Luís Ferreira Pires

A methodology for the development of RESTful semantic web services for gene expression analysis

Gene expression studies are generally performed through multi-step analysis processes, which require the integrated use of a number of analysis tools. In order to facilitate tool/data integration, an increasing number of analysis tools have been developed as or adapted to semantic web services. In recent years, some approaches have been defined for the development and semantic annotation of web services created from legacy software tools, but these approaches still present many limitations. In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain. Therefore, this paper aims at defining an integrated methodology for the implementation of RESTful semantic web services created from gene expression analysis tools and the semantic annotation of such services. We have applied our methodology to the development of a number of services to support the analysis of different types of gene expression data, including microarray and RNASeq. All developed services are publicly available in the Gene Expression Analysis Services (GEAS) Repository at http://dcm.ffclrp.usp.br/lssb/geas. Additionally, we have used a number of the developed services to create different integrated analysis scenarios to reproduce parts of two gene expression studies documented in the literature. The first study involves the analysis of one-color microarray data obtained from multiple sclerosis patients and healthy donors. The second study comprises the analysis of RNA-Seq data obtained from melanoma cells to investigate the role of the remodeller BRG1 in the proliferation and morphology of these cells. Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services. Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis.

Towards ontology-driven situation-aware disaster management

Over the last years, numerous ICT applications with mechanisms to detect situations have been developed to support disaster management (DM), which is a field of a great societal and economic importance. Those applications are termed situation-aware (SA) because they try, in near real-time, to perceive and comprehend a situation of some type (e.g. disease epidemics) and project a reaction to the detected situation (e.g. isolate diseased people). An obstacle to the modelling of SA applications is the lack of well-founded structural and temporal constructs, which is inherent to conventional design techniques. Ontology-driven conceptual modelling has been successfully applied to overcome this issue, where ontological analysis based on a foundational ontology supports the modelling of concepts within a specific field as a well-founded core ontology. In this paper we discuss the importance of a well-founded core ontology for DM to support the specification of SA applications. We give an overview of the comprehensive framework we are developing, in which the DM core ontology plays a prominent role in the development of SA applications. In particular, we discuss the challenge of harmonizing concepts related to the modelling of situations in a foundational ontology in the lights of the Barwisean situation theory, Situoid theory and Situation awareness theory. This challenge has to be addressed to properly support SA applications in DM.

Ontology-Driven Conceptual Modeling for Early Warning Systems: Redesigning the Situation Modeling Language

An early warning system (EWS) is an integrated system that supports the detection, monitoring and alerting of emergency situations. A possible application of an EWS is in epidemiological surveillance, to detect infectious disease outbreaks in geographical areas. In this scenario, a challenge in the development and integration of applications on top of EWS is to achieve common understanding between epidemiologists and software developers, allowing the specification of rules resulted from epidemiological studies. To address this challenge this paper describes an ontology-based model-driven engineering (MDE) framework that relies on the Situation Modelling Language (SML), a knowledge specification technique for situation identification. Some requirements are realized by revisiting SML, which resulted in a complete redesign of its semantics, abstract and concrete syntaxes. The initial validation shows that our framework can accelerate the generation of high quality situation-aware applica tions, being suitable for other application scenarios.

SemanticSCo: a platform to support the semantic composition of services for gene expression analysis

Gene expression studies often require the combined use of a number of analysis tools. However, manual integration of analysis tools can be cumbersome and error prone. To support a higher level of automation in the integration process, efforts have been made in the biomedical domain towards the development of semantic web services and supporting composition environments. Yet, most environments consider only the execution of simple service behaviours and requires users to focus on technical details of the composition process. We propose a novel approach to the semantic composition of gene expression analysis services that addresses the shortcomings of the existing solutions. Our approach includes an architecture designed to support the service composition process for gene expression analysis, and a flexible strategy for the (semi) automatic composition of semantic web services. Finally, we implement a supporting platform called SemanticSCo to realize the proposed composition approach and demonstrate its functionality by successfully reproducing a microarray study documented in the literature. The SemanticSCo platform provides support for the composition of RESTful web services semantically annotated using SAWSDL. Our platform also supports the definition of constraints/conditions regarding the order in which service operations should be invoked, thus enabling the definition of complex service behaviours. Our proposed solution for semantic web service composition takes into account the requirements of different stakeholders and addresses all phases of the service composition process. It also provides support for the definition of analysis workflows at a high-level of abstraction, thus enabling users to focus on biological research issues rather than on the technical details of the composition process. The SemanticSCo source code is available at https://github.com/usplssb/SemanticSCo.

Architectural Design: Conception and Specification of Interactive Systems

This book presents a design methodology that is practically applicable to the architectural design of a broad range of systems. It is based on fundamental design concepts to conceive and specify the required functional properties of a system, while abstracting from the specific implementation functions and technologies that can be chosen to build the system. Abstraction and precision are indispensable when it comes to understanding complex systems and precisely creating and representing them at a high functional level. Once understood, these concepts appear natural, self-evident and extremely powerful, since they can directly, precisely and concisely reflect what is considered essential for the functional behavior of a system. The first two chapters present the global views on how to design systems and how to interpret terms and meta-concepts. This informal introduction provides the general context for the remainder of the book. On a more formal level, Chapters 3 through 6 present the main basic design concepts, illustrating them with examples. Language notations are introduced along with the basic design concepts. Lastly, Chapters 7 to 12 discuss the more intricate basic design concepts of interactive systems by focusing on their common functional goal. These chapters are recommended to readers who have a particular interest in the design of protocols and interfaces for various systems. The didactic approach makes it suitable for graduate students who want to develop insights into and skills in developing complex systems, as well as practitioners in industry and large organizations who are responsible for the design and development of large and complex systems. It includes numerous tangible examples from various fields, and several appealing exercises with their solutions.

Rule-based support for situation management

The notion of situation enables designers, maintainers, and users to abstract from lower-level entities and properties and to focus on the higher-level patterns that emerge in time. Situation management concerns a number of tasks including situation specification, situation detection (which may involve composite situation pattern recognition), and situation’s life cycle control. This chapter discusses how to approach situation management from a rule-based perspective. We present a rule-based situation management infrastructure to support the development of situation-aware applications and show its applicability to a scenario in the public health domain, concerning situations for detecting influenza epidemics.