title: What's What: The (Nearly) Definitive Guide to Reaction Role Assignment.
abstract: When analyzing chemical reactions it is essential to know which molecules are actively involved in the reaction and which educts will form the product molecules. Assigning reaction roles, like reactant, reagent, or product, to the molecules of a chemical reaction might be a trivial problem for hand-curated reaction schemes but it is more difficult to automate, an essential step when handling large amounts of reaction data. Here, we describe a new fingerprint-based and data-driven approach to assign reaction roles which is also applicable to rather unbalanced and noisy reaction schemes. Given a set of molecules involved and knowing the product(s) of a reaction we assign the most probable reactants and sort out the remaining reagents. Our approach was validated using two different data sets: one hand-curated data set comprising about 680 diverse reactions extracted from patents which span more than 200 different reaction types and include up to 18 different reactants. A second set consists of 50 000 randomly picked reactions from US patents. The results of the second data set were compared to results obtained using two different atom-to-atom mapping algorithms. For both data sets our method assigns the reaction roles correctly for the vast majority of the reactions, achieving an accuracy of 88% and 97% respectively. The median time needed, about 8 ms, indicates that the algorithm is fast enough to be applied to large collections. The new method is available as part of the RDKit toolkit and the data sets and Jupyter notebooks used for evaluation of the new method are available in the Supporting Information of this publication.
authors.affiliation: Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, 4002 Basel, Switzerland.
authors.forename: Nadine
authors.identifier: 0000-0001-5824-2764
authors.initials: N
authors.lastname: Schneider
authors.affiliation: Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, 4002 Basel, Switzerland.
authors.forename: Nikolaus
authors.initials: N
authors.lastname: Stiefl
authors.affiliation: T5 Informatics GmbH , Spalenring 11, 4055 Basel, Switzerland.
authors.forename: Gregory A
authors.identifier: 0000-0001-6279-4481
authors.initials: GA
authors.lastname: Landrum
mesh_terms: D000465:Algorithms; D062126:Databases, Chemical; D055808:Drug Discovery / Q000379:methods; D007202:Indicators and Reagents / Q000737:chemistry; D008956:Models, Chemical; D010330:Patents as Topic; D012984:Software
chemical_list: D007202:Indicators and Reagents