HUDDL for description and archive of hydrographic binary data

Many of the attempts to introduce a universal hydrographic binary data format have failed or have been only partially successful. In essence, this is because such formats either have to simplify the data to such an extent that they only support the lowest common subset of all the formats covered, or they attempt to be a superset of all formats and quickly become cumbersome. Neither choice works well in practice. This paper presents a different approach: a standardized description of (past, present, and future) data formats using the Hydrographic Universal Data Description Language (HUDDL), a descriptive language implemented using the Extensible Markup Language (XML). That is, XML is used to provide a structural and physical description of a data format, rather than the content of a particular file. Done correctly, this opens the possibility of automatically generating both multi-language data parsers and documentation for format specification based on their HUDDL descriptions, as well as providing easy version control of them. This solution also provides a powerful approach for archiving a structural description of data along with the data, so that binary data will be easy to access in the future. Intending to provide a relatively low-effort solution to index the wide range of existing formats, we suggest the creation of a catalogue of format descriptions, each of them capturing the logical and physical specifications for a given data format (with its subsequent upgrades). A C/C++ parser code generator is used as an example prototype of one of the possible advantages of the adoption of such a hydrographic data format catalogue

Huddl: the Hydrographic Universal Data Description Language

Since many of the attempts to introduce a universal hydrographic data format have failed or have been only partially successful, a different approach is proposed. Our solution is the Hydrographic Universal Data Description Language (HUDDL), a descriptive XML-based language that permits the creation of a standardized description of (past, present, and future) data formats, and allows for applications like HUDDLER, a compiler that automatically creates drivers for data access and manipulation. HUDDL also represents a powerful solution for archiving data along with their structural description, as well as for cataloguing existing format specifications and their version control. HUDDL is intended to be an open, community-led initiative to simplify the issues involved in hydrographic data access

A practical mandatory access control model for XML databases

A practical mandatory access control (MAC) model for XML databases is presented in this paper. The label type and label access policy can be defined according to the requirements of different applications. In order to preserve the integrity of data in XML databases, a constraint between a read-access rule and a write-access rule in label access policy is introduced. Rules for label assignment and propagation are presented to alleviate the workload of label assignments. Furthermore, a solution for resolving conflicts in label assignments is proposed. Rules for update-related operations, rules for exceptional privileges of ordinary users and the administrator are also proposed to preserve the security of operations in XML databases. The MAC model, we proposed in this study, has been implemented in an XML database. Test results demonstrated that our approach provides rational and scalable performance

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

Dealing with large schema sets in mobile SOS-based applications

Although the adoption of OGC Web Services for server, desktop and web applications has been successful, its penetration in mobile devices has been slow. One of the main reasons is the performance problems associated with XML processing as it consumes a lot of memory and processing time, which are scarce resources in a mobile device. In this paper we propose an algorithm to generate efficient code for XML data binding for mobile SOS-based applications. The algorithm take advantage of the fact that individual implementations use only some portions of the standards' schemas, which allows the simplification of large XML schema sets in an application-specific manner by using a subset of XML instance files conforming to these schemas.Comment: 9 pages, 2 tables, 7 figure

Xml Interfaces: a Growing Need for Standardization

The incentive for this research came from the need to solve a fundamental problem many companies face when transferring data across multi-platform applications: how to deploy XML interfaces that integrate easily with other systems. The goal of this project was to identify a solution for Company ABC when integrating XML interfaces with customers, partners, and vendors. The project researches the need and development of data standards that can solve one of the key problems with XML - interoperability. Through the use of a common language, companies can utilize data formats and schemas developed by data standards organizations operating in their vertical industry. Implementing a standard XML interface will help Company ABC reduce the expense of customizing all of their XML interfaces

REST service testing based on inferred XML schemas

The concept of service oriented architecture has been extensively explored in software engineering, due to the fact that it produces architectures made up of several interconnected modules, easy to reuse when building new systems. This approach to design would be impossible without interconnection mechanisms such as REST (Representationa State Transfer) services, which allow module communication while minimizing coupling. . However, this low coupling brings disadvantages, such as the lack of transparency, which makes it difficult to sistematically create tests without knowledge of the inner working of a system. In this article, we present an automatic error detection system for REST services, based on a statistical analysis over responses produced at multiple service invocations. Thus, a service can be systematically tested without knowing its full specification. The method can find errors in REST services which could not be identified by means of traditional testing methods, and provides limited testing coverage for services whose response format is unknown. It can be also useful as a complement to other testing mechanisms