Lost in translation: data integration tools meet the Semantic Web (experiences from the Ondex project)

TL;DR

This paper examines how data integration and visualization platforms like Ondex, developed for Life Sciences, face challenges adapting to Semantic Web data due to semantic mismatches and structural discrepancies.

Contribution

The paper analyzes Ondex's data structure and usage to identify semantic mismatches with Semantic Web data, proposing a methodology for such analysis and highlighting relevant issues.

Findings

Discrepancies between Ondex data structures and Semantic Web representations

Semantic mismatches lead to errors in data integration and analysis

Identified issues are relevant for similar network analysis platforms

Abstract

More information is now being published in machine processable form on the web and, as de-facto distributed knowledge bases are materializing, partly encouraged by the vision of the Semantic Web, the focus is shifting from the publication of this information to its consumption. Platforms for data integration, visualization and analysis that are based on a graph representation of information appear first candidates to be consumers of web-based information that is readily expressible as graphs. The question is whether the adoption of these platforms to information available on the Semantic Web requires some adaptation of their data structures and semantics. Ondex is a network-based data integration, analysis and visualization platform which has been developed in a Life Sciences context. A number of features, including semantic annotation via ontologies and an attention to provenance and evidence, make this an ideal candidate to consume Semantic Web information, as well as a prototype for the application of network analysis tools in this context. By analyzing the Ondex data structure and its usage, we have found a set of discrepancies and errors arising from the semantic mismatch between a procedural approach to network analysis and the implications of a web-based representation of information. We report in the paper on the simple methodology that we have adopted to conduct such analysis, and on issues that we have found which may be relevant for a range of similar platforms