The Digitalization of Bioassays in the Open Research Knowledge Graph

Background: Recent years are seeing a growing impetus in the semantification of scholarly knowledge at the fine-grained level of scientific entities in knowledge graphs. The Open Research Knowledge Graph (ORKG) https://www.orkg.org/ represents an important step in this direction, with thousands of scholarly contributions as structured, fine-grained, machine-readable data. There is a need, however, to engender change in traditional community practices of recording contributions as unstructured, non-machine-readable text. For this in turn, there is a strong need for AI tools designed for scientists that permit easy and accurate semantification of their scholarly contributions. We present one such tool, ORKG-assays. Implementation: ORKG-assays is a freely available AI micro-service in ORKG written in Python designed to assist scientists obtain semantified bioassays as a set of triples. It uses an AI-based clustering algorithm which on gold-standard evaluations over 900 bioassays with 5,514 unique property-value pairs for 103 predicates shows competitive performance. Results and Discussion: As a result, semantified assay collections can be surveyed on the ORKG platform via tabulation or chart-based visualizations of key property values of the chemicals and compounds offering smart knowledge access to biochemists and pharmaceutical researchers in the advancement of drug development.
Comment: 12 pages, 5 figures, In Review at DeXa 2022 https://www.dexa.org/dexa2022