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Unintended consequences of existential quantifications in biomedical ontologies

Martin Boeker, Ilinca Tudose, Janna Hastings, Daniel Schober, Stefan Schulz
2011 BMC Bioinformatics  
We further describe several usability issues with OBO ontologies, including the lack of ontological commitment for several common terms, and the proliferation of domain-specific relations.  ...  Based on the interpretations underlying OWL description logics (OWL-DL) semantics, we scrutinize the OWL-DL releases of OBO ontologies to assess whether their logical axioms correspond to the meaning intended  ...  unintended consequences in biomedical ontologies.  ... 
doi:10.1186/1471-2105-12-456 pmid:22115278 pmcid:PMC3280341 fatcat:uby7pqivcff4tdyatoqqx7phd4

A methodology for asynchronous multi-user editing of semantic web ontologies

Julian Seidenberg, Alan Rector
2007 Proceedings of the 4th international conference on Knowledge capture - K-CAP '07  
Current tools, techniques and methodologies for multiuser editing of semantic web ontologies are inadequate. The vast majority of ontologies are maintained by single individuals.  ...  This technique fits into a methodology for ontology editing in which multiple ontology engineers concurrently lock, extract, modify, error-check and re-merge individual segments of a large ontology.  ...  This set is comparable to a commit of a long transaction in a conventional database application.  ... 
doi:10.1145/1298406.1298430 dblp:conf/kcap/SeidenbergR07 fatcat:gjtvnjithbh3fl3mr35eiw5zx4

Building Ontologies Collaboratively Using ContentCVS

Ernesto Jiménez-Ruiz, Bernardo Cuenca Grau, Ian Horrocks, Rafael Berlanga Llavori
2009 International Workshop on Description Logics  
from different developers, minimising the introduction of errors (e.g., ensuring that the ontology does not have unintended logical consequences), and so on.  ...  These errors may manifest themselves both as structural (i.e., syntactic) mismatches between developers' ontological descriptions, and as unintended logical consequences.  ...  For example, discussion threads and annotations could be used in ContentCVS to assist users in selecting intended and unintended consequences (i.e. in Steps 9 and 10 of Table 1 ), and for recording the  ... 
dblp:conf/dlog/Jimenez-RuizGHL09 fatcat:zstvwmqm3ncibghq4exbseg2by

Foundationless Ontologies

Michael Grüninger, Megan Katsumi
2019 Joint Ontology Workshops  
One of the purported benefits of foundational ontologies is that they facilitate the design of sharable and reusable domain ontologies.  ...  In this paper we explore the role of foundational ontologies in axiomatizing the intended semantics of the signature of a domain ontology.  ...  The next Theorem shows that the answer to this question is based on the distinction between elementary and pseudoelementary classes of structures. Theorem 2.  ... 
dblp:conf/jowo/GruningerK19a fatcat:icj7x7w4f5bupih4tyhwpqgazm

On the Definition of 'Ontology'

Fabian Neuhaus
2017 Joint Ontology Workshops  
In this paper we offer six arguments against their proposed analysis of 'ontology'. It has technical flaws that lead to absurd consequences.  ...  According to them an ontology is, roughly speaking, a logical theory, which models approximate, as best as possible, the intended models according to a given ontological commitment (which is based on a  ...  Acknowledgments I would like to thank Till Mossakowski for an interesting discussion on the nature of ontologies, which lead to this work.  ... 
dblp:conf/jowo/Neuhaus17 fatcat:b3qifw5xznfdfijtjmt5tcvtnm

Ontological Patterns, Anti-Patterns and Pattern Languages for Next-Generation Conceptual Modeling [chapter]

Giancarlo Guizzardi
2014 Lecture Notes in Computer Science  
In particular, the paper discusses three of these tools, namely, ontological patterns, ontological anti-patterns and pattern languages.  ...  Thus, we might say that data are fragments of a theory of the real world, and data processing juggles representations of these fragments of theory...The issue is ontology, or the question of what exists  ...  Mylopoulos and the members of NEMO for many years of fruitful collaboration. This research was partially supported by the Lucretius ERC Advanced Grant # 267856.  ... 
doi:10.1007/978-3-319-12206-9_2 fatcat:7pjdlifflzhvbgrbckstorxcvy

Thoughts on the complex relation between linked data, semantic annotations, and ontologies

Krzysztof Janowicz, Pascal Hitzler
2013 Proceedings of the sixth international workshop on Exploiting semantic annotations in information retrieval - ESAIR '13  
We will report from our own experience and from observations gathered by editing papers about ontologies and Linked Data for the Semantic Web journal.  ...  straightforward at first: Data are annotated with additional meta information according to some schemata in order to expose additional non-intrinsic characteristics relevant to the meaningful interpretation of  ...  These ontologies introduce classes such as Endurant and Perdurant together with numerous complex ontological commitments.  ... 
doi:10.1145/2513204.2513218 dblp:conf/cikm/JanowiczH13 fatcat:g4vsdnnlnzamfps42vgimrn2uy

Supporting concurrent ontology development: Framework, algorithms and tool

E. Jiménez Ruiz, B. Cuenca Grau, I. Horrocks, R. Berlanga
2011 Data & Knowledge Engineering  
consequences).  ...  and reconcile conflicting views of the domain by merging different ontology versions; and 6. to minimise the introduction of errors (e.g., to ensure that the ontology does not have unintended logical  ...  The authors also wish to acknowledge Alan Rector (Information Management Group, University of Manchester) for providing us with a valuable ontology test sequence.  ... 
doi:10.1016/j.datak.2010.10.001 fatcat:h54e2gtnkzgmxnqotmxrnmdvoe

A Model Theoretic Semantics for Ontology Versioning [chapter]

Jeff Heflin, Zhengxiang Pan
2004 Lecture Notes in Computer Science  
We show that the Semantic Web needs a formal semantics for the various kinds of links between ontologies and other documents.  ...  Since the Web is the product of a diverse community, as opposed to a single agent, this semantics accommodates different viewpoints by having different entailment relations for different ontology perspectives  ...  Since the ontology can only restrict unintended models, there is no way to formally describe the intended models of an ontology.  ... 
doi:10.1007/978-3-540-30475-3_6 fatcat:v3iklfpzkjf65ftrybes52sjxa

PriGuardTool: A Web-Based Tool to Detect Privacy Violations Semantically [chapter]

Nadin Kökciyan, Pınar Yolum
2016 Lecture Notes in Computer Science  
The system then monitors which commitments are violated based on the content shown to users, such that a violated commitment represents a privacy violation in the system.  ...  This paper presents PriGuardTool, a Web-based tool that can detect privacy violations in online social networks.  ...  Post class is the most general class to represent a post. In an ontology, one can define complex classes.  ... 
doi:10.1007/978-3-319-50983-9_5 fatcat:gxiij75dzrexrcgl72qmmvy4g4

The Pitfalls of Thesaurus Ontologization - the Case of the NCI Thesaurus

Stefan Schulz, Daniel Schober, Ilinca Tudose, Holger Stenzhorn
2010 AMIA Annual Symposium Proceedings  
These axioms therefore constitute a huge source for unintended models, rendering most logic-based reasoning unreliable. After identifying typical error patterns we discuss some possible improvements.  ...  According to a rating performed by two domain experts, roughly half of these examples, and in consequence more than 76,000 axioms in the OWL-DL version, make incorrect assertions if interpreted according  ...  DL-based ontologies allow describing classes via the properties their members have in common.  ... 
pmid:21347074 pmcid:PMC3041372 fatcat:cvx6hvo565b4texahrnvkhokde

Quality Assurance of Ontology Content Reuse

Michael Halper, Christopher Ochs, Yehoshua Perl, Sivaram Arabandi, Mark A. Musen
2018 International Conference on Biomedical Ontology  
Some heuristic-based approaches are proposed for analyzing ontologies for these kinds of quality assurance issues.  ...  An analysis is carried out on a sample of the large collection of BioPortal-hosted ontologies, many of which employ reuse.  ...  The content is solely the responsibility of the authors and does not necessarily represent the views of the National Institutes of Health.  ... 
dblp:conf/icbo/HalperOPAM18 fatcat:dhydd7ygobfknnhes5klnbzttm

Providing Conceptual Disambiguation for Terms in Reusable Ontologies: A Case Study from FIBO

Michael G. Bennett
2018 Joint Ontology Workshops  
An example is given in the applications of the Interest Rate Swaps (IR Swaps) FIBO ontology, where some ontology elements may be re-used to represent different concepts in different kinds of ontology application  ...  This paper describes a number of design techniques employed in the Financial Industry Business Ontology (FIBO) series of standards.  ...  There is considerable scope for further investigation and research in these areas as well as in the potential for providing practical methodological support for ontologies across the engineering development  ... 
dblp:conf/jowo/Bennett18 fatcat:x54p5hw6nbddlgq2s3alikppk4

An Ontology for Formal Models of Kinship [chapter]

Carmen Chui, Michael Grüninger, Janette Wong
2020 Frontiers in Artificial Intelligence and Applications  
The near ubiquity of family relationship ontologies in the Semantic Web has brought on the question of whether any formal analysis has been done in this domain.  ...  Based on these algebraic models, we provide an ontology for kinship written in first-order logic and demonstrate how the ontology can be used to validate definitions found in Canadian legal laws and data  ...  Consequently, ancestorO f (x, y) was selected as a primitive in the ontology. Ancestors, Spouses, and Unintended Models The axioms in T ancestor and T spouse alone are not sufficient.  ... 
doi:10.3233/faia200663 fatcat:bfc4e6ucuzbejdjxvk3rhcvvim

Theoretical foundations and engineering tools for building ontologies as reference conceptual models

Giancarlo Guizzardi
2010 Semantic Web Journal  
Furthermore, it discusses the importance of foundational theories and principles to the design of ontology (conceptual) modeling languages and models, emphasizing the fundamental role played by true ontological  ...  In this context, ontologies have been more and more recognized as one of the enabling technologies.  ...  of the underlying domain and in making explicit the underlying ontological commitments.  ... 
doi:10.3233/sw-2010-0015 fatcat:e62docpjiff25bgzvm67s2kgom
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