Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

Reasoning over Ontologies with Hidden Content: The Import-by-Query Approach

There is currently a growing interest in techniques for hiding parts of the signature of an ontology Kh that is being reused by another ontology Kv. Towards this goal, in this paper we propose the import-by-query framework, which makes the content of Kh accessible through a limited query interface. If Kv reuses the symbols from Kh in a certain restricted way, one can reason over Kv U Kh by accessing only Kv and the query interface. We map out the landscape of the import-by-query problem. In particular, we outline the limitations of our framework and prove that certain restrictions on the expressivity of Kh and the way in which Kv reuses symbols from Kh are strictly necessary to enable reasoning in our setting. We also identify cases in which reasoning is possible and we present suitable import-by-query reasoning algorithms

vSPARQL: A View Definition Language for the Semantic Web

Translational medicine applications would like to leverage the biological and biomedical ontologies, vocabularies, and data sets available on the semantic web. We present a general solution for RDF information set reuse inspired by database views. Our view definition language, vSPARQL, allows applications to specify the exact content that they are interested in and how that content should be restructured or modified. Applications can access relevant content by querying against these view definitions. We evaluate the expressivity of our approach by defining views for practical use cases and comparing our view definition language to existing query languages

Subontology Extraction Using Hyponym and Hypernym Closure on is-a Directed Acyclic Graphs

International audienceOntologies are successfully used as semantic guides when navigating through the huge and ever increasing quantity of digital documents. Nevertheless, the size of numerous domain ontologies tends to grow beyond the human capacity to grasp information. This growth is problematic for a lot of key applications that require user interactions such as document annotation or ontology modification/evolution. The problem could be partially overcome by providing users with a sub-ontology focused on their current concepts of interest. A sub-ontology restricted to this sole set of concepts is of limited interest since their relationships can generally not be explicit without adding some of their hyponyms and hypernyms. This paper proposes efficient algorithms to identify these additional key concepts based on the closure of two common graph operators: the least common-ancestor and greatest common descendant. The resulting method produces ontology excerpts focused on a set of concepts of interest and is fast enough to be used in interactive environments. As an example, we use the resulting program, called OntoFocus (http://www.ontotoolkit.mines-ales.fr/), to restrict, in few seconds, the large Gene Ontology (~30,000 concepts) to a sub-ontology focused on concepts annotating a gene related to breast cancer

Dutch hypernym detection : does decompounding help?

This research presents experiments carried out to improve the precision and recall of Dutch hypernym detection. To do so, we applied a data-driven semantic relation finder that starts from a list of automatically extracted domain-specific terms from technical corpora, and generates a list of hypernym relations between these terms. As Dutch technical terms often consist of compounds written in one orthographic unit, we investigated the impact of a decompounding module on the performance of the hypernym detection system. In addition, we also improved the precision of the system by designing filters taking into account statistical and linguistic information. The experimental results show that both the precision and recall of the hypernym detection system improved, and that the decompounding module is especially effective for hypernym detection in Dutch

Deductive Module Extraction for Expressive Description Logics: Extended Version

In deductive module extraction, we determine a small subset of an ontology for a given vocabulary that preserves all logical entailments that can be expressed in that vocabulary. While in the literature stronger module notions have been discussed, we argue that for applications in ontology analysis and ontology reuse, deductive modules, which are decidable and potentially smaller, are often sufficient. We present methods based on uniform interpolation for extracting different variants of deductive modules, satisfying properties such as completeness, minimality and robustness under replacements, the latter being particularly relevant for ontology reuse. An evaluation of our implementation shows that the modules computed by our method are often significantly smaller than those computed by existing methods.This is an extended version of the article in the proceedings of IJCAI 2020

05371 Abstracts Collection -- Principles and Practices of Semantic Web Reasoning

From 11.09.05 to 16.09.05, the Dagstuhl Seminar 05371 ``Principles and Practices of Semantic Web Reasoning\u27\u27 % generate automaticall was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available