Semantic integration of gene expression analysis tools and data sources using software connectors

Abstract Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data.

Sistemas certificáveis de gestão ambiental e da qualidade: práticas para integração em empresas do setor moveleiro

O principal objetivo deste artigo é propor, a partir do referencial teórico e de um estudo de caso em uma empresa moveleira, práticas para integração de sistemas certificáveis de gestão ambiental e da qualidade. A coleta de dados do estudo de caso se deu por meio de entrevistas semiestruturadas com o responsável direto pelos dois sistemas e com alguns colaboradores-chave do nível operacional, além de análise documental e de visitas in loco. Ao final deste artigo, são propostas práticas para integração desses sistemas, relacionadas aos seguintes elementos: alta administração; apoio administrativo, financeiro e pessoal; serviço de consultoria; coordenação do programa de integração; interface entre os sistemas; capacitação técnico-gerencial; sistema de liderança, prospecção, avaliação e desenvolvimento de fornecedores; sistema de informação; indicadores; comunicação com o cliente, e integração contínua.

Sistemas de gestão integrados como indutor para a sustentabilidade: uma análise do impacto no desempenho das organizações baseado no Triple Bottom Line.

O objetivo deste trabalho é analisar o impacto dos Sistemas de Gestão Integrados (SGI) no desempenho organizacional sob a óptica do Triple Bottom Line (TBL), verificando se esta implementação auxilia a empresa a se tornar mais sustentável. A abordagem multi-método utilizada está dividida em três partes. A primeira compreende uma revisão sistemática da literatura, tendo como base a abordagem bibliométrica. A base de dados escolhida para a seleção dos artigos que compõem a amostra foi a ISI Web of Knowledge (Web of Science). As análises conduzidas sugerem lacunas na literatura a serem pesquisadas de modo a relacionar a integração dos sistemas de gestão como meio para as organizações tornarem-se mais sustentáveis, auxiliando assim na elaboração de um modelo teórico e das hipóteses de pesquisa. Os resultados parciais obtidos ressaltam a lacuna na literatura de estudos nessa área, principalmente que contemplem a dimensão social do Triple Bottom Line. Lacunas na literatura foram identificadas também no que se refere à análise do impacto da adoção dessas abordagens normativas no desempenho organizacional. A segunda etapa da metodologia é composta por estudos de casos múltiplos em empresas de diferentes setores e que tenham implantado sistemas de gestão de maneira integrada. Os resultados obtidos mostram que a certificação auxilia no desenvolvimento de ações sustentáveis, resultando em impactos econômicos, ambientais e sociais positivos. Nesta etapa, testou-se o modelo e as hipóteses levantadas na abordagem bibliométrica. A terceira etapa da metodologia é composta por análises estatísticas de dados secundários extraídos da revista Exame ?Maiores e Melhores\'. Os dados do ano de 2014 das empresas foram tratados por meio do software MINITAB 17 ®. Por meio do teste de mediana de mood, as amostras foram testadas e apresentaram diferenças estatisticamente significativas para o desempenho das empresas em diferentes setores. De maneira geral, as empresas com SGI apresentam melhor desempenho econômico do que as demais. Com a mesma base de dados, utilizando o modelo de equações estruturais e o software Smart PLS 2.0, criou-se um diagrama de caminhos analisando os constructos (SGI) com variáveis de desempenho (Endividamento, Lucratividade, Patrimônio, Crescimento e Retorno). O modelo de equações estruturais testado apresentou força para a relação entre SGI com Endividamento, Lucratividade, Patrimônio e Crescimento. As diferentes metodologias apresentadas contribuíram para responder a hipótese e afirmar com base na amostra deste trabalho que o SGI leva as empresas a terem melhor desempenho econômico, ambiental e social (baseado no TBL).

Content Based Integration of Construction Site Images in Architecture, Engineering, Construction, and Facilities Management (AEC/FM) Model based Systems

This book explores the processes for retrieval, classification, and integration of construction images in AEC/FM model based systems. The author describes a combination of techniques from the areas of image and video processing, computer vision, information retrieval, statistics and content-based image and video retrieval that have been integrated into a novel method for the retrieval of related construction site image data from components of a project model. This method has been tested on available construction site images from a variety of sources like past and current building construction and transportation projects and is able to automatically classify, store, integrate and retrieve image data files in inter-organizational systems so as to allow their usage in project management related tasks. objects. Therefore, automated methods for the integration of construction images are important for construction information management. During this research, processes for retrieval, classification, and integration of construction images in AEC/FM model based systems have been explored. Specifically, a combination of techniques from the areas of image and video processing, computer vision, information retrieval, statistics and content-based image and video retrieval have been deployed in order to develop a methodology for the retrieval of related construction site image data from components of a project model. This method has been tested on available construction site images from a variety of sources like past and current building construction and transportation projects and is able to automatically classify, store, integrate and retrieve image data files in inter-organizational systems so as to allow their usage in project management related tasks.

A design pattern for integration of business process management systems

A cross-domain workflow application may be constructed using a standard reference model such as the one by the Workflow Management Coalition (WfMC) [7] but the requirements for this type of application are inherently different from one organization to another. The existing models and systems built around them meet some but not all the requirements from all the organizations involved in a collaborative process. Furthermore the requirements change over time. This makes the applications difficult to develop and distribute. Service Oriented Architecture (SOA) based approaches such as the BPET (Business Process Execution Language) intend to provide a solution but fail to address the problems sufficiently, especially in the situations where the expectations and level of skills of the users (e.g. the participants of the processes) in different organisations are likely to be different. In this paper, we discuss a design pattern that provides a novel approach towards a solution. In the solution, business users can design the applications at a high level of abstraction: the use cases and user interactions; the designs are documented and used, together with the data and events captured later that represents the user interactions with the systems, to feed an intermediate component local to the users -the IFM (InterFace Mapper) -which bridges the gaps between the users and the systems. We discuss the main issues faced in the design and prototyping. The approach alleviates the need for re-programming with the APIs to any back-end service thus easing the development and distribution of the applications

A generic model for integration of Quality, Environment and Safety Management Systems

Purpose – The purpose of this paper is to propose a generic model of Integrated Management System of Quality, Environment and Safety (IMS-QES) that can be adapted and progressively to assimilate various Management Systems, of which highlights: ISO 9001 for Quality; ISO 14001 for Environment; OHSAS 18001 for Occupational Health and Safety. Design/methodology/approach – The model was designed in the real environment of a Portuguese Organization and 160 employees were surveyed. The rate response was equal to 86 percent. The conceived model was implemented in a first phase for the integration of Quality, Environment and Safety Management Systems. Findings – Among the main findings of the survey the paper highlights: the elimination of conflicts between individual systems with resources optimization; creation of added value to the business by eliminating several types of wastes; the integrated management of sustainability components in a global market; the improvement of partnerships with suppliers of goods and services; reducing the number of internal and external audits. Originality/value – This case study is one of the first Portuguese empirical researches about IMS-QES and the paper believes that it can be useful in the creation of a Portuguese guideline for integration, namely the Quality Management Systems; Environmental Management Systems and Occupational Health and Safety Management Systems among others.

Guidelines for the integration of certifiable management systems in industrial companies

Organizations often operate in turbulent environments characterized by intense competitiveness, constant technological progress, new market requirements, and scarce natural resources. This scenario imposes the constant need for change in the operation and companies' management. The integration of certifiable management systems is an effective alternative in this sense. The objective of the present study is to propose guidelines for the integration of the ISO 9001 Quality Management System (QMS), ISO 14001 Environmental Management System (EMS) and OHSAS 18001 Occupational Health and Safety Management System (OHSMS) in industrial companies. These guidelines were developed based on a theoretical framework and on the results from fourteen case studies performed in Brazilian industrial companies. The proposed guidelines were divided into three phases: A) integration planning, b) integration development, and c) integration control and improvement.

Integration of Year-round Forage Management Systems for Spring-calving and Fall-calving Beef Cows (A Progress Report)

Animal production, hay production and feeding, winter forage composition changes, and summer pasture yields and nutrient composition of a year-round grazing system for spring-calving and fall-calving cows were compared to those of a conventional, minimal land system. Cows in the year-round and minimal land systems grazed forage from smooth bromegrassorchardgrass-birdsfoot trefoil (SB-O-T) pastures at 1.67 and 3.33 acres, respectively, per cow in the summer. During the summer, SB-O-T pastures in the year-round grazing system also were grazed by stockers at 1.67 stockers per acre, and spring-calving and fall-calving cows grazed smooth bromegrass–red clover (SB-RC) and endophyte-free tall fescue–red clover (TF-RC) at 2.5 acres per cow for approximately 45 days in midsummer. In the year-round grazing system, spring-calving cows grazed corn crop residues at 2.5 acres per cow and stockpiled SB-RC pastures at 2.5 acres per cow; fallcalving cows grazed stockpiled TF-RC pastures at 2.5 acres per cow during winter. In the minimal land system, in winter, cows were maintained in a drylot on first-cutting hay harvested from 62.5–75% of the pasture acres during summer. Hay was fed to maintain a body condition score of 5 on a 9-point scale for springcalving cows in both systems and a body condition score of 3 for fall-calving cows in the year-round system. Over 3 years, mean body weights of fall-calving cows in the year-round system did not differ from the body weights of spring-calving cows in either system, but fall-calving cows had higher (P < .05) body condition scores compared to spring-calving cows in either system. There were no differences among all groups of cows in body condition score changes over the winter grazing season (P > .05). During the summer grazing season, fall-calving cows in the year- round system and springcalving cows in the minimal land system gained more body condition and more weight (P < .05) than springcalving cows in the year-round grazing system. Fall calves in the year-round system had higher birth weights, lower weaning weights, and lower average preweaning daily gains compared to either group of spring calves (P < .05). However, there were no significant differences for birth weights, weaning weights, or average pre-weaning daily gains between spring calves in either system over the 3-year experiment (P > .05). The amount of total growing animal production (calves and stockers) per acre for each system did not differ in any year (P > .05). Over the 3-year experiment, 1.9 ton more hay was fed per cow and 1 ton more hay was fed per cow–calf pair in the minimal land system compared to the year-round grazing system (P < .05).

The Barriers to the Integration of the Uterine Balloon Tamponade into South Africa and Ghana's Health Systems for the Management of Postpartum Hemorrhage

Background

Postpartum hemorrhage is the most significant contributor to maternal mortality globally, claiming 140,000 lives annually. Postpartum hemorrhage is a leading cause of maternal death in South Africa, with the literature indicating that 80 percent of the postpartum hemorrhage deaths in South Africa are avoidable. Ghana, as of 2010, witnesses 2700 maternal deaths annually, primarily because of poor quality of care in health facilities and services being difficult to access. As per WHO recommendations, uterotonics are integral to treating postpartum hemorrhage as soon as it is diagnosed. In case of persistent bleeding or limited availability of uterotonics, the uterine balloon tamponade (UBT) can be used as a second line of defense. If both these measures are unable to counter the bleeding, providers must perform surgical interventions. Literature on the UBT, as one tool in the protocol to address postpartum hemorrhage, has shown it to have success rates ranging from 60 to 100 percent. Despite the potential to lower the number of postpartum hemorrhage deaths in South Africa and Ghana, the UBT has not been incorporated widely in South Africa and Ghana. The aim of this study is to describe the barriers involved with integrating the UBT into South Africa and Ghana’s health systems to address postpartum hemorrhage.

Methods

The study took place in multiple sites in South Africa (Cape Town, Johannesburg, Durban and Mpumalanga) and in Accra, Ghana. South Africa and Ghana were selected because postpartum hemorrhage contributes greatly to their maternal mortality numbers and there is potential in both countries to lower those rates through greater use of the UBT. A total of 25 participants were interviewed through purposive sampling, snowball sampling and participant referrals, and included various categories of stakeholders integral to the integration process of a medical device. Individual in-depth interviews were used for data collection, with interview questions being tailored to each stakeholder category. The focus of the interviews was on the protocol used to counter postpartum hemorrhage, the frequency with which the UBT is used as part of the protocol, and the process of integrating it into the South Africa and Ghana’s health systems. The data collected were coded using NVivo and analyzed using content analysis.

Results

The barriers to integration of the uterine balloon tamponade to address postpartum hemorrhage in South Africa and Ghana were evident on the political, economic and health delivery levels. The results indicated that the barriers to integration in South Africa included the low recognition of postpartum hemorrhage as a problem, the lack of clarity surrounding the role of the Medicines Control Council as a regulatory body for medical devices, and low awareness of the UBT as an intervention to control postpartum hemorrhage. The barriers in Ghana were the cash constraints experienced by the Ghana Health Services to fund medical devices, a heavy reliance on donors for funding, and the lack of consistent knowledge on processes involving clinical trials for new medical devices in Ghana.

Conclusion

Existing literature on methods to counter postpartum hemorrhage to reduce maternal mortality has focused on and emphasized the efficacy of the UBT. Despite overwhelming evidence supporting the use of the UBT, many health systems across the world, particularly low-income countries, do not have access to the device owing to numerous barriers in integrating the device into obstetric care. This study illustrates the need to focus on incorporating the UBT into health systems for greater availability to health workers and its use as standard of care. Ultimately, this study can be used as a stepping-stone for more research on this subject, providing evidence to influence policymakers to integrate the UBT into their protocols for postpartum hemorrhage response.

AgroDB - integration of database management systems with crop models.

2016

Sustainable urban infrastructure management : integration of urban computer modelling

Purpose - This paper seeks to examine the complex relationships between urban planning, infrastructure management, sustainable urban development, and to illustrate why there is an urgent need for local governments to develop a robust planning support system which integrates with advance urban computer modelling tools to facilitate better infrastructure management and improve knowledge sharing between the community, urban planners, engineers and decision makers. Design/methodology/approach - The methods used in this paper includes literature review and practical project case observations. Originality/value - This paper provides an insight of how the Brisbane's planning support system established by Brisbane City Council has significantly improved the effectiveness of urban planning, infrastructure management and community engagement through better knowledge management processes. Practical implications - This paper presents a practical framework for setting up a functional planning support system within local government. The integration of the Brisbane Urban Growth model, Virtual Brisbane and the Brisbane Economic Activity Monitoring (BEAM) database have proven initially successful to provide a dynamic platform to assist elected officials, planners and engineers to understand the limitations of the local environment, its urban systems and the planning implications on a city. With the Brisbane's planning support system, planners and decision makers are able to provide better planning outcomes, policy and infrastructure that adequately address the local needs and achieve sustainable spatial forms.

Specifying information systems for business process integration : a management perspective

Supply chain management and customer relationship management are concepts for optimizing the provision of goods to customers. Information sharing and information estimation are key tools used to implement these two concepts. The reduction of delivery times and stock levels can be seen as the main managerial objectives of an integrative supply chain and customer relationship management. To achieve this objective, business processes need to be integrated along the entire supply chain including the end consumer. Information systems form the backbone of any business process integration. The relevant information system architectures are generally well-understood, but the conceptual specification of information systems for business process integration from a management perspective, remains an open methodological problem. To address this problem, we will show how customer relationship management and supply chain management information can be integrated at the conceptual level in order to provide supply chain managers with relevant information. We will further outline how the conceptual management perspective of business process integration can be supported by deriving specifications for enabling information system from business objectives.

Efficiency of knowledge integration in enterprise systems implementation

Recent literature has emphasized the pivotal role of knowledge integration in Enterprise Systems (ES) success. This research-in-progress paper, building upon Knowledge Based Theory of the firm (KBT), examines the efficiency of knowledge integration in the context of ES implementation and identifies the factors contributing to its enhancement. The proposed model in this paper suggests that the efficiency of knowledge integration in an ES implementation process depends upon the level of common knowledge and the level of coordination in the ES adopting organization. It further suggests that the level of common knowledge can be enhanced by proper training, improving ES users’intrinsic and extrinsic motivations and business process modeling and the level of coordination can be improved by articulating a clear unified organizational goal for the ES adoption in the organization, forming a competent ES team, enhancing interdepartmental communication and the cross-functionality in the organization structure.