136 research outputs found

    Measuring the impact of COVID-19 on hospital care pathways

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    Care pathways in hospitals around the world reported significant disruption during the recent COVID-19 pandemic but measuring the actual impact is more problematic. Process mining can be useful for hospital management to measure the conformance of real-life care to what might be considered normal operations. In this study, we aim to demonstrate that process mining can be used to investigate process changes associated with complex disruptive events. We studied perturbations to accident and emergency (A &E) and maternity pathways in a UK public hospital during the COVID-19 pandemic. Co-incidentally the hospital had implemented a Command Centre approach for patient-flow management affording an opportunity to study both the planned improvement and the disruption due to the pandemic. Our study proposes and demonstrates a method for measuring and investigating the impact of such planned and unplanned disruptions affecting hospital care pathways. We found that during the pandemic, both A &E and maternity pathways had measurable reductions in the mean length of stay and a measurable drop in the percentage of pathways conforming to normative models. There were no distinctive patterns of monthly mean values of length of stay nor conformance throughout the phases of the installation of the hospital’s new Command Centre approach. Due to a deficit in the available A &E data, the findings for A &E pathways could not be interpreted

    Methodological approaches and techniques for designing ontologies in information systems requirements engineering

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    Programa doutoral em Information Systems and TechnologyThe way we interact with the world around us is changing as new challenges arise, embracing innovative business models, rethinking the organization and processes to maximize results, and evolving change management. Currently, and considering the projects executed, the methodologies used do not fully respond to the companies' needs. On the one hand, organizations are not familiar with the languages used in Information Systems, and on the other hand, they are often unable to validate requirements or business models. These are some of the difficulties encountered that lead us to think about formulating a new approach. Thus, the state of the art presented in this paper includes a study of the models involved in the software development process, where traditional methods and the rivalry of agile methods are present. In addition, a survey is made about Ontologies and what methods exist to conceive, transform, and represent them. Thus, after analyzing some of the various possibilities currently available, we began the process of evolving a method and developing an approach that would allow us to design ontologies. The method we evolved and adapted will allow us to derive terminologies from a specific domain, aggregating them in order to facilitate the construction of a catalog of terminologies. Next, the definition of an approach to designing ontologies will allow the construction of a domain-specific ontology. This approach allows in the first instance to integrate and store the data from different information systems of a given organization. In a second instance, the rules for mapping and building the ontology database are defined. Finally, a technological architecture is also proposed that will allow the mapping of an ontology through the construction of complex networks, allowing mapping and relating terminologies. This doctoral work encompasses numerous Research & Development (R&D) projects belonging to different domains such as Software Industry, Textile Industry, Robotic Industry and Smart Cities. Finally, a critical and descriptive analysis of the work done is performed, and we also point out perspectives for possible future work.A forma como interagimos com o mundo à nossa volta está a mudar à medida que novos desafios surgem, abraçando modelos empresariais inovadores, repensando a organização e os processos para maximizar os resultados, e evoluindo a gestão da mudança. Atualmente, e considerando os projetos executados, as metodologias utilizadas não respondem na totalidade às necessidades das empresas. Por um lado, as organizações não estão familiarizadas com as linguagens utilizadas nos Sistemas de Informação, por outro lado, são muitas vezes incapazes de validar requisitos ou modelos de negócio. Estas são algumas das dificuldades encontradas que nos levam a pensar na formulação de uma nova abordagem. Assim, o estado da arte apresentado neste documento inclui um estudo dos modelos envolvidos no processo de desenvolvimento de software, onde os métodos tradicionais e a rivalidade de métodos ágeis estão presentes. Além disso, é efetuado um levantamento sobre Ontologias e quais os métodos existentes para as conceber, transformar e representar. Assim, e após analisarmos algumas das várias possibilidades atualmente disponíveis, iniciou-se o processo de evolução de um método e desenvolvimento de uma abordagem que nos permitisse conceber ontologias. O método que evoluímos e adaptamos permitirá derivar terminologias de um domínio específico, agregando-as de forma a facilitar a construção de um catálogo de terminologias. Em seguida, a definição de uma abordagem para conceber ontologias permitirá a construção de uma ontologia de um domínio específico. Esta abordagem permite em primeira instância, integrar e armazenar os dados de diferentes sistemas de informação de uma determinada organização. Num segundo momento, são definidas as regras para o mapeamento e construção da base de dados ontológica. Finalmente, é também proposta uma arquitetura tecnológica que permitirá efetuar o mapeamento de uma ontologia através da construção de redes complexas, permitindo mapear e relacionar terminologias. Este trabalho de doutoramento engloba inúmeros projetos de Investigação & Desenvolvimento (I&D) pertencentes a diferentes domínios como por exemplo Indústria de Software, Indústria Têxtil, Indústria Robótica e Smart Cities. Finalmente, é realizada uma análise critica e descritiva do trabalho realizado, sendo que apontamos ainda perspetivas de possíveis trabalhos futuros

    Semiring Provenance for Lightweight Description Logics

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    We investigate semiring provenance--a successful framework originally defined in the relational database setting--for description logics. In this context, the ontology axioms are annotated with elements of a commutative semiring and these annotations are propagated to the ontology consequences in a way that reflects how they are derived. We define a provenance semantics for a language that encompasses several lightweight description logics and show its relationships with semantics that have been defined for ontologies annotated with a specific kind of annotation (such as fuzzy degrees). We show that under some restrictions on the semiring, the semantics satisfies desirable properties (such as extending the semiring provenance defined for databases). We then focus on the well-known why-provenance, which allows to compute the semiring provenance for every additively and multiplicatively idempotent commutative semiring, and for which we study the complexity of problems related to the provenance of an axiom or a conjunctive query answer. Finally, we consider two more restricted cases which correspond to the so-called positive Boolean provenance and lineage in the database setting. For these cases, we exhibit relationships with well-known notions related to explanations in description logics and complete our complexity analysis. As a side contribution, we provide conditions on an ELHI_bot ontology that guarantee tractable reasoning.Comment: Paper currently under review. 102 page

    Knowledge Graph Building Blocks: An easy-to-use Framework for developing FAIREr Knowledge Graphs

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    Knowledge graphs and ontologies provide promising technical solutions for implementing the FAIR Principles for Findable, Accessible, Interoperable, and Reusable data and metadata. However, they also come with their own challenges. Nine such challenges are discussed and associated with the criterion of cognitive interoperability and specific FAIREr principles (FAIR + Explorability raised) that they fail to meet. We introduce an easy-to-use, open source knowledge graph framework that is based on knowledge graph building blocks (KGBBs). KGBBs are small information modules for knowledge-processing, each based on a specific type of semantic unit. By interrelating several KGBBs, one can specify a KGBB-driven FAIREr knowledge graph. Besides implementing semantic units, the KGBB Framework clearly distinguishes and decouples an internal in-memory data model from data storage, data display, and data access/export models. We argue that this decoupling is essential for solving many problems of knowledge management systems. We discuss the architecture of the KGBB Framework as we envision it, comprising (i) an openly accessible KGBB-Repository for different types of KGBBs, (ii) a KGBB-Engine for managing and operating FAIREr knowledge graphs (including automatic provenance tracking, editing changelog, and versioning of semantic units); (iii) a repository for KGBB-Functions; (iv) a low-code KGBB-Editor with which domain experts can create new KGBBs and specify their own FAIREr knowledge graph without having to think about semantic modelling. We conclude with discussing the nine challenges and how the KGBB Framework provides solutions for the issues they raise. While most of what we discuss here is entirely conceptual, we can point to two prototypes that demonstrate the principle feasibility of using semantic units and KGBBs to manage and structure knowledge graphs

    NeuroBridge ontology: computable provenance metadata to give the long tail of neuroimaging data a FAIR chance for secondary use

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    Background Despite the efforts of the neuroscience community, there are many published neuroimaging studies with data that are still not findable or accessible. Users face significant challenges in reusing neuroimaging data due to the lack of provenance metadata, such as experimental protocols, study instruments, and details about the study participants, which is also required for interoperability. To implement the FAIR guidelines for neuroimaging data, we have developed an iterative ontology engineering process and used it to create the NeuroBridge ontology. The NeuroBridge ontology is a computable model of provenance terms to implement FAIR principles and together with an international effort to annotate full text articles with ontology terms, the ontology enables users to locate relevant neuroimaging datasets. Methods Building on our previous work in metadata modeling, and in concert with an initial annotation of a representative corpus, we modeled diagnosis terms (e.g., schizophrenia, alcohol usage disorder), magnetic resonance imaging (MRI) scan types (T1-weighted, task-based, etc.), clinical symptom assessments (PANSS, AUDIT), and a variety of other assessments. We used the feedback of the annotation team to identify missing metadata terms, which were added to the NeuroBridge ontology, and we restructured the ontology to support both the final annotation of the corpus of neuroimaging articles by a second, independent set of annotators, as well as the functionalities of the NeuroBridge search portal for neuroimaging datasets. Results The NeuroBridge ontology consists of 660 classes with 49 properties with 3,200 axioms. The ontology includes mappings to existing ontologies, enabling the NeuroBridge ontology to be interoperable with other domain specific terminological systems. Using the ontology, we annotated 186 neuroimaging full-text articles describing the participant types, scanning, clinical and cognitive assessments. ConclusionThe NeuroBridge ontology is the first computable metadata model that represents the types of data available in recent neuroimaging studies in schizophrenia and substance use disorders research; it can be extended to include more granular terms as needed. This metadata ontology is expected to form the computational foundation to help both investigators to make their data FAIR compliant and support users to conduct reproducible neuroimaging research

    Documenting Data Integration Using Knowledge Graphs

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    With the increasing volume of data on the Web and the proliferation of published knowledge graphs, there is a growing need for improved data management and information extraction. However, heterogeneity issues across the data sources, i.e., various formats and systems, negatively impact efficient access, manage, reuse, and analyze the data. A data integration system (DIS) provides uniform access to heterogeneous data sources and their relationships; it offers a unified and comprehensive view of the data. DISs resort to mapping rules, expressed in declarative languages like RML, to align data from various sources to classes and properties defined in an ontology. This work defines a knowledge graph where data integration systems are represented as factual statements. The aim of this work is to provide the basis for integrated analysis of data collected from heterogeneous data silos. The proposed knowledge graph is also specified as a data integration system, that integrates all data integration systems. The proposed solution includes a unified schema, which defines and explains the relationships between all elements in the data integration system DIS=⟨G, S, M, F⟩. The results suggest that factual statements from the proposed knowledge graph, improve the understanding of the features that characterize knowledge graphs declaratively defined like data integration systems

    Semantic data integration and knowledge graph creation at scale

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    Contrary to data, knowledge is often abstract. Concrete knowledge can be achieved through the inclusion of semantics in the data models, highlighting the role of data integration. The massive growing number of data, in recent years, has promoted the demand for scaling up data management techniques; materializing data integration, a.k.a., knowledge graph creation falls in that category. In this thesis, we investigate efficient methods and techniques for materializing data integration. We formalize the process of materializing data integration. We formally define the characteristics of a materialized data integration system that merge the data operators and sources. Owing to this formalism, both layers of data integration, including data and schema-level integration, are formalized in the context of mapping assertions. We explore optimization opportunities for improving the materialization of data integration systems. We recognize three angles including intra/inter-mapping assertions from which the materialization can be improved. Accordingly, we propose source-based, mapping-based, and inter-mapping assertion groups of optimization techniques. We utilize our proposed techniques in three real-world projects. We illustrate how applying these optimization techniques contribute to meeting the objectives of the mentioned projects. Furthermore, we study the parameters impacting the performance of materialization of data integration. Relying on reported parameters and the presumably impacting parameters, we build four groups of testbeds. We empirically study the performances of these different testbeds in the presence and absence of our proposed techniques, in terms of execution time. We observe that the savings can be up to 75%. Lastly, we contribute to facilitating the process of declarative data integration system definition. We propose two data operation function signatures in Function Ontology (FnO). The first set of functions is designed to perform the task of entity alignment by resorting to an entity and relation linking tool. The second library consists of domain-specific functions to align genomic entities by harmonizing their representations. Finally, we introduce a tool equipped with a user interface to facilitate the process of defining declarative mapping rules by allowing users to explore the data sources and unified schema while defining their correspondences.Im Gegensatz zu den Daten ist das Wissen oft abstrakt. Konkretes Wissen kann durch die Einbeziehung von Semantik in die Datenmodelle erreicht werden, was die Rolle der Datenintegration unterstreicht. Die massiv wachsende Zahl von Daten hat in den letzten Jahren die Nachfrage nach einer Ausweitung der Datenverwaltungstechnikengef¨ordert; die materialisierende Datenintegration, auch bekannt als die Erstellung von Wissensgraphen, f¨allt in diese Kategorie. In dieser Arbeit untersuchen wir effiziente Methoden und Techniken zur Materialisierung der Datenintegration. Wir formalisieren den Prozess der Materialisierung der Datenintegration. Wir definieren formal die Eigenschaften eines materialisierten Datenintegrationssystems, so dass die Datenoperatoren und -quellen zusammengef¨uhrt werden. Dank dieses Formalismus werden beide Ebenen der Datenintegration, einschließlich der Integration auf Daten- und Schemaebene, im Kontext von Mapping-Assertions formalisiert. Wir untersuchen die Optimierungsm¨oglichkeiten zur Verbesserung der Materialisierung von Datenintegrationssystemen. Wir erkennen drei Gesichtspunkte, einschließlich Intra-/Inter-Mapping-Assertions, unter denen die Materialisierung verbessert werden kann. Dementsprechend schlagen wir quellenbasierte, mappingbasierte und inter-mapping Assertionsgruppen von Optimierungstechniken vor. Wir setzen die von uns vorgeschlagenen Techniken in drei Forschungsprojekte ein. Wir veranschaulichen, wie die Anwendung dieser Optimierungstechniken dazu beitr¨agt, die Ziele der genannten Projekte zu erreichen. Wir untersuchen die Parameter, die sich auf die Leistung der Materialisierung der Datenintegration auswirken. Auf der Grundlage der gemeldeten Parameter und der vermutlich ausschlaggebenden Parameter erstellen wir vier Gruppen von Testumgebungen. Wir untersuchen empirisch die Leistung dieser verschiedenen Testbeds mit und ohne die von uns vorgeschlagenen Techniken in Bezug auf die Ausf¨uhrungszeit. Wir stellen fest, dass die Einsparungen bis zu 75% betragen k¨onnen. Schließlich tragen wir zur Erleichterung des Prozesses der deklarativen Definition von Datenintegrationssystemen bei, indem wir zwei Funktionssignaturen f¨ur Datenoperationen in der Function Ontology (FnO) vorschlagen. Die erste Gruppe von Funktionen ist f¨ur die Aufgabe des Entit¨atsabgleichs konzipiert, w¨ahrend die zweite Bibliothek aus dom¨anenspezifischen Funktionen zum Abgleich genomischer Entit¨aten durch Harmonisierung ihrer Darstellungen besteht. Schließlich stellen wir ein Tool vor, das mit einer Benutzeroberfl¨ache ausgestattet ist, um den Prozess der Definition deklarativer Mapping-Regeln zu erleichtern, indem es den Benutzern erm¨oglicht, die Datenquellen und das einheitliche Schema zu erkunden

    Spider4SPARQL: A Complex Benchmark for Evaluating Knowledge Graph Question Answering Systems

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    With the recent spike in the number and availability of Large Language Models (LLMs), it has become increasingly important to provide large and realistic benchmarks for evaluating Knowledge Graph Question Answering (KBQA) systems. So far the majority of benchmarks rely on pattern-based SPARQL query generation approaches. The subsequent natural language (NL) question generation is conducted through crowdsourcing or other automated methods, such as rule-based paraphrasing or NL question templates. Although some of these datasets are of considerable size, their pitfall lies in their pattern-based generation approaches, which do not always generalize well to the vague and linguistically diverse questions asked by humans in real-world contexts. In this paper, we introduce Spider4SPARQL - a new SPARQL benchmark dataset featuring 9,693 previously existing manually generated NL questions and 4,721 unique, novel, and complex SPARQL queries of varying complexity. In addition to the NL/SPARQL pairs, we also provide their corresponding 166 knowledge graphs and ontologies, which cover 138 different domains. Our complex benchmark enables novel ways of evaluating the strengths and weaknesses of modern KGQA systems. We evaluate the system with state-of-the-art KGQA systems as well as LLMs, which achieve only up to 45\% execution accuracy, demonstrating that Spider4SPARQL is a challenging benchmark for future research

    Research Paper: Process Mining and Synthetic Health Data: Reflections and Lessons Learnt

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    Analysing the treatment pathways in real-world health data can provide valuable insight for clinicians and decision-makers. However, the procedures for acquiring real-world data for research can be restrictive, time-consuming and risks disclosing identifiable information. Synthetic data might enable representative analysis without direct access to sensitive data. In the first part of our paper, we propose an approach for grading synthetic data for process analysis based on its fidelity to relationships found in real-world data. In the second part, we apply our grading approach by assessing cancer patient pathways in a synthetic healthcare dataset (The Simulacrum provided by the English National Cancer Registration and Analysis Service) using process mining. Visualisations of the patient pathways within the synthetic data appear plausible, showing relationships between events confirmed in the underlying non-synthetic data. Data quality issues are also present within the synthetic data which reflect real-world problems and artefacts from the synthetic dataset’s creation. Process mining of synthetic data in healthcare is an emerging field with novel challenges. We conclude that researchers should be aware of the risks when extrapolating results produced from research on synthetic data to real-world scenarios and assess findings with analysts who are able to view the underlying data

    Ein ontologiebasiertes Verfahren zur automatisierten Bewertung von Bauwerksschäden in einer digitalen Datenumgebung

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    Neue Technologien im Bereich der Bauwerks- und Schadenserfassung führen zu einer Automatisierung und damit verbundenen Effizienzsteigerung von Inspektionsprozessen. Eine adäquate Digitalisierung des erfassten Bauwerkzustandes in ein BIM-Modell ist jedoch gegenwärtig nicht problemlos möglich. Eine Hauptursache hierfür sind fehlende Spezifikationen für ein digitales Modell, das aufgenommene Schäden repräsentieren kann. Ein Problem bilden dabei Unschärfen in der Informationsmodellierung, die üblicherweise bei BIM-Verfahren im Neubau nicht auftreten. Unscharfe Informationen, wie z.B. die Klassifizierung detektierter Schäden oder Annahme weiterer verborgener Schäden, werden derzeit manuell von Experten evaluiert, was oftmals eine aufwendige Auswertung kontextueller Informationen in einer Vielzahl verteilter Bauwerksdokumente erfordert. Eine automatisierte Bewertung detektierter Schäden anhand des Bauwerkskontextes wird derzeit noch nicht in der Praxis umgesetzt. In dieser Dissertation wird ein Konzept zur Repräsentation von Bauwerksschäden in einem digitalen, generisch strukturierten Schadensmodell vorgestellt. Das entwickelte Konzept bietet hierbei Lösungsansätze für Probleme gegenwärtiger Schadensmodellierung, wie z.B. die Verwaltung heterogener Dokumentationsdaten, Versionierung von Schadensobjekten oder Verarbeitung der Schadensgeometrie. Das modulare Schema des Schadensmodells besteht aus einer generischen Kernkomponente, die eine allgemeine Beschreibung von Schäden ermöglicht, unabhängig von spezifizierenden Faktoren, wie dem betroffenen Bauwerkstyp oder Baumaterial. Zur Definition domänenspezifischer Informationen kann die Kernkomponente durch entsprechende Erweiterungsschemata ergänzt werden. Als präferierte Serialisierungsmöglichkeit wird das Schadensmodell in einer wissensbasierten Ontologie umgesetzt. Dies erlaubt eine automatisierte Bewertung der modellierten Schadens- und Kontextinformationen unter Nutzung digitalisierten Wissens. Zur Evaluation unscharfer Schadensinformationen wird ein wissensbasiertes Bewertungsverfahren vorgestellt. Das hierbei entwickelte Schadensbewertungssystem ermöglicht eine Klassifizierung detektierter Schäden, sowie Folgerung impliziter Bewertungsinformationen, die für die weitere instandhalterische Planung relevant sind. Außerdem ermöglicht das Verfahren eine Annahme undetektierter Schäden, die potentiell im Inneren des Bauwerks oder schwer erreichbaren Stellen auftreten können. In der ontologischen Bewertung werden dabei nicht nur Schadensmerkmale berücksichtigt, sondern auch Informationen bezüglich des Bauwerkskontext, wie z.B. der betroffene Bauteil- oder Materialtyp oder vorliegende Umweltbedingungen. Zur Veranschaulichung der erarbeiteten Spezifikationen und Methoden, werden diese abschließend an zwei Testszenarien angewendet.New technologies in the field of building and damage detection lead to an automation of inspection processes and thus an increase in efficiency. However, an adequate digitalisation of the recorded building data into a BIM model is currently not possible without problems. One main reason for this is the lack of specifications for a digital model that can represent recorded damages. Thereby, a primary problem are uncertainties and fuzzy data in the information modelling, which usually does not occur when applying BIM for new buildings. Fuzzy information, such as the classification of detected damages or the assumption of further hidden damages, is currently evaluated manually by experts, which often requires a complex evaluation of contextual information in a multitude of distributed building documents. An automated evaluation of detected damages based on the building context is applied or implemented in practice. In this thesis a concept for the representation of structural damages in a digital, generically structured damage model is presented. The developed concept offers solutions for problems of current damage modelling, e.g. the management of heterogeneous documentation data, versioning of damage objects or processing of the damage geometry. The modular scheme of the damage model consists of a generic core component, which allows a general description of damages, independent of specifying factors, such as the type of construction or building material concerned. For the definition of domain-specific information, the core component can be supplemented by corresponding extension schemes. As a preferred serialisation option, the damage model is implemented in a knowledge-based ontology. This allows an automated evaluation of the modelled damage and context information using digitised knowledge. For the evaluation of fuzzy damage information, a knowledge-based evaluation procedure is presented. The developed damage evaluation system allows a classification of detected damages as well as the conclusion of implicit evaluation information relevant for further maintenance planning. In addition, the method allows the assumption of undetected damages that can potentially occur inside the structure or in places that are difficult to reach. In the ontological assessment, not only damage characteristics are considered, but also information regarding the building context, such as the affected component or material type as well as existing environmental conditions. To illustrate the developed specifications and methods, the whole concept is applied to two test scenarios
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