Natural Language Processing for Drug Discovery Knowledge Graphs: Promises and Pitfalls

Methods Mol Biol. 2024:2716:223-240. doi: 10.1007/978-1-0716-3449-3_10.


Building and analyzing knowledge graphs (KGs) to aid drug discovery is a topical area of research. A salient feature of KGs is their ability to combine many heterogeneous data sources in a format that facilitates discovering connections. The utility of KGs has been exemplified in areas such as drug repurposing, with insights made through manual exploration and modeling of the data. In this chapter, we discuss promises and pitfalls of using natural language processing (NLP) to mine "unstructured text"- typically from scientific literature- as a data source for KGs. This draws on our experience of initially parsing "structured" data sources-such as ChEMBL-as the basis for data within a KG, and then enriching or expanding upon them using NLP. The fundamental promise of NLP for KGs is the automated extraction of data from millions of documents-a task practically impossible to do via human curation alone. However, there are many potential pitfalls in NLP-KG pipelines, such as incorrect named entity recognition and ontology linking, all of which could ultimately lead to erroneous inferences and conclusions.

Keywords: Database; DrugBank; Heterogeneous data; NLP; Named entity linking; Named entity recognition; Normalization; Ontologies; PubTator; SemMedDB; Unstructured text.

MeSH terms

  • Drug Discovery
  • Drug Repositioning
  • Humans
  • Natural Language Processing*
  • Pattern Recognition, Automated*