NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

Molecular biology knowledge can be systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist a number of maps of molecular interactions containing detailed description of various cell mechanisms. It is difficult to explore these large maps, to comment their content and to maintain them. Though there exist several tools addressing these problems individually, the scientific community still lacks an environment that combines these three capabilities together. NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. NaviCell combines three features: (1) efficient map browsing based on Google Maps engine; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting the community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of their interest in the context of signaling pathways and cross-talks between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive fashion due to an imbedded blogging system. NaviCell provides an easy way to explore large-scale maps of molecular interactions, thanks to the Google Maps and WordPress interfaces, already familiar to many users. Semantic zooming used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization meaningful to the user. In addition, NaviCell provides a framework for community-based map curation.Comment: 20 pages, 5 figures, submitte

Blueprint model and language for engineering cloud applications

Abstract: The research presented in this thesis is positioned within the domain of engineering CSBAs. Its contribution is twofold: (1) a uniform specification language, called the Blueprint Specification Language (BSL), for specifying cloud services across several cloud vendors and (2) a set of associated techniques, called the Blueprint Manipulation Techniques (BMTs), for publishing, querying, and composing cloud service specifications with aim to support the flexible design and configuration of an CSBA.

From the web of bibliographic data to the web of bibliographic meaning: structuring, interlinking and validating ontologies on the semantic web

Bibliographic data sets have revealed good levels of technical interoperability observing the principles and good practices of linked data. However, they have a low level of quality from the semantic point of view, due to many factors: lack of a common conceptual framework for a diversity of standards often used together, reduced number of links between the ontologies underlying data sets, proliferation of heterogeneous vocabularies, underuse of semantic mechanisms in data structures, "ontology hijacking" (Feeney et al., 2018), point-to-point mappings, as well as limitations of semantic web languages for the requirements of bibliographic data interoperability. After reviewing such issues, a research direction is proposed to overcome the misalignments found by means of a reference model and a superontology, using Shapes Constraint Language (SHACL) to solve current limitations of RDF languages.info:eu-repo/semantics/acceptedVersio

VAMP: semantic validation for MPEG-7 profile descriptions

MPEG-7 can be used to create complex and comprehensive metadata descriptions of multimedia content. Since MPEG-7 is defined in terms of an XML schema, the semantics of its elements has no formal grounding. In addition, certain features can be described in multiple ways. MPEG-7 profiles are subsets of the standard that apply to specific application areas and that aim to reduce this syntactic variability, but they still lack formal semantics. We propose an approach for expressing the semantics explicitly

Computerization of workflows, guidelines and care pathways: a review of implementation challenges for process-oriented health information systems

There is a need to integrate the various theoretical frameworks and formalisms for modeling clinical guidelines, workflows, and pathways, in order to move beyond providing support for individual clinical decisions and toward the provision of process-oriented, patient-centered, health information systems (HIS). In this review, we analyze the challenges in developing process-oriented HIS that formally model guidelines, workflows, and care pathways. A qualitative meta-synthesis was performed on studies published in English between 1995 and 2010 that addressed the modeling process and reported the exposition of a new methodology, model, system implementation, or system architecture. Thematic analysis, principal component analysis (PCA) and data visualisation techniques were used to identify and cluster the underlying implementation ‘challenge’ themes. One hundred and eight relevant studies were selected for review. Twenty-five underlying ‘challenge’ themes were identified. These were clustered into 10 distinct groups, from which a conceptual model of the implementation process was developed. We found that the development of systems supporting individual clinical decisions is evolving toward the implementation of adaptable care pathways on the semantic web, incorporating formal, clinical, and organizational ontologies, and the use of workflow management systems. These architectures now need to be implemented and evaluated on a wider scale within clinical settings

Management information systems in social safety net programs : a look at accountability and control mechanisms

This paper is intended to provide task managers and World Bank Group clients working on Social Safety Net (SSN) programs with practical and systematic ways to use information management practices to mitigate risks by strengthening control and accountability mechanisms. It lays out practices and options to consider in the design and implementation of the Management Information System (MIS), and how to evaluate and mitigate operational risks originating from running a MIS. The findings of the paper are based on the review of several Conditional Cash Transfer (CCT) programs in the Latin American Region and various World Bank publications on CCTs. The paper presents a framework for the implementation of MIS and cross-cutting information management systems that is based on industry standards and information management practices. This framework can be applied both to programs that make use of information and communications technology (ICT) and programs that are paper based. It includes examples of MIS practices that can strengthen control and accountability mechanisms of SSN programs, and presents a roadmap for the design and implementation of an MIS in these programs. The application of the framework is illustrated through case studies from three fictitious countries. The paper concludes with some considerations and recommendations for task managers and government officials in charge of implementing CCTs and other safety nets program, and with a checklist for the implementation and monitoring of MIS.E-Business,Technology Industry,Education for Development (superceded),Labor Policies,Knowledge Economy

Designing Community Collaboration Support System to Facilitate the Resilience of Supply Chains During Crises

This study explores how to design an information system that facilitates the resilience of supply chains and the collaboration of different stakeholders during various crises. The ultimate objective of this study is to develop a knowledge base for formalizing design principles essential for designing and conceptualizing the Community Collaboration Support System to facilitate the resilience of supply chains during a crisis. To derive the design principles, we followed the design science research approach. Drawing from the literature, this paper used kernel theories as a part of the process. The design principles are well positioned and aligned with the acquired knowledge base. This study contributes to the existing research in distributed and collaboration technology. Additional explanatory studies are needed to validate posited design principles