Linked Data based Health Information Representation, Visualization and Retrieval System on the Semantic Web

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.To better facilitate health information dissemination, using flexible ways to represent, query and visualize health data becomes increasingly important. Semantic Web technologies, which provide a common framework by allowing data to be shared and reused between applications, can be applied to the management of health data. Linked open data - a new semantic web standard to publish and link heterogonous data- allows not only human, but also machine to brows data in unlimited way. Through a use case of world health organization HIV data of sub Saharan Africa - which is severely affected by HIV epidemic, this thesis built a linked data based health information representation, querying and visualization system. All the data was represented with RDF, by interlinking it with other related datasets, which are already on the cloud. Over all, the system have more than 21,000 triples with a SPARQL endpoint; where users can download and use the data and – a SPARQL query interface where users can put different type of query and retrieve the result. Additionally, It has also a visualization interface where users can visualize the SPARQL result with a tool of their preference. For users who are not familiar with SPARQL queries, they can use the linked data search engine interface to search and browse the data. From this system we can depict that current linked open data technologies have a big potential to represent heterogonous health data in a flexible and reusable manner and they can serve in intelligent queries, which can support decision-making. However, in order to get the best from these technologies, improvements are needed both at the level of triple stores performance and domain-specific ontological vocabularies

An integrated approach to deliver OLAP for multidimensional Semantic Web Databases

Semantic Webs (SW) and web data have become increasingly important sources to support Business Intelligence (BI), but they are difficult to manage due to the exponential increase in their volumes, inconsistency in semantics and complexity in representations. On-Line Analytical Processing (OLAP) is an important tool in analysing large and complex BI data, but it lacks the capability of processing disperse SW data due to the nature of its design. A new concept with a richer vocabulary than the existing ones for OLAP is needed to model distributed multidimensional semantic web databases. A new OLAP framework is developed, with multiple layers including additional vocabulary, extended OLAP operators, and usage of SPARQL to model heterogeneous semantic web data, unify multidimensional structures, and provide new enabling functions for interoperability. The framework is presented with examples to demonstrate its capability to unify existing vocabularies with additional vocabulary elements to handle both informational and topological data in Graph OLAP. The vocabularies used in this work are: the RDF Cube Vocabulary (QB) – proposed by the W3C to allow multi-dimensional, mostly statistical, data to be published in RDF; and the QB4OLAP – a QB extension introducing standard OLAP operators. The framework enables the composition of multiple databases (e.g. energy consumptions and property market values etc.) to generate observations through semantic pipe-like operators. This approach is demonstrated through Use Cases containing highly valuable data collected from a real-life environment. Its usability is proved through the development and usage of semantic pipe-like operators able to deliver OLAP specific functionalities. To the best of my knowledge there is no available data modelling approach handling both informational and topological Semantic Web data, which is designed either to provide OLAP capabilities over Semantic Web databases or to provide a means to connect such databases for further OLAP analysis. The thesis proposes that the presented work provides a wider understanding of: ways to access Semantic Web data; ways to build specialised Semantic Web databases, and, how to enrich them with powerful capabilities for further Business Intelligence

Semantically defined Analytics for Industrial Equipment Diagnostics

In this age of digitalization, industries everywhere accumulate massive amount of data such that it has become the lifeblood of the global economy. This data may come from various heterogeneous systems, equipment, components, sensors, systems and applications in many varieties (diversity of sources), velocities (high rate of changes) and volumes (sheer data size). Despite significant advances in the ability to collect, store, manage and filter data, the real value lies in the analytics. Raw data is meaningless, unless it is properly processed to actionable (business) insights. Those that know how to harness data effectively, have a decisive competitive advantage, through raising performance by making faster and smart decisions, improving short and long-term strategic planning, offering more user-centric products and services and fostering innovation. Two distinct paradigms in practice can be discerned within the field of analytics: semantic-driven (deductive) and data-driven (inductive). The first emphasizes logic as a way of representing the domain knowledge encoded in rules or ontologies and are often carefully curated and maintained. However, these models are often highly complex, and require intensive knowledge processing capabilities. Data-driven analytics employ machine learning (ML) to directly learn a model from the data with minimal human intervention. However, these models are tuned to trained data and context, making it difficult to adapt. Industries today that want to create value from data must master these paradigms in combination. However, there is great need in data analytics to seamlessly combine semantic-driven and data-driven processing techniques in an efficient and scalable architecture that allows extracting actionable insights from an extreme variety of data. In this thesis, we address these needs by providing: • A unified representation of domain-specific and analytical semantics, in form of ontology models called TechOnto Ontology Stack. It is highly expressive, platform-independent formalism to capture conceptual semantics of industrial systems such as technical system hierarchies, component partonomies etc and its analytical functional semantics. • A new ontology language Semantically defined Analytical Language (SAL) on top of the ontology model that extends existing DatalogMTL (a Horn fragment of Metric Temporal Logic) with analytical functions as first class citizens. • A method to generate semantic workflows using our SAL language. It helps in authoring, reusing and maintaining complex analytical tasks and workflows in an abstract fashion. • A multi-layer architecture that fuses knowledge- and data-driven analytics into a federated and distributed solution. To our knowledge, the work in this thesis is one of the first works to introduce and investigate the use of the semantically defined analytics in an ontology-based data access setting for industrial analytical applications. The reason behind focusing our work and evaluation on industrial data is due to (i) the adoption of semantic technology by the industries in general, and (ii) the common need in literature and in practice to allow domain expertise to drive the data analytics on semantically interoperable sources, while still harnessing the power of analytics to enable real-time data insights. Given the evaluation results of three use-case studies, our approach surpass state-of-the-art approaches for most application scenarios.Im Zeitalter der Digitalisierung sammeln die Industrien überall massive Daten-mengen, die zum Lebenselixier der Weltwirtschaft geworden sind. Diese Daten können aus verschiedenen heterogenen Systemen, Geräten, Komponenten, Sensoren, Systemen und Anwendungen in vielen Varianten (Vielfalt der Quellen), Geschwindigkeiten (hohe Änderungsrate) und Volumina (reine Datengröße) stammen. Trotz erheblicher Fortschritte in der Fähigkeit, Daten zu sammeln, zu speichern, zu verwalten und zu filtern, liegt der eigentliche Wert in der Analytik. Rohdaten sind bedeutungslos, es sei denn, sie werden ordnungsgemäß zu verwertbaren (Geschäfts-)Erkenntnissen verarbeitet. Wer weiß, wie man Daten effektiv nutzt, hat einen entscheidenden Wettbewerbsvorteil, indem er die Leistung steigert, indem er schnellere und intelligentere Entscheidungen trifft, die kurz- und langfristige strategische Planung verbessert, mehr benutzerorientierte Produkte und Dienstleistungen anbietet und Innovationen fördert. In der Praxis lassen sich im Bereich der Analytik zwei unterschiedliche Paradigmen unterscheiden: semantisch (deduktiv) und Daten getrieben (induktiv). Die erste betont die Logik als eine Möglichkeit, das in Regeln oder Ontologien kodierte Domänen-wissen darzustellen, und wird oft sorgfältig kuratiert und gepflegt. Diese Modelle sind jedoch oft sehr komplex und erfordern eine intensive Wissensverarbeitung. Datengesteuerte Analysen verwenden maschinelles Lernen (ML), um mit minimalem menschlichen Eingriff direkt ein Modell aus den Daten zu lernen. Diese Modelle sind jedoch auf trainierte Daten und Kontext abgestimmt, was die Anpassung erschwert. Branchen, die heute Wert aus Daten schaffen wollen, müssen diese Paradigmen in Kombination meistern. Es besteht jedoch ein großer Bedarf in der Daten-analytik, semantisch und datengesteuerte Verarbeitungstechniken nahtlos in einer effizienten und skalierbaren Architektur zu kombinieren, die es ermöglicht, aus einer extremen Datenvielfalt verwertbare Erkenntnisse zu gewinnen. In dieser Arbeit, die wir auf diese Bedürfnisse durch die Bereitstellung: • Eine einheitliche Darstellung der Domänen-spezifischen und analytischen Semantik in Form von Ontologie Modellen, genannt TechOnto Ontology Stack. Es ist ein hoch-expressiver, plattformunabhängiger Formalismus, die konzeptionelle Semantik industrieller Systeme wie technischer Systemhierarchien, Komponenten-partonomien usw. und deren analytische funktionale Semantik zu erfassen. • Eine neue Ontologie-Sprache Semantically defined Analytical Language (SAL) auf Basis des Ontologie-Modells das bestehende DatalogMTL (ein Horn fragment der metrischen temporären Logik) um analytische Funktionen als erstklassige Bürger erweitert. • Eine Methode zur Erzeugung semantischer workflows mit unserer SAL-Sprache. Es hilft bei der Erstellung, Wiederverwendung und Wartung komplexer analytischer Aufgaben und workflows auf abstrakte Weise. • Eine mehrschichtige Architektur, die Wissens- und datengesteuerte Analysen zu einer föderierten und verteilten Lösung verschmilzt. Nach unserem Wissen, die Arbeit in dieser Arbeit ist eines der ersten Werke zur Einführung und Untersuchung der Verwendung der semantisch definierten Analytik in einer Ontologie-basierten Datenzugriff Einstellung für industrielle analytische Anwendungen. Der Grund für die Fokussierung unserer Arbeit und Evaluierung auf industrielle Daten ist auf (i) die Übernahme semantischer Technologien durch die Industrie im Allgemeinen und (ii) den gemeinsamen Bedarf in der Literatur und in der Praxis zurückzuführen, der es der Fachkompetenz ermöglicht, die Datenanalyse auf semantisch inter-operablen Quellen voranzutreiben, und nutzen gleichzeitig die Leistungsfähigkeit der Analytik, um Echtzeit-Daten-einblicke zu ermöglichen. Aufgrund der Evaluierungsergebnisse von drei Anwendungsfällen Übertritt unser Ansatz für die meisten Anwendungsszenarien Modernste Ansätze

Automating the multidimensional design of data warehouses

Les experiències prèvies en l'àmbit dels magatzems de dades (o data warehouse), mostren que l'esquema multidimensional del data warehouse ha de ser fruit d'un enfocament híbrid; això és, una proposta que consideri tant els requeriments d'usuari com les fonts de dades durant el procés de disseny.Com a qualsevol altre sistema, els requeriments són necessaris per garantir que el sistema desenvolupat satisfà les necessitats de l'usuari. A més, essent aquest un procés de reenginyeria, les fonts de dades s'han de tenir en compte per: (i) garantir que el magatzem de dades resultant pot ésser poblat amb dades de l'organització, i, a més, (ii) descobrir capacitats d'anàlisis no evidents o no conegudes per l'usuari.Actualment, a la literatura s'han presentat diversos mètodes per donar suport al procés de modelatge del magatzem de dades. No obstant això, les propostes basades en un anàlisi dels requeriments assumeixen que aquestos són exhaustius, i no consideren que pot haver-hi informació rellevant amagada a les fonts de dades. Contràriament, les propostes basades en un anàlisi exhaustiu de les fonts de dades maximitzen aquest enfocament, i proposen tot el coneixement multidimensional que es pot derivar des de les fonts de dades i, conseqüentment, generen massa resultats. En aquest escenari, l'automatització del disseny del magatzem de dades és essencial per evitar que tot el pes de la tasca recaigui en el dissenyador (d'aquesta forma, no hem de confiar únicament en la seva habilitat i coneixement per aplicar el mètode de disseny elegit). A més, l'automatització de la tasca allibera al dissenyador del sempre complex i costós anàlisi de les fonts de dades (que pot arribar a ser inviable per grans fonts de dades).Avui dia, els mètodes automatitzables analitzen en detall les fonts de dades i passen per alt els requeriments. En canvi, els mètodes basats en l'anàlisi dels requeriments no consideren l'automatització del procés, ja que treballen amb requeriments expressats en llenguatges d'alt nivell que un ordenador no pot manegar. Aquesta mateixa situació es dona en els mètodes híbrids actual, que proposen un enfocament seqüencial, on l'anàlisi de les dades es complementa amb l'anàlisi dels requeriments, ja que totes dues tasques pateixen els mateixos problemes que els enfocament purs.En aquesta tesi proposem dos mètodes per donar suport a la tasca de modelatge del magatzem de dades: MDBE (Multidimensional Design Based on Examples) and AMDO (Automating the Multidimensional Design from Ontologies). Totes dues consideren els requeriments i les fonts de dades per portar a terme la tasca de modelatge i a més, van ser pensades per superar les limitacions dels enfocaments actuals.1. MDBE segueix un enfocament clàssic, en el que els requeriments d'usuari són coneguts d'avantmà. Aquest mètode es beneficia del coneixement capturat a les fonts de dades, però guia el procés des dels requeriments i, conseqüentment, és capaç de treballar sobre fonts de dades semànticament pobres. És a dir, explotant el fet que amb uns requeriments de qualitat, podem superar els inconvenients de disposar de fonts de dades que no capturen apropiadament el nostre domini de treball.2. A diferència d'MDBE, AMDO assumeix un escenari on es disposa de fonts de dades semànticament riques. Per aquest motiu, dirigeix el procés de modelatge des de les fonts de dades, i empra els requeriments per donar forma i adaptar els resultats generats a les necessitats de l'usuari. En aquest context, a diferència de l'anterior, unes fonts de dades semànticament riques esmorteeixen el fet de no tenir clars els requeriments d'usuari d'avantmà.Cal notar que els nostres mètodes estableixen un marc de treball combinat que es pot emprar per decidir, donat un escenari concret, quin enfocament és més adient. Per exemple, no es pot seguir el mateix enfocament en un escenari on els requeriments són ben coneguts d'avantmà i en un escenari on aquestos encara no estan clars (un cas recorrent d'aquesta situació és quan l'usuari no té clares les capacitats d'anàlisi del seu propi sistema). De fet, disposar d'uns bons requeriments d'avantmà esmorteeix la necessitat de disposar de fonts de dades semànticament riques, mentre que a l'inversa, si disposem de fonts de dades que capturen adequadament el nostre domini de treball, els requeriments no són necessaris d'avantmà. Per aquests motius, en aquesta tesi aportem un marc de treball combinat que cobreix tots els possibles escenaris que podem trobar durant la tasca de modelatge del magatzem de dades.Previous experiences in the data warehouse field have shown that the data warehouse multidimensional conceptual schema must be derived from a hybrid approach: i.e., by considering both the end-user requirements and the data sources, as first-class citizens. Like in any other system, requirements guarantee that the system devised meets the end-user necessities. In addition, since the data warehouse design task is a reengineering process, it must consider the underlying data sources of the organization: (i) to guarantee that the data warehouse must be populated from data available within the organization, and (ii) to allow the end-user discover unknown additional analysis capabilities.Currently, several methods for supporting the data warehouse modeling task have been provided. However, they suffer from some significant drawbacks. In short, requirement-driven approaches assume that requirements are exhaustive (and therefore, do not consider the data sources to contain alternative interesting evidences of analysis), whereas data-driven approaches (i.e., those leading the design task from a thorough analysis of the data sources) rely on discovering as much multidimensional knowledge as possible from the data sources. As a consequence, data-driven approaches generate too many results, which mislead the user. Furthermore, the design task automation is essential in this scenario, as it removes the dependency on an expert's ability to properly apply the method chosen, and the need to analyze the data sources, which is a tedious and timeconsuming task (which can be unfeasible when working with large databases). In this sense, current automatable methods follow a data-driven approach, whereas current requirement-driven approaches overlook the process automation, since they tend to work with requirements at a high level of abstraction. Indeed, this scenario is repeated regarding data-driven and requirement-driven stages within current hybrid approaches, which suffer from the same drawbacks than pure data-driven or requirement-driven approaches.In this thesis we introduce two different approaches for automating the multidimensional design of the data warehouse: MDBE (Multidimensional Design Based on Examples) and AMDO (Automating the Multidimensional Design from Ontologies). Both approaches were devised to overcome the limitations from which current approaches suffer. Importantly, our approaches consider opposite initial assumptions, but both consider the end-user requirements and the data sources as first-class citizens.1. MDBE follows a classical approach, in which the end-user requirements are well-known beforehand. This approach benefits from the knowledge captured in the data sources, but guides the design task according to requirements and consequently, it is able to work and handle semantically poorer data sources. In other words, providing high-quality end-user requirements, we can guide the process from the knowledge they contain, and overcome the fact of disposing of bad quality (from a semantical point of view) data sources.2. AMDO, as counterpart, assumes a scenario in which the data sources available are semantically richer. Thus, the approach proposed is guided by a thorough analysis of the data sources, which is properly adapted to shape the output result according to the end-user requirements. In this context, disposing of high-quality data sources, we can overcome the fact of lacking of expressive end-user requirements.Importantly, our methods establish a combined and comprehensive framework that can be used to decide, according to the inputs provided in each scenario, which is the best approach to follow. For example, we cannot follow the same approach in a scenario where the end-user requirements are clear and well-known, and in a scenario in which the end-user requirements are not evident or cannot be easily elicited (e.g., this may happen when the users are not aware of the analysis capabilities of their own sources). Interestingly, the need to dispose of requirements beforehand is smoothed by the fact of having semantically rich data sources. In lack of that, requirements gain relevance to extract the multidimensional knowledge from the sources.So that, we claim to provide two approaches whose combination turns up to be exhaustive with regard to the scenarios discussed in the literaturePostprint (published version

Semantic Integration of Cervical Cancer Data Repositories to Facilitate Multicenter Association Studies: The ASSIST Approach

The current work addresses the unifi cation of Electronic Health Records related to cervical cancer into a single medical knowledge source, in the context of the EU-funded ASSIST research project. The project aims to facilitate the research for cervical precancer and cancer through a system that virtually unifi es multiple patient record repositories, physically located in different medical centers/hospitals, thus, increasing fl exibility by allowing the formation of study groups “on demand” and by recycling patient records in new studies. To this end, ASSIST uses semantic technologies to translate all medical entities (such as patient examination results, history, habits, genetic profi le) and represent them in a common form, encoded in the ASSIST Cervical Cancer Ontology. The current paper presents the knowledge elicitation approach followed, towards the defi nition and representation of the disease’s medical concepts and rules that constitute the basis for the ASSIST Cervical Cancer Ontology. The proposed approach constitutes a paradigm for semantic integration of heterogeneous clinical data that may be applicable to other biomedical application domains

Model driven design and data integration in semantic web information systems

The Web is quickly evolving in many ways. It has evolved from a Web of documents into a Web of applications in which a growing number of designers offer new and interactive Web applications with people all over the world. However, application design and implementation remain complex, error-prone and laborious. In parallel there is also an evolution from a Web of documents into a Web of `knowledge' as a growing number of data owners are sharing their data sources with a growing audience. This brings the potential new applications for these data sources, including scenarios in which these datasets are reused and integrated with other existing and new data sources. However, the heterogeneity of these data sources in syntax, semantics and structure represents a great challenge for application designers. The Semantic Web is a collection of standards and technologies that offer solutions for at least the syntactic and some structural issues. If offers semantic freedom and flexibility, but this leaves the issue of semantic interoperability. In this thesis we present Hera-S, an evolution of the Model Driven Web Engineering (MDWE) method Hera. MDWEs allow designers to create data centric applications using models instead of programming. Hera-S especially targets Semantic Web sources and provides a flexible method for designing personalized adaptive Web applications. Hera-S defines several models that together define the target Web application. Moreover we implemented a framework called Hydragen, which is able to execute the Hera-S models to run the desired Web application. Hera-S' core is the Application Model (AM) in which the main logic of the application is defined, i.e. defining the groups of data elements that form logical units or subunits, the personalization conditions, and the relationships between the units. Hera-S also uses a so-called Domain Model (DM) that describes the content and its structure. However, this DM is not Hera-S specific, but instead allows any Semantic Web source representation as its DM, as long as its content can be queried by the standardized Semantic Web query language SPARQL. The same holds for the User Model (UM). The UM can be used for personalization conditions, but also as a source of user-related content if necessary. In fact, the difference between DM and UM is conceptual as their implementation within Hydragen is the same. Hera-S also defines a presentation model (PM) which defines presentation details of elements like order and style. In order to help designers with building their Web applications we have introduced a toolset, Hera Studio, which allows to build the different models graphically. Hera Studio also provides some additional functionality like model checking and deployment of the models in Hydragen. Both Hera-S and its implementation Hydragen are designed to be flexible regarding the user of models. In order to achieve this Hydragen is a stateless engine that queries for relevant information from the models at every page request. This allows the models and data to be changed in the datastore during runtime. We show that one way to exploit this flexibility is by applying aspect-orientation to the AM. Aspect-orientation allows us to dynamically inject functionality that pervades the entire application. Another way to exploit Hera-S' flexibility is in reusing specialized components, e.g. for presentation generation. We present a configuration of Hydragen in which we replace our native presentation generation functionality by the AMACONT engine. AMACONT provides more extensive multi-level presentation generation and adaptation capabilities as well aspect-orientation and a form of semantic based adaptation. Hera-S was designed to allow the (re-)use of any (Semantic) Web datasource. It even opens up the possibility for data integration at the back end, by using an extendible storage layer in our database of choice Sesame. However, even though theoretically possible it still leaves much of the actual data integration issue. As this is a recurring issue in many domains, a broader challenge than for Hera-S design only, we decided to look at this issue in isolation. We present a framework called Relco which provides a language to express data transformation operations as well as a collection of techniques that can be used to (semi-)automatically find relationships between concepts in different ontologies. This is done with a combination of syntactic, semantic and collaboration techniques, which together provide strong clues for which concepts are most likely related. In order to prove the applicability of Relco we explore five application scenarios in different domains for which data integration is a central aspect. This includes a cultural heritage portal, Explorer, for which data from several datasources was integrated and was made available by a mapview, a timeline and a graph view. Explorer also allows users to provide metadata for objects via a tagging mechanism. Another application is SenSee: an electronic TV-guide and recommender. TV-guide data was integrated and enriched with semantically structured data from several sources. Recommendations are computed by exploiting the underlying semantic structure. ViTa was a project in which several techniques for tagging and searching educational videos were evaluated. This includes scenarios in which user tags are related with an ontology, or other tags, using the Relco framework. The MobiLife project targeted the facilitation of a new generation of mobile applications that would use context-based personalization. This can be done using a context-based user profiling platform that can also be used for user model data exchange between mobile applications using technologies like Relco. The final application scenario that is shown is from the GRAPPLE project which targeted the integration of adaptive technology into current learning management systems. A large part of this integration is achieved by using a user modeling component framework in which any application can store user model information, but which can also be used for the exchange of user model data

On the Foundations of Data Interoperability and Semantic Search on the Web

This dissertation studies the problem of facilitating semantic search across disparate ontologies that are developed by different organizations. There is tremendous potential in enabling users to search independent ontologies and discover knowledge in a serendipitous fashion, i.e., often completely unintended by the developers of the ontologies. The main difficulty with such search is that users generally do not have any control over the naming conventions and content of the ontologies. Thus terms must be appropriately mapped across ontologies based on their meaning. The meaning-based search of data is referred to as semantic search, and its facilitation (aka semantic interoperability) then requires mapping between ontologies. In relational databases, searching across organizational boundaries currently involves the difficult task of setting up a rigid information integration system. Linked Data representations more flexibly tackle the problem of searching across organizational boundaries on the Web. However, there exists no consensus on how ontology mapping should be performed for this scenario, and the problem is open. We lay out the foundations of semantic search on the Web of Data by comparing it to keyword search in the relational model and by providing effective mechanisms to facilitate data interoperability across organizational boundaries. We identify two sharply distinct goals for ontology mapping based on real-world use cases. These goals are: (i) ontology development, and (ii) facilitating interoperability. We systematically analyze these goals, side-by-side, and contrast them. Our analysis demonstrates the implications of the goals on how to perform ontology mapping and how to represent the mappings. We rigorously compare facilitating interoperability between ontologies to information integration in databases. Based on the comparison, class matching is emphasized as a critical part of facilitating interoperability. For class matching, various class similarity metrics are formalized and an algorithm that utilizes these metrics is designed. We also experimentally evaluate the effectiveness of the class similarity metrics on real-world ontologies. In order to encode the correspondences between ontologies for interoperability, we develop a novel W3C-compliant representation, named skeleton