Schema for Lens Patents - Lens PatSeq Patent Document Sequences
  Database: mm10    Primary Table: patBulk Data last updated: 2016-03-14
Big Bed File Download: /gbdb/mm10/bbi/patBulk.bb
Item Count: 8,474,445
The data is stored in the binary BigBed format.

Format description: Summary information about a patent sequence derived from all documents that reference the sequence
fieldexampledescription
chromchr1Chromosome (or contig, scaffold, etc.)
chromStart130315656Start position in chromosome
chromEnd130315676End position in chromosome
nameoOiW0XchHC1DC3cBy5b1bgName of item
score0Score from 0-1000
strand-+ or
thickStart130315656Start of where display should be thick (start codon)
thickEnd130315676End of where display should be thick (stop codon)
reserved227,180,2Used as itemRgb as of 2004-11-22
blockCount1Number of blocks
blockSizes20,Comma separated list of block sizes
chromStarts0,Start positions relative to chromStart
docCount6Number of documents
claimCount0Documents with this sequence in the claims
grantCount1Granted patents
orgHomo sapiensDeclared organisms
dateRange21. Feb 2008 - 17. Apr 2014Publication dates
(earliest - latest)
patTitleORGAN-SPECIFIC PROTEINS AND METHODS OF THEIR USE (5); no title (1)Patent document titles
and document counts
(max. 10 titles)
intDocIdsWO_2008_021290_A2,EP_2057465_A2,JP_2010500568_A,US_2012_0087862_A1,US_8586006_B2,US_2014_0106981_A1Links to documents
claimGrantSeqIdsPatents with this sequence in the claims
grantSeqIdsUS_8586006_B2/sequences/view/64332|US_8586006_B2-64332 (46687)Patents with this sequence
claimSeqIdsApplications with this sequence in the claims
appSeqIdsWO_2008_021290_A2/sequences/view/64332|WO_2008_021290_A2-64332 (46687),EP_2057465_A2/sequences/view/64332|EP_2057465_A2-64332 (46686),JP_2010500568_A/sequences/view/30235|JP_2010500568_A-30235 (46687),US_2012_0087862_A1/sequences/view/64332|US_2012_0087862_A1-64332 (46687),US_2014_0106981_A1/sequences/view/64332|US_2014_0106981_A1-64332 (46687)Applications with this sequence
mouseOverORGAN-SPECIFIC PROTEINS AND METHODS OF THEIR USE (6 documents, 0 in claims, 1 granted)Mouseover
fprintPatSeq Fingerprint

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsdocCountclaimCountgrantCountorgdateRangepatTitleintDocIdsclaimGrantSeqIdsgrantSeqIdsclaimSeqIdsappSeqIdsmouseOverfprint
chr1130315656130315676oOiW0XchHC1DC3cBy5b1bg0-130315656130315676227,180,2120,0,601Homo sapiens21. Feb 2008 - 17. Apr 2014ORGAN-SPECIFIC PROTEINS AND METHODS OF THEIR USE (5); no title (1)WO_2008_021290_A2,EP_2057465_A2,JP_2010500568_A,US_2012_0087862_A1,US_8586006_B2,US_2014_0106981_A1US_8586006_B2/sequences/view/64332|US_8586006_B2-64332 (46687)WO_2008_021290_A2/sequences/view/64332|WO_2008_021290_A2-64332 (46687),EP_2057465_A2/sequences/view/64332|EP_2057465_A2-64332 (4 ...ORGAN-SPECIFIC PROTEINS AND METHODS OF THEIR USE (6 documents, 0 in claims, 1 granted)
chr1130316258130316277HglceO3mSmL6xowi75zKLA1-13031625813031627710,116,178119,0,610Artificial13. Jan 2011 - 05. Jun 2014COMPOSITIONS AND METHODS FOR ENHANCING PRODUCTION OF A BIOLOGICAL PRODUCT (2); CELL-BASED BIOPROCESSING (2); CHINESE HAMSTER OVA ...CA_2767225_A1,CA_2767231_A1,WO_2012_005898_A2,US_2014_0004565_A1,US_2014_0099666_A1,US_2014_0154783_A1WO_2012_005898_A2/sequences/view/2534175|WO_2012_005898_A2-2534175 (54137)CA_2767225_A1/sequences/view/2534175|CA_2767225_A1-2534175 (56682),CA_2767231_A1/sequences/view/2534175|CA_2767231_A1-2534175 (5 ...COMPOSITIONS AND METHODS FOR ENHANCING PRODUCTION OF A BIOLOGICAL PRODUCT (6 documents, 1 in claims, 0 granted)
chr1130316553130316572gd1E43SrHl6hrCx5U9ffGw0-130316553130316572227,180,2119,0,402Homo sapiens09. Mar 2006 - 10. Oct 2012siRNA molecules targeting Bcl-2 (2); no title (2)JP_2006507841_A,JP_2006507841_A,EP_2213738_B1,EP_2213738_B1EP_2213738_B1/sequences/view/928419|EP_2213738_B1-928419 (1560618),EP_2213738_B1/sequences/view/928519|EP_2213738_B1-928519 (156 ...JP_2006507841_A/sequences/view/928419|JP_2006507841_A-928419 (1562373),JP_2006507841_A/sequences/view/928519|JP_2006507841_A-928 ...siRNA molecules targeting Bcl-2 (4 documents, 0 in claims, 2 granted)
chr1130316591130316610w7VX9DzzB9P4ryjFSodm0g0-130316591130316610227,180,2119,0,201Homo sapiens05. Jan 2006 - 31. Jul 2007Bioinformatically detectable group of novel regulatory genes and uses thereof (2)US_2006_0003322_A1,US_7250496_B2US_7250496_B2/sequences/view/146506|US_7250496_B2-146506 (250627)US_2006_0003322_A1/sequences/view/146506|US_2006_0003322_A1-146506 (250625)Bioinformatically detectable group of novel regulatory genes and uses thereof (2 documents, 0 in claims, 1 granted)
chr1130316604130316617YefAzLJPK5_DH_WrhSC7sg0-130316604130316617227,180,2113,0,201C. elegans21. Jul 2011 - 15. May 2012Ribonucleic acid interference molecules and binding sites derived by analyzing intergenic and intronic regions of genomes (2)US_2011_0178283_A1,US_8178503_B2US_8178503_B2/sequences/view/710689|US_8178503_B2-710689 (744661)US_2011_0178283_A1/sequences/view/710689|US_2011_0178283_A1-710689 (744661)Ribonucleic acid interference molecules and binding sites derived by analyzing intergenic and intronic regions of genomes (2 doc ...
chr1130316679130316701Rou609-KDsRQc2C118t6_g0-130316679130316701227,180,2122,0,401Mus musculus17. Aug 2006 - 21. May 2013Ribonucleic acid interference molecules (3); RIBONUCLEIC ACID INTERFERERNCE MOLECULES AND METHODS FOR GENERATING PRECURSOR/MATUR ...CA_2588023_A1,US_2008_0125583_A1,US_2012_0040460_A1,US_8445666_B2US_8445666_B2/sequences/view/179055|US_8445666_B2-179055 (167247)CA_2588023_A1/sequences/view/179055|CA_2588023_A1-179055 (167247),US_2008_0125583_A1/sequences/view/179055|US_2008_0125583_A1-17 ...Ribonucleic acid interference molecules (4 documents, 0 in claims, 1 granted)
chr1130316742130316762ZKOJslMSLSz91py7KWaZTg0-130316742130316762227,180,2120,0,2505Unspecified23. Sep 2004 - 25. Sep 2012POLYPEPTIDE COMPOUNDS FOR INHIBITING ANGIOGENESIS AND TUMOR GROWTH (11); NUCLEIC ACID COMPOUNDS FOR INHIBITING ANGIOGENESIS AND ...CA_2518898_A1,CA_2518912_A1,US_2005_0084873_A1,US_2005_0164965_A1,US_2005_0249736_A1,EP_1605961_A2,CA_2581430_A1,WO_2006_034456_ ...US_7381410_B2/sequences/view/324|US_7381410_B2-324 (359),US_7585967_B2/sequences/view/324|US_7585967_B2-324 (347),US_7862816_B2/ ...CA_2518898_A1/sequences/view/324|CA_2518898_A1-324 (347),CA_2518912_A1/sequences/view/324|CA_2518912_A1-324 (347),US_2005_008487 ...POLYPEPTIDE COMPOUNDS FOR INHIBITING ANGIOGENESIS AND TUMOR GROWTH (25 documents, 0 in claims, 5 granted)
chr11303178191303178399IeBjGWwZN5D4oYniXs1FA0+13031781913031783920,178,187120,0,300Artificial05. Jan 2011 - 04. Aug 2011GENOME-WIDE CONSTRUCTION OF SCHIZOSACCHAROMYCES POMBE HETEROZYGOUS DELETION MUTANTS CONTAINING GENE-SPECIFIC BARCODES BY THE MET ...EP_2268808_A1,JP_2011517957_A,US_2011_0190163_A1EP_2268808_A1/sequences/view/9915|EP_2268808_A1-9915 (8397),JP_2011517957_A/sequences/view/9915|JP_2011517957_A-9915 (8397),US_2 ...GENOME-WIDE CONSTRUCTION OF SCHIZOSACCHAROMYCES POMBE HETEROZYGOUS DELETION MUTANTS CONTAINING GENE-SPECIFIC BARCODES BY THE MET ...
chr1130318280130318293ezvXOOpypGeskhGPHkT5Ng0+130318280130318293227,180,2113,0,101Homo sapiens02. Feb 2010Bioinformatically detectable group of novel regulatory oligonucleotides and uses thereofUS_7655785_B1US_7655785_B1/sequences/view/2048447|US_7655785_B1-2048447 (139851)Bioinformatically detectable group of novel regulatory oligonucleotides and uses thereof (1 documents, 0 in claims, 1 granted)
chr1130318351130318364U42D1QLF1zti4yWUuEvwqg1+130318351130318364187,20,50113,0,412Mycobacterium avium subsp. paratuberculosis08. Feb 2007 - 17. May 2011BIOINFORMATICALLY DETECTABLE GROUP OF NOVEL REGULATORY BACTERIAL AND BACTERIAL ASSOCIATED OLIGONUCLEOTIDES AND USES THEREOF (4)US_2007_0031843_A1,US_2007_0031843_A1,US_7943754_B2,US_7943754_B2US_7943754_B2/sequences/view/2877970|US_7943754_B2-2877970 (690833),US_7943754_B2/sequences/view/969749|US_7943754_B2-969749 (69 ...US_2007_0031843_A1/sequences/view/2877970|US_2007_0031843_A1-2877970 (690833)US_2007_0031843_A1/sequences/view/969749|US_2007_0031843_A1-969749 (690833)BIOINFORMATICALLY DETECTABLE GROUP OF NOVEL REGULATORY BACTERIAL AND BACTERIAL ASSOCIATED OLIGONUCLEOTIDES AND USES THEREOF (4 d ...

Lens Patents (patSeq) Track Description
 

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/mm10/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