The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing

Warren J. Read, George Demetriou, Goran Nenadic, Noel Ruddock, Robert Stevens, Jerry Winter

Research output: Contribution to journalArticlepeer-review

Abstract

Background: The motivation for the BioHub project is to create an Integrated Knowledge Management System (IKMS) that will enable chemists to source ingredients from bio-renewables, rather than from non-sustainable sources such as fossil oil and its derivatives. Method: The BioHubKB is the data repository of the IKMS; it employs Semantic Web technologies, especially OWL, to host data about chemical transformations, bio-renewable feedstocks, co-product streams and their chemical components. Access to this knowledge base is provided to other modules within the IKMS through a set of RESTful web services, driven by SPARQL queries to a Sesame back-end. The BioHubKB re-uses several bio-ontologies and bespoke extensions, primarily for chemical feedstocks and products, to form its knowledge organisation schema. Results: Parts of plants form feedstocks, while various processes generate co-product streams that contain certain chemicals. Both chemicals and transformations are associated with certain qualities, which the BioHubKB also attempts to capture. Of immediate commercial and industrial importance is to estimate the cost of particular sets of chemical transformations (leading to candidate surfactants) performed in sequence, and these costs too are captured. Data are sourced from companies' internal knowledge and document stores, and from the publicly available literature. Both text analytics and manual curation play their part in populating the ontology. We describe the prototype IKMS, the BioHubKB and the services that it supports for the IKMS. Availability: The BioHubKB can be found via http://biohub.cs.manchester.ac.uk/ontology/biohub-kb.owl.

Original languageEnglish
Article number30
JournalJournal of Biomedical Semantics
Volume7
DOIs
Publication statusPublished - 1 Jun 2016

Keywords

  • Chemistry
  • Environmental sustainability
  • Ontology
  • Repository

Research Beacons, Institutes and Platforms

  • Manchester Institute of Biotechnology

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