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Towards Dataset Dynamics: Change Frequency of Linked Open Data Sources
"... Datasets in the LOD cloud are far from being static in their nature and how they are exposed. As resources are added and new links are set, applications consuming the data should be able to deal with these changes. In this paper we investigate how LOD datasets change and what sensible measures there ..."
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Cited by 30 (8 self)
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Datasets in the LOD cloud are far from being static in their nature and how they are exposed. As resources are added and new links are set, applications consuming the data should be able to deal with these changes. In this paper we investigate how LOD datasets change and what sensible measures there are to accommodate dataset dynamics. We compare our findings with traditional, document-centric studies concerning the “freshness ” of the document collections and propose metrics for LOD datasets. 1.
On Matching Large Life Science Ontologies in Parallel
"... Abstract. Matching life science ontologies to determine ontology mappings has recently become an active field of research. The large size of existing ontologies and the application of complex match strategies for obtaining high quality mappings makes ontology matching a resource- and time-intensive ..."
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Cited by 11 (5 self)
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Abstract. Matching life science ontologies to determine ontology mappings has recently become an active field of research. The large size of existing ontologies and the application of complex match strategies for obtaining high quality mappings makes ontology matching a resource- and time-intensive process. To improve performance we investigate different approaches for parallel matching on multiple compute nodes. In particular, we consider inter-matcher and intramatcher parallelism as well as the parallel execution of element- and structurelevel matching. We implemented a distributed infrastructure for parallel ontology matching and evaluate different approaches for parallel matching of large life science ontologies in the field of anatomy and molecular biology.
Ontology Evolution Under Semantic Constraints
"... The dynamic nature of ontology development has motivated the formal study of ontology evolution problems. This paper presents a logical framework that enables fine-grained investigation of evolution problems at a deductive level. In our framework, the optimal evolutions of an ontology O are those on ..."
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Cited by 10 (4 self)
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The dynamic nature of ontology development has motivated the formal study of ontology evolution problems. This paper presents a logical framework that enables fine-grained investigation of evolution problems at a deductive level. In our framework, the optimal evolutions of an ontology O are those ontologies O ′ that maximally preserve both the structure of O, and its entailments in a given preservation language. We show that our framework is compatible with the postulates of Belief Revision, and we investigate the existence of optimal evolutions in various settings. In particular, we present first results on TBox-level revision and contraction in the EL and FL0 families of Description Logics.
Estimating the Quality of Ontology-Based Annotations by Considering Evolutionary Changes
"... Abstract. Ontology-based annotations associate objects, such as genes and proteins, with well-defined ontology concepts to semantically and uniformly describe object properties. Such annotation mappings are utilized in different applications and analysis studies whose results strongly depend on the ..."
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Abstract. Ontology-based annotations associate objects, such as genes and proteins, with well-defined ontology concepts to semantically and uniformly describe object properties. Such annotation mappings are utilized in different applications and analysis studies whose results strongly depend on the quality of the used annotations. To study the quality of annotations we propose a generic evaluation approach considering the annotation generation methods (provenance) as well as the evolution of ontologies, object sources, and annotations. Thus, it facilitates the identification of reliable annotations, e.g., for use in analysis applications. We evaluate our approach for functional protein annotations in Ensembl and Swiss-Prot using the Gene Ontology.
Building Ontologies Collaboratively Using ContentCVS
"... OWL Ontologies are already being used in many application domains. In particular, OWL is extensively used in the clinical sciences; prominent examples of OWL ontologies are the National Cancer Institute (NCI) Thesaurus, SNOMED CT, the Gene Ontology (GO), the Foundational Model of Anatomy (FMA), and ..."
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Cited by 9 (1 self)
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OWL Ontologies are already being used in many application domains. In particular, OWL is extensively used in the clinical sciences; prominent examples of OWL ontologies are the National Cancer Institute (NCI) Thesaurus, SNOMED CT, the Gene Ontology (GO), the Foundational Model of Anatomy (FMA), and GALEN. These ontologies are large and complex; for example, SNOMED currently describes more than 350.000 concepts whereas NCI and GALEN describe around 50.000 concepts. Furthermore, these ontologies are in continuous evolution; for example the developers of NCI and GO perform approximately 350 additions of new entities and 25 deletions of obsolete entities each month [1]. Most realistic ontologies, including the ones just mentioned, are being developed collaboratively. The developers of an ontology can be geographically distributed and may contribute in different ways and to different extents. Maintaining such large ontologies in a collaborative way is a highly complex process, which involves tracking and managing the frequent changes to the ontology, reconciling conflicting views of the domain from different developers, minimising the introduction of errors (e.g., ensuring
Efficient Management of Biomedical Ontology Versions
"... Abstract. Ontologies have become very popular in life sciences and other domains. They mostly undergo continuous changes and new ontology versions are frequently released. However, current analysis studies do not consider the ontology changes reflected in different versions but typically limit thems ..."
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Cited by 7 (3 self)
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Abstract. Ontologies have become very popular in life sciences and other domains. They mostly undergo continuous changes and new ontology versions are frequently released. However, current analysis studies do not consider the ontology changes reflected in different versions but typically limit themselves to a specific ontology version which may quickly become obsolete. To allow applications easy access to different ontology versions we propose a central and uniform management of the versions of different biomedical ontologies. The proposed database approach takes concept and structural changes of succeeding ontology versions into account thereby supporting different kinds of change analysis. Furthermore, it is very space-efficient by avoiding redundant storage of ontology components which remain unchanged in different versions. We evaluate the storage requirements and query performance of the proposed approach for the Gene Ontology.
Supporting Concurrent Ontology Development: Framework, Algorithms and Tool
, 2010
"... We propose a novel approach to facilitate the concurrent development of ontologies by different groups of experts. Our approach adapts Concurrent Versioning, a successful paradigm in software development, to allow several developers to make changes concurrently to an ontology. Conflict detection and ..."
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Cited by 4 (0 self)
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We propose a novel approach to facilitate the concurrent development of ontologies by different groups of experts. Our approach adapts Concurrent Versioning, a successful paradigm in software development, to allow several developers to make changes concurrently to an ontology. Conflict detection and resolution are based on novel techniques that take into account the structure and semantics of the ontology versions to be reconciled by using precisely-defined notions of structural and semantic differences between ontologies and by extending state-of-the-art ontology debugging and repair techniques. We also present ContentCVS, a system that implements our approach, and a preliminary empirical evaluation which suggests that our approach is both computationally feasible and useful in practice.
Ontology Contraction: Beyond the Propositional Paradise
"... Abstract. The dynamic nature of ontology development has motivated the formal study of ontology evolution problem. This paper addresses contraction —the problem of retracting information that should no longer hold in an ontology. We survey existing model and formula based semantics to contraction an ..."
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Cited by 3 (1 self)
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Abstract. The dynamic nature of ontology development has motivated the formal study of ontology evolution problem. This paper addresses contraction —the problem of retracting information that should no longer hold in an ontology. We survey existing model and formula based semantics to contraction and investigate their properties for the description logics DL-Lite and EL, which underpin the QL and EL profiles of OWL 2. Our results suggest that these contraction semantics, which are well-understood and well-behaved for propositional logics, are intrinsically problematical in the context of ontology languages. We believe that a starting point for addressing these problems might be the recent semantics proposed in [1]. 1
Semi-Automatic Adaptation of Mappings between Life Science Ontologies
"... Abstract. The continuous evolution of life science ontologies requires the adaptation of their associated mappings. We propose two approaches for tackling this problem in a largely automatic way: (1) a compositionbased adaptation relying on the principle of mapping composition and (2) a diff-based a ..."
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Cited by 2 (1 self)
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Abstract. The continuous evolution of life science ontologies requires the adaptation of their associated mappings. We propose two approaches for tackling this problem in a largely automatic way: (1) a compositionbased adaptation relying on the principle of mapping composition and (2) a diff-based adaptation algorithm individually handling change operations to update the mapping. Both techniques reuse unaffected correspondences, and adapt only the affected mapping part. We experimentally assess and confirm the effectiveness of our approaches for evolving mappings between large life science ontologies.
