Targeted Multi-Modal Passage Search for Molecules and their Synthesis Pathways

We present a chemical extraction and search pipeline intended to support information tasks related to drug discovery. Commonly used search tools for drug discovery such as Reaxys and SciFinder do not allow users to obtain retrieval results at the passage level. To address this, we present a passage retrieval tool for chemical patents that supports queries combining text and molecule diagrams expressed in SMILES. When SMILES is provided as a part of a query, the system refines text retrieval results through matching both textual names and drawn figures based on extracted SMILES representations. Molecule matches are obtained through substructure matching and structural similarity. This functionality was motivated by a chemist's need to find synthesis pathways for specific molecules containing a substructure of interest that binds and thus inhibits specific human genes. For this demonstration, we index a collection of 131 PDF patents categorized into 12 specific genes enabling a user to search on them. There are 32,301 document pages in the collection. Our user interface can be accessed at https://unichemfinder.gccis.rit.edu/. Our source code and data is available at https://gitlab.com/dprl/unichemfinder.