Network Analysis of the Organic Chemistry in Patents, Literature, and Pharmaceutical Industry

Journal article, 2025

Chemical reactions can be connected in large networks such as knowledge graphs. In this way, prior work has been able to draw meaningful conclusions about the properties and structures involved in organic chemistry reactions. However, the research has focused on public sources of organic synthesis that might lack the intricate details of the synthetic routes used in in-house drug discovery. In this work, previous analyses are expanded to also include an in-house electronic lab notebook (ELN) source, such that we can compare it to knowledge graphs that were constructed from US Patent and Trademark Office (USPTO) and Reaxys. We found that the Reaxys knowledge graph is the most interconnected and has the largest proportion of nodes belonging to the core, whereas the USPTO is much less connected and only has a small core. The ELN knowledge graph falls between these extremes in connectivity and it does not have any core. The hub molecules of ELN and USPTO are most similar, primarily represented by small, organic building blocks. We hypothesize that these differences can be attributed to the different origins of the data in the three sources. We discuss what impact this might have on synthesis prediction modelling.