Knowledge management for systems biology a general and visually driven framework applied to translational medicine

Background: To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results: To address this challenge we previously developed a generic knowledge management framework, BioXM , which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions: We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development

A common type system for clinical natural language processing

Background: One challenge in reusing clinical data stored in electronic medical records is that these data are heterogenous. Clinical Natural Language Processing (NLP) plays an important role in transforming information in clinical text to a standard representation that is comparable and interoperable. Information may be processed and shared when a type system specifies the allowable data structures. Therefore, we aim to define a common type system for clinical NLP that enables interoperability between structured and unstructured data generated in different clinical settings. Results: We describe a common type system for clinical NLP that has an end target of deep semantics based on Clinical Element Models (CEMs), thus interoperating with structured data and accommodating diverse NLP approaches. The type system has been implemented in UIMA (Unstructured Information Management Architecture) and is fully functional in a popular open-source clinical NLP system, cTAKES (clinical Text Analysis and Knowledge Extraction System) versions 2.0 and later. Conclusions: We have created a type system that targets deep semantics, thereby allowing for NLP systems to encapsulate knowledge from text and share it alongside heterogenous clinical data sources. Rather than surface semantics that are typically the end product of NLP algorithms, CEM-based semantics explicitly build in deep clinical semantics as the point of interoperability with more structured data types

Towards Complex Real-World Safety Factory Inspection: A High-Quality Dataset for Safety Clothing and Helmet Detection

Safety clothing and helmets play a crucial role in ensuring worker safety at construction sites. Recently, deep learning methods have garnered significant attention in the field of computer vision for their potential to enhance safety and efficiency in various industries. However, limited availability of high-quality datasets has hindered the development of deep learning methods for safety clothing and helmet detection. In this work, we present a large, comprehensive, and realistic high-quality dataset for safety clothing and helmet detection, which was collected from a real-world chemical plant and annotated by professional security inspectors. Our dataset has been compared with several existing open-source datasets, and its effectiveness has been verified applying some classic object detection methods. The results demonstrate that our dataset is more complete and performs better in real-world settings. Furthermore, we have released our deployment code to the public to encourage the adoption of our dataset and improve worker safety. We hope that our efforts will promote the convergence of academic research and industry, ultimately contribute to the betterment of society.Comment: 11 pages, 7 figure

Embedding Predications

Written communication is rarely a sequence of simple assertions. More often, in addition to simple assertions, authors express subjectivity, such as beliefs, speculations, opinions, intentions, and desires. Furthermore, they link statements of various kinds to form a coherent discourse that reflects their pragmatic intent. In computational semantics, extraction of simple assertions (propositional meaning) has attracted the greatest attention, while research that focuses on extra-propositional aspects of meaning has remained sparse overall and has been largely limited to narrowly defined categories, such as hedging or sentiment analysis, treated in isolation. In this thesis, we contribute to the understanding of extra-propositional meaning in natural language understanding, by providing a comprehensive account of the semantic phenomena that occur beyond simple assertions and examining how a coherent discourse is formed from lower level semantic elements. Our approach is linguistically based, and we propose a general, unified treatment of the semantic phenomena involved, within a computationally viable framework. We identify semantic embedding as the core notion involved in expressing extra-propositional meaning. The embedding framework is based on the structural distinction between embedding and atomic predications, the former corresponding to extra-propositional aspects of meaning. It incorporates the notions of predication source, modality scale, and scope. We develop an embedding categorization scheme and a dictionary based on it, which provide the necessary means to interpret extra-propositional meaning with a compositional semantic interpretation methodology. Our syntax-driven methodology exploits syntactic dependencies to construct a semantic embedding graph of a document. Traversing the graph in a bottom-up manner guided by compositional operations, we construct predications corresponding to extra-propositional semantic content, which form the basis for addressing practical tasks. We focus on text from two distinct domains: news articles from the Wall Street Journal, and scientific articles focusing on molecular biology. Adopting a task-based evaluation strategy, we consider the easy adaptability of the core framework to practical tasks that involve some extra-propositional aspect as a measure of its success. The computational tasks we consider include hedge/uncertainty detection, scope resolution, negation detection, biological event extraction, and attribution resolution. Our competitive results in these tasks demonstrate the viability of our proposal

Metodología de implantación de modelos de gestión de la información dentro de los sistemas de planificación de recursos empresariales. Aplicación en la pequeña y mediana empresa

La Siguiente Generación de Sistemas de Fabricación (SGSF) trata de dar respuesta a los requerimientos de los nuevos modelos de empresas, en contextos de inteligencia, agilidad y adaptabilidad en un entono global y virtual. La Planificación de Recursos Empresariales (ERP) con soportes de gestión del producto (PDM) y el ciclo de vida del producto (PLM) proporciona soluciones de gestión empresarial sobre la base de un uso coherente de tecnologías de la información para la implantación en sistemas CIM (Computer-Integrated Manufacturing), con un alto grado de adaptabilidad a la estnictura organizativa deseada. En general, esta implementación se lleva desarrollando hace tiempo en grandes empresas, siendo menor (casi nula) su extensión a PYMEs. La presente Tesis Doctoral, define y desarrolla una nueva metodología de implementación pan la generación automática de la información en los procesos de negocio que se verifican en empresas con requerimientos adaptados a las necesidades de la SGSF, dentro de los sistemas de gestión de los recursos empresariales (ERP), atendiendo a la influencia del factor humano. La validez del modelo teórico de la metodología mencionada se ha comprobado al implementarlo en una empresa del tipo PYME, del sector de Ingeniería. Para el establecimiento del Estado del Arte de este tema se ha diseñado y aplicado una metodología específica basada en el ciclo de mejora continua de Shewhart/Deming, aplicando las herramientas de búsqueda y análisis bibliográfico disponibles en la red con acceso a las correspondientes bases de datos

Z-Numbers-Based Approach to Hotel Service Quality Assessment

In this study, we are analyzing the possibility of using Z-numbers for measuring the service quality and decision-making for quality improvement in the hotel industry. Techniques used for these purposes are based on consumer evalu- ations - expectations and perceptions. As a rule, these evaluations are expressed in crisp numbers (Likert scale) or fuzzy estimates. However, descriptions of the respondent opinions based on crisp or fuzzy numbers formalism not in all cases are relevant. The existing methods do not take into account the degree of con- fidence of respondents in their assessments. A fuzzy approach better describes the uncertainties associated with human perceptions and expectations. Linguis- tic values are more acceptable than crisp numbers. To consider the subjective natures of both service quality estimates and confidence degree in them, the two- component Z-numbers Z = (A, B) were used. Z-numbers express more adequately the opinion of consumers. The proposed and computationally efficient approach (Z-SERVQUAL, Z-IPA) allows to determine the quality of services and iden- tify the factors that required improvement and the areas for further development. The suggested method was applied to evaluate the service quality in small and medium-sized hotels in Turkey and Azerbaijan, illustrated by the example