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

Coherent Integration of Databases by Abductive Logic Programming

We introduce an abductive method for a coherent integration of independent data-sources. The idea is to compute a list of data-facts that should be inserted to the amalgamated database or retracted from it in order to restore its consistency. This method is implemented by an abductive solver, called Asystem, that applies SLDNFA-resolution on a meta-theory that relates different, possibly contradicting, input databases. We also give a pure model-theoretic analysis of the possible ways to `recover' consistent data from an inconsistent database in terms of those models of the database that exhibit as minimal inconsistent information as reasonably possible. This allows us to characterize the `recovered databases' in terms of the `preferred' (i.e., most consistent) models of the theory. The outcome is an abductive-based application that is sound and complete with respect to a corresponding model-based, preferential semantics, and -- to the best of our knowledge -- is more expressive (thus more general) than any other implementation of coherent integration of databases

A Comprehensive Framework for Controlled Query Evaluation, Consistent Query Answering and KB Updates in Description Logics

In this extended abstract we discuss the relationship between confidentiality-preserving frameworks and inconsistency-tolerant repair and update semantics in Description Logics (DL). In particular, we consider the well-known problems of Consistent Query Answering, Controlled Query Evaluation, and Knowledge Base Update in DL and introduce a unifying framework that can be naturally instantiated to capture significant settings for the above problems, previously investigated in the literature

Using Ontologies for Semantic Data Integration

While big data analytics is considered as one of the most important paths to competitive advantage of today’s enterprises, data scientists spend a comparatively large amount of time in the data preparation and data integration phase of a big data project. This shows that data integration is still a major challenge in IT applications. Over the past two decades, the idea of using semantics for data integration has become increasingly crucial, and has received much attention in the AI, database, web, and data mining communities. Here, we focus on a specific paradigm for semantic data integration, called Ontology-Based Data Access (OBDA). The goal of this paper is to provide an overview of OBDA, pointing out both the techniques that are at the basis of the paradigm, and the main challenges that remain to be addressed

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

BlogForever D2.6: Data Extraction Methodology

This report outlines an inquiry into the area of web data extraction, conducted within the context of blog preservation. The report reviews theoretical advances and practical developments for implementing data extraction. The inquiry is extended through an experiment that demonstrates the effectiveness and feasibility of implementing some of the suggested approaches. More specifically, the report discusses an approach based on unsupervised machine learning that employs the RSS feeds and HTML representations of blogs. It outlines the possibilities of extracting semantics available in blogs and demonstrates the benefits of exploiting available standards such as microformats and microdata. The report proceeds to propose a methodology for extracting and processing blog data to further inform the design and development of the BlogForever platform