Datalog± Ontology Consolidation

Knowledge bases in the form of ontologies are receiving increasing attention as they allow to clearly represent both the available knowledge, which includes the knowledge in itself and the constraints imposed to it by the domain or the users. In particular, Datalog ± ontologies are attractive because of their property of decidability and the possibility of dealing with the massive amounts of data in real world environments; however, as it is the case with many other ontological languages, their application in collaborative environments often lead to inconsistency related issues. In this paper we introduce the notion of incoherence regarding Datalog± ontologies, in terms of satisfiability of sets of constraints, and show how under specific conditions incoherence leads to inconsistent Datalog ± ontologies. The main contribution of this work is a novel approach to restore both consistency and coherence in Datalog± ontologies. The proposed approach is based on kernel contraction and restoration is performed by the application of incision functions that select formulas to delete. Nevertheless, instead of working over minimal incoherent/inconsistent sets encountered in the ontologies, our operators produce incisions over non-minimal structures called clusters. We present a construction for consolidation operators, along with the properties expected to be satisfied by them. Finally, we establish the relation between the construction and the properties by means of a representation theorem. Although this proposal is presented for Datalog± ontologies consolidation, these operators can be applied to other types of ontological languages, such as Description Logics, making them apt to be used in collaborative environments like the Semantic Web.Fil: Deagustini, Cristhian Ariel David. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación. Instituto de Ciencias e Ingeniería de la Computación; ArgentinaFil: Martinez, Maria Vanina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación. Instituto de Ciencias e Ingeniería de la Computación; ArgentinaFil: Falappa, Marcelo Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación. Instituto de Ciencias e Ingeniería de la Computación; ArgentinaFil: Simari, Guillermo Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación. Instituto de Ciencias e Ingeniería de la Computación; Argentin

Biomedical ontology alignment: An approach based on representation learning

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results

DOOR: towards a formalization of ontology relations

In this paper, we describe our ongoing effort in describing and formalizing semantic relations that link ontolo- gies with each others on the Semantic Web in order to create an ontology, DOOR, to represent, manipulate and reason upon these relations. DOOR is a Descriptive Ontology of Ontology Relations which intends to define relations such as inclusion, versioning, similarity and agreement using ontological primitives as well as rules. Here, we provide a detailed description of the methodology used to design the DOOR ontology, as well as an overview of its content. We also describe how DOOR is used in a complete framework (called KANNEL) for detecting and managing semantic relations between ontologies in large ontology repositories. Applied in the context of a large collection of automatically crawled ontologies, DOOR and KANNEL provide a starting point for analyzing the underlying structure of the network of ontologies that is the Semantic Web

Reasoning with concept diagrams about antipatterns

Ontologies are notoriously hard to define, express and reason about. Many tools have been developed to ease the debugging and the reasoning process with ontologies, however they often lack accessibility and formalisation. A visual representation language, concept diagrams, was developed for expressing and reasoning about ontologies in an accessible way. Indeed, empirical studies show that concept diagrams are cognitively more accessible to users in ontology debugging tasks. In this paper we answer the question of “ How can concept diagrams be used to reason about inconsistencies and incoherence of ontologies?”. We do so by formalising a set of inference rules for concept diagrams that enables stepwise verification of the inconsistency and/or incoherence of a set of ontology axioms. The design of inference rules is driven by empirical evidence that concise (merged) diagrams are easier to comprehend for users than a set of lower level diagrams that offer a one-to-one translation of OWL ontology axioms into concept diagrams. We prove that our inference rules are sound, and exemplify how they can be used to reason about inconsistencies and incoherence. Finally, we indicate how our rules can serve as a foundation for new rules required when representing ontologies in diverse new domains

Repairing Ontologies via Axiom Weakening.

Ontology engineering is a hard and error-prone task, in which small changes may lead to errors, or even produce an inconsistent ontology. As ontologies grow in size, the need for automated methods for repairing inconsistencies while preserving as much of the original knowledge as possible increases. Most previous approaches to this task are based on removing a few axioms from the ontology to regain consistency. We propose a new method based on weakening these axioms to make them less restrictive, employing the use of refinement operators. We introduce the theoretical framework for weakening DL ontologies, propose algorithms to repair ontologies based on the framework, and provide an analysis of the computational complexity. Through an empirical analysis made over real-life ontologies, we show that our approach preserves significantly more of the original knowledge of the ontology than removing axioms

Completing and Debugging Ontologies: state of the art and challenges

As semantically-enabled applications require high-quality ontologies, developing and maintaining ontologies that are as correct and complete as possible is an important although difficult task in ontology engineering. 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 do this by formalizing the repairing step as an abduction problem and situating the state of the art with respect to this framework. We show that there are still many open research problems and show opportunities for further work and advancing the field.Comment: 56 page