Towards a service-oriented e-infrastructure for multidisciplinary environmental research

Research e-infrastructures are considered to have generic and thematic parts. The generic part provids high-speed networks, grid (large-scale distributed computing) and database systems (digital repositories and data transfer systems) applicable to all research commnities irrespective of discipline. Thematic parts are specific deployments of e-infrastructures to support diverse virtual research communities. The needs of a virtual community of multidisciplinary envronmental researchers are yet to be investigated. We envisage and argue for an e-infrastructure that will enable environmental researchers to develop environmental models and software entirely out of existing components through loose coupling of diverse digital resources based on the service-oriented achitecture. We discuss four specific aspects for consideration for a future e-infrastructure: 1) provision of digital resources (data, models & tools) as web services, 2) dealing with stateless and non-transactional nature of web services using workflow management systems, 3) enabling web servce discovery, composition and orchestration through semantic registries, and 4) creating synergy with existing grid infrastructures

Automatic annotation of bioinformatics workflows with biomedical ontologies

Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community. This paper presents an approach to annotating workflows and their subcomponents with ontology terms, in an attempt to describe these artifacts in a structured way. Despite a dearth of even textual descriptions, we automatically annotated 530 myExperiment bioinformatics-related workflows, including more than 2600 workflow-associated services, with relevant ontological terms. Quantitative evaluation of the Information Content of these terms suggests that, in cases where annotation was possible at all, the annotation quality was comparable to manually curated bioinformatics resources.Comment: 6th International Symposium on Leveraging Applications (ISoLA 2014 conference), 15 pages, 4 figure

Report of the Stanford Linked Data Workshop

The Stanford University Libraries and Academic Information Resources (SULAIR) with the Council on Library and Information Resources (CLIR) conducted at week-long workshop on the prospects for a large scale, multi-national, multi-institutional prototype of a Linked Data environment for discovery of and navigation among the rapidly, chaotically expanding array of academic information resources. As preparation for the workshop, CLIR sponsored a survey by Jerry Persons, Chief Information Architect emeritus of SULAIR that was published originally for workshop participants as background to the workshop and is now publicly available. The original intention of the workshop was to devise a plan for such a prototype. However, such was the diversity of knowledge, experience, and views of the potential of Linked Data approaches that the workshop participants turned to two more fundamental goals: building common understanding and enthusiasm on the one hand and identifying opportunities and challenges to be confronted in the preparation of the intended prototype and its operation on the other. In pursuit of those objectives, the workshop participants produced:1. a value statement addressing the question of why a Linked Data approach is worth prototyping;2. a manifesto for Linked Libraries (and Museums and Archives and …);3. an outline of the phases in a life cycle of Linked Data approaches;4. a prioritized list of known issues in generating, harvesting & using Linked Data;5. a workflow with notes for converting library bibliographic records and other academic metadata to URIs;6. examples of potential “killer apps” using Linked Data: and7. a list of next steps and potential projects.This report includes a summary of the workshop agenda, a chart showing the use of Linked Data in cultural heritage venues, and short biographies and statements from each of the participants

Web Service Discovery – Reality Check 2.0

In practice the ability to find the right Web service decides between a functionality being implemented anew and at least the possibility of executing it via a service. This report evaluates existing public portals for Web service discovery with respect to their characteristics and their acceptance by developers. For this, we distinguish different possible settings and use cases and evaluate how these are supported in practice. Only few of the publicly available Web service registries are growing in size and importance, with the use case best supported being the pre-programming phase of evaluation of the service landscape. <br