A formal foundation for ontology alignment interaction models

Ontology alignment foundations are hard to find in the literature. The abstract nature of the topic and the diverse means of practice makes it difficult to capture it in a universal formal foundation. We argue that such a lack of formality hinders further development and convergence of practices, and in particular, prevents us from achieving greater levels of automation. In this article we present a formal foundation for ontology alignment that is based on interaction models between heterogeneous agents on the Semantic Web. We use the mathematical notion of information flow in a distributed system to ground our three hypotheses of enabling semantic interoperability and we use a motivating example throughout the article: how to progressively align two ontologies of research quality assessment through meaning coordination. We conclude the article with the presentation---in an executable specification language---of such an ontology-alignment interaction model

Dividing the Ontology Alignment Task with Semantic Embeddings and Logic-based Modules

Large ontologies still pose serious challenges to state-of-the-art ontology alignment systems. In this paper we present an approach that combines a neural embedding model and logic-based modules to accurately divide an input ontology matching task into smaller and more tractable matching (sub)tasks. We have conducted a comprehensive evaluation using the datasets of the Ontology Alignment Evaluation Initiative. The results are encouraging and suggest that the proposed method is adequate in practice and can be integrated within the workflow of systems unable to cope with very large ontologies

Results of the ontology alignment evaluation initiative 2019

The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems on precisely defined test cases. These test cases can be based on ontologies of different levels of complexity (from simple thesauri to expressive OWL ontologies) and use different evaluation modalities (e.g., blind evaluation, open evaluation, or consensus). The OAEI 2019 campaign offered 11 tracks with 29 test cases, and was attended by 20 participants. This paper is an overall presentation of that campaign

Ontology alignment through argumentation

Currently, the majority of matchers are able to establish simple correspondences between entities, but are not able to provide complex alignments. Furthermore, the resulting alignments do not contain additional information on how they were extracted and formed. Not only it becomes hard to debug the alignment results, but it is also difficult to justify correspondences. We propose a method to generate complex ontology alignments that captures the semantics of matching algorithms and human-oriented ontology alignment definition processes. Through these semantics, arguments that provide an abstraction over the specificities of the alignment process are generated and used by agents to share, negotiate and combine correspondences. After the negotiation process, the resulting arguments and their relations can be visualized by humans in order to debug and understand the given correspondences.(undefined

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

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