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Root Justifications for Ontology Repair [chapter]

Kodylan Moodley, Thomas Meyer, Ivan José Varzinczak
2011 Lecture Notes in Computer Science  
In recent years, there has been significant progress in developing tools for debugging and repairing Description Logic (DL)-based ontologies with erroneous consequences.  ...  By extending existing principles in ontology repair, our goal is to define one such a common approach.  ...  Conclusion We have presented an alternative approach for ontology repair using the notion of root justifications.  ... 
doi:10.1007/978-3-642-23580-1_24 fatcat:yinrqimfsjel3f42ckf3dzkqba

The Justificatory Structure of the NCBO BioPortal Ontologies [chapter]

Samantha Bail, Matthew Horridge, Bijan Parsia, Ulrike Sattler
2011 Lecture Notes in Computer Science  
Current ontology development tools offer debugging support by presenting justifications for entailments of OWL ontologies.  ...  In many cases even a single entailment may have many distinct justifications, and justifications for distinct entailments may be critically related.  ...  The focus of the work of root and derived justifications is to provide improved ontology debugging and repair support; there is no indication of inferring information about the ontology from its root and  ... 
doi:10.1007/978-3-642-25073-6_5 fatcat:qotu7nj66ne3np2umkljqeitpq

ORE - A Tool for Repairing and Enriching Knowledge Bases [chapter]

Jens Lehmann, Lorenz Bühmann
2010 Lecture Notes in Computer Science  
In this article, we present ORE, a tool for repairing and enriching OWL ontologies.  ...  Furthermore, the tool allows to extend an ontology through (semi-)automatic supervised learning.  ...  Ontology Repair For a single entailment, e.g. an unsatisfiable class, there can be many justifications.  ... 
doi:10.1007/978-3-642-17749-1_12 fatcat:u4ch5bi4efechd3htxugxggcim

Explaining Inconsistencies in OWL Ontologies [chapter]

Matthew Horridge, Bijan Parsia, Ulrike Sattler
2009 Lecture Notes in Computer Science  
This is despite the fact that justifications are important for repairing inconsistent ontologies, and can be used as a basis for paraconsistent reasoning.  ...  Justifications play a central role as the basis for explaining entailments in OWL ontologies.  ...  Using justifications for inconsistent ontologies for repair.  ... 
doi:10.1007/978-3-642-04388-8_11 fatcat:fy5qfqig5zhd5a6vykq46azbzq

Union and Intersection of all Justifications [article]

Jieying Chen, Yue Ma, Rafael Peñaloza, Hui Yang
2021 arXiv   pre-print
We present new algorithm for computing the union and intersection of all justifications for a given ontological consequence without first computing the set of all justifications.  ...  We further discuss how to use these results to repair ontologies efficiently.  ...  For this paper, we are interested in the notions of justification and repair. Definition 1 (Justification, repair). Let O be an ontology and α a GCI.  ... 
arXiv:2109.11216v1 fatcat:uwoarazgtza4bdksj4m3znlroa

Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies

Luke T Slater, Georgios V Gkoutos, Robert Hoehndorf
2020 BMC Medical Informatics and Decision Making  
In addition, we designed and implemented a novel algorithm that can determine justifications for contradictions across extremely large and complicated ontologies, and use these justifications to semi-automatically  ...  We also applied our semi-automatic repair algorithm to each combination of OBO ontologies that resulted in unsatisfiable classes, finding that only 117 axioms could be removed to account for all cases  ...  Acknowledgements We would like to thank Dr Paul Schofield and Dr Egon Willighagen for helpful conversations surrounding the described experiments.  ... 
doi:10.1186/s12911-020-01336-2 pmid:33319712 fatcat:qixgz75fxbcw5mgexutjjldmbq

Completing and Debugging Ontologies: state of the art and challenges [article]

Patrick Lambrix
2020 arXiv   pre-print
A key step is ontology debugging and completion. In general, there are two steps: detecting defects and repairing defects. In this paper we discuss the state of the art regarding the repairing step.  ...  We show that there are still many open research problems and show opportunities for further work and advancing the field.  ...  Acknowledgements We thank the anonymous referees for comments that have led to improvements of the paper as well as Mina Abd Nikooie Pour, Ying Li and Chunyan Wang for proofreading and checking the examples  ... 
arXiv:1908.03171v2 fatcat:mztcxefbqndebd6cvj5wgz2de4

Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies [article]

Luke T Slater, Georgios V Gkoutos, Robert Hoehndorf
2020 biorxiv/medrxiv   pre-print
We design and implement a novel algorithm that can determine justifications for contradictions across extremely large and complicated ontologies, and use these justifications to semi-automatically repair  ...  Results: We developed a method that tests for hidden unsatisfiabilities in an ontology that arise when combined with other ontologies.  ...  to make an ontology coherent, it does not 343 repair the root cause of the contradiction.  ... 
doi:10.1101/2020.05.16.099309 fatcat:4rr5bjr4drecldakravt32gqse

Reasoning based quality assurance of medical ontologies: a case study

Matthew Horridge, Bijan Parsia, Natalya F Noy, Mark A Musenm
2014 AMIA Annual Symposium Proceedings  
Specifically, we found that a logically inconsistent version of the ICTM ontology could be repaired using justifications (minimal entailing subsets of an ontology).  ...  In this paper we investigate how automated OWL reasoning, along with a Justification Finding Service can be used as a Quality Assurance technique for the development of large and complex ontologies such  ...  a repair plan for the ontology.  ... 
pmid:25954373 pmcid:PMC4420015 fatcat:nrvi7iazefd5xjz7amogzm4ium

A unified approach for debugging is-a structure and mappings in networked taxonomies

Patrick Lambrix, Valentina Ivanova
2013 Journal of Biomedical Semantics  
With the increased use of ontologies and ontology mappings in semantically-enabled applications such as ontology-based search and data integration, the issue of detecting and repairing defects in ontologies  ...  Results: We propose a unified framework for debugging the is-a structure of and mappings between taxonomies, the most used kind of ontologies.  ...  We thank Qiang Liu for the implementation work on an earlier version of the RepOSE system.  ... 
doi:10.1186/2041-1480-4-10 pmid:23548155 pmcid:PMC3851282 fatcat:7xq4zn5sozhalkrclmrufn27cu

Extracting Justifications from BioPortal Ontologies [chapter]

Matthew Horridge, Bijan Parsia, Ulrike Sattler
2012 Lecture Notes in Computer Science  
The results paint a picture of the performance that can be expected when finding all justifications for entailments using black box justification finding techniques.  ...  The results also show that many naturally occurring ontologies exhibit a rich justificatory structure, with some ontologies having extremely high numbers of justifications per entailment.  ...  each repair.  ... 
doi:10.1007/978-3-642-35173-0_19 fatcat:oqnwdm6zgjfgtcqkdop2vjlhuy

Ontology based Clinical Practice Justification in Natural Language

David Mendes, Irene Pimenta Rodrigues, Carlos Baeta
2013 Procedia Technology - Elsevier  
Our work has two main contributions, consolidating the use of OGCP (Ontology for General Clinical Practice) as foundation and providing controlled English justifications of the extracted suggestions.  ...  In this article we demonstrate the use of an ontological framework as inferencing basis for automatic sound clinical suggestions providing.  ...  -Center for Research in Artificial Intelligence of Faculdade de Ciências e Tecnologia of Universidade Nova de Lisboa for its continuous financial support of our work. § § § Description Logic **** Discourse  ... 
doi:10.1016/j.protcy.2013.12.144 fatcat:5ncvemszendxvdgpypcahzbr7m

Finding All Justifications of OWL DL Entailments [chapter]

Aditya Kalyanpur, Bijan Parsia, Matthew Horridge, Evren Sirin
2007 Lecture Notes in Computer Science  
Justifications are essential for debugging unsatisfiable classes and contradictions.  ...  Finding the justifications of an entailment (that is, all the minimal set of axioms sufficient to produce an entailment) has emerged as a key inference service for the Web Ontology Language (OWL).  ...  ), we find any one justification and set it as the root node of the HST.  ... 
doi:10.1007/978-3-540-76298-0_20 fatcat:pqtfq6wcsbfwjnausesctjisdq

Knowledge Base Creation, Enrichment and Repair [chapter]

Sebastian Hellmann, Volha Bryl, Lorenz Bühmann, Milan Dojchinovski, Dimitris Kontokostas, Jens Lehmann, Uroš Milošević, Petar Petrovski, Vojtěch Svátek, Mladen Stanojević, Ondřej Zamazal
2014 Lecture Notes in Computer Science  
This chapter focuses on data transformation to RDF and Linked Data and furthermore on the improvement of existing or extracted data especially with respect to schema enrichment and ontology repair.  ...  However, schema information is needed for consistency checking and finding modelling problems.  ...  Ontology Repair with PatOMat The PatOMat is a pattern-based ontology transformation framework specifically designed for OWL ontologies [23] .  ... 
doi:10.1007/978-3-319-09846-3_3 fatcat:fuymcvwpibbvbkaooq33opmga4

Ontology Evaluation through Assessment of Inferred Statements: Study of a Prototypical Implementation of an Ontology Questionnaire for OWL DL Ontologies [chapter]

Viktoria Pammer, Stefanie Lindstaedt
2009 Lecture Notes in Computer Science  
We study this process by means of a prototypical implementation for OWL DL ontologies, called ontology questionnaire, and discuss support for dealing with unwanted inferences based on experiences with  ...  Evaluation and consequent revision of ontologies is a critical task in the process of ontology engineering.  ...  Justifications in OWL The second question has been treated with slightly varying focus under the names of ontology debugging, ontology repair and ontology explanations.  ... 
doi:10.1007/978-3-642-10488-6_38 fatcat:tebkoo33w5bh7gmaesz7nlyp54
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