Controlled vocabularies and semantics in systems biology

The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the tools frequently used for this purpose. We describe here three ontologies created specifically to address the needs of the systems biology community. The Systems Biology Ontology (SBO) provides semantic information about the model components. The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. The Terminology for the Description of Dynamics (TEDDY) categorizes dynamical features of the simulation results and general systems behavior. The provision of semantic information extends a model's longevity and facilitates its reuse. It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments

Cadastral data integration through Linked Data

Ponencias, comunicaciones y pósters presentados en el 17th AGILE Conference on Geographic Information Science "Connecting a Digital Europe through Location and Place", celebrado en la Universitat Jaume I del 3 al 6 de junio de 2014.Cadastral data is one of the more important types of geospatial data. Taking into account the importance of these data, several international bodies have worked for creating a standardised model for land administration. However, in spite of existing efforts, there are several open issues for the development of a harmonized vision of cadastral data. Taking into account this scenario, Linked Open Data may allow addressing some of these challenges, by proposing best practices for exposing, sharing, and integrating data on the Web. This paper shows a use case where two cadastral information sources are semantically integrated according to Linked Data principles. These sources belong to different Colombian cadastral producers and are characterized by different heterogeneity issues. Herein, we describe an implementation of Linked Data principles in the cadastral domain using LADM standard (ISO 19152) and GeoSPARQL. Besides, our original data are enriched with different dataset of Linked Data cloud (LinkedGeoData and GeoNames)

Towards a formal manufacturing reference ontology

Due to the advancement in the application of Information and Communication Technology (ICT), manufacturing industry and its many domains employ a wide range of different ICT tools. To be competitive, industries need to communicate effectively within and across their many system domains. This communication is hindered by the diversity in the semantics of concepts and information structures of these different domain systems. Whilst international standards provide an effective route to information sharing within narrowly specified domains, they are themselves not interoperable across the wide range of application domains needed to support manufacturing industry due to the inconsistency of concept semantics. Formal ontologies have shown promise in removing interpretation problems by computationally capturing the semantics of concepts, ensuring their consistency and thus providing a verifiable and shared understanding across multiple domains. The research work reported in this paper contributes to the development of formal reference ontology for manufacturing, which is envisaged as a key component in future interoperable manufacturing systems. A set of core manufacturing concepts are identified and their semantics have been captured in formal logic based on exploiting and extending existing standards definitions, where possible combined with an industrial investigation of the concepts required. A successful experimental investigation has been conducted to verify the application of the ontology based on the interaction between concepts in the design and manufacturing domains of an aerospace component

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

Construals as a complement to intelligent tutoring systems in medical education

This is a preliminary version of a report prepared by Meurig and Will Beynon in conjunction with a poster paper "Mediating Intelligence through Observation, Dependency and Agency in Making Construals of Malaria" at the 11th International Conference on Intelligent Tutoring Systems (ITS 2012) and a paper "Construals to Support Exploratory and Collaborative Learning in Medicine" at the associated workshop on Intelligent Support for Exploratory Environments (ISEE 2012). A final version of the report will be published at a later stage after feedback from presentations at these events has been taken into account, and the experimental versions of the JS-EDEN interpreter used in making construals have been developed to a more mature and stable form

A Methodology for a Performance Information Model to support Facility Management

Current facility management practice relies on different systems which require new technologies to integrate and manage information more easily. Building information modeling offers a good opportunity to improve facility information management by providing a unified platform for various data sources rather than an intuitive information interface. Although current research trends reveal that there is a continuously growing interest in facility management aided by building information modeling, an integrated model is still hard to obtain. This paper aims at developing a novel methodology based on building information modeling and facility management systems integration, underpinned by a performance information model. The implementation process of a performance information model is described, including information technologies involved, the data and process requirements, and the building performance assessment methods used. A first pilot case-study has been conducted with regards to surgery rooms in healthcare buildings. The proposal can support condition-based maintenance work schedule, as well as the achievement of organizational, environmental, and technical requirements. Among the practical implications found: Improved technological and environmental performances assessment; better visualization of building condition; improved decision-making process; facilitated maintenance tasks planning and maintenance records management

Modeling coherent social systems for learning

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Multi-process modelling approach to complex organisation design

Present day markets require manufacturing enterprises (MEs) to be designed and run in a flexibly structured yet optimised way. However, contemporary approaches to ME engineering do not enable this requirement to capture ME attributes such that suitable processes, resource systems and support services can be readily implemented and changed. This study has developed and prototyped a model-driven environment for the design, optimisation and control of MEs with an embedded capability to handle various types of change. This so called Enriched-Process Modelling (E-MPM) Environment can support the engineering of strategic, tactical and operational processes and comprises two parts: (1) an E-MPM Method that informs, structures, and guides modelling activities required at different stages of ME systems design; and (2) an E-MPM Modelling Framework that specifies interconnections between modelling concepts necessary for the design and run time operation of ME systems. [Continues.