The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

Background. 
The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.

Description. 
SADI – Semantic Automated Discovery and Integration – is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services “stack”, SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers.

Conclusions.
SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behavior we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies

BioCatalogue: a universal catalogue of web services for the life sciences

The use of Web Services to enable programmatic access to on-line bioinformatics is becoming increasingly important in the Life Sciences. However, their number, distribution and the variable quality of their documentation can make their discovery and subsequent use difficult. A Web Services registry with information on available services will help to bring together service providers and their users. The BioCatalogue (http://www.biocatalogue.org/) provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Services in the BioCatalogue can be described and searched in multiple ways based upon their technical types, bioinformatics categories, user tags, service providers or data inputs and outputs. They are also subject to constant monitoring, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. The system is accessible via a human-readable ‘Web 2.0’-style interface and a programmatic Web Service interface. The BioCatalogue follows a community approach in which all services can be registered, browsed and incrementally documented with annotations by any member of the scientific community

Web services approach for ambient assisted living in mobile environments

Web services appeared as a promising technology for Web environments independent of technologies, services, and applications. First, a performance comparison study between the two most used Web service architectures, SOAP and REST, is presented, considering messages exchange between clients and a server. Based on this study, the REST architecture was chosen to deploy the system because it gets better results compared to SOAP architecture. Currently, there are some issues related with this approach that should be studied. For instance, if massive quantities of data are sent to databases it can influence significantly the performance of the whole system. The Advanced Message Queuing Protocol (AMPQ) appears as a promising solution to address this problem. Then, in order to evaluate the performance of this approach, this work presents a performance evaluation and a comparison study of RESTful Web services and the AMQP Protocol considering exchanging messages between clients and a server. The study is based on the averaged exchanged messages for a certain period of time. It was observed and concluded that, for large quantities of messages exchange, the best results comes from the Advanced Message Queuing Protocol. Message Queuing Telemetry Transport (MQTT) was addressed in this work because it is a similar protocol to AMQP but it can be used by mobile devices with a processing capacity smallest unlike the AMQP that needs greater processing capacity. These studies are performed in the context of Ambient Assisted Living environments, since the work was applied to this topic in order to experiment the effectiveness and evaluate the performance of these protocols in this scenario

A Service-Oriented Approach for Network-Centric Data Integration and Its Application to Maritime Surveillance

Maritime-surveillance operators still demand for an integrated maritime picture better supporting international coordination for their operations, as looked for in the European area. In this area, many data-integration efforts have been interpreted in the past as the problem of designing, building and maintaining huge centralized repositories. Current research activities are instead leveraging service-oriented principles to achieve more flexible and network-centric solutions to systems and data integration. In this direction, this article reports on the design of a SOA platform, the Service and Application Integration (SAI) system, targeting novel approaches for legacy data and systems integration in the maritime surveillance domain. We have developed a proof-of-concept of the main system capabilities to assess feasibility of our approach and to evaluate how the SAI middleware architecture can fit application requirements for dynamic data search, aggregation and delivery in the distributed maritime domain

SysML-Based Domain-Specific Executable Workflows

The Systems Modeling Language (SysML) is a general-purpose graphical modeling language for specifying, analyzing, designing, and verifying complex systems. This thesis presents a tool called SysFlow Workflow Engine (SWE) that is being developed to execute a domain workflow defined using SysML\u27s Activity Diagram. The thesis also describes extensions added to the SysML semantics to make them SWE executable. SWE focuses on grid computing, cyberinfrastructure and related domains; however, support for other domains can be easily added. SWE aims to provide a common interface to grid, cyberinfrastructure and other domain-specific software by abstracting their complexity and idiosyncrasies. To create a workflow, users can use SysML modelers such as Topcased, which allow them to create and validate SysML models. Before submitting a workflow to SWE for execution, users have to ensure that their workflow is not only a valid SysML model but also a valid SWE executable model. SWE receives a SysML workflow in XML Metadata Interchange (XMI) format and after performing certain validation checks, it parses and executes the workflow

A geo-database for potentially polluting marine sites and associated risk index

The increasing availability of geospatial marine data provides an opportunity for hydrographic offices to contribute to the identification of Potentially Polluting Marine Sites (PPMS). To adequately manage these sites, a PPMS Geospatial Database (GeoDB) application was developed to collect and store relevant information suitable for site inventory and geo-spatial analysis. The benefits of structuring the data to conform to the Universal Hydrographic Data Model (IHO S-100) and to use the Geographic Mark-Up Language (GML) for encoding are presented. A storage solution is proposed using a GML-enabled spatial relational database management system (RDBMS). In addition, an example of a risk index methodology is provided based on the defined data structure. The implementation of this example was performed using scripts containing SQL statements. These procedures were implemented using a cross-platform C++ application based on open-source libraries and called PPMS GeoDB Manager

An integrated computational pipeline and database to support whole-genome sequence annotation

We describe here our experience in annotating the Drosophila melanogaster genome sequence, in the course of which we developed several new open-source software tools and a database schema to support large-scale genome annotation. We have developed these into an integrated and reusable software system for whole-genome annotation. The key contributions to overall annotation quality are the marshalling of high-quality sequences for alignments and the design of a system with an adaptable and expandable flexible architecture