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Nucleic Acids Research Advance Access published online on November 1, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp960
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

Non-redundant patent sequence databases with value-added annotations at two levels

Weizhong Li1, Hamish McWilliam1, Ana Richart de la Torre2, Adam Grodowski2, Irina Benediktovich2, Mickael Goujon1, Stephane Nauche2 and Rodrigo Lopez1,*

1European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and 2European Patent Office, IQ Life Sciences, Patentlaan 3-9, 2288 EE Rijswijk, The Netherlands

*To whom correspondence should be addressed. Tel: +44 1223 494423; Fax: +44 1223 494468; Email: rls{at}ebi.ac.uk.

Received August 25, 2009. Revised September 22, 2009. Accepted October 13, 2009.

The European Bioinformatics Institute (EMBL-EBI) provides public access to patent data, including abstracts, chemical compounds and sequences. Sequences can appear multiple times due to the filing of the same invention with multiple patent offices, or the use of the same sequence by different inventors in different contexts. Information relating to the source invention may be incomplete, and biological information available in patent documents elsewhere may not be reflected in the annotation of the sequence. Search and analysis of these data have become increasingly challenging for both the scientific and intellectual-property communities. Here, we report a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents. The databases were created at two levels by the use of sequence MD5 checksums. Sequences within a level-1 cluster are 100% identical over their whole length. Level-2 clusters were defined by sub-grouping level-1 clusters based on patent family information. Value-added annotations, such as publication number corrections, earliest publication dates and feature collations, significantly enhance the quality of the data, allowing for better tracking and cross-referencing. The databases are available format: http://www.ebi.ac.uk/patentdata/nr/.


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