Developing an alternative VIVO frontend based on Triple Pattern Fragments for Metabolomics

Taeber Rapczak, Michael Conlon, Kevin S. Hanson, Samantha G. Emerson, Christopher P. Barnes

TL;DR: A technical overview of the software and architecture developed by the NIH Metabolomics Consortium for their People Portal VIVO.

Abstract: At the 2019 VIVO Conference, Dr Michael Conlon presented "A cross-institutional, FAIR VIVO for Metabolomics" in which he introduced the NIH Metabolomics Consortium's Metabolomics.info website and its VIVO-backed, People Portal (https://people.metabolomics.info). This presentation is a technical follow-up in which we discuss our VIVO implementation, the parts of VIVO we used, and the software we developed to make it all function. More specifically, we discuss Triple Pattern Fragments (TPF) (which were added to version 1.10 of VIVO), our backend Python programs and architectural design, and how we use our software along with VIVO’s TPF endpoint to power an alternative frontend using plain JavaScript, HTML, and CSS. Finally, we'll show that all of our software is open-source and that our data is freely available so that other users in the metabolomics community are empowered to use it in their preferred applications or even develop their own tools.

Keywords: metabolomics, Triple Pattern Fragments, JavaScript, Python, Linked Data, Open-source software