SADI, SHARE, and the in silico scientific method

Abstract

BackgroundThe emergence and uptake of Semantic Web technologies by the Life Sciences provides exciting opportunities for exploring novel ways to conduct in silico science. Web Service Workflows are already becoming first-class objects in “the new way”, and serve as explicit, shareable, referenceable representations of how an experiment was done. In turn, Semantic Web Service projects aim to facilitate workflow construction by biological domain-experts such that workflows can be edited, re-purposed, and re-published by non-informaticians. However the aspects of the scientific method relating to explicit discourse, disagreement, and hypothesis generation have remained relatively impervious to new technologies.ResultsHere we present SADI and SHARE - a novel Semantic Web Service framework, and a reference implementation of its client libraries. Together, SADI and SHARE allow the semi- or fully-automatic discovery and pipelining of Semantic Web Services in response to ad hoc user queries.ConclusionsThe semantic behaviours exhibited by SADI and SHARE extend the functionalities provided by Description Logic Reasoners such that novel assertions can be automatically added to a data-set without logical reasoning, but rather by analytical or annotative services. This behaviour might be applied to achieve the “semantification” of those aspects of the in silico scientific method that are not yet supported by Semantic Web technologies. We support this suggestion using an example in the clinical research space.

Opportunités du web social et du web sémantique pour la recherche biomédicale ?

“…Les futures avancées scientifiques ne dépendent-elles pas de plus en plus de la façon dont les chercheurs partagent leurs données et collaborent entre eux ? Le web sémantique n'est-il pas une entrée majeure de la recherche in silico et de la e-science [8] ? Un deuxième défi pour la recherche est certainement l'innovation ouverte que l'ont peut adosser à l'horizontalité du web social.…”

Data Integration in Bioinformatics: Current Efforts and Challenges

“…Therefore, to deal with such large-scale data management and analysis, Semantic WS necessitate to adopt advances in high performance computing (Schadt, et al, 2010), such as, cloud/grid computing (Bateman and Wood, 2009;Stein, 2010) and Service-Oriented Computing (Papazoglou, et al, 2008). In addition, a Semantic WS framework (Wilkinson, et al, 2010) is also needed, in order to set up Semantic WS workflows or pipelines.…”

Leveraging Fragmental Semantic Data to Enhance Services Discovery

“…Semantic Automated Discovery and Integration (SADI) [8] framework is able to retrieve SADI services. While SADI search only compares the input/output OWL class URLs in SADI services, our work considers more semantic conditions (e.g., functional profile and tags).…”