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

Abstract

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/.

Figure 1.

Data growth of EMBL-Bank patent class. The curve indicates the number of entries in the EMBL-Bank patent class has increased dramatically during the past decade.

Figure 2.

Steps to create non-redundant patent sequence databases at two levels. Squares of the same colour represent level-1 sequences, 100% identical over the whole length. Squares of the same colour and pattern represent level-2 sequences, which are identical and belong to the same invention (i.e. patent family).

Figure 3.

Publication number error types detected in the sequence data set (both nucleotide and protein). ‘KC only’ represents the errors of incorrect KC only; ‘KC completeness only’ represents the errors of incomplete KC only; ‘KC + PN’ represents the errors of wrong PN and wrong KC; ‘KC completeness + PN’ represents the errors of incomplete KC and wrong PN; ‘PN only’ represents the errors of wrong PN only; ‘Publication Level only’ represents errors of publication level only; and ‘Pending’ represents publication numbers which currently cannot be resolved and are pending for corrections.