Deploying mutation impact text-mining software with the SADI Semantic Web Services framework

Abstract

Background: Mutation impact extraction is an important task designed to harvest relevant annotations from scientific documents for reuse in multiple contexts. Our previous work on text mining for mutation impacts resulted in (i) the development of a GATE-based pipeline that mines texts for information about impacts of mutations on proteins, (ii) the population of this information into our OWL DL mutation impact ontology, and (iii) establishing an experimental semantic database for storing the results of text mining.Results: This article explores the possibility of using the SADI framework as a medium for publishing our mutation impact software and data. SADI is a set of conventions for creating web services with semantic descriptions that facilitate automatic discovery and orchestration. We describe a case study exploring and demonstrating the utility of the SADI approach in our context. We describe several SADI services we created based on our text mining API and data, and demonstrate how they can be used in a number of biologically meaningful scenarios through a SPARQL interface (SHARE) to SADI services. In all cases we pay special attention to the integration of mutation impact services with external SADI services providing information about related biological entities, such as proteins, pathways, and drugs.Conclusion: We have identified that SADI provides an effective way of exposing our mutation impact data such that it can be leveraged by a variety of stakeholders in multiple use cases. The solutions we provide for our use cases can serve as examples to potential SADI adopters trying to solve similar integration problems. © 2011 Riazanov et al; licensee BioMed Central Ltd.