title: Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents.
abstract: BACKGROUND
  First public disclosure of new chemical entities often takes place in patents, which makes them an important source of information. However, with an ever increasing number of patent applications, manual processing and curation on such a large scale becomes even more challenging. An alternative approach better suited for this large corpus of documents is the automated extraction of chemical structures. A number of patent chemistry databases generated by using the latter approach are now available but little is known that can help to manage expectations when using them. This study aims to address this by comparing two such freely available sources, SureChEMBL and IBM SIIP (IBM Strategic Intellectual Property Insight Platform), with manually curated commercial databases.
  
  
  RESULTS
  When looking at the percentage of chemical structures successfully extracted from a set of patents, using SciFinder as our reference, 59 and 51 % were also found in our comparison in SureChEMBL and IBM SIIP, respectively. When performing this comparison with compounds as starting point, i.e. establishing if for a list of compounds the databases provide the links between chemical structures and patents they appear in, we obtained similar results. SureChEMBL and IBM SIIP found 62 and 59 %, respectively, of the compound-patent pairs obtained from Reaxys.
  
  
  CONCLUSIONS
  In our comparison of automatically generated vs. manually curated patent chemistry databases, the former successfully provided approximately 60 % of links between chemical structure and patents. It needs to be stressed that only a very limited number of patents and compound-patent pairs were used for our comparison. Nevertheless, our results will hopefully help to manage expectations of users of patent chemistry databases of this type and provide a useful framework for more studies like ours as well as guide future developments of the workflows used for the automated extraction of chemical structures from patents. The challenges we have encountered whilst performing this study highlight that more needs to be done to make such assessments easier. Above all, more adequate, preferably open access to relevant 'gold standards' is required.
authors.affiliation: GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY UK.
authors.forename: Stefan
authors.identifier: 0000-0002-7188-9607
authors.initials: S
authors.lastname: Senger
authors.affiliation: GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY UK.
authors.forename: Luca
authors.initials: L
authors.lastname: Bartek
authors.affiliation: European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK.
authors.forename: George
authors.initials: G
authors.lastname: Papadatos
authors.affiliation: European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK.
authors.forename: Anna
authors.initials: A
authors.lastname: Gaulton
keywords: IBM SIIP; Patent chemistry databases; Patents; SureChEMBL