Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD)

Complex human traits such as chronic kidney disease (CKD) are a major health and financial burden in modern societies. Currently, the description of the CKD onset and progression at the molecular level is still not fully understood. Meanwhile, the prolific use of high-throughput omic technologies in disease biomarker discovery studies yielded a vast amount of disjointed data that cannot be easily collated. Therefore, we aimed to develop a molecule-centric database featuring CKD-related experiments from available literature publications. We established the Chronic Kidney Disease database CKDdb, an integrated and clustered information resource that covers multi-omic studies (microRNAs, genomics, peptidomics, proteomics and metabolomics) of CKD and related disorders by performing literature data mining and manual curation. The CKDdb database contains differential expression data from 49395 molecule entries (redundant), of which 16885 are unique molecules (non-redundant) from 377 manually curated studies of 230 publications. This database was intentionally built to allow disease pathway analysis through a systems approach in order to yield biological meaning by integrating all existing information and therefore has the potential to unravel and gain an in-depth understanding of the key molecular events that modulate CKD pathogenesis

The NASA Astrophysics Data System: Architecture

The powerful discovery capabilities available in the ADS bibliographic services are possible thanks to the design of a flexible search and retrieval system based on a relational database model. Bibliographic records are stored as a corpus of structured documents containing fielded data and metadata, while discipline-specific knowledge is segregated in a set of files independent of the bibliographic data itself. The creation and management of links to both internal and external resources associated with each bibliography in the database is made possible by representing them as a set of document properties and their attributes. To improve global access to the ADS data holdings, a number of mirror sites have been created by cloning the database contents and software on a variety of hardware and software platforms. The procedures used to create and manage the database and its mirrors have been written as a set of scripts that can be run in either an interactive or unsupervised fashion. The ADS can be accessed at http://adswww.harvard.eduComment: 25 pages, 8 figures, 3 table

A semantic and agent-based approach to support information retrieval, interoperability and multi-lateral viewpoints for heterogeneous environmental databases

PhDData stored in individual autonomous databases often needs to be combined and interrelated. For example, in the Inland Water (IW) environment monitoring domain, the spatial and temporal variation of measurements of different water quality indicators stored in different databases are of interest. Data from multiple data sources is more complex to combine when there is a lack of metadata in a computation forin and when the syntax and semantics of the stored data models are heterogeneous. The main types of information retrieval (IR) requirements are query transparency and data harmonisation for data interoperability and support for multiple user views. A combined Semantic Web based and Agent based distributed system framework has been developed to support the above IR requirements. It has been implemented using the Jena ontology and JADE agent toolkits. The semantic part supports the interoperability of autonomous data sources by merging their intensional data, using a Global-As-View or GAV approach, into a global semantic model, represented in DAML+OIL and in OWL. This is used to mediate between different local database views. The agent part provides the semantic services to import, align and parse semantic metadata instances, to support data mediation and to reason about data mappings during alignment. The framework has applied to support information retrieval, interoperability and multi-lateral viewpoints for four European environmental agency databases. An extended GAV approach has been developed and applied to handle queries that can be reformulated over multiple user views of the stored data. This allows users to retrieve data in a conceptualisation that is better suited to them rather than to have to understand the entire detailed global view conceptualisation. User viewpoints are derived from the global ontology or existing viewpoints of it. This has the advantage that it reduces the number of potential conceptualisations and their associated mappings to be more computationally manageable. Whereas an ad hoc framework based upon conventional distributed programming language and a rule framework could be used to support user views and adaptation to user views, a more formal framework has the benefit in that it can support reasoning about the consistency, equivalence, containment and conflict resolution when traversing data models. A preliminary formulation of the formal model has been undertaken and is based upon extending a Datalog type algebra with hierarchical, attribute and instance value operators. These operators can be applied to support compositional mapping and consistency checking of data views. The multiple viewpoint system was implemented as a Java-based application consisting of two sub-systems, one for viewpoint adaptation and management, the other for query processing and query result adjustment

QueryOR: a comprehensive web platform for genetic variant analysis and prioritization

Background: Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to facilitate data analysis. Results: Here we describe QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. Instead of being designed on specific datasets, it works on a general XML schema specifying formats and criteria of each data source. Thanks to this flexibility, new criteria can be easily added for future expansion. Currently, up to 70 user-selectable criteria are available, including a wide range of gene and variant features. Moreover, rather than progressively discarding variants taking one criterion at a time, the prioritization is achieved by a global positive selection process that considers all transcript isoforms, thus producing reliable results. QueryOR is easy to use and its intuitive interface allows to handle different kinds of inheritance as well as features related to sharing variants in different patients. QueryOR is suitable for investigating single patients, families or cohorts. Conclusions: QueryOR is a comprehensive and flexible web platform eligible for an easy user-driven variant prioritization. It is freely available for academic institutions at http://queryor.cribi.unipd.it/

Data Management in the APPA System

International audienceCombining Grid and P2P technologies can be exploited to provide high-level data sharing in large-scale distributed environments. However, this combination must deal with two hard problems: the scale of the network and the dynamic behavior of the nodes. In this paper, we present our solution in APPA (Atlas Peer-to-Peer Architecture), a data management system with high-level services for building large-scale distributed applications. We focus on data availability and data discovery which are two main requirements for implementing large-scale Grids. We have validated APPA's services through a combination of experimentation over Grid5000, which is a very large Grid experimental platform, and simulation using SimJava. The results show very good performance in terms of communication cost and response time

Non-invasive lightweight integration engine for building EHR from autonomous distributed systems

[EN] In this paper we describe Pangea-LE, a message-oriented lightweight data integration engine that allows homogeneous and concurrent access to clinical information from disperse and heterogeneous data sources. The engine extracts the information and passes it to the requesting client applications in a flexible XML format. The XML response message can be formatted on demand by appropriate Extensible Stylesheet Language (XSL) transformations in order to meet the needs of client applications. We also present a real deployment in a hospital where Pangea-LE collects and generates an XML view of all the available patient clinical information. The information is presented to healthcare professionals in an Electronic Health Record (EHR) viewer Web application with patient search and EHR browsing capabilities. Implantation in a real setting has been a success due to the non-invasive nature of Pangea-LE which respects the existing information systems.This work was partially funded by the Spanish Ministry of Science and Technology (MEC-TSI2004-06475-102-01) and the Spanish Ministry of Health (PI052245)Angulo Fernández, C.; Crespo Molina, PM.; Maldonado Segura, JA.; Moner Cano, D.; Perez Cuesta, D.; Abad, I.; Mandingorra Gimenez, J.... (2007). Non-invasive lightweight integration engine for building EHR from autonomous distributed systems. International Journal of Medical Informatics. 76(Supplement 3):417-424. https://doi.org/10.1016/j.ijmedinf.2007.05.002S41742476Supplement

The role of earth observation in an integrated deprived area mapping “system” for low-to-middle income countries

Urbanization in the global South has been accompanied by the proliferation of vast informal and marginalized urban areas that lack access to essential services and infrastructure. UN-Habitat estimates that close to a billion people currently live in these deprived and informal urban settlements, generally grouped under the term of urban slums. Two major knowledge gaps undermine the efforts to monitor progress towards the corresponding sustainable development goal (i.e., SDG 11—Sustainable Cities and Communities). First, the data available for cities worldwide is patchy and insufficient to differentiate between the diversity of urban areas with respect to their access to essential services and their specific infrastructure needs. Second, existing approaches used to map deprived areas (i.e., aggregated household data, Earth observation (EO), and community-driven data collection) are mostly siloed, and, individually, they often lack transferability and scalability and fail to include the opinions of different interest groups. In particular, EO-based-deprived area mapping approaches are mostly top-down, with very little attention given to ground information and interaction with urban communities and stakeholders. Existing top-down methods should be complemented with bottom-up approaches to produce routinely updated, accurate, and timely deprived area maps. In this review, we first assess the strengths and limitations of existing deprived area mapping methods. We then propose an Integrated Deprived Area Mapping System (IDeAMapS) framework that leverages the strengths of EO- and community-based approaches. The proposed framework offers a way forward to map deprived areas globally, routinely, and with maximum accuracy to support SDG 11 monitoring and the needs of different interest groups

Green BPM as a business-oriented discipline : a systematic mapping study and research agenda

Green Business Process Management (BPM) focuses on the ecological impact of business processes. This article provides a systematic mapping study of Green BPM literature to evaluate five attributes of the Green BPM research area: (1) scope, (2) disciplines, (3) accountability, (4) researchers and (5) quality control. The results allow developing a research agenda to enhance Green BPM as an approach for environmentally sustainable organizations. We rely on a dichotomy of knowledge production to present research directives relevant for both academics and practitioners in order to help close a rigor-relevance gap. The involvement of both communities is crucial for Green BPM to advance as an applied, business-oriented discipline

Heterogeneous network embedding enabling accurate disease association predictions.

BackgroundIt is significant to identificate complex biological mechanisms of various diseases in biomedical research. Recently, the growing generation of tremendous amount of data in genomics, epigenomics, metagenomics, proteomics, metabolomics, nutriomics, etc., has resulted in the rise of systematic biological means of exploring complex diseases. However, the disparity between the production of the multiple data and our capability of analyzing data has been broaden gradually. Furthermore, we observe that networks can represent many of the above-mentioned data, and founded on the vector representations learned by network embedding methods, entities which are in close proximity but at present do not actually possess direct links are very likely to be related, therefore they are promising candidate subjects for biological investigation.ResultsWe incorporate six public biological databases to construct a heterogeneous biological network containing three categories of entities (i.e., genes, diseases, miRNAs) and multiple types of edges (i.e., the known relationships). To tackle the inherent heterogeneity, we develop a heterogeneous network embedding model for mapping the network into a low dimensional vector space in which the relationships between entities are preserved well. And in order to assess the effectiveness of our method, we conduct gene-disease as well as miRNA-disease associations predictions, results of which show the superiority of our novel method over several state-of-the-arts. Furthermore, many associations predicted by our method are verified in the latest real-world dataset.ConclusionsWe propose a novel heterogeneous network embedding method which can adequately take advantage of the abundant contextual information and structures of heterogeneous network. Moreover, we illustrate the performance of the proposed method on directing studies in biology, which can assist in identifying new hypotheses in biological investigation