Ontology similarity in the alignment space

david2010bInternational audienceMeasuring similarity between ontologies can be very useful for different purposes, e.g., finding an ontology to replace another, or finding an ontology in which queries can be translated. Classical measures compute similarities or distances in an ontology space by directly comparing the content of ontologies. We introduce a new family of ontology measures computed in an alignment space: they evaluate the similarity between two ontologies with regard to the available alignments between them. We define two sets of such measures relying on the existence of a path between ontologies or on the ontology entities that are preserved by the alignments. The former accounts for known relations between ontologies, while the latter reflects the possibility to perform actions such as instance import or query translation. All these measures have been implemented in the OntoSim library, that has been used in experiments which showed that entity preserving measures are comparable to the best ontology space measures. Moreover, they showed a robust behaviour with respect to the alteration of the alignment space

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

MeLinDa: an interlinking framework for the web of data

The web of data consists of data published on the web in such a way that they can be interpreted and connected together. It is thus critical to establish links between these data, both for the web of data and for the semantic web that it contributes to feed. We consider here the various techniques developed for that purpose and analyze their commonalities and differences. We propose a general framework and show how the diverse techniques fit in the framework. From this framework we consider the relation between data interlinking and ontology matching. Although, they can be considered similar at a certain level (they both relate formal entities), they serve different purposes, but would find a mutual benefit at collaborating. We thus present a scheme under which it is possible for data linking tools to take advantage of ontology alignments.Comment: N° RR-7691 (2011

Cross-lingual Entity Alignment via Joint Attribute-Preserving Embedding

Entity alignment is the task of finding entities in two knowledge bases (KBs) that represent the same real-world object. When facing KBs in different natural languages, conventional cross-lingual entity alignment methods rely on machine translation to eliminate the language barriers. These approaches often suffer from the uneven quality of translations between languages. While recent embedding-based techniques encode entities and relationships in KBs and do not need machine translation for cross-lingual entity alignment, a significant number of attributes remain largely unexplored. In this paper, we propose a joint attribute-preserving embedding model for cross-lingual entity alignment. It jointly embeds the structures of two KBs into a unified vector space and further refines it by leveraging attribute correlations in the KBs. Our experimental results on real-world datasets show that this approach significantly outperforms the state-of-the-art embedding approaches for cross-lingual entity alignment and could be complemented with methods based on machine translation

A Large Scale Dataset for the Evaluation of Ontology Matching Systems

Recently, the number of ontology matching techniques and systems has increased significantly. This makes the issue of their evaluation and comparison more severe. One of the challenges of the ontology matching evaluation is in building large scale evaluation datasets. In fact, the number of possible correspondences between two ontologies grows quadratically with respect to the numbers of entities in these ontologies. This often makes the manual construction of the evaluation datasets demanding to the point of being infeasible for large scale matching tasks. In this paper we present an ontology matching evaluation dataset composed of thousands of matching tasks, called TaxME2. It was built semi-automatically out of the Google, Yahoo and Looksmart web directories. We evaluated TaxME2 by exploiting the results of almost two dozen of state of the art ontology matching systems. The experiments indicate that the dataset possesses the desired key properties, namely it is error-free, incremental, discriminative, monotonic, and hard for the state of the art ontology matching systems. The paper has been accepted for publication in "The Knowledge Engineering Review", Cambridge Universty Press (ISSN: 0269-8889, EISSN: 1469-8005)

Towards automated knowledge-based mapping between individual conceptualisations to empower personalisation of Geospatial Semantic Web

Geospatial domain is characterised by vagueness, especially in the semantic disambiguation of the concepts in the domain, which makes defining universally accepted geo- ontology an onerous task. This is compounded by the lack of appropriate methods and techniques where the individual semantic conceptualisations can be captured and compared to each other. With multiple user conceptualisations, efforts towards a reliable Geospatial Semantic Web, therefore, require personalisation where user diversity can be incorporated. The work presented in this paper is part of our ongoing research on applying commonsense reasoning to elicit and maintain models that represent users' conceptualisations. Such user models will enable taking into account the users' perspective of the real world and will empower personalisation algorithms for the Semantic Web. Intelligent information processing over the Semantic Web can be achieved if different conceptualisations can be integrated in a semantic environment and mismatches between different conceptualisations can be outlined. In this paper, a formal approach for detecting mismatches between a user's and an expert's conceptual model is outlined. The formalisation is used as the basis to develop algorithms to compare models defined in OWL. The algorithms are illustrated in a geographical domain using concepts from the SPACE ontology developed as part of the SWEET suite of ontologies for the Semantic Web by NASA, and are evaluated by comparing test cases of possible user misconceptions

Automated Annotation-Based Bio-Ontology Alignment with Structural Validation

We outline the structure of an automated process to both align multiple bio-ontologies in terms of their genomic co-annotations, and then to measure the structural quality of that alignment. We illustrate the method with a genomic analysis of 70 genes implicated in lung disease against the Gene Ontology

Two-fold Semantic Web service matchmaking – applying ontology mapping for service discovery

Semantic Web Services (SWS) aim at the automated discovery and orchestration of Web services on the basis of comprehensive, machine-interpretable semantic descriptions. Since SWS annotations usually are created by distinct SWS providers, semantic-level mediation, i.e. mediation between concurrent semantic representations, is a key requirement for SWS discovery. Since semantic-level mediation aims at enabling interoperability across heterogeneous semantic representations, it can be perceived as a particular instantiation of the ontology mapping problem. While recent SWS matchmakers usually rely on manual alignments or subscription to a common ontology, we propose a two-fold SWS matchmaking approach, consisting of (a) a general-purpose semantic-level mediator and (b) comparison and matchmaking of SWS capabilities. Our semantic-level mediation approach enables the implicit representation of similarities across distinct SWS by grounding service descriptions in so-called Mediation Spaces (MS). Given a set of SWS and their respective grounding, a SWS matchmaker automatically computes instance similarities across distinct SWS ontologies and matches the request to the most suitable SWS. A prototypical application illustrates our approach