Description

This track shows genome matches to biomedical sequences submitted with patent application documents to patent offices around the world. The sequences, their mappings, and selected patent information were graciously provided by PatSeq, a search tool part of The Lens, Cambia.

This track contains more data than the NCBI Genbank Division "Patents", as the sequences were extracted from patents directly.

Display Convention and Configuration

The data is split into two subtracks: one for sequences that are only part of patents that have submitted more than 100 sequences ("bulk patents") and a second track for all other sequences ("non-bulk patents").

A sequence can be part of many patent documents, with some being found in several thousand patents. This track shows only a single alignment for every sequence, colored based on its occurrence in the different patent documents and using a color schema similar to The Lens.

Based on the first sequence match, the four different item colors follow this priority ranking in descending order:

	the sequence is referenced in the claims of a granted patent
	the sequence is disclosed in a granted patent
	the sequence is referenced in the claims of a patent application
	the sequence is disclosed in a patent application

Sequences referenced in the claims section of a patent document define the scope of the invention and are important during litigation. Therefore, they are given priority in the color scheme. Patent grant documents form the basis of patent protection and are prioritized over applications.

Hover over a feature with the mouse to see the total number of documents where the sequence has been referenced, how many of these documents are granted patents and how often the sequence has been referenced in the claims. A randomly selected document title is also shown in the mouseover.

Clicking on a feature will bring up the details page, which contains information about the sequence and alignment of that feature. The link at the top of the page opens the PatSeq Analyzer with the chromosomal region covered by the feature that was clicked. The PatSeq Analyzer is a specialized genome browser that allows for the viewing and filtering of patent sequence matches in detail.

The next section of the details page is a list of up to ten patent documents that include this sequence, with the number of occurrences within each document in parentheses. This is followed by up to thirty links to patent documents. The patent documents listed in these sections are displayed in order of the number of sequence occurrences in the document. Shown below these are the links to the sequence in The Lens, in the format "patentDocumentIdentifier-SEQIDNO (docSequenceCount)". The "SEQ ID NO" is an integer number, the unique identifier of a patent sequence in a patent document. When a protein sequence has been annotated on a nucleotide sequence, the "SEQ ID NO" contains the reading frame separated by a ".", e.g. "1.1" would indicate the first frame of SEQIDNO 1. The total number of sequences submitted with the patent document ("docSequenceCount") is shown in parentheses after the SEQIDNO. The links to the sequence are separated into the categories "granted and in claims", "granted", "in claims" and "applications" (=all others). Sequence identifiers link to the respective pages on PatSeq. A maximum of thirty documents are linked from this page per category listed in order of the number of sequence occurrences; please use PatSeq Analyzer to view all matching documents.

The score of the features in this track is the number of documents where the sequence appears in the claims. For example, by setting the score filter to 1, only sequences are shown that have been referenced at least once in the claims.

Methods

More than 96 million patent document files were collected by The Lens. The ST.25-formatted sequences were extracted and mapped to genomes with the aligners BLAT and BWA. The minimal identity of the query over the alignment is 95%. Note that for hg19, no patents are shown on chrM, as the mitochondrial chromosome used for the mapping was the one from the Ensembl genome FASTA files.

Credits

Thanks to the team behind The Lens, in particular, Osmat Jefferson and Deniz Koellhofer, for making these data available.

Feedback

Send suggestions on the way data in this track is visualized to our support address genome@soe.ucsc.edu. Questions on the data itself are best directed to support@cambia.org.

Data access

The raw data can be explored interactively with the Table Browser. For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The files for this track are called patNonBulk.bb and patBulk.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here.

The command to obtain the data as a tab-separated table looks like this:

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/patNonBulk.bb -chrom=chr5 -start=1000000 -end=2000000 output.tsv

A full log of the commands that were used to build this annotation is available from our database build description. In this text file, search for "patNonBulk" to find the right section.

References

Editorial: The patent bargain Nature. 2013 Dec 12;504(7479):187-188.

Patently transparent. Nat Biotechnol. 2006 May;24(5):474. PMID: 16680110

Jefferson OA, Köllhofer D, Ehrich TH, Jefferson RA. Transparency tools in gene patenting for informing policy and practice. Nat Biotechnol. 2013 Dec;31(12):1086-93. PMID: 24316644