Resource discovery in heterogeneous digital content environments

The concept of 'resource discovery' is central to our understanding of how users explore, navigate, locate and retrieve information resources. This submission for a PhD by Published Works examines a series of 11 related works which explore topics pertaining to resource discovery, each demonstrating heterogeneity in their digital discovery context. The assembled works are prefaced by nine chapters which seek to review and critically analyse the contribution of each work, as well as provide contextualization within the wider body of research literature. A series of conceptual sub-themes is used to organize and structure the works and the accompanying critical commentary. The thesis first begins by examining issues in distributed discovery contexts by studying collection level metadata (CLM), its application in 'information landscaping' techniques, and its relationship to the efficacy of federated item-level search tools. This research narrative continues but expands in the later works and commentary to consider the application of Knowledge Organization Systems (KOS), particularly within Semantic Web and machine interface contexts, with investigations of semantically aware terminology services in distributed discovery. The necessary modelling of data structures to support resource discovery - and its associated functionalities within digital libraries and repositories - is then considered within the novel context of technology-supported curriculum design repositories, where questions of human-computer interaction (HCI) are also examined. The final works studied as part of the thesis are those which investigate and evaluate the efficacy of open repositories in exposing knowledge commons to resource discovery via web search agents. Through the analysis of the collected works it is possible to identify a unifying theory of resource discovery, with the proposed concept of (meta)data alignment described and presented with a visual model. This analysis assists in the identification of a number of research topics worthy of further research; but it also highlights an incremental transition by the present author, from using research to inform the development of technologies designed to support or facilitate resource discovery, particularly at a 'meta' level, to the application of specific technologies to address resource discovery issues in a local context. Despite this variation the research narrative has remained focussed on topics surrounding resource discovery in heterogeneous digital content environments and is noted as having generated a coherent body of work. Separate chapters are used to consider the methodological approaches adopted in each work and the contribution made to research knowledge and professional practice.The concept of 'resource discovery' is central to our understanding of how users explore, navigate, locate and retrieve information resources. This submission for a PhD by Published Works examines a series of 11 related works which explore topics pertaining to resource discovery, each demonstrating heterogeneity in their digital discovery context. The assembled works are prefaced by nine chapters which seek to review and critically analyse the contribution of each work, as well as provide contextualization within the wider body of research literature. A series of conceptual sub-themes is used to organize and structure the works and the accompanying critical commentary. The thesis first begins by examining issues in distributed discovery contexts by studying collection level metadata (CLM), its application in 'information landscaping' techniques, and its relationship to the efficacy of federated item-level search tools. This research narrative continues but expands in the later works and commentary to consider the application of Knowledge Organization Systems (KOS), particularly within Semantic Web and machine interface contexts, with investigations of semantically aware terminology services in distributed discovery. The necessary modelling of data structures to support resource discovery - and its associated functionalities within digital libraries and repositories - is then considered within the novel context of technology-supported curriculum design repositories, where questions of human-computer interaction (HCI) are also examined. The final works studied as part of the thesis are those which investigate and evaluate the efficacy of open repositories in exposing knowledge commons to resource discovery via web search agents. Through the analysis of the collected works it is possible to identify a unifying theory of resource discovery, with the proposed concept of (meta)data alignment described and presented with a visual model. This analysis assists in the identification of a number of research topics worthy of further research; but it also highlights an incremental transition by the present author, from using research to inform the development of technologies designed to support or facilitate resource discovery, particularly at a 'meta' level, to the application of specific technologies to address resource discovery issues in a local context. Despite this variation the research narrative has remained focussed on topics surrounding resource discovery in heterogeneous digital content environments and is noted as having generated a coherent body of work. Separate chapters are used to consider the methodological approaches adopted in each work and the contribution made to research knowledge and professional practice

Towards a system of concepts for Family Medicine. Multilingual indexing in General Practice/ Family Medicine in the era of Semantic Web

UNIVERSITY OF LIÈGE, BELGIUM Executive Summary Faculty of Medicine Département Universitaire de Médecine Générale. Unité de recherche Soins Primaires et Santé Doctor in biomedical sciences Towards a system of concepts for Family Medicine. Multilingual indexing in General Practice/ Family Medicine in the era of SemanticWeb by Dr. Marc JAMOULLE Introduction This thesis is about giving visibility to the often overlooked work of family physicians and consequently, is about grey literature in General Practice and Family Medicine (GP/FM). It often seems that conference organizers do not think of GP/FM as a knowledge-producing discipline that deserves active dissemination. A conference is organized, but not much is done with the knowledge shared at these meetings. In turn, the knowledge cannot be reused or reapplied. This these is also about indexing. To find knowledge back, indexing is mandatory. We must prepare tools that will automatically index the thousands of abstracts that family doctors produce each year in various languages. And finally this work is about semantics1. It is an introduction to health terminologies, ontologies, semantic data, and linked open data. All are expressions of the next step: Semantic Web for health care data. Concepts, units of thought expressed by terms, will be our target and must have the ability to be expressed in multiple languages. In turn, three areas of knowledge are at stake in this study: (i) Family Medicine as a pillar of primary health care, (ii) computational linguistics, and (iii) health information systems. Aim • To identify knowledge produced by General practitioners (GPs) by improving annotation of grey literature in Primary Health Care • To propose an experimental indexing system, acting as draft for a standardized table of content of GP/GM • To improve the searchability of repositories for grey literature in GP/GM. 1For specific terms, see the Glossary page 257 x Methods The first step aimed to design the taxonomy by identifying relevant concepts in a compiled corpus of GP/FM texts. We have studied the concepts identified in nearly two thousand communications of GPs during conferences. The relevant concepts belong to the fields that are focusing on GP/FM activities (e.g. teaching, ethics, management or environmental hazard issues). The second step was the development of an on-line, multilingual, terminological resource for each category of the resulting taxonomy, named Q-Codes. We have designed this terminology in the form of a lightweight ontology, accessible on-line for readers and ready for use by computers of the semantic web. It is also fit for the Linked Open Data universe. Results We propose 182 Q-Codes in an on-line multilingual database (10 languages) (www.hetop.eu/Q) acting each as a filter for Medline. Q-Codes are also available under the form of Unique Resource Identifiers (URIs) and are exportable in Web Ontology Language (OWL). The International Classification of Primary Care (ICPC) is linked to Q-Codes in order to form the Core Content Classification in General Practice/Family Medicine (3CGP). So far, 3CGP is in use by humans in pedagogy, in bibliographic studies, in indexing congresses, master theses and other forms of grey literature in GP/FM. Use by computers is experimented in automatic classifiers, annotators and natural language processing. Discussion To the best of our knowledge, this is the first attempt to expand the ICPC coding system with an extension for family physician contextual issues, thus covering non-clinical content of practice. It remains to be proven that our proposed terminology will help in dealing with more complex systems, such as MeSH, to support information storage and retrieval activities. However, this exercise is proposed as a first step in the creation of an ontology of GP/FM and as an opening to the complex world of Semantic Web technologies. Conclusion We expect that the creation of this terminological resource for indexing abstracts and for facilitating Medline searches for general practitioners, researchers and students in medicine will reduce loss of knowledge in the domain of GP/FM. In addition, through better indexing of the grey literature (congress abstracts, master’s and doctoral theses), we hope to enhance the accessibility of research results and give visibility to the invisible work of family physicians

Knowledge-driven entity recognition and disambiguation in biomedical text

Entity recognition and disambiguation (ERD) for the biomedical domain are notoriously difficult problems due to the variety of entities and their often long names in many variations. Existing works focus heavily on the molecular level in two ways. First, they target scientific literature as the input text genre. Second, they target single, highly specialized entity types such as chemicals, genes, and proteins. However, a wealth of biomedical information is also buried in the vast universe of Web content. In order to fully utilize all the information available, there is a need to tap into Web content as an additional input. Moreover, there is a need to cater for other entity types such as symptoms and risk factors since Web content focuses on consumer health. The goal of this thesis is to investigate ERD methods that are applicable to all entity types in scientific literature as well as Web content. In addition, we focus on under-explored aspects of the biomedical ERD problems -- scalability, long noun phrases, and out-of-knowledge base (OOKB) entities. This thesis makes four main contributions, all of which leverage knowledge in UMLS (Unified Medical Language System), the largest and most authoritative knowledge base (KB) of the biomedical domain. The first contribution is a fast dictionary lookup method for entity recognition that maximizes throughput while balancing the loss of precision and recall. The second contribution is a semantic type classification method targeting common words in long noun phrases. We develop a custom set of semantic types to capture word usages; besides biomedical usage, these types also cope with non-biomedical usage and the case of generic, non-informative usage. The third contribution is a fast heuristics method for entity disambiguation in MEDLINE abstracts, again maximizing throughput but this time maintaining accuracy. The fourth contribution is a corpus-driven entity disambiguation method that addresses OOKB entities. The method first captures the entities expressed in a corpus as latent representations that comprise in-KB and OOKB entities alike before performing entity disambiguation.Die Erkennung und Disambiguierung von Entitäten für den biomedizinischen Bereich stellen, wegen der vielfältigen Arten von biomedizinischen Entitäten sowie deren oft langen und variantenreichen Namen, große Herausforderungen dar. Vorhergehende Arbeiten konzentrieren sich in zweierlei Hinsicht fast ausschließlich auf molekulare Entitäten. Erstens fokussieren sie sich auf wissenschaftliche Publikationen als Genre der Eingabetexte. Zweitens fokussieren sie sich auf einzelne, sehr spezialisierte Entitätstypen wie Chemikalien, Gene und Proteine. Allerdings bietet das Internet neben diesen Quellen eine Vielzahl an Inhalten biomedizinischen Wissens, das vernachlässigt wird. Um alle verfügbaren Informationen auszunutzen besteht der Bedarf weitere Internet-Inhalte als zusätzliche Quellen zu erschließen. Außerdem ist es auch erforderlich andere Entitätstypen wie Symptome und Risikofaktoren in Betracht zu ziehen, da diese für zahlreiche Inhalte im Internet, wie zum Beispiel Verbraucherinformationen im Gesundheitssektor, relevant sind. Das Ziel dieser Dissertation ist es, Methoden zur Erkennung und Disambiguierung von Entitäten zu erforschen, die alle Entitätstypen in Betracht ziehen und sowohl auf wissenschaftliche Publikationen als auch auf andere Internet-Inhalte anwendbar sind. Darüber hinaus setzen wir Schwerpunkte auf oft vernachlässigte Aspekte der biomedizinischen Erkennung und Disambiguierung von Entitäten, nämlich Skalierbarkeit, lange Nominalphrasen und fehlende Entitäten in einer Wissensbank. In dieser Hinsicht leistet diese Dissertation vier Hauptbeiträge, denen allen das Wissen von UMLS (Unified Medical Language System), der größten und wichtigsten Wissensbank im biomedizinischen Bereich, zu Grunde liegt. Der erste Beitrag ist eine schnelle Methode zur Erkennung von Entitäten mittels Lexikonabgleich, welche den Durchsatz maximiert und gleichzeitig den Verlust in Genauigkeit und Trefferquote (precision and recall) balanciert. Der zweite Beitrag ist eine Methode zur Klassifizierung der semantischen Typen von Nomen, die sich auf gebräuchliche Nomen von langen Nominalphrasen richtet und auf einer selbstentwickelten Sammlung von semantischen Typen beruht, die die Verwendung der Nomen erfasst. Neben biomedizinischen können diese Typen auch nicht-biomedizinische und allgemeine, informationsarme Verwendungen behandeln. Der dritte Beitrag ist eine schnelle Heuristikmethode zur Disambiguierung von Entitäten in MEDLINE Kurzfassungen, welche den Durchsatz maximiert, aber auch die Genauigkeit erhält. Der vierte Beitrag ist eine korpusgetriebene Methode zur Disambiguierung von Entitäten, die speziell fehlende Entitäten in einer Wissensbank behandelt. Die Methode wandelt erst die Entitäten, die in einem Textkorpus ausgedrückt aber nicht notwendigerweise in einer Wissensbank sind, in latente Darstellungen um und führt anschließend die Disambiguierung durch

Linked Data para la generación de conocimiento financiero a partir de la extracción de información semiestructurada

En la actualidad, la información es generada por datos ubicados en un entorno distribuido pero vinculado. Con relación a esta premisa, las tecnologías semánticas y Linked Data, proporcionan un paradigma en el que no sólo los documentos, sino que también los datos son recursos de primera clase en la Web, permitiendo su extensión y la compartición de conocimientos hacia un espacio global de datos basado en estándares abiertos, mejor conocido como Web de datos. En este trabajo de tesis, se presenta un modelo semántico inspirado en los principios de Linked Data que ofrece una alternativa de solución a los problemas de integración de datos que se manifiestan en los Estados financieros publicados por las empresas bajo el estándar XBRL a través de la Web. En este sentido, mediante el modelo semántico se identifican y subsanan ciertas limitaciones existentes en las Hojas de Balance, Cuentas de resultados y Estados de flujos de efectivo. Entre estas limitaciones destacan la falta de una semántica que permita la integración de sus datos para hacerlos navegables, la dificultad para el acceso a los mismos a través de protocolos asociados a Internet como el HTTP para la navegación e interconexión con otras fuentes de información, y la carente capacidad para la búsqueda de ratios financieros, así como el procesamiento de cálculos permitan un análisis fundamental o clásico que sirva de apoyo a la toma de decisiones. El modelo semántico, se integra de taxonomías financieras basadas en la norma US-GAAP, y es el soporte fundamental de una base de conocimientos financieros reutilizable inspirada en Linked Data. En relación con lo anterior, la investigación que se realiza en este trabajo de tesis se sintetiza a través de la solución que se proporciona a las hipótesis que en ella se plantean, y mediante la que se busca demostrar que el modelo semántico tiene la capacidad para poblar una base de conocimientos financieros a partir de la integración de fuentes de datos externas, facilitar la reutilización de sus datos con terceros a través de Linked Data, ayudar a mejorar la calidad estructural de los datos financieros y comprobar que este modelo también facilita el análisis fundamental financiero para apoyar la toma de decisiones tanto automatizada como por parte de las personas.At present, the information is generated by data located in a distributed environment but linked. In relation to this premise, semantic and Linked Data technologies provide a paradigm in which not only documents but also the data are first-class resources on the Web, allowing its extension and sharing of knowledge towards a global space data based on open standards, better known as Web of data. In this thesis, a semantic model based on the principles of Linked Data that provides an alternative solution to the problems presented data integration that are manifested in the financial statements published by the company under the XBRL standard through Web. In this sense, using the semantic model are identified and remedied certain limitations in Balance Sheets, Income Statements and Cash Flow Statements. These limitations include the lack of a semantics that allow the integration of their data to make it navigable, difficulty accessing them through associated Internet protocols like HTTP for navigation and interconnection with other sources of information and lacking ability for search of financial ratios, as well as processing calculations that allow a fundamental or classical financial analysis that supports the decision making. The semantic model integrated financial taxonomies based on US-GAAP standard, and is the main support base of reusable financial knowledge inspired Linked Data. In connection with this, the research conducted in this thesis is synthesized through the solution provided to the hypothesis raised therein, and by which seeks to demonstrate that the semantic model has the ability to financial populate a knowledge base from the integration of external data sources, facilitating the reuse of data with third parties via Linked data, help improve the structural quality of financial data and verify that this model also facilitates analysis financial crucial to support decision-making both automated and by the people.Programa Oficial de Doctorado en Ciencia y Tecnología InformáticaPresidente: Juan Bautista Llorens Morillo.- Secretario: Carlos Ángel Iglesias Fernández.- Vocal: Manuel Fernández-Utrilla Migue

On Making in the Digital Humanities

On Making in the Digital Humanities fills a gap in our understanding of digital humanities projects and craft by exploring the processes of making as much as the products that arise from it. The volume draws focus to the interwoven layers of human and technological textures that constitute digital humanities scholarship. To do this, it assembles a group of well-known, experienced and emerging scholars in the digital humanities to reflect on various forms of making (we privilege here the creative and applied side of the digital humanities). The volume honours the work of John Bradley, as it is totemic of a practice of making that is deeply informed by critical perspectives. A special chapter also honours the profound contributions that this volume’s co-editor, Stéfan Sinclair, made to the creative, applied and intellectual praxis of making and the digital humanities. Stéfan Sinclair passed away on 6 August 2020. The chapters gathered here are individually important, but together provide a very human view on what it is to do the digital humanities, in the past, present and future. This book will accordingly be of interest to researchers, teachers and students of the digital humanities; creative humanities, including maker spaces and culture; information studies; the history of computing and technology; and the history of science and the humanities

An ontology for formal representation of medication adherence-related knowledge : case study in breast cancer

Indiana University-Purdue University Indianapolis (IUPUI)Medication non-adherence is a major healthcare problem that negatively impacts the health and productivity of individuals and society as a whole. Reasons for medication non-adherence are multi-faced, with no clear-cut solution. Adherence to medication remains a difficult area to study, due to inconsistencies in representing medicationadherence behavior data that poses a challenge to humans and today’s computer technology related to interpreting and synthesizing such complex information. Developing a consistent conceptual framework to medication adherence is needed to facilitate domain understanding, sharing, and communicating, as well as enabling researchers to formally compare the findings of studies in systematic reviews. The goal of this research is to create a common language that bridges human and computer technology by developing a controlled structured vocabulary of medication adherence behavior—“Medication Adherence Behavior Ontology” (MAB-Ontology) using breast cancer as a case study to inform and evaluate the proposed ontology and demonstrating its application to real-world situation. The intention is for MAB-Ontology to be developed against the background of a philosophical analysis of terms, such as belief, and desire to be human, computer-understandable, and interoperable with other systems that support scientific research. The design process for MAB-Ontology carried out using the METHONTOLOGY method incorporated with the Basic Formal Ontology (BFO) principles of best practice. This approach introduces a novel knowledge acquisition step that guides capturing medication-adherence-related data from different knowledge sources, including adherence assessment, adherence determinants, adherence theories, adherence taxonomies, and tacit knowledge source types. These sources were analyzed using a systematic approach that involved some questions applied to all source types to guide data extraction and inform domain conceptualization. A set of intermediate representations involving tables and graphs was used to allow for domain evaluation before implementation. The resulting ontology included 629 classes, 529 individuals, 51 object property, and 2 data property. The intermediate representation was formalized into OWL using Protégé. The MAB-Ontology was evaluated through competency questions, use-case scenario, face validity and was found to satisfy the requirement specification. This study provides a unified method for developing a computerized-based adherence model that can be applied among various disease groups and different drug categories

A framework for the analysis and evaluation of enterprise models

Bibliography: leaves 264-288.The purpose of this study is the development and validation of a comprehensive framework for the analysis and evaluation of enterprise models. The study starts with an extensive literature review of modelling concepts and an overview of the various reference disciplines concerned with enterprise modelling. This overview is more extensive than usual in order to accommodate readers from different backgrounds. The proposed framework is based on the distinction between the syntactic, semantic and pragmatic model aspects and populated with evaluation criteria drawn from an extensive literature survey. In order to operationalize and empirically validate the framework, an exhaustive survey of enterprise models was conducted. From this survey, an XML database of more than twenty relatively large, publicly available enterprise models was constructed. A strong emphasis was placed on the interdisciplinary nature of this database and models were drawn from ontology research, linguistics, analysis patterns as well as the traditional fields of data modelling, data warehousing and enterprise systems. The resultant database forms the test bed for the detailed framework-based analysis and its public availability should constitute a useful contribution to the modelling research community. The bulk of the research is dedicated to implementing and validating specific analysis techniques to quantify the various model evaluation criteria of the framework. The aim for each of the analysis techniques is that it can, where possible, be automated and generalised to other modelling domains. The syntactic measures and analysis techniques originate largely from the disciplines of systems engineering, graph theory and computer science. Various metrics to measure model hierarchy, architecture and complexity are tested and discussed. It is found that many are not particularly useful or valid for enterprise models. Hence some new measures are proposed to assist with model visualization and an original "model signature" consisting of three key metrics is proposed.Perhaps the most significant contribution ofthe research lies in the development and validation of a significant number of semantic analysis techniques, drawing heavily on current developments in lexicography, linguistics and ontology research. Some novel and interesting techniques are proposed to measure, inter alia, domain coverage, model genericity, quality of documentation, perspicuity and model similarity. Especially model similarity is explored in depth by means of various similarity and clustering algorithms as well as ways to visualize the similarity between models. Finally, a number of pragmatic analyses techniques are applied to the models. These include face validity, degree of use, authority of model author, availability, cost, flexibility, adaptability, model currency, maturity and degree of support. This analysis relies mostly on the searching for and ranking of certain specific information details, often involving a degree of subjective interpretation, although more specific quantitative procedures are suggested for some of the criteria. To aid future researchers, a separate chapter lists some promising analysis techniques that were investigated but found to be problematic from methodological perspective. More interestingly, this chapter also presents a very strong conceptual case on how the proposed framework and the analysis techniques associated vrith its various criteria can be applied to many other information systems research areas. The case is presented on the grounds of the underlying isomorphism between the various research areas and illustrated by suggesting the application of the framework to evaluate web sites, algorithms, software applications, programming languages, system development methodologies and user interfaces