Unified Access Research Articles

Providing an Integrated Access to EHR Using Electronic Health Records Aggregators.

The integration of health data systems is an open problem. Most of the active initiatives are based on the use of standards, each one proposed for a concrete use, without integrating other needs or standards allowing on homogenous use. We propose an alternative to get an unified view of health related data, valid for several uses, that can integrate heterogeneous sources. The proposal set the framework to integrate the developments made so far to automatically learn the extraction and conversion of the data. All the sources are integrated under a single access point. We present the main concepts of EHRagg as a middleware between systems that can incorporate several sources giving an unified access following the FAIR principles.

Using RGISTools to Estimate Water Levels in Reservoirs and Lakes

The combination of freely accessible satellite imagery from multiple programs improves the spatio-temporal coverage of remote sensing data, but it exhibits barriers regarding the variety of web services, file formats, and data standards. Ris an open-source software environment with state-of-the-art statistical packages for the analysis of optical imagery. However, it lacks the tools for providing unified access to multi-program archives to customize and process the time series of images. This manuscript introduces RGISTools, a new software that solves these issues, and provides a working example on water mapping, which is a socially and environmentally relevant research field. The case study uses a digital elevation model and a rarely assessed combination of Landsat-8 and Sentinel-2 imagery to determine the water level of a reservoir in Northern Spain. The case study demonstrates how to acquire and process time series of surface reflectance data in an efficient manner. Our method achieves reasonably accurate results, with a root mean squared error of 0.90 m. Future improvements of the package involve the expansion of the workflow to cover the processing of radar images. This should counteract the limitation of the cloud coverage with multi-spectral images.

Unifying access

Since Hansen’s seminal 1959 paper, measures of access have evolved with technology and through practical applications. The myriad of distinct but familially related access measures created many more options to measure places, but has sown needless confusion. This paper systematically reviews measures of access across disciplines. We categorize measures of access, covering both mainstream and innovative but less widely-used techniques; each access measure (topological, contiguous, cumulative opportunities, utility, flow-based measures) is separated into Primal and Dual measure, based on whether accessibility is represented by the level of reachable opportunities or by the travel impedance. We show access measures are unified by the same intrinsic structure consisting of travel impedance and the opportunities reachable, and that access measured by different methods are equivalent under specific assumptions on travel impedance, and the accounting of relevant opportunities. This paper overviews the use of access measures from the existing literature, and clarifies measures of access, which should help users in the selection and appropriate use of access measures for the relevant context.

Task scheduling based on swarm intelligence algorithms in high performance computing environment

The high-performance computing environment is a computing platform, which aggregates multiple distributed high-performance computers from indifferent organizations, providing users with unified access and usage patterns. Since the task scheduling strategy is lack of flexibility, an optimized task scheduling model in the high-performance computing environment is proposed in this paper, which introduces an improved swarm intelligence algorithm in task queues, refines the Core Scheduler for each task, and increases the configuration of task scheduling strategy. In core task scheduling, swarm intelligence algorithm is adopted to minimize the average scheduling time for completion tasks through optimal task allocation on each node. Simulation results show that the proposed scheduling algorithm is better than the traditional task scheduling algorithm. Therefore, according to the task scheduling strategy based on swarm intelligence algorithm, it can effectively reduce the task waiting, improve the system’s throughput, the task response and system resource utilization has a better effect.

MONET: a toolbox integrating top-performing methods for network modularization.

SummaryWe define a disease module as a partition of a molecular network whose components are jointly associated with one or several diseases or risk factors thereof. Identification of such modules, across different types of networks, has great potential for elucidating disease mechanisms and establishing new powerful biomarkers. To this end, we launched the ‘Disease Module Identification (DMI) DREAM Challenge’, a community effort to build and evaluate unsupervised molecular network modularization algorithms. Here, we present MONET, a toolbox providing easy and unified access to the three top-performing methods from the DMI DREAM Challenge for the bioinformatics community.Availability and implementation MONET is a command line tool for Linux, based on Docker and Singularity containers; the core algorithms were written in R, Python, Ada and C++. It is freely available for download at https://github.com/BergmannLab/MONET.git.Supplementary information Supplementary data are available at Bioinformatics online.

Effective Dynamic Integration and Utilization of Heterogenous Compute Resources

Increased operational effectiveness and the dynamic integration of only temporarily available compute resources (opportunistic resources) becomes more and more important in the next decade, due to the scarcity of resources for future high energy physics experiments as well as the desired integration of cloud and high performance computing resources. This results in a more heterogenous compute environment, which gives rise to huge challenges for the computing operation teams of the experiments. At the Karlsruhe Institute of Technology (KIT) we design solutions to tackle these challenges. In order to ensure an efficient utilization of opportunistic resources and unified access to the entire infrastructure, we developed the Transparent Adaptive Resource Dynamic Integration System (TARDIS). A scalable multi-agent resource manager providing interfaces to provision as well as dynamically and transparently integrate resources of various providers into one common overlay batch system. Operational effectiveness is guaranteed by relying on COBalD – the Opportunistic Balancing Daemon and its simple approach of taking into account the utilization and allocation of the different resource types, in order to run the individual workflows on the best-suited resource respectively. In this contribution we will present the current status of integrating various HPC centers and cloud providers into the compute infrastructure at the Karlsruhe Institute of Technology as well as our experiences gained in a production environment.

Immunedeconv: An R Package for Unified Access to Computational Methods for Estimating Immune Cell Fractions from Bulk RNA-Sequencing Data.

Since the performance of in silico approaches for estimating immune-cell fractions from bulk RNA-seq data can vary, it is often advisable to compare results of several methods. Given numerous dependencies and differences in input and output format of the various computational methods, comparative analyses can become quite complex. This motivated us to develop immunedeconv, an R package providing uniform and user-friendly access to seven state-of-the-art computational methods for deconvolution of cell-type fractions from bulk RNA-seq data. Here, we show how immunedeconv can be installed and applied to a typical dataset. First, we give an example for obtaining cell-type fractions using quanTIseq. Second, we show how dimensionless scores produced by MCP-counter can be used for cross-sample comparisons. For each of these examples, we provide R code illustrating how immunedeconv results can be summarized graphically.

A Lightweight Collaborative GIS Data Editing Approach to Support Urban Planning

Collaborative geospatial data editing is different from other collaborative editing systems, such as textual editing, owing to its geospatial nature. This paper presents a version-based lightweight collaborative geospatial editing method for urban planning. This method extracts editing data and generates a version for collaborative editing, which reduces the data size and thus allows for a high feedback speed. A replication mechanism is engaged to replicate a version for the client to freely edit, which ensures constraint-free editing in collaboration. Based on this method, realizing the fact that heterogeneous geospatial data and non-professional users are involved, a lightweight architecture, integrating web services, and component technologies, was proposed. This architecture provides a unified data access interface and powerful editing ability and ensures a high feedback speed and constraint-free editing. The result of the application of the proposed approach in a practical project demonstrates the usability of collaborative geospatial editing in urban planning. While this approach has been designed for urban planning, it can be modified for use in other domains.

DiSSCo as a New Regional Model for Scientific Collections in Europe

European Natural Science Collections (NSC) are part of the global natural and cultural capital and represent 80% of the world bio-and geo-diversity. Data derived from these collections underpin thousands of scholarly publications and official reports (used to support legislative and regulatory processes relating to health, food, security, sustainability and environmental change) and let to inventions and products that today play an important role in our bio-economy. In the last decades, the research practice in natural sciences changed dramatically. Advances in digital, genomic and information technologies enable natural science collections to provide new insights but also ask for changing the current operational and business models of individual collections held at local natural history museums and universities. A new business model that provides unified access to collection objects and all scientific data derived from them. Although aggregating infrastructures like the Global Biodiversity Information Facility, GenBank and Catalogue of Life now successfully aggregate data on specific data classes, the landscape remains fragmented with limited capacity to bring together this information in a systematic and robust manner and with scattered access to the physical objects. The Distributed System of Scientific Collections (DiSSCo) represents a pan-European initiative, and the largest ever agreement of natural science museums, to jointly address the fragmentation of European collections. DiSSCo is unifying European natural science collections into a coherent new research infrastructure, able to provide bio- and geo-diversity data at the scale, form and precision required by a multi-disciplinary user base in science. DiSSCo is harmonising digitisation, curation and publication processes and workflows across the scientific collections in Europe and enables linking of occurrence, genomic, chemical and morphological data classes as well as publications and experts to the physical object. In this paper we will present the socio-cultural and governance aspects of this research infrastructure. DiSSCo is receiving political support from 11 countries in Europe and will gradually change its funding model from institutional to national funding, with temporary funding from the EC to support the preparation and development. Solutions to achieve large scale digitisation are currently designed in the EC funded ICEDIG project to underpin the future large scale digitisation carried out by the countries. Unified virtual (digitisation on demand) and transnational physical access to the collections is over the next four years being developed in the EC funded SYNTHESYS+ project. The governance of DiSSCo is designed to gradually change from a steering committee composed of a few large natural history museums contributing in cash to initiate the development into a legal entity in which national consortia are represented, with a central coordination office for daily management. Each country individually decides how its entities (scientific collection facilities, research councils, governmental bodies) are organised in their national consortium. A stakeholder and user forum, Scientific Advisory Board and International Advisory Board will ensure that DiSSCo will be functional in enabling science across disciplines and within the international landscape of infrastructures. Training and short scientific missions are being developed in the MOBILISE COST Action to build capacity in FAIR data production, publication and usage of scientific collection-derived data in Europe and to initiate the socio-cultural changes needed in the collection-holding institutes. A Helpdesk is being constructed in the SYNTHESYS+ and DiSSCo Prepare projects to further facilitate the use and scientific use cases have been collected in ICEDIG to develop and facilitate e-services tailored to scientific needs.

SwissCollNet – A National Initiative for Natural History Collections in Switzerland

More than 60 million specimens are housed in geological and biological collections in numerous museums and botanical gardens located all over Switzerland. They are of national and international origin. Taken together they form an entity with a high scientific value and international recognition for their contribution to scientific research. Due to the federalistic organisation of Switzerland, natural history collections are located and curated in numerous institutions. So far, no common strategy for digitisation, documentation and long-term data archiving has been developed. This shortcoming has been widely identified by concerned parties. Under the lead of the Swiss Academy of Sciences, several organisations have assembled information about Swiss natural history collections. They identified measures to be taken to promote the scientific and educational potential of natural history collections in Switzerland (Beer et al. 2019). With a national initiative, the Swiss Natural History Collections Network (SwissCollNet) aims to unite Swiss natural history collections under a common vision and with a common strategy. The goal is to promote the collections themselves and to harness the scientific and educational potential of these collections for research and training. SwissCollNet consists of representatives of research, teaching, museums and botanical gardens, the data centers for information on the national fauna and flora, the Swiss Systematics Society and the Swiss node of GBIF, the Global Biodiversity Information Facility. The initiative aims to foster research on natural history collections. It will provide a single decentralised data infrastructure framework for Swiss research related to natural history. It will help to harmonise nationwide collection data management, digitisation and long-term data archiving. It will facilitate identification of specimens and revision of taxonomic groups. New research techniques, fast-evolving computer technologies and internet connectivity, create new opportunities for deciphering and using the wealth of information housed in Swiss and international collections. The development of an agreed strategy and research priorities on a national scale will allow fluent, fluid and permanent collaboration across all Swiss natural history collections by promoting interoperability and unified access to collections as well as creating opportunities for scientific collaboration and innovation. This national approach will create an internationally compatible research data infrastructure, while respecting and integrating regional and decentralized conditions and requirements. Thus, it will maximize the impact for science, policy and society.

An Evolving Business Model for a Biodiversity Biobank Network: GGBN

GGBN, the Global Genome Biodiversity Network, is a consortium of virtually linked biodiversity biobanks that provide unified open access to their sample data through a web portal (www.ggbn.org), together improve best practices and develop standards. Since its inception in 2011, GGBN has largely been supported by external grants and in-kind support from its members. Starting with representatives from thirteen organizations across Africa, Australia, Europe, North, Central, and South America, preliminary plans for an international coordinating mechanism for biodiversity biobanks was developed. In 2013, an interim executive committee was established and an MOU (memorandum of understanding) was distributed to 17 potential collaborators for signature. Subsequently a governance and business model were developed based on input from across the collections and research communities. As the network grew, the interim executive committee solicited letters of intent to transition GGBN into a formal member-driven organization. In 2016 with 12 biodiversity collections online through GGBN’s data portal, the organization was launched and the business model implemented. This included a general and a technical secretariat, an executive committee and general assembly of its, at that time, 41 members. Having grown to encompass 87 general assembly members and 22 collections online in two years, GGBN is assessing its current business model, with focus on increasing revenue, and marketing strategy. Results of this assessment and associated next steps for GGBN are presented and discussed.

ELEMENTOS PARA UMA POLÍTICA BRASILEIRA DE ACESSO INTEGRADO, UTILIZAÇÃO E PRESERVAÇÃO DE ACERVOS DIGITAIS EM MEMÓRIA E CULTURA

Há vários anos instituições de Memória e Cultura brasileiras vêm desenvolvendo projetos de digitalização, preservação e acesso a acervos digitais. No entanto poucas dessas iniciativas são colaborativas e mesmo ainda envolvem acesso unificado a acervos de mais de uma instituição, além de sofrerem descontinuidades e de falta de recursos para sustentação continuada. Acervos digitais em memória e cultura têm potencialidades educacionais, culturais e econômicas que os acervos físicos não possuem. Esse trabalho revê as experiências brasileiras e internacionais de digitalização, preservação e acesso a acervos digitais e consulta documentos, projetos e literatura a respeito para ressaltar na tentativa de esboçar uma política brasileira de acesso unificado, preservação e utilização de acervos digitais em Memória e Cultura.

Invited commentary: “Everybody has won, and all must have prizes” (Carroll, 1865)

Invited commentary: “Everybody has won, and all must have prizes” (Carroll, 1865)

Data Science, Analytics and Collaboration for a Biosurveillance Ecosystem

Data Science, Analytics and Collaboration for a Biosurveillance Ecosystem

LitSense: making sense of biomedical literature at sentence level.

Literature search is a routine practice for scientific studies as new discoveries build on knowledge from the past. Current tools (e.g. PubMed, PubMed Central), however, generally require significant effort in query formulation and optimization (especially in searching the full-length articles) and do not allow direct retrieval of specific statements, which is key for tasks such as comparing/validating new findings with previous knowledge and performing evidence attribution in biocuration. Thus, we introduce LitSense, which is the first web-based system that specializes in sentence retrieval for biomedical literature. LitSense provides unified access to PubMed and PMC content with over a half-billion sentences in total. Given a query, LitSense returns best-matching sentences using both a traditional term-weighting approach that up-weights sentences that contain more of the rare terms in the user query as well as a novel neural embedding approach that enables the retrieval of semantically relevant results without explicit keyword match. LitSense provides a user-friendly interface that assists its users to quickly browse the returned sentences in context and/or further filter search results by section or publication date. LitSense also employs PubTator to highlight biomedical entities (e.g. gene/proteins) in the sentences for better result visualization. LitSense is freely available at https://www.ncbi.nlm.nih.gov/research/litsense.

The Wireless Access for Future Smart Cities as a Large Scale Complex Cyber Physical System

In future smart cities (SCs) highly developed and smart wireless communication access infrastructures will be needed for the connection of a huge number of different types of objects, sensors and user terminals. Such access networks must have the necessary autonomic and intelligent mechanisms to respond to the needs of an increasing variety of users (human and non-human), to cope with the high user density in SCs, their mobility, new and increasing service requirements, traffic dynamics, SC complex wireless channel conditions, etc. The wireless AN of a future SC must be a type of network which is able to offer revolutionary services, capabilities, and facilities that are hard to be provided via the heterogeneous network (HetNet) infrastructures that are implemented today. This paper introduces the concept of the unified wireless access (UWA) for SCs and considers some of the challenges related to its functional requirements and design. The structure of a sample UWA network illustrating the functional relations between its components is given. It is envisaged that such UWA architecture will perform and could be considered from the aspect of a large scale complex and intelligent cyber physical system (CPS) with control feedbacks and different types of users introducing stochasticity in the loop of the system. For the goal of analyzing the performance and functional relationships between the elements of such UWA a general modeling approach is introduced taking into consideration some of the basic approaches applied for CPS analysis.

An IoT Unified Access Platform for Heterogeneity Sensing Devices Based on Edge Computing

With the rapid development of the Internet of Things (IoT), a large number of heterogeneous sensing devices are accessed in their proprietary ways to IoT applications, formed “silos” application mode. The growth of IoT applications has been hampered by this mode due to the barriers of resource sharing of heterogeneous sensing devices. This paper proposes an IoT access platform deployed at the network edge near the sensing devices. This architecture can enable more responsive IoT applications and provide efficient privacy protection for sensitive data. We propose a general ontology-based resource description model of IoT devices to provide a consistent view of heterogeneous sensing devices for IoT applications in the cloud. Based on this model, we propose an adaptive access method to provide unified access, control, and management of IoT devices with various intelligence levels. The access platform turns the “silos” application mode of IoT into a horizontal application mode, supports applications to share and reuse the resources of IoT devices. We demonstrate the efficacy of our architecture with an application case study that highlights our proposed resource description model and adaptive access method and evaluate performance improvement with experiments.

Semantic Integration and Enrichment of Heterogeneous Biological Databases.

Biological databases are growing at an exponential rate, currently being among the major producers of Big Data, almost on par with commercial generators, such as YouTube or Twitter. While traditionally biological databases evolved as independent silos, each purposely built by a different research group in order to answer specific research questions; more recently significant efforts have been made toward integrating these heterogeneous sources into unified data access systems or interoperable systems using the FAIR principles of data sharing. Semantic Web technologies have been key enablers in this process, opening the path for new insights into the unified data, which were not visible at the level of each independent database. In this chapter, we first provide an introduction into two of the most used database models for biological data: relational databases and RDF stores. Next, we discuss ontology-based data integration, which serves to unify and enrich heterogeneous data sources. We present an extensive timeline of milestones in data integration based on Semantic Web technologies in the field of life sciences. Finally, we discuss some of the remaining challenges in making ontology-based data access (OBDA) systems easily accessible to a larger audience. In particular, we introduce natural language search interfaces, which alleviate the need for database users to be familiar with technical query languages. We illustrate the main theoretical concepts of data integration through concrete examples, using two well-known biological databases: a gene expression database, Bgee, and an orthology database, OMA.

Autotransformer fed traction power supply system: analysis, modeling and simulation

For many decades, Ethiopia had been using a meter gauge railway from Addis Ababa to the red sea port of Djibouti. Currently, the century old railway is completely replaced by a brand new standard gauge electrified railway line aiming to connect the country to the global market by guaranteeing a unified access to different regions of the country. In order to meet modern railway standards, a 1 × 25 kV catenary system is adopted in Ethio-Djibouti railway line corridor. In this paper, an alternative and a more superior 2 × 25 kV traction power supply system is presented. The modeling and analysis of the 2 × 25 kV traction supply system including the traction load, the substation power transformer, the autotransformer (AT), the catenary line impedance, etc., are performed. In addition, in order to validate the benefits of the proposed system, a comparative analysis of the two types of traction power supply arrangement has been conducted using MATLAB simulation. The analysis focuses on evaluating the voltage profiles of both power supply configurations on the basis of BS EN 50163:2004 international standard.

Модель интегрированной распределенной библиотечной информационной системы Академгородка г. Алматы

Описана модель интегрированной распределенной библиотечной информационной системы, объединяющей оцифровываемый книжный фонд и научные труды Казахстанского инженерно-технологического университета и ряда научно-исследовательских институтов, расположенных в Академгородке г. Алматы. Проанализированы возможности и потребности всех участников научно-образовательного кластера для построения оптимальной архитектуры распределенной информационной системы. Приведено описание и представлены результаты реализации подсистем цифрового репозитория интегрированной распределенной библиотечной информационной системы Академгородка г. Алматы. The purpose of the work is to create an integrated distributed library information system that allows preserving the result of intellectual activity of Kazakhstan Engineering Technological University and a number of research institutes located in the Academgorodok of Almaty in an actual form and to provide access to them based on Web technologies. The relevance of the work is related to the fact that significant amounts of information obtained as a result of research of these institutions, their continuous expansion and heterogeneity in the nature of storage and distribution, along with the lack of unified access to them create significant problems of their effective use. These problems lead to the need to find new approaches and solutions to the problems of creating a repository of information resources, their organization, means and ways to access users. In addition, the work is consistent with the goals set within the framework of the State Program “Digital Kazakhstan” for 2017-2020. The following results were obtained in the present work: 1. The analysis of the capabilities and needs of all participants of the scientificand educational cluster for building the optimal architecture of the distributed information system is carried out. 2. The model of integrated distributed library information system of Almaty Akademgorodok was developed. 3. The results of the implementation of its subsystems are presented. As a result of the conducted research, it was concluded that this system corresponds to the needs of participants in the scientific and educational cluster both in terms of information content and support for sectoral and linguistic specifics, since it solves the main tasks for these systems: providing a system for reliable long-term storage of digital (electronic) documents with preservation of all semantic and functional characteristics of source documents; ensuring “transparent” search and access of users to documents, both for familiarization and for the analysis of the facts contained therein; organization of collection of information on remote digital repositories supporting the OAI-PMH, SRW/SRU, and Z39.50 protocols.