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Register a new userAn Ontology for the Materials Design Domain
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Added by
Patrick Lambrix
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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In the materials design domain, much of the data from materials calculations are stored in different heterogeneous databases. Materials databases usually have different data models. Therefore, the users have to face the challenges to find the data from adequate sources and integrate data from multiple sources. Ontologies and ontology-based techniques can address such problems as the formal representation of domain knowledge can make data more available and interoperable among different systems. In this paper, we introduce the Materials Design Ontology (MDO), which defines concepts and relations to cover knowledge in the field of materials design. MDO is designed using domain knowledge in materials science (especially in solid-state physics), and is guided by the data from several databases in the materials design field. We show the application of the MDO to materials data retrieved from well-known materials databases.
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In ontology-mediated querying, description logic (DL) ontologies are used to enrich incomplete data with domain knowledge which results in more complete answers to queries. However, the evaluation of ontology-mediated queries (OMQs) over relational databases is computationally hard. This raises the question when OMQ evaluation is efficient, in the sense of being tractable in combined complexity or fixed-parameter tractable. We study this question for a range of ontology-mediated query languages based on several important and widely-used DLs, using unions of conjunctive queries as the actual queries. For the DL ELHI extended with the bottom concept, we provide a characterization of the classes of OMQs that are fixed-parameter tractable. For its fragment EL extended with domain and range restrictions and the bottom concept (which restricts the use of inverse roles), we provide a characterization of the classes of OMQs that are tractable in combined complexity. Both results are in terms of equivalence to OMQs of bounded tree width and rest on a reasonable assumption from parameterized complexity theory. They are similar in spirit to Grohes seminal characterization of the tractable classes of conjunctive queries over relational databases. We further study the complexity of the meta problem of deciding whether a given OMQ is equivalent to an OMQ of bounded tree width, providing several completeness results that range from NP to 2ExpTime, depending on the DL used. We also consider the DL-Lite family of DLs, including members that admit functional roles.
The Virtual Materials Marketplace (VIMMP) project, which develops an open platform for providing and accessing services related to materials modelling, is presented with a focus on its ontology development and data technology aspects. Within VIMMP, a system of marketplace-level ontologies is developed to characterize services, models, and interactions between users; the European Materials and Modelling Ontology (EMMO) is employed as a top-level ontology. The ontologies are used to annotate data that are stored in the ZONTAL Space component of VIMMP and to support the ingest and retrieval of data and metadata at the VIMMP marketplace frontend.
Ontology-based data access (OBDA) is a popular paradigm for querying heterogeneous data sources by connecting them through mappings to an ontology. In OBDA, it is often difficult to reconstruct why a tuple occurs in the answer of a query. We address this challenge by enriching OBDA with provenance semirings, taking inspiration from database theory. In particular, we investigate the problems of (i) deciding whether a provenance annotated OBDA instance entails a provenance annotated conjunctive query, and (ii) computing a polynomial representing the provenance of a query entailed by a provenance annotated OBDA instance. Differently from pure databases, in our case these polynomials may be infinite. To regain finiteness, we consider idempotent semirings, and study the complexity in the case of DL-Lite ontologies. We implement Task (ii) in a state-of-the-art OBDA system and show the practical feasibility of the approach through an extensive evaluation against two popular benchmarks.
We focus on ontology-mediated queries (OMQs) based on (frontier-)guarded existential rules and (unions of) conjunctive queries, and we investigate the problem of FO-rewritability, i.e., whether an OMQ can be rewritten as a first-order query. We adopt two different approaches. The first approach employs standard two-way alternating parity tree automata. Although it does not lead to a tight complexity bound, it provides a transparent solution based on widely known tools. The second approach relies on a sophisticated automata model, known as cost automata. This allows us to show that our problem is 2ExpTime-complete. In both approaches, we provide semantic characterizations of FO-rewritability that are of independent interest.
The Center for Expanded Data Annotation and Retrieval (CEDAR) aims to revolutionize the way that metadata describing scientific experiments are authored. The software we have developed--the CEDAR Workbench--is a suite of Web-based tools and REST APIs that allows users to construct metadata templates, to fill in templates to generate high-quality metadata, and to share and manage these resources. The CEDAR Workbench provides a versatile, REST-based environment for authoring metadata that are enriched with terms from ontologies. The metadata are available as JSON, JSON-LD, or RDF for easy integration in scientific applications and reusability on the Web. Users can leverage our APIs for validating and submitting metadata to external repositories. The CEDAR Workbench is freely available and open-source.
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