S yn KB : Semantic Search for Synthetic Procedures (2022)

Abstract: In this paper we present SynKB, an open-source, automatically extracted knowledge base of chemical synthesis protocols. Similar to proprietary chemistry databases such as Reaxsys, SynKB allows chemists to retrieve structured knowledge about synthetic procedures. By taking advantage of recent advances in natural language processing for procedural texts, SynKB supports more flexible queries about reaction conditions, and thus has the potential to help chemists search the literature for conditions used in relevant reactions as they design new synthetic routes. Using customized Transformer models to automatically extract information from 6 million synthesis procedures described in U.S. and EU patents, we show that for many queries, SynKB has higher recall than Reaxsys, while maintaining high precision. We plan to make SynKB available as an open-source tool; in contrast, proprietary chemistry databases require costly subscriptions.

## introduction commercial chemistry databases, such as reaxys 3 are invaluable tools for chemists, who issue structured sql-like queries to retrieve precise information about chemical reactions described in the literature. large, high-quality datasets are also crucial for synthetic route planning @xcite , automation @xcite , and machine learning approaches to retrosynthesis @xcite . in addition to proprietary, manually curated databases such as reaxys, recent work has begun to use automatically extracted data from reactions described in patents @xcite , however existing databases are limited to basic reaction information, and do not include important details such as concentrations or order of additions @xcite . the lack of high-quality data has been identified as a key challenge in developing recommendation models for reaction conditions @xcite . in this paper, we present synkb, a working system that demonstrates the application of modern nlp methods to extract large quantities of structured information about chemical synthesis procedures from text. synkb has a number of advantages with respect to existing chemistry databases such as reaxys: (1) we show that by automatically extracting information from millions of synthesis procedures described in u.s. and european patents using state-of-the-art nlp methods, we can achieve significantly higher recall than existing chemistry databases while maintaining high precision. in §3, we demonstrate synkb's coverage is complementary to reaxys; see figure 2 for details. (2) synkb's novel graph search supports better coverage of reaction conditions than existing chemistry databases; this includes concentrations, reaction times, order of the addition of reagents, catalysts, etc. (3) we will make synkb available as opensource software on publication, in contrast, most existing chemistry databases are proprietary, with the notable exception of @xcite , which we compare to in §3. we have built an online demo, which can be viewed at the following url: https://tinyurl. com/synkb . we will also release the source code and patent-based extractions used to build synkb on publication. ## synkb synkb is an open-source system that allows chemists to perform structured queries over large corpora of synthesis procedures. in this section, we present each component of synkb, as illustrated in figure 1 . our corpus collection is first presented in §2.1. section 2.2 describes how a corpus of six (6 million synth. procedures) ## empirical comparison in §2, we described the design and implementation of synkb including the underlying models, data preparation, and semantic search features. to demonstrate the utility of synkb for assisting chemists to search the literature for reaction details, we now evaluate its search features on ten example questions (q1-q10 in ## conclusion in this paper, we present synkb, a system for large-scale extraction and querying of chemical synthesis procedures. synkb provides efficient searches against semantic action graphs and chemical reaction slots derived from 6 million synthesis procedures contained in chemical patents. a quantitative comparison with reaxys, one of the leading commercial databases of reaction information, demonstrates the competence and versatility of our freely accessible system.