An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows

Abstract

Abstract With the capacity to produce and record data electronically, Scientific research and the data associated with it have grown at an unprecedented rate. However, despite a decent amount of data now existing in an electronic form, it is still common for scientific research to be recorded in an unstructured text format with inconsistent context (vocabularies) which vastly reduces the potential for direct intelligent analysis. Research has demonstrated that the use of semantic technologies such as ontologies to structure and enrich scientific data can greatly improve this potential. However, whilst there are many ontologies that can be used for this purpose, there is still a vast quantity of scientific terminology that does not have adequate semantic representation. A key area for expansion identified by the authors was the pharmacokinetic/pharmacodynamic (PK/PD) domain due to its high usage across many areas of Pharma. As such we have produced a set of these terms and other bioassay related terms to be incorporated into the BioAssay Ontology (BAO), which was identified as the most relevant ontology for this work. A number of use cases developed by experts in the field were used to demonstrate how these new ontology terms can be used, and to set the scene for the continuation of this work with a look to expanding this work out into further relevant domains. The work done in this paper was part of Phase 1 of the SEED project (Semantically Enriching electronic laboratory notebook (eLN) Data).

Keywords

• ADME (Absorption, Distribution, Metabolism, Excretion)
• BioAssay
• Drug safety
• Electronic lab notebook
• FAIR (Findable, Accessible, Interoperable and Reusable) principles
• Ontologies