1. |
- Lambrix, Patrick, Professor, 1965-, et al.
(author)
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The materials design ontology
- 2024
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In: Semantic Web. - : IOS Press. - 1570-0844 .- 2210-4968. ; 15:2, s. 481-515
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Journal article (peer-reviewed)abstract
- In the materials design domain, much of the data from materials calculations is stored in different heterogeneous databases with different data and access models. Therefore, accessing and integrating data from different sources is challenging. As ontology-based access and integration alleviates these issues, in this paper we address data access and interoperability for computational materials databases by developing the Materials Design Ontology. This ontology is inspired by and guided by the OPTIMADE effort that aims to make materials databases interoperable and includes many of the data providers in computational materials science. In this paper, first, we describe the development and the content of the Materials Design Ontology. Then, we use a topic model-based approach to propose additional candidate concepts for the ontology. Finally, we show the use of the Materials Design Ontology by a proof-of-concept implementation of a data access and integration system for materials databases based on the ontology.
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2. |
- Li, Huanyu, 1992-, et al.
(author)
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OBG-gen: Ontology-Based GraphQL Server Generation for Data Integration
- 2023
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In: Proceedings of the ISWC 2023 Posters, Demos and Industry Tracks: From Novel Ideas to Industrial Practice.
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Conference paper (peer-reviewed)abstract
- A GraphQL server contains two building blocks: (1) a GraphQL schema defining the types of data objects that can be requested; (2) resolver functions fetching the relevant data from underlying data sources. GraphQL can be used for data integration if the GraphQL schema provides an integrated view of data from multiple data sources, and the resolver functions are implemented accordingly.However, there does not exist a semantics-aware approach to use GraphQL for data integration.We proposed a framework using GraphQL for data integration in which a global domain ontology informs the generation of a GraphQL server. Furthermore, we implemented a prototype of this framework, OBG-gen. In this paper, we demonstrate OBG-gen in a real-world data integration scenario in the materials design domain and in a synthetic benchmark scenario.
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3. |
- Li, Huanyu, 1992-, et al.
(author)
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Ontology-based GraphQL server generation for data access and data integration
- 2024
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In: Semantic Web. - : IOS Press. - 1570-0844 .- 2210-4968. ; , s. 1-37
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Journal article (peer-reviewed)abstract
- In a GraphQL Web API, a so-called GraphQL schema defines the types of data objects that can be queried, and so-called resolver functions are responsible for fetching the relevant data from underlying data sources. Thus, we can expect to use GraphQL not only for data access but also for data integration, if the GraphQL schema reflects the semantics of data from multiple data sources, and the resolver functions can obtain data from these data sources and structure the data according to the schema. However, there does not exist a semantics-aware approach to employ GraphQL for data integration. Furthermore, there are no formal methods for defining a GraphQL API based on an ontology.In this work, we introduce a framework for using GraphQL in which a global domain ontology informs the generation of a GraphQL server that answers requests by querying heterogeneous data sources.The core of this framework consists of an algorithm to generate a GraphQL schema based on an ontology and a generic resolver function based on semantic mappings. We provide a prototype, OBG-gen, of this framework, and we evaluate our approach over a real-world data integration scenario in the materials design domain and two synthetic benchmark scenarios (Linköping GraphQL Benchmark and GTFS-Madrid-Bench). The experimental results of our evaluation indicate that: (i) our approach is feasible to generate GraphQL servers for data access and integration over heterogeneous data sources, thus avoiding a manual construction of GraphQL servers, and (ii) our data access and integration approach is general and applicable to different domains where data is shared or queried via different ways.
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4. |
- Li, Huanyu, 1992-
(author)
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Ontology-Driven Data Access and Data Integration with an Application in the Materials Design Domain
- 2022
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Doctoral thesis (other academic/artistic)abstract
- The Semantic Web aims to make data on the web machine-readable by introducing semantics to the data. Ontologies are one of the critical technologies in the Semantic Web. Ontologies, which provide a formal definition of a domain of interest, can play an important role in enabling semantics-aware data access and data integration over heterogeneous data sources. Traditionally, ontology-based data access and integration methods focus on data that follows relational data models. However, in some domains, such as materials design, the models that data follows and the methods by which it is shared differ today. Data may be based on different data models (i.e., relational models and non-relational models) and may be shared in different ways (e.g., as tabular data via SQL queries or API (Application Programming Interface) requests, or as JSON-formatted data via API requests). To address these challenges, conventional ontology-based data access and integration approaches must be adapted. The recently developed GraphQL, a framework for building APIs, is an interesting candidate for providing such an approach, although the use of GraphQL for integration has not yet been studied.In this thesis, we propose a GraphQL-based framework for data access and integration. As part of this framework, we propose and implement a novel approach that enables automatic generation of GraphQL servers based on ontologies rather than building them from scratch. The framework is evaluated via experiments based on a synthetic benchmark dataset. Further, we utilize the field of materials design as a target domain to evaluate the feasibility of our framework by showing the use of the framework for the Open Databases Integration for Materials Design (OPTIMADE), which is a community effort aiming to develop a specification for a common API to make materials databases interoperable. At the beginning of this work, no ontologies existed for the domain of computational materials databases. As our approach requires the use of an ontology, we developed one: the Materials Design Ontology (MDO). Furthermore, when new databases are added or new kinds of data are added to existing databases, the coverage of the ontology driving the GraphQL server generation may need to be enlarged. Therefore, we study how ontologies can be extended and propose an approach based on phrase-based topic modeling, formal topical concept analysis and domain expert validation. In addition to extending MDO, we also use this approach to extend two ontologies in the nanotechnology domain.
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5. |
- Abd Nikooie Pour, Mina, et al.
(author)
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A First Step Towards a Tool for Extending Ontologies
- 2021
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In: Proceedings of the Sixth International Workshop on the Visualization and Interaction for Ontologies and Linked Data. - : CEUR Workshop proceedings. ; , s. 1-12
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Conference paper (peer-reviewed)abstract
- Ontologies have been proposed as a means towards making data FAIR (Findable, Accessible, Interoperable, Reusable). This has attracted much interest in several communities and ontologies are being developed. However, to obtain good results when using ontologies in semantically-enabled applications, the ontologies need to be of high quality. One of the quality aspects is that the ontologies should be as complete as possible. In this paper we propose a first version of a tool that supports users in extending ontologies using a phrase-based approach. To demonstrate the usefulness of our proposed tool, we exemplify the use by extending the Materials Design Ontology.
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6. |
- Abd Nikooie Pour, Mina, et al.
(author)
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A First Step towards Extending the Materials Design Ontology
- 2021
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In: <em>Workshop on Domain Ontologies for Research Data Management in Industry Commons of Materials and Manufacturing - DORIC-MM 2021</em>. ; , s. 1-11
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Conference paper (peer-reviewed)abstract
- Ontologies have been proposed as a means towards making data FAIR (Findable, Accessible, Interoperable, Reusable) and has recently attracted much interest in the materials science community. Ontologies for this domain are being developed and one such effort is the Materials Design Ontology. However, to obtain good results when using ontologies in semantically-enabled applications, the ontologies need to be of high quality. One of the quality aspects is that the ontologies should be as complete as possible. In this paper we show preliminary results regarding extending the Materials Design Ontology using a phrase-based topic model.
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7. |
- Abd Nikooie Pour, Mina, et al.
(author)
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Phrase2Onto: A Tool to Support Ontology Extension
- 2023
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In: Procedia Computer Science. - : Elsevier. - 1877-0509. ; 225, s. 1415-1424, s. 1415-1424
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Journal article (peer-reviewed)abstract
- Due to importance of data FAIRness (Findable, Accessible, Interoperable, Reusable), ontologies as a means to make data FAIR have attracted more and more attention in different communities and are being used in semantically-enabled applications. However, to obtain good results while using ontologies in these applications, high quality ontologies are needed of which completeness is one of the important aspects. An ontology lacking information can lead to missing results. In this paper we present a tool, Phrase2Onto, that supports users in extending ontologies to make the ontologies more complete. It is particularly suited for ontology extension using a phrase-based topic model approach, but the tool can support any extension approach where a user needs to make decisions regarding the appropriateness of using phrases to define new concepts. We describe the functionality of the tool and a user study using Pizza Ontology. The user study showed a good usability of the system and high task completion. Further, we report on a real application where we extend the Materials Design Ontology.
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8. |
- Davidsson, Joel, 1989-, et al.
(author)
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ADAQ : Automatic workflows for magneto-optical properties of point defects in semiconductors
- 2021
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In: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 269
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Journal article (peer-reviewed)abstract
- Automatic Defect Analysis and Qualification (ADAQ) is a collection of automatic workflows developed for high-throughput simulations of magneto-optical properties of point defects in semiconductors. These workflows handle the vast number of defects by automating the processes to relax the unit cell of the host material, construct supercells, create point defect clusters, and execute calculations in both the electronic ground and excited states. The main outputs are the magneto-optical properties which include zero-phonon lines, zero-field splitting, and hyperfine coupling parameters. In addition, the formation energies are calculated. We demonstrate the capability of ADAQ by performing a complete characterization of the silicon vacancy in silicon carbide in the polytype 4H (4H-SiC).
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9. |
- Davidsson, Joel, 1989-
(author)
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Color Centers in Semiconductors for Quantum Applications : A High-Throughput Search of Point Defects in SiC
- 2021
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Doctoral thesis (other academic/artistic)abstract
- Point defects in semiconductors have been and will continue to be relevant for applications. Shallow defects realize transistors, which power the modern age of information, and in the not-too-distant future, deep-level defects could provide the foundation for a revolution in quantum information processing. Deep-level defects (in particular color centers) are also of interest for other applications such as a single photon emitter, especially one that emits at 1550 nm, which is the optimal frequency for long-range communication via fiber optics.First-principle calculations can predict the energies and optical properties of point defects. I performed extensive convergence tests for magneto-optical properties, such as zero phonon lines, hyperfine coupling parameters, and zero-field splitting for the four different configurations of the divacancy in 4H-SiC. Comparing the converged results with experimental measurements, a clear identification of the different configurations was made. With this approach, I also identified all configurations for the silicon vacancy in 4H-SiC as well as the divacancy and silicon vacancy in 6H-SiC. The same method was further used to identify two additional configurations belonging to the divacancy present in a 3C stacking fault inclusion in 4H-SiC. I extended the calculated properties to include the transition dipole moment which provides the polarization, intensity, and lifetime of the zero phonon lines. When calculating the transition dipole moment, I show that it is crucial to include the self-consistent change of the electronic orbitals in the excited state due to the geometry relaxation. I tested the method on the divacancy in 4H-SiC, further strengthening the previous identification and providing accurate photoluminescence intensities and lifetimes.Finding stable point defects with the right properties for a given application is a challenging task. Due to the vast number of possible point defects present in bulk semiconductor materials, I designed and implemented a collection of automatic workflows to systematically investigate any point defects. This collection is called ADAQ (Automatic Defect Analysis and Qualification) and automates every step of the theoretical process, from creating defects to predicting their properties. Using ADAQ, I screened about 8000 intrinsic point defect clusters in 4H-SiC. This thesis presents an overview of the formation energy and the most relevant optical properties for these single and double point defects. These results show great promise for finding new color centers suitable for various quantum applications.
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10. |
- Davidsson, Joel, 1989-, et al.
(author)
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Exhaustive characterization of modified Si vacancies in 4H-SiC
- 2022
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In: Nanophotonics. - : Walter de Gruyter. - 2192-8606 .- 2192-8614. ; 11:20, s. 4565-4580
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Journal article (peer-reviewed)abstract
- The negatively charged silicon vacancy (V-Si(-)) in silicon carbide is a well-studied point defect for quantum applications. At the same time, a closer inspection of ensemble photoluminescence and electron paramagnetic resonance measurements reveals an abundance of related but so far unidentified signals. In this study, we search for defects in 4H-SiC that explain the above magneto-optical signals in a defect database generated by automatic defect analysis and qualification (ADAQ) workflows. This search reveals only one class of atomic structures that exhibit silicon-vacancy-like properties in the data: a carbon anti-site (C-Si) within sub-nanometer distances from the silicon vacancy only slightly alters the latter without affecting the charge or spin state. Such a perturbation is energetically bound. We consider the formation of V-Si(-) + C-Si; up to 2 nm distance and report their zero phonon lines and zero field splitting values. In addition, we perform high-resolution photoluminescence experiments in the silicon vacancy region and find an abundance of lines. Comparing our computational and experimental results, several configurations show great agreement. Our work demonstrates the effectiveness of a database with high-throughput results in the search for defects in quantum applications.
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