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Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents.

Senger S, Bartek L, Papadatos G, Gaulton A - J Cheminform (2015)

Bottom Line: 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.SureChEMBL and IBM SIIP found 62 and 59 %, respectively, of the compound-patent pairs obtained from Reaxys.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.

View Article: PubMed Central - PubMed

Affiliation: GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY UK.

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.

No MeSH data available.


Distribution of SureChEMBL-SciFinder overlap. Number of patents where the percentage of hits from SciFinder that are also present in SureChEMBL is within a given range
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Fig1: Distribution of SureChEMBL-SciFinder overlap. Number of patents where the percentage of hits from SciFinder that are also present in SureChEMBL is within a given range

Mentions: As can be seen in Fig. 1, for seven patents no more than 30 % of the molecules in SciFinder were also found in SureChEMBL. We decided to investigate in more detail why the overlap for these patents was so small.Fig. 1


Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents.

Senger S, Bartek L, Papadatos G, Gaulton A - J Cheminform (2015)

Distribution of SureChEMBL-SciFinder overlap. Number of patents where the percentage of hits from SciFinder that are also present in SureChEMBL is within a given range
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4594083&req=5

Fig1: Distribution of SureChEMBL-SciFinder overlap. Number of patents where the percentage of hits from SciFinder that are also present in SureChEMBL is within a given range
Mentions: As can be seen in Fig. 1, for seven patents no more than 30 % of the molecules in SciFinder were also found in SureChEMBL. We decided to investigate in more detail why the overlap for these patents was so small.Fig. 1

Bottom Line: 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.SureChEMBL and IBM SIIP found 62 and 59 %, respectively, of the compound-patent pairs obtained from Reaxys.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.

View Article: PubMed Central - PubMed

Affiliation: GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY UK.

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.

No MeSH data available.