Lost in Translation: Data Integration Tools Meet the Semantic Web (Experiences from the Ondex Project)

Abstract

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.

Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach

“…The new format will be both a reference for converting external data of interest into a unified data format, and a source of queries, data access and exchange for applications. We have achieved a first concrete result by reviewing past work [59], and developing an Ondex plug-in to export OXL data as RDF that instantiates our ontology [60].…”

Combining computational models, semantic annotations and simulation experiments in a graph database

“…NoSQL approaches, together with semantic web applications, more recently gained popularity in the life sciences ( 22 ), e.g. as Key-Value Stores, BigTable ( 23 ), document databases, triple stores or graph databases ( 24 ).…”

Developing integrated crop knowledge networks to advance candidate gene discovery

“…The scripting syntax is based on a bespoke language developed in Lysenko 2012. Ondex networks can be exported in several formats such as the Ondex exchange format OXL (Taubert et al, 2007), RDF (Splendiani et al, 2012) or Cytoscape-compatible JSON. Networks can be visualised and inspected using tools like Cytoscape (Shannon et al, 2003) or in the Ondex User Interface (Ondex UI) (Fig.…”

“…Furthermore, a Cytoscape plugin, called OndexView allows for concise graphical representations of integrated knowledge networks (Weile et al, 2011). Some studies were undertaken to evaluate the utility of semantic web technologies (RDF, SPARQL) within the umbrella of Ondex (Splendiani et al, 2012, Canevet et al, 2010). Two studies showed the contributions of Ondex towards Bayesian data integration (Weile et al, 2012) and towards logic-based modelling (Lesk et al, 2011).…”