Semantic mediation to improve reproducibility for biomolecular NMR analysis

Michael R. Gryk, Bertram Ludäscher

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Two barriers to computational reproducibility are the ability to record the critical metadata required for rerunning a computation, as well as translating the semantics of the metadata so that alternate approaches can easily be configured for verifying computational reproducibility. We are addressing this problem in the context of biomolecular NMR computational analysis by developing a series of linked ontologies which define the semantics of the various software tools used by researchers for data transformation and analysis. Building from a core ontology representing the primary observational data of NMR, the linked data approach allows for the translation of metadata in order to configure alternate software approaches for given computational tasks. In this paper we illustrate the utility of this with a small sample of the core ontology as well as tool-specific semantics for two third-party software tools. This approach to semantic mediation will help support an automated approach to validating the reliability of computation in which the same processing workflow is implemented with different software tools. In addition, the detailed semantics of both the data and the processing functionalities will provide a method for software tool classification.

Original languageEnglish (US)
Title of host publicationTransforming Digital Worlds - 13th International Conference, iConference 2018, Proceedings
EditorsGobinda Chowdhury, Julie McLeod, Val Gillet, Peter Willett
PublisherSpringer-Verlag Berlin Heidelberg
Pages620-625
Number of pages6
ISBN (Print)9783319781044
DOIs
StatePublished - Jan 1 2018
Event13th International Conference on Transforming Digital Worlds, iConference 2018 - Sheffield, United Kingdom
Duration: Mar 25 2018Mar 28 2018

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10766 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other13th International Conference on Transforming Digital Worlds, iConference 2018
CountryUnited Kingdom
CitySheffield
Period3/25/183/28/18

Keywords

  • Computational reproducibility
  • Ontology
  • Provenance

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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  • Cite this

    Gryk, M. R., & Ludäscher, B. (2018). Semantic mediation to improve reproducibility for biomolecular NMR analysis. In G. Chowdhury, J. McLeod, V. Gillet, & P. Willett (Eds.), Transforming Digital Worlds - 13th International Conference, iConference 2018, Proceedings (pp. 620-625). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 10766 LNCS). Springer-Verlag Berlin Heidelberg. https://doi.org/10.1007/978-3-319-78105-1_70