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Structure-Activity Relationship (SAR) analysis is important for the development of novel small molecule drugs. Such analyses rely on bioactivity data either from in-house or published data, with data from the latter currently being extracted manually at much expensive.
Here we report on an entirely automated system for extracting bioactivity data that we are developing, initially targeting US patents. The system relies on combining the results of many technologies: chemical entity recognition, chemical name to structure, table processing, chemical compound number resolution, chemical sketch interpretation, and even in some cases reconstitution of molecules from a generic core and R-group definitions. Where possible, the target and the assay description are also identified.
To assess the precision/recall of our system we compare our results with those manually extracted from US patents by BindingDB. We also compare the data we’ve extracted with the data present in ChEMBL from journal articles, to analyse whether there are significant differences between activity data in journal articles and patents e.g. differences in targets of interest.