Biomedical data integration in computational drug design and bioinformatics

[Abstract In recent years, in the post genomic era, more and more data is being generated by biological high throughput technologies, such as proteomics and transcriptomics. This omics data can be very useful, but the real challenge is to analyze all this data, as a whole, after integrating it. Biomedical data integration enables making queries to different, heterogeneous and distributed biomedical data sources. Data integration solutions can be very useful not only in the context of drug design, but also in biomedical information retrieval, clinical diagnosis, system biology, etc. In this review, we analyze the most common approaches to biomedical data integration, such as federated databases, data warehousing, multi-agent systems and semantic technology, as well as the solutions developed using these approaches in the past few years.Red Gallega de Investigación sobre Cáncer Colorrectal; Ref. 2009/58Programa Iberoamericano de Ciencia y Tecnología para el Desarrollo; 209RT- 0366Instituto de Salud Carlos III; PIO52048Instituto de Salud Carlos III; RD07/0067/0005Ministerio de Industria, Turismo y Comercio; TSI-020110-2009-

Active Ontology: An Information Integration Approach for Dynamic Information Sources

In this paper we describe an ontology-based information integration approach that is suitable for highly dynamic distributed information sources, such as those available in Grid systems. The main challenges addressed are: 1) information changes frequently and information requests have to be answered quickly in order to provide up-to-date information; and 2) the most suitable information sources have to be selected from a set of different distributed ones that can provide the information needed. To deal with the first challenge we use an information cache that works with an update-on-demand policy. To deal with the second we add an information source selection step to the usual architecture used for ontology-based information integration. To illustrate our approach, we have developed an information service that aggregates metadata available in hundreds of information services of the EGEE Grid infrastructure

Multi-Paradigm Reasoning for Access to Heterogeneous GIS

Accessing and querying geographical data in a uniform way has become easier in recent years. Emerging standards like WFS turn the web into a geospatial web services enabled place. Mediation architectures like VirGIS overcome syntactical and semantical heterogeneity between several distributed sources. On mobile devices, however, this kind of solution is not suitable, due to limitations, mostly regarding bandwidth, computation power, and available storage space. The aim of this paper is to present a solution for providing powerful reasoning mechanisms accessible from mobile applications and involving data from several heterogeneous sources. By adapting contents to time and location, mobile web information systems can not only increase the value and suitability of the service itself, but can substantially reduce the amount of data delivered to users. Because many problems pertain to infrastructures and transportation in general and to way finding in particular, one cornerstone of the architecture is higher level reasoning on graph networks with the Multi-Paradigm Location Language MPLL. A mediation architecture is used as a “graph provider” in order to transfer the load of computation to the best suited component – graph construction and transformation for example being heavy on resources. Reasoning in general can be conducted either near the “source” or near the end user, depending on the specific use case. The concepts underlying the proposal described in this paper are illustrated by a typical and concrete scenario for web applications

Ontology Based Integration of Distributed and Heterogeneous Data Sources in ACGT.

In this work, we describe the set of tools comprising the Data Access Infrastructure within Advancing Clinic-genomic Trials on Cancer (ACGT), a R&D Project funded in part by the European. This infrastructure aims at improving Post-genomic clinical trials by providing seamless access to integrated clinical, genetic, and image databases. A data access layer, based on OGSA-DAI, has been developed in order to cope with syntactic heterogeneities in databases. The semantic problems present in data sources with different nature are tackled by two core tools, namely the Semantic Mediator and the Master Ontology on Cancer. The ontology is used as a common framework for semantics, modeling the domain and acting as giving support to homogenization. SPARQL has been selected as query language for the Data Access Services and the Mediator. Two experiments have been carried out in order to test the suitability of the selected approach, integrating clinical and DICOM image databases

Semantic Mediation of Environmental Observation Datasets through Sensor Observation Services

A large volume of environmental observation data is being generated as a result of the observation of many properties at the Earth surface. In parallel, there exists a clear interest in accessing data from different data providers related to the same property, in order to solve concrete problems. Based on such fact, there is also an increasing interest in publishing the above data through open interfaces in the scope of Spatial Data Infraestructures. There have been important advances in the definition of open standards of the Open Geospatial Consortium (OGC) that enable interoperable access to sensor data. Among the proposed interfaces, the Sensor Observation Service (SOS) is having an important impact. We have realized that currently there is no available solution to provide integrated access to various data sources through a SOS interface. This problem shows up two main facets. On the one hand, the heterogeneity among different data sources has to be solved. On the other hand, semantic conflicts that arise during the integration process must also resolved with the help of relevant domain expert knowledge. To solve the problems, the main goal of this thesis is to design and develop a semantic data mediation framework to access any kind of environmental observation dataset, including both relational data sources and multidimensional arrays

Augmenting applications with hyper media, functionality and meta-information

The Dynamic Hypermedia Engine (DHE) enhances analytical applications by adding relationships, semantics and other metadata to the application\u27s output and user interface. DHE also provides additional hypermedia navigational, structural and annotation functionality. These features allow application developers and users to add guided tours, personal links and sharable annotations, among other features, into applications. DHE runs as a middleware between the application user interface and its business logic and processes, in a n-tier architecture, supporting the extra functionalities without altering the original systems by means of application wrappers. DHE automatically generates links at run-time for each of those elements having relationships and metadata. Such elements are previously identified using a Relation Navigation Analysis. DHE also constructs more sophisticated navigation techniques not often found on the Web on top of these links. The metadata, links, navigation and annotation features supplement the application\u27s primary functionality. This research identifies element types, or classes , in the application displays. A mapping rule encodes each relationship found between two elements of interest at the class level . When the user selects a particular element, DHE instantiates the commands included in the rules with the actual instance selected and sends them to the appropriate destination system, which then dynamically generates the resulting virtual (i.e. not previously stored) page. DHE executes concurrently with these applications, providing automated link generation and other hypermedia functionality. DHE uses the extensible Markup Language (XMQ -and related World Wide Web Consortium (W3C) sets of XML recommendations, like Xlink, XML Schema, and RDF -to encode the semantic information required for the operation of the extra hypermedia features, and for the transmission of messages between the engine modules and applications. DHE is the only approach we know that provides automated linking and metadata services in a generic manner, based on the application semantics, without altering the applications. DHE will also work with non-Web systems. The results of this work could also be extended to other research areas, such as link ranking and filtering, automatic link generation as the result of a search query, metadata collection and support, virtual document management, hypermedia functionality on the Web, adaptive and collaborative hypermedia, web engineering, and the semantic Web

Querying Web-Sources within a Data Federation

The Web is undoubtedly the largest and most diverse repository of data, but it was not designed to offer the capabilities of traditional data base management systems – which is unfortunate. In a true data federation, all types of data sources, such as relational databases and semi-structured Web sites, could be used together. IBM WebSphere uses the “request-reply-compensate” protocol to communicate with wrappers in a data federation. This protocol expects wrappers to reply to query requests by indicating the portion of the queries they can answer. While this provides a very generic approach to data federation, it also requires the wrapper developer to deal with some of the complexities of capability considerations through custom coding. Alternative approaches based on declarative capability restrictions have been proposed in the literature, but they have not found their way into commercial systems, perhaps due to their complexity. We offer a practical middle-ground solution to querying Web-sources, using IBM’s data federation system as an example. In lieu of a two-layered architecture consisting of wrapper and source layers, we propose to move the capability declaration from the wrapper layer to a single component between the wrapper and the native data source. The advantage of this three-layered architecture is that each new Web-source only needs to register its capability with the capability-declaration component once, which saves the work of writing a new wrapper each time. Thus the inclusion of Web-sources through this mechanism can be accelerated in a way that doesn\u27t require a change in existing data federation technology

A unified view of data-intensive flows in business intelligence systems : a survey

Data-intensive flows are central processes in today’s business intelligence (BI) systems, deploying different technologies to deliver data, from a multitude of data sources, in user-preferred and analysis-ready formats. To meet complex requirements of next generation BI systems, we often need an effective combination of the traditionally batched extract-transform-load (ETL) processes that populate a data warehouse (DW) from integrated data sources, and more real-time and operational data flows that integrate source data at runtime. Both academia and industry thus must have a clear understanding of the foundations of data-intensive flows and the challenges of moving towards next generation BI environments. In this paper we present a survey of today’s research on data-intensive flows and the related fundamental fields of database theory. The study is based on a proposed set of dimensions describing the important challenges of data-intensive flows in the next generation BI setting. As a result of this survey, we envision an architecture of a system for managing the lifecycle of data-intensive flows. The results further provide a comprehensive understanding of data-intensive flows, recognizing challenges that still are to be addressed, and how the current solutions can be applied for addressing these challenges.Peer ReviewedPostprint (author's final draft