RDF Triples Research Articles

An Ontology-Based Automation System

This paper presents an ontology-based approach to benefit automatic fertilization management for citrus orchards located in mountainous region. The core of the fertilization approach is the citrus fertilization ontology, which covers knowledge about citrus fertilizers and fertilization application. Specially, our approach can provide not only the yearly fertilization quantities of required pure nitrogen, phosphorus, and potassium according to their disease symptoms, but also the suitable fertilizing recommendations for the citrus orchards with different soil properties. The current version of the ontology (ver. 2.9.10) contains 103 classes, 34 properties, 800 instances, which are defined by 3056 RDF triples and is evaluated by using 90 competency questions. Furthermore, we run experiments with our proposal targeting at four citrus orchards in Chongqing, and compare its outputs with the reference values advised by the agri-professionals of citrus planting.

Medical Knowledge Graph Completion Based on Word Embeddings

The aim of Medical Knowledge Graph Completion is to automatically predict one of three parts (head entity, relationship, and tail entity) in RDF triples from medical data, mainly text data. Following their introduction, the use of pretrained language models, such as Word2vec, BERT, and XLNET, to complete Medical Knowledge Graphs has become a popular research topic. The existing work focuses mainly on relationship completion and has rarely solved entities and related triples. In this paper, a framework to predict RDF triples for Medical Knowledge Graphs based on word embeddings (named PTMKG-WE) is proposed, for the specific use for the completion of entities and triples. The framework first formalizes existing samples for a given relationship from the Medical Knowledge Graph as prior knowledge. Second, it trains word embeddings from big medical data according to prior knowledge through Word2vec. Third, it can acquire candidate triples from word embeddings based on analogies from existing samples. In this framework, the paper proposes two strategies to improve the relation features. One is used to refine the relational semantics by clustering existing triple samples. Another is used to accurately embed the expression of the relationship through means of existing samples. These two strategies can be used separately (called PTMKG-WE-C and PTMKG-WE-M, respectively), and can also be superimposed (called PTMKG-WE-C-M) in the framework. Finally, in the current study, PubMed data and the National Drug File-Reference Terminology (NDF-RT) were collected, and a series of experiments was conducted. The experimental results show that the framework proposed in this paper and the two improvement strategies can be used to predict new triples for Medical Knowledge Graphs, when medical data are sufficiently abundant and the Knowledge Graph has appropriate prior knowledge. The two strategies designed to improve the relation features have a significant effect on the lifting precision, and the superposition effect becomes more obvious. Another conclusion is that, under the same parameter setting, the semantic precision of word embedding can be improved by extending the breadth and depth of data, and the precision of the prediction framework in this paper can be further improved in most cases. Thus, collecting and training big medical data is a viable method to learn more useful knowledge.

Knowledge Graph Construction for SOFL Formal Specifications

Formal specifications can provide a solid foundation for software development and support for techniques of software quality assurance, such as specification-based inspection and testing. To ensure that these techniques can be applied effectively in practice, efficiently and accurately understanding specifications becomes extremely important. While this may be relatively easy for well-trained developers in formal methods, it can be rather difficult for computer since computer does not easily understand specifications. This difficulty poses a challenge for realizing automatic specification-based verification techniques that are in high demand for reducing development cost and improving software reliability. In this paper, we address this problem by discussing how the formal specification can be transformed into a knowledge graph to provide comprehensible, well-organized details of the specification for developers and computers. The transformation is done by extracting and storing information about attributes of each component and by establishing relationships between components in a formal specification. We elaborate on a top-down approach of constructing a knowledge graph from a specification, including creating an ontology, designing the Entity–Relationship (ER) diagram of the relational database based on the created ontology, extracting and storing attribute and relationship information in the relational database, mapping ontology to its instances and relational data to RDF triples, and displaying knowledge graph. Further, we present a case study to show how our approach works on the formal specification of an ATM system. Finally, we describe three experiments to evaluate its performance in improving specification readability, effectively guiding inspectors to establish traceability links between specifications and programs, and detecting defects through program inspection, respectively.

A fuzzy semantic representation and reasoning model for multiple associative predicates in knowledge graph

As the latest achievement of the development in semiotics, knowledge graph has been recognized and widely used by more and more researchers for its rich semantic information and clear logical structure. How to discovery the deep relevant knowledge from the massive graph-structured data has become a hot spot of artificial intelligence. Considering that some predicates in knowledge graph express fuzzy relationships whose semantics are not certain, the basic schema of classical knowledge graph in the form of RDF triple cannot describe the fuzzy semantic information effectively. To counter above problems, in this paper, we present a new semantic representation and reasoning model for multiple associative predicates by introducing fuzzy theory. Concretely, the presented method defines a new fuzzy annotating strategy to represent the fuzzy semantics between associative predicates in different RDF triples. On this basis, some fuzzy reasoning rules are presented to realize fuzzy semantic extension for classical knowledge graph. Lastly, the experimental results show that our proposal can discover more implicit valid knowledge with fuzzy semantic and have a good consistency with the intuition of human judgments. Overall, the methods proposed in this paper constitute some effective ways of knowledge discovery of structured semantic data.

A formalization of one of the main claims of “OpenBiodiv: A knowledge graph for literature-extracted linked open data in biodiversity science” by Penev et al. 20191

Penev et al. claimed in previous work that triples in the OpenBiodiv knowledge graph releases are generally semantic triples extracted from biodiversity literature. We present here a formalization of that claim, stating that all things of class “triple in OpenBiodiv knowledge graph” that are in the context of a thing of class “release of OpenBiodiv knowledge graph” generally have a relation of type “is same as” to a thing of class “semantic triple extracted from biodiversity literature” in the same context.

An Ontology for Modeling Cultural Heritage Knowledge in Urban Tourism

Urban tourism information available on Internet has been of enormous relevance to motivate the tourism in many countries. There exist many applications focused on promoting and preserving the cultural heritage, through urban tourism, which in turn demand a well-defined and standard model for representing the whole knowledge of this domain, thus ensuring interoperable and flexible applications. Current studies propose the use of ontologies to formally model such knowledge. Nonetheless, most of them only represent partial knowledge of cultural heritage or are restrictive to an indoor perspective (i.e., museum ontologies). In this context, we propose the ontology CURIOCITY (Cultural Heritage for Urban Tourism in Indoor/Outdoor environments of the CITY), to represent the cultural heritage knowledge based on UNESCO’s definitions. CURIOCITY ontology has a three-level architecture (Upper, Middle, and Lower ontologies) in accordance with a purpose of modularity and levels of specificity. In this paper, we describe in detail all modules of CURIOCITY ontology and perform a comparative evaluation with state-of-the-art ontologies. Additionally, to demonstrate the suitability of CURIOCITY ontology, we show several touristic services offered through a framework supported in the ontology. The framework includes an automatic population process, that allows transforming a museum data repository (in CSV format) into RDF triples of CURIOCITY ontology to automatically populate the CURIOCITY repository, and facilities to develop a set of tourism applications and services, following the UNESCO’s definitions.

Query Answer Reformulation over Knowledge Bases

The answer of a query, submitted to a database or a knowledge base, is often long and may contain redundant data. The user is frequently forced to browse through a long answer or refine and repeat the query until the answer reaches a manageable size. Without proper treatment, consuming the answer may indeed become a tedious task. This article then proposes a process that modifies the presentation of a query answer to improve the quality of the user’s experience in the context of an RDF knowledge base. The process reorganizes the original query answer by applying heuristics to summarize the results and to select template questions that create a user dialog that guides the presentation of the results. The article also includes experiments based on RDF versions of MusicBrainz, enriched with DBpedia data, and IMDb, each with over 200 million RDF triples. The experiments use sample queries from well-known benchmarks.

RDFFrames: knowledge graph access for machine learning tools

Knowledge graphs represented as RDF datasets are integral to many machine learning applications. RDF is supported by a rich ecosystem of data management systems and tools, most notably RDF database systems that provide a SPARQL query interface. Surprisingly, machine learning tools for knowledge graphs do not use SPARQL, despite the obvious advantages of using a database system. This is due to the mismatch between SPARQL and machine learning tools in terms of data model and programming style. Machine learning tools work on data in tabular format and process it using an imperative programming style, while SPARQL is declarative and has as its basic operation matching graph patterns to RDF triples. We posit that a good interface to knowledge graphs from a machine learning software stack should use an imperative, navigational programming paradigm based on graph traversal rather than the SPARQL query paradigm based on graph patterns. In this paper, we present RDFFrames, a framework that provides such an interface. RDFFrames provides an imperative Python API that gets internally translated to SPARQL, and it is integrated with the PyData machine learning software stack. RDFFrames enables the user to make a sequence of Python calls to define the data to be extracted from a knowledge graph stored in an RDF database system, and it translates these calls into a compact SPQARL query, executes it on the database system, and returns the results in a standard tabular format. Thus, RDFFrames is a useful tool for data preparation that combines the usability of PyData with the flexibility and performance of RDF database systems.

Semantic 3D City Database — An enabler for a dynamic geospatial knowledge graph

This paper presents a dynamic geospatial knowledge graph as part of The World Avatar project, with an underlying ontology based on CityGML 2.0 for three-dimensional geometrical city objects. We comprehensively evaluated, repaired and refined an existing CityGML ontology to produce an improved version that could pass the necessary tests and complete unit test development. A corresponding data transformation tool, originally designed to work alongside CityGML, was extended. This allowed for the transformation of original data into a form of semantic triples. We compared various scalable technologies for this semantic data storage and chose Blazegraph™ as it provided the required geospatial search functionality. We also evaluated scalable hardware data solutions and file systems using the publicly available CityGML 2.0 data of Charlottenburg in Berlin, Germany as a working example. The structural isomorphism of the CityGML schemas and the OntoCityGML Tbox allowed the data to be transformed without loss of information. Efficient geospatial search algorithms allowed us to retrieve building data from any point in a city using coordinates. The use of named graphs and namespaces for data partitioning ensured the system performance stayed well below its capacity limits. This was achieved by evaluating scalable and dedicated data storage hardware capable of hosting expansible file systems, which strengthened the architectural foundations of the target system.

Agent-Based Semantic Role Mining for Intelligent Access Control in Multi-Domain Collaborative Applications of Smart Cities

Significance and popularity of Role-Based Access Control (RBAC) is inevitable; however, its application is highly challenging in multi-domain collaborative smart city environments. The reason is its limitations in adapting the dynamically changing information of users, tasks, access policies and resources in such applications. It also does not incorporate semantically meaningful business roles, which could have a diverse impact upon access decisions in such multi-domain collaborative business environments. We propose an Intelligent Role-based Access Control (I-RBAC) model that uses intelligent software agents for achieving intelligent access control in such highly dynamic multi-domain environments. The novelty of this model lies in using a core I-RBAC ontology that is developed using real-world semantic business roles as occupational roles provided by Standard Occupational Classification (SOC), USA. It contains around 1400 business roles, from nearly all domains, along with their detailed task descriptions as well as hierarchical relationships among them. The semantic role mining process is performed through intelligent agents that use word embedding and a bidirectional LSTM deep neural network for automated population of organizational ontology from its unstructured text policy and, subsequently, matching this ontology with core I-RBAC ontology to extract unified business roles. The experimentation was performed on a large number of collaboration case scenarios of five multi-domain organizations and promising results were obtained regarding the accuracy of automatically derived RDF triples (Subject, Predicate, Object) from organizational text policies as well as the accuracy of extracted semantically meaningful roles.

Improving text-to-image generation with object layout guidance

The automatic generation of realistic images directly from a story text is a very challenging problem, as it cannot be addressed using a single image generation approach due mainly to the semantic complexity of the story text constituents. In this work, we propose a new approach that decomposes the task of story visualization into three phases: semantic text understanding, object layout prediction, and image generation and refinement. We start by simplifying the text using a scene graph triple notation that encodes semantic relationships between the story objects. We then introduce an object layout module to capture the features of these objects from the corresponding scene graph. Specifically, the object layout module aggregates individual object features from the scene graph as well as averaged or likelihood object features generated by a graph convolutional neural network. All these features are concatenated to form semantic triples that are then provided to the image generation framework. For the image generation phase, we adopt a scene graph image generation framework as stage-I, which is refined using a StackGAN as stage-II conditioned on the object layout module and the generated output image from stage-I. Our approach renders object details in high-resolution images while keeping the image structure consistent with the input text. To evaluate the performance of our approach, we use the COCO dataset and compare it with three baseline approaches, namely, sg2im, StackGAN and AttnGAN, in terms of image quality and user evaluation. According to the obtained assessment results, our object layout guidance-based approach significantly outperforms the abovementioned baseline approaches in terms of the accuracy of semantic matching and realism of the generated images representing the story text sentences.

Relational schema optimization for RDF-based knowledge graphs

Characteristic sets (CS) organize RDF triples based on the set of properties associated with their subject nodes. This concept was recently used in indexing techniques, as it can capture the implicit schema of RDF data. While most CS-based approaches yield significant improvements in space and query performance, they fail to perform well when answering complex query workloads in the presence of schema heterogeneity, i.e., when the number of CSs becomes very large, resulting in a highly partitioned data organization. In this paper, we address this problem by introducing a novel technique, for merging CSs based on their hierarchical structure. Our method employs a lattice to capture the hierarchical relationships between CSs, identifies dense CSs and merges dense CSs with their ancestors. We have implemented our algorithm on top of a relational backbone, where each merged CS is stored in a relational table, and therefore, CS merging results in a smaller number of required tables to host the source triples of a dataset. Moreover, we perform an extensive experimental study to evaluate the performance and impact of merging to the storage and querying of RDF datasets, indicating significant improvements. We also conduct a sensitivity analysis to identify the stability and any possible weaknesses of our algorithm, and report on our results.

Drug repurposing for COVID-19 via knowledge graph completion

ObjectiveTo discover candidate drugs to repurpose for COVID-19 using literature-derived knowledge and knowledge graph completion methods. MethodsWe propose a novel, integrative, and neural network-based literature-based discovery (LBD) approach to identify drug candidates from PubMed and other COVID-19-focused research literature. Our approach relies on semantic triples extracted using SemRep (via SemMedDB). We identified an informative and accurate subset of semantic triples using filtering rules and an accuracy classifier developed on a BERT variant. We used this subset to construct a knowledge graph, and applied five state-of-the-art, neural knowledge graph completion algorithms (i.e., TransE, RotatE, DistMult, ComplEx, and STELP) to predict drug repurposing candidates. The models were trained and assessed using a time slicing approach and the predicted drugs were compared with a list of drugs reported in the literature and evaluated in clinical trials. These models were complemented by a discovery pattern-based approach. ResultsAccuracy classifier based on PubMedBERT achieved the best performance (F1 = 0.854) in identifying accurate semantic predications. Among five knowledge graph completion models, TransE outperformed others (MR = 0.923, Hits@1 = 0.417). Some known drugs linked to COVID-19 in the literature were identified, as well as others that have not yet been studied. Discovery patterns enabled identification of additional candidate drugs and generation of plausible hypotheses regarding the links between the candidate drugs and COVID-19. Among them, five highly ranked and novel drugs (i.e., paclitaxel, SB 203580, alpha 2-antiplasmin, metoclopramide, and oxymatrine) and the mechanistic explanations for their potential use are further discussed. ConclusionWe showed that a LBD approach can be feasible not only for discovering drug candidates for COVID-19, but also for generating mechanistic explanations. Our approach can be generalized to other diseases as well as to other clinical questions. Source code and data are available at https://github.com/kilicogluh/lbd-covid.

The Use of National Strategic Reference Framework Data in Knowledge Graphs and Data Mining to Identify Red Flags

Red Flags in fiscal projects are warning signs that may indicate underlying problems with their implementation. In this paper, we present how National Strategic Reference Framework Open Data can be used to take full advantage of semantic web technologies and data mining techniques to build a knowledge-based system that identifies Red Flags. We collected the data from the Open Data API provided by the Greek Ministry of Economy and Finance. Data modeling consist of two ontologies; the Vocabulary of Fiscal Projects, describing the fiscal projects and the National Strategic Reference Framework Greece Vocabulary, illustrating the Greek National Strategic Reference Framework data. We transformed the data into RDF triples and uploaded them onto an OpenLink Virtuoso Server, so that we could retrieve them via SPARQL queries. Performance indicators were defined to assess the state of the project and Density-Based Spatial Clustering of Applications with Noise, (DBSCAN) was used to identify Red Flags. User’s demands is that rejected projects should raise Red Flags, to avoid project failure and assist the auditor to organize the monitoring process efficiently, by avoiding to examine most of the non-problematic projects. We performed a use case scenario in which an auditor has to examine NSRF projects, approximately 12 months before the end of the programming period. The system retrieved the fiscal information, calculated the performance indicators and identified the Red Flags. The last update of the projects status after the end of the programming period was retrieved and extracted the number of rejected projects, to test whether the user requirements are satisfied. Rejected projects consist of 3.8% of the total projects. The results of the use case scenario show that RedFlags platform is more likely to identify project failures and not raise Red Flags on not rejected projects. Therefore, the RedFlags platform using open data, assists the auditor to organize the monitoring process better.

Knowledge Graph Construction of High-Performance Computing Learning Platform

With the development of intelligent education, it has become one of the more efficient learning schemes to construct the knowledge graph which can excavate the knowledge base. People generally use RDF triples and use languages such as OWL to construct knowledge graphs, but this method has problems such as limited expression ability and too much manual annotation. In this paper, we propose a framework that combines statistical language models, neural network language models, and clustering and clipping algorithms. When processing unstructured text data, unsupervised extraction of representative key words as features of the structured graphs’ entities, so that the processed entity information has more accurate semantics and human learning relevance, and the method of clustering and calculating the learning rate is used to further clarify the learning order and mastery of knowledge points. We have conducted extensive experiments to collect data from the two major modules of HPC high-performance computing courses and domains as datasets, and used this framework to build many knowledge graphs which can provide practical learning. The knowledge graph of this paper can be obtained from: https://v2.easyhpc.net:10000/knowledge Knowledge Graph Module.

Mining information from sentences through Semantic Web data and Information Extraction tasks

The Semantic Web provides guidelines for the representation of information about real-world objects (entities) and their relations (properties). This is helpful for the dissemination and consumption of information by people and applications. However, the information is mainly contained within natural language sentences, which do not have a structure or linguistic descriptions ready to be directly processed by computers. Thus, the challenge is to identify and extract the elements of information that can be represented. Hence, this article presents a strategy to extract information from sentences and its representation with Semantic Web standards. Our strategy involves Information Extraction tasks and a hybrid semantic similarity measure to get entities and relations that are later associated with individuals and properties from a Knowledge Base to create RDF triples (Subject–Predicate–Object structures). The experiments demonstrate the feasibility of our method and that it outperforms the accuracy provided by a pattern-based method from the literature.

MELODI Presto: a fast and agile tool to explore semantic triples derived from biomedical literature.

ABSTRACTSummaryThe field of literature-based discovery is growing in step with the volume of literature being produced. From modern natural language processing algorithms to high quality entity tagging, the methods and their impact are developing rapidly. One annotation object that arises from these approaches, the subject–predicate–object triple, is proving to be very useful in representing knowledge. We have implemented efficient search methods and an application programming interface, to create fast and convenient functions to utilize triples extracted from the biomedical literature by SemMedDB. By refining these data, we have identified a set of triples that focus on the mechanistic aspects of the literature, and provide simple methods to explore both enriched triples from single queries, and overlapping triples across two query lists.Availability and Implementationhttps://melodi-presto.mrcieu.ac.uk/.Supplementary information Supplementary data are available at Bioinformatics online.

RDFFrames

Knowledge graphs represented in RDF are becoming increasingly popular and are essential to many machine learning applications. A rich ecosystem of RDF data management systems and tools has evolved over the years, most notably RDF database management systems that support the SPARQL query language. Surprisingly, machine learning tools for knowledge graphs typically do not use SPARQL despite the obvious advantages of using a database system. This is due to the mismatch between SPARQL and machine learning tools in terms of expected data model and interface style. Machine learning tools work on data in tabular format and process it using imperative relational API calls, while SPARQL matches graph patterns to RDF triples. To access knowledge graphs for machine learning, we observe that it is more natural to use a navigational paradigm based on graph traversal rather than the SPARQL paradigm based on triple patterns. We demonstrate RDFFrames, a framework that bridges the gap between machine learning tools and RDF database systems by offering the usability and flexibility of machine learning tools together with the performance of a database system. RDFFrames enables the user to make a sequence of Python calls to define the data to be extracted from a knowledge graph stored in an RDF database system, and it translates these calls into a compact SPARQL query, executes it on the database system, and returns the results in a standard tabular format.

Mapping Manuscript Migrations Knowledge Graph: Data for Tracing the History and Provenance of Medieval and Renaissance Manuscripts

The Mapping Manuscript Migrations (MMM) project transformed three separate datasets relating to the history and provenance of medieval and Renaissance manuscripts into a unified knowledge graph. The source databases are: Schoenberg Database of Manuscripts, from the Schoenberg Institute for Manuscript Studies, University of Pennsylvania; Bibale, from the Institut de recherche et d’histoire des textes (IRHT-CNRS, Paris); and Medieval Manuscripts in Oxford Libraries, from the Bodleian Libraries, University of Oxford. The data consist of more than 20 million RDF triples which have been mapped to the MMM Data Model. The model combines classes and properties from CIDOC-CRM and FRBR, together with some specific MMM elements. The Knowledge Graph was created using the MMM data transformation pipeline. The MMM dataset is available from the Zenodo repository, and can be directly deployed on a SPARQL endpoint using a docker recipe. To test and demonstrate its usefulness, the MMM Knowledge Graph is in use in the MMM Semantic Portal: https://mappingmanuscriptmigrations.org.

Entity summarization with high readability and low redundancy

The development of the World Wide Web has triggered substantial growth of knowledge graphs (KG). Research into using KGs for intelligent applications has increased significantly. A KG describes facts about entities using RDF triples, and an entity description may contain a large number of triples. In applications where entity information is presented directly, entity summarization is required to prevent user information overload and to fit the presentation capacity. Here, the task is to select the most representative subset of triples from the rich entity description. In this paper, we propose an innovative entity summarization method, which we refer to as ESSTER, to generate summaries with both high readability and low redundancy. The proposed method combines structural and textual features. The importance of a triple is measured based on its structural features in the KG. The text readability of a triple is measured based on n-grams in a text corpus, and redundancy in a set of triples is measured by logical reasoning, numeric comparison, and text similarity. Entity summations is modeled and by combining these three measures and solved as a combinatorial optimization problem. We conducted experiments and compared the proposed method to six existing methods on two publicly available datasets of manually labeled summaries. Experimental results demonstrate that the proposed method achieves state of the art results.