Generating Linked-Data based Domain-Specific Sentiment Lexicons from Legacy Language and Semantic Resources

We present a methodology for legacy language resource adaptation that generates domain-specific sentiment lexicons organized around domain entities described with lexical information and sentiment words described in the context of these entities. We explain the steps of the methodology and we give a working example of our initial results. The resulting lexicons are modelled as Linked Data resources by use of established formats for Linguistic Linked Data (lemon, NIF) and for linked sentiment expressions (Marl), thereby contributing and linking to existing Language Resources in the Linguistic Linked Open Data cloud.

SMART Protocols: seMAntic represenTation for experimental protocols

Two important characteristics of science are the ?reproducibility? and ?clarity?. By rigorous practices, scientists explore aspects of the world that they can reproduce under carefully controlled experimental conditions. The clarity, complementing reproducibility, provides unambiguous descriptions of results in a mechanical or mathematical form. Both pillars depend on well-structured and accurate descriptions of scientific practices, which are normally recorded in experimental protocols, scientific workflows, etc. Here we present SMART Protocols (SP), our ontology-based approach for representing experimental protocols and our contribution to clarity and reproducibility. SP delivers an unambiguous description of processes by means of which data is produced; by doing so, we argue, it facilitates reproducibility. Moreover, SP is thought to be part of e-science infrastructures. SP results from the analysis of 175 protocols; from this dataset, we extracted common elements. From our analysis, we identified document, workflow and domain-specific aspects in the representation of experimental protocols. The ontology is available at http://purl.org/net/SMARTprotocol

A semantic-based approach to attain reproducibility of computational environments in scientific workflows: a case study

Reproducible research in scientific workflows is often addressed by tracking the provenance of the produced results. While this approach allows inspecting intermediate and final results, improves understanding, and permits replaying a workflow execution, it does not ensure that the computational environment is available for subsequent executions to reproduce the experiment. In this work, we propose describing the resources involved in the execution of an experiment using a set of semantic vocabularies, so as to conserve the computational environment. We define a process for documenting the workflow application, management system, and their dependencies based on 4 domain ontologies. We then conduct an experimental evaluation using a real workflow application on an academic and a public Cloud platform. Results show that our approach can reproduce an equivalent execution environment of a predefined virtual machine image on both computing platforms.

A Focused Crawler in order to Get Semantic Web Resources (CSR)

This paper presents a Focused Crawler in order to Get Semantic Web Resources (CSR). Structured data web are available in formats such as Extensible Markup Language (XML), Resource Description Framework (RDF) and Ontology Web Language (OWL) that can be used for processing. One of the main challenges for performing a manual search and download semantic web resources is that this task consumes a lot of time. Our research work propose a focused crawler which allow to download these resources automatically and store them on disk in order to have a collection that will be used for data processing. CRS consists of three layers: (a) The User Interface Layer, (b) The Focus Crawler Layer and (c) The Base Crawler Layer. CSR uses as a selection policie the Shark-Search method. CSR was conducted with two experiments. The first one starts on December 15 2012 at 7:11 am and ends on December 16 2012 at 4:01 were obtained 448,123,537 bytes of data. The CSR ends by itself after to analyze 80,4375 seeds with an unlimited depth. CSR got 16,576 semantic resources files where the 89 % was RDF, the 10 % was XML and the 1% was OWL. The second one was based on the Web Data Commons work of the Research Group Data and Web Science at the University of Mannheim and the Institute AIFB at the Karlsruhe Institute of Technology. This began at 4:46 am of June 2 2013 and 1:37 am June 9 2013. After 162.51 hours of execution the result was 285,279 semantic resources where predominated the XML resources with 99 % and OWL and RDF with 1 % each one.

Analysis of the suitability of existing medical ontologies for building a scalable semantic interoperability solution supporting multi-site collaboration in oncology

Semantic interoperability is essential to facilitate efficient collaboration in heterogeneous multi-site healthcare environments. The deployment of a semantic interoperability solution has the potential to enable a wide range of informatics supported applications in clinical care and research both within as ingle healthcare organization and in a network of organizations. At the same time, building and deploying a semantic interoperability solution may require significant effort to carryout data transformation and to harmonize the semantics of the information in the different systems. Our approach to semantic interoperability leverages existing healthcare standards and ontologies, focusing first on specific clinical domains and key applications, and gradually expanding the solution when needed. An important objective of this work is to create a semantic link between clinical research and care environments to enable applications such as streamlining the execution of multi-centric clinical trials, including the identification of eligible patients for the trials. This paper presents an analysis of the suitability of several widely-used medical ontologies in the clinical domain: SNOMED-CT, LOINC, MedDRA, to capture the semantics of the clinical trial eligibility criteria, of the clinical trial data (e.g., Clinical Report Forms), and of the corresponding patient record data that would enable the automatic identification of eligible patients. Next to the coverage provided by the ontologies we evaluate and compare the sizes of the sets of relevant concepts and their relative frequency to estimate the cost of data transformation, of building the necessary semantic mappings, and of extending the solution to new domains. This analysis shows that our approach is both feasible and scalable.

A Semantic Approach to Problem-Based Learning with Conceptual Models

El aprendizaje basado en problemas se lleva aplicando con éxito durante las últimas tres décadas en un amplio rango de entornos de aprendizaje. Este enfoque educacional consiste en proponer problemas a los estudiantes de forma que puedan aprender sobre un dominio particular mediante el desarrollo de soluciones a dichos problemas. Si esto se aplica al modelado de conocimiento, y en particular al basado en Razonamiento Cualitativo, las soluciones a los problemas pasan a ser modelos que representan el compotamiento del sistema dinámico propuesto. Por lo tanto, la tarea del estudiante en este caso es acercar su modelo inicial (su primer intento de representar el sistema) a los modelos objetivo que proporcionan soluciones al problema, a la vez que adquieren conocimiento sobre el dominio durante el proceso. En esta tesis proponemos KaiSem, un método que usa tecnologías y recursos semánticos para guiar a los estudiantes durante el proceso de modelado, ayudándoles a adquirir tanto conocimiento como sea posible sin la directa supervisión de un profesor. Dado que tanto estudiantes como profesores crean sus modelos de forma independiente, estos tendrán diferentes terminologías y estructuras, dando lugar a un conjunto de modelos altamente heterogéneo. Para lidiar con tal heterogeneidad, proporcionamos una técnica de anclaje semántico para determinar, de forma automática, enlaces entre la terminología libre usada por los estudiantes y algunos vocabularios disponibles en la Web de Datos, facilitando con ello la interoperabilidad y posterior alineación de modelos. Por último, proporcionamos una técnica de feedback semántico para comparar los modelos ya alineados y generar feedback basado en las posibles discrepancias entre ellos. Este feedback es comunicado en forma de sugerencias individualizadas que el estudiante puede utilizar para acercar su modelo a los modelos objetivos en cuanto a su terminología y estructura se refiere. ABSTRACT Problem-based learning has been successfully applied over the last three decades to a diverse range of learning environments. This educational approach consists of posing problems to learners, so they can learn about a particular domain by developing solutions to them. When applied to conceptual modeling, and particularly to Qualitative Reasoning, the solutions to problems are models that represent the behavior of a dynamic system. Therefore, the learner's task is to move from their initial model, as their first attempt to represent the system, to the target models that provide solutions to that problem while acquiring domain knowledge in the process. In this thesis we propose KaiSem, a method for using semantic technologies and resources to scaffold the modeling process, helping the learners to acquire as much domain knowledge as possible without direct supervision from the teacher. Since learners and experts create their models independently, these will have different terminologies and structure, giving rise to a pool of models highly heterogeneous. To deal with such heterogeneity, we provide a semantic grounding technique to automatically determine links between the unrestricted terminology used by learners and some online vocabularies of the Web of Data, thus facilitating the interoperability and later alignment of the models. Lastly, we provide a semantic-based feedback technique to compare the aligned models and generate feedback based on the possible discrepancies. This feedback is communicated in the form of individualized suggestions, which can be used by the learner to bring their model closer in terminology and structure to the target models.

SemQuaRE - An extension of the SQuaRE quality model for the evaluation of semantic technologies

To correctly evaluate semantic technologies and to obtain results that can be easily integrated, we need to put evaluations under the scope of a unique software quality model. This paper presents SemQuaRE, a quality model for semantic technologies. SemQuaRE is based on the SQuaRE standard and describes a set of quality characteristics specific to semantic technologies and the quality measures that can be used for their measurement. It also provides detailed formulas for the calculation of such measures. The paper shows that SemQuaRE is complete with respect to current evaluation trends and that it has been successfully applied in practice.

Desarrollo de ontología de títulos de grado

Dada la amplia información que rodea el dominio de programas de estudios superiores, específicamente los estudios de grado, este trabajo fin de grado propone la construcción de un modelo para representar dicha información mediante la construcción de una red de ontologías, proporcionando una definición común de conceptos importantes, y que posteriormente puede ser reutilizada para la construcción de aplicaciones que ayuden a las partes interesadas, como, estudiantes, personal académico y administrativo, a la búsqueda y acceso de información oportuna. Para la construcción de esta red de ontologías, se siguen las recomendaciones y pautas propuestas por la metodología NeOn [1a] [1b], que sigue un paradigma basado en la reutilización de recursos de conocimiento. Por otra parte, se realiza una populación de dicha red de ontologías mediante datos específicos del grado en Ingeniería Informática de la Universidad Politécnica de Madrid. La construcción de una red de ontologías siguiendo las directrices de la metodología NeOn requiere la realización de distintas actividades y tareas, como el estudio del dominio, estudio de la viabilidad, especificación de requisitos, conceptualización, formalización, implementación y mantenimiento. Se realizan también muchas otras actividades y tareas dependiendo del contexto en el que se construye la ontología. En este proyecto se hace un especial énfasis en las actividades de especificación de requisitos, conceptualización e implementación, además de la actividad de búsqueda de recursos ontológicos para su posterior reutilización. Se ha construido una red de ontologías llamada: European Bachelor Degree Ontology (EBDO) que incluye términos y conceptos importantes que se han detectado en la etapa de especificación de requisitos y que las ontologías a reutilizar no contemplan. Las decisiones de diseño para la construcción de esta nueva red de ontologías y su alineamiento con las ontologías a reutilizar se han basado en la especificación de requisitos ontológicos. Una vez definidos los conceptos relevantes de la red de ontologías, se ha implementado la red de ontologías en un lenguaje computable. Una vez que la red de ontologías se ha implementado se han realizado tareas de evaluación para corregir posible errores. Finalmente, cuando se ha obtenido una versión estable de la ontología, se ha realizado la instanciación de individuos del plan de estudios del grado en Ingeniería Informática de la Universidad Politécnica de Madrid.---ABSTRACT---Given the extensive information surrounding the domain of higher education programs, specifically bachelor degree studies, this bachelor degree project proposes the construction of a model to represent this information by building an ontology network, providing a common definition of important concepts. This network can be reused to build semantic applications that help stakeholders, such as, students, academic and organisational staff, to search and access to timely information. For the construction of this network of ontologies, guidelines and recommendations proposed by the NeOn Methodology [1a] [1b] have been followed. This methodology follows a paradigm based on the reuse of knowledge resources. Moreover, a population of this ontology network is performed with specific data of the Computer Science Degree from Universidad Politécnica de Madrid Building a network of ontologies following the guidelines of the NeOn Methodology requires the completion of various activities and tasks such as, the study of the domain, study of the feasibility, requirements specification, conceptualization, formalization, implementation and maintenance. Many other activities and tasks are also performed depending on the context in which the ontology is built. In this project a special emphasis is made on the activities of requirements specification, conceptualization and search of ontological resources for reuse and implementation. A new network of ontologies, named European Bachelor Degree Ontology (EBDO), has been built. This network includes terms and concepts that have been detected at the stage of requirements specification and that the reused ontologies have not contemplated. Design principles for the construction of this new network of ontologies and for the reused ontologies alignment have been based on the ontological specification requirements. Once the relevant concepts of the ontology network are defined, the network has been implemented in a computable ontology language. Once the network ontology is implemented, the evaluation activity has been conducted to correct the errors that the network presented. Finally, when a stable version of the ontology has been obtained, the instantiation of individuals of the study program of the Bachelor Degree in Computer Science from Universidad Politécnica de Madrid has been performed.

Using WYSIWYM to Create an Open-ended Interface for the Semantic Grid

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A Semantic Workflow Mechanism to Realize Experimental Goals and Constraints

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Semantic Support for Computational Land-Use Modelling

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Characteristics of patients making serious inhaler errors with a dry powder inhaler and association with asthma-related events in a primary care setting

Acknowledgements The iHARP database was funded by unrestricted grants from Mundipharma International Ltd and Research in Real-Life Ltd; these analyses were funded by an unrestricted grant from Teva Pharmaceuticals. Mundipharma and Teva played no role in study conduct or analysis and did not modify or approve the manuscript. The authors wish to direct a special appreciation to all the participants of the iHARP group who contributed data to this study and to Mundipharma, sponsors of the iHARP group. In addition, we thank Julie von Ziegenweidt for assistance with data extraction and Anna Gilchrist and Valerie L. Ashton, PhD, for editorial assistance. Elizabeth V. Hillyer, DVM, provided editorial and writing support, funded by Research in Real-Life, Ltd.

Cultural universals: Measuring the semantic structure of emotion terms in English and Japanese

Research is presented on the semantic structure of 15 emotion terms as measured by judged-similarity tasks for monolingual English-speaking and monolingual and bilingual Japanese subjects. A major question is the relative explanatory power of a single shared model for English and Japanese versus culture-specific models for each language. The data support a shared model for the semantic structure of emotion terms even though some robust and significant differences are found between English and Japanese structures. The Japanese bilingual subjects use a model more like English when performing tasks in English than when performing the same task in Japanese.

Role of left inferior prefrontal cortex in retrieval of semantic knowledge: A reevaluation

A number of neuroimaging findings have been interpreted as evidence that the left inferior frontal gyrus (IFG) subserves retrieval of semantic knowledge. We provide a fundamentally different interpretation, that it is not retrieval of semantic knowledge per se that is associated with left IFG activity but rather selection of information among competing alternatives from semantic memory. Selection demands were varied across three semantic tasks in a single group of subjects. Functional magnetic resonance imaging signal in overlapping regions of left IFG was dependent on selection demands in all three tasks. In addition, the degree of semantic processing was varied independently of selection demands in one of the tasks. The absence of left IFG activity for this comparison counters the argument that the effects of selection can be attributed solely to variations in degree of semantic retrieval. Our findings suggest that it is selection, not retrieval, of semantic knowledge that drives activity in the left IFG.

Ancient mtDNA sequences in the human nuclear genome: A potential source of errors in identifying pathogenic mutations

Nuclear-localized mtDNA pseudogenes might explain a recent report describing a heteroplasmic mtDNA molecule containing five linked missense mutations dispersed over the contiguous mtDNA CO1 and CO2 genes in Alzheimer’s disease (AD) patients. To test this hypothesis, we have used the PCR primers utilized in the original report to amplify CO1 and CO2 sequences from two independent ρ° (mtDNA-less) cell lines. CO1 and CO2 sequences amplified from both of the ρ° cells, demonstrating that these sequences are also present in the human nuclear DNA. The nuclear pseudogene CO1 and CO2 sequences were then tested for each of the five “AD” missense mutations by restriction endonuclease site variant assays. All five mutations were found in the nuclear CO1 and CO2 PCR products from ρ° cells, but none were found in the PCR products obtained from cells with normal mtDNA. Moreover, when the overlapping nuclear CO1 and CO2 PCR products were cloned and sequenced, all five missense mutations were found, as well as a linked synonymous mutation. Unlike the findings in the original report, an additional 32 base substitutions were found, including two in adjacent tRNAs and a two base pair deletion in the CO2 gene. Phylogenetic analysis of the nuclear CO1 and CO2 sequences revealed that they diverged from modern human mtDNAs early in hominid evolution about 770,000 years before present. These data would be consistent with the interpretation that the missense mutations proposed to cause AD may be the product of ancient mtDNA variants preserved as nuclear pseudogenes.