usable via an EHR prototype. The main challenges include the provision of a more comprehensive account of different patient groups as well as the representation of uncertain knowledge, ambiguous concepts, and negative statements and more complicated and detailed molecular mechanisms or pathway information about cystic fibrosis. CONCLUSIONS Although cystic fibrosis is just one example, based on the current structure of OntoKBCF, it should be relatively straightforward to extend the prototype to cover different topics. Moreover, the principles underpinning its development could be reused for building alternative human monogenetic diseases knowledge bases.

An Ontology-Based Information Extraction System for Organic Farming

2021 ◽  
Vol 17 (2) ◽  
pp. 79-99
Author(s):  
Adebayo Adewumi Abayomi-Alli ◽  
Oluwasefunmi 'Tale Arogundade ◽  
Sanjay Misra ◽  
Mulkah Opeyemi Akala ◽  
Abiodun Motunrayo Ikotun ◽  
...  
Keyword(s):  
Information Extraction ◽  
Knowledge Base ◽  
Organic Farming ◽  
Description Logic ◽  
Query Language ◽  
Relevant Information ◽  
Extraction System ◽  
Ontology Development ◽  
Ontology Language ◽  
Information Extraction System

In the existing farming system, information is obtained manually, and most times, farmers act based on their discretion. Sometimes, farmers rely on information from experts and extension officers for decision making. In recent times, a lot of information systems are available with relevant information on organic farming practices; however, such information is scattered in different context, form, and media all over the internet, making their retrieval difficult. The use of ontology with the aid of a conceptual scheme makes the comprehensive and detailed formalization of any subject domain possible. This study is aimed at acquiring, storing, and providing organic farming-based information available to current and intending software developer who may wish to develop applications for farmers. It employs information extraction (IE) and ontology development techniques to develop an ontology-based information extraction (OBIE) system called ontology-based information extraction system for organic farming (OBIESOF). The knowledge base was built using protégé editor; Java was used for the implementation of the ontology knowledge base with the aid of the high-level application programming language for working web ontology language application program interface (OWL API). In contrast, HermiT was used to checking the consistencies of the ontology and for submitting queries in order to verify their validity. The queries were expressed in description logic (DL) query language. The authors tested the capability of the ontology to respond to user queries by posing instances of the competency questions from DL query interface. The answers generated by the ontology were promising and serve as positive pointers to its usefulness as a knowledge repository.

scholarly journals ASP for minimal entailment in a rational extension of SROEL

2016 ◽  
Vol 16 (5-6) ◽  
pp. 738-754 ◽  
Author(s):  
LAURA GIORDANO ◽  
DANIELE THESEIDER DUPRÉ
Keyword(s):  
Description Logic ◽  
Polynomial Complexity ◽  
Answer Set Programming ◽  
Low Complexity ◽  
Knowledge Bases ◽  
Ontology Language ◽  
Rational Extension ◽  
Small Model ◽  
Answer Sets ◽  
Answer Set

AbstractIn this paper we exploit Answer Set Programming (ASP) for reasoning in a rational extensionSROEL(⊓,×)RTof the low complexity description logicSROEL(⊓, ×), which underlies the OWL EL ontology language. In the extended language, a typicality operatorTis allowed to define conceptsT(C) (typicalC's) under a rational semantics. It has been proven that instance checking under rational entailment has a polynomial complexity. To strengthen rational entailment, in this paper we consider a minimal model semantics. We show that, for arbitrarySROEL(⊓,×)RTknowledge bases, instance checking under minimal entailment is ΠP2-complete. Relying on a Small Model result, where models correspond to answer sets of a suitable ASP encoding, we exploit Answer Set Preferences (and, in particular, theasprinframework) for reasoning under minimal entailment.

A Design for Additive Manufacturing Ontology

2017 ◽  
Vol 17 (2) ◽  
Author(s):  
Mahmoud Dinar ◽  
David W. Rosen
Keyword(s):  
Additive Manufacturing ◽  
Knowledge Base ◽  
System Integration ◽  
Domain Knowledge ◽  
Description Logic ◽  
Design For Additive Manufacturing ◽  
Ontology Language ◽  
Subtractive Manufacturing ◽  
Description Framework ◽  
Future Work

Design for additive manufacturing (DFAM) gives designers new freedoms to create complex geometries and combine parts into one. However, it has its own limitations, and more importantly, requires a shift in thinking from traditional design for subtractive manufacturing. There is a lack of formal and structured guidelines, especially for novice designers. To formalize knowledge of DFAM, we have developed an ontology using formal web ontology language (OWL)/resource description framework (RDF) representations in the Protégé tool. The description logic formalism facilitates expressing domain knowledge as well as capturing information from benchmark studies. This is demonstrated in a case study with three design features: revolute joint, threaded assembly (screw connection), and slider–crank. How multiple instances (build events) are stored and retrieved in the knowledge base is discussed in light of modeling requirements for the DFAM knowledge base: knowledge capture and reuse, supporting a tutoring system, integration into cad tools. A set of competency questions are described to evaluate knowledge retrieval. Examples are given with SPARQL queries. Reasoning with semantic web rule language (SWRL) is exemplified for manufacturability analysis. Knowledge documentation is the main objective of the current ontology. However, description logic creates multiple opportunities for future work, including representing and reasoning about DFAM rules in a structured modular hierarchy, discovering new rules with induction, and recognizing patterns with classification, e.g., what leads to “successful” versus “unsuccessful” fabrications.

scholarly journals Reverse Engineering Queries in Ontology-Enriched Systems: The Case of Expressive Horn Description Logic Ontologies

2018 ◽  
Author(s):  
Víctor Gutiérrez-Basulto ◽  
Jean Christoph Jung ◽  
Leif Sabellek
Keyword(s):  
Reverse Engineering ◽  
Knowledge Base ◽  
Description Logic ◽  
Knowledge Bases ◽  
Query Answering ◽  
Conjunctive Queries ◽  
Complexity Bounds ◽  
Query By Example

We introduce the query-by-example (QBE) paradigm for query answering in the presence of ontologies. Intuitively, QBE permits non-expert users to explore the data by providing examples of the information they (do not) want, which the system then generalizes into a query. Formally, we study the following question: given a knowledge base and sets of positive and negative examples, is there a query that returns all positive but none of the negative examples?  We focus on description logic knowledge bases with ontologies formulated in Horn-ALCI and (unions of) conjunctive queries. Our main contributions are characterizations, algorithms and tight complexity bounds for QBE.  

scholarly journals Ontology for preserving the knowledge base of traditional dances (OTD)

2020 ◽  
Vol 38 (4) ◽  
pp. 785-803
Author(s):  
Deepjyoti Kalita ◽  
Dipen Deka
Keyword(s):  
Knowledge Base ◽  
Domain Knowledge ◽  
Description Logic ◽  
Cultural Knowledge ◽  
Strong Base ◽  
Content Type ◽  
North East India ◽  
North East ◽  
Ontology Language ◽  
Traditional Dance

Purpose Systematic organization of domain knowledge has many advantages in archiving, sharing and retrieval of information. Ontologies provide a cushion for such practices in the semantic Web environment. This study aims to develop an ontology that can preserve the knowledge base of traditional dance practices. Design/methodology/approach It is hypothesized that an ontology-based approach for the chosen domain might boost collaborative research prospects in the domain. A systematic methodology was developed for modeling the ontology based on the analytico-synthetic rule of library classification. Protégé 5.2 was used as an editor for the ontology using the Web ontology language combined with description logic axioms. Ontology was later implemented in a local GraphDB repository to run queries over it. Findings The developed ontology on traditional dances (OTD) was tested using the dances of the Rabha tribes of North East India. Rabha tribes are from an indigenous mongoloid community and have a robust presence in Southeast Asian countries, such as Myanmar, Thailand, Bangladesh, Bhutan and Nepal. The result from HermiT reasoner found the presence of no logical inconsistency in the ontology, while the OOPS! pitfall checker tool reported no major internal inconsistency. The induced knowledge base of traditional dances of the Rabha’s in the developed OTD was further validated based on some competency questions. Research limitations/implications In the growing trend of globalization, preservation of the cultural knowledge base of human societies is an important issue. Traditional dances reflect a strong base of the cultural heritage of human societies as they are closely related to the lifestyle, habitat, religious practices and festivals of a specific community. Originality/value The current study is exclusively designed, keeping in mind the variables of traditional dance domain based on a survey of the user- and domain-specific needs. The ontology finds probable uses in traditional knowledge information systems, lifestyle-based e-commerce sites and e-learning platforms.

New Model for Handling Inconsistency Issues in DL-Lite Knowledge Bases

2021 ◽  
Author(s):  
Ghassen Hamdi ◽  
Mohamed Nazih Omri
Keyword(s):  
Experimental Study ◽  
Knowledge Base ◽  
Performance Measures ◽  
Description Logic ◽  
Knowledge Bases ◽  
Topical Issue ◽  
New Model ◽  
F Measure ◽  
Main Factor

The lightweight description logic (DL-lite) represents one of the most important logic specially dedicated to applications that handle large volumes of data. Managing inconsistency issues, in order to effectively query inconsistent DL-Lite knowledge bases, is a topical issue. Since assertions (ABoxes) come from a variety of sources with varying degrees of reliability, there is confusion in hierarchical knowledge bases. As a consequence, the inclusion of new axioms is a main factor that causes inconsistency in this type of knowledge base. Often, it is too expensive to manually verify and validate all assertions. In this article, we study the problem of inconsistencies in the DL-Lite family and we propose a new algorithm to resolve the inconsistencies in prioritized knowledge bases. We carried out an experimental study to analyze and compare the results obtained by our proposed algorithm, in the framework of this work, and the main algorithms studied in the literature. The results obtained show that our algorithm is more productive than the others, compared to standard performance measures, namely precision, recall and F-measure.

Knowledge-Based Description Logic ALCO Knowledge Compiled Algorithm to Determine Consistency

2012 ◽  
Vol 487 ◽  
pp. 347-351
Author(s):  
Ya Qiong Jiang ◽  
Jun Wang
Keyword(s):  
Normal Form ◽  
Knowledge Base ◽  
Propositional Logic ◽  
Description Logic ◽  
Knowledge Bases ◽  
Knowledge Compilation ◽  
Knowledge Based ◽  
Common Technique ◽  
Compilation Techniques

Knowledge compilation is a common technique for propositional logic knowledge bases. A given knowledge base is transformed into a normal form, for which reasoning can be answered efficiently. The precompilation of description logic knowledge base is important for reasoning and services of description logic. This paper gives precompilation about the description logic ALCO TBox based on knowledge compilation techniques, for which the consistency of TBox can be determined.

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