EMBL-EBI Patent Services

Transcription

1 EMBL-EBI Patent Services 5 th Annual Forum for SMEs October 6-7 th 2011 Jennifer McDowall EBI is an Outstation of the European Molecular Biology Laboratory.

2 Patent resources at EBI 2

3 International sequence DB agreement GenBank DDBJ Fourth INSDC level INSDC agreement: Free unrestricted access All data exchanged daily ENA How do they differ? organization of data 3 tools and database links

4 Distributing patent sequences USPTO other patent offices 4 GenBank DDBJ Fourth INSDC level ENA EPO NR patent sequence databases JPO KIPO

5 Why new patent sequence databases? Patent proteins: Patent nucleotides: EPO USPTO JPO KIPO ENA (EPO, USPTO, JPO, KIPO) 5 Non-redundant sequence data Patent family classification Enriched with patent information

6 Searching redundant databases Protein Example: Search patent protein sequence Patent proteins 6

7 Results from redundant databases. >260 identical results too much to analyze 7

8 NR patent sequence databases removes Fourth redundancy level LEVEL1 NR patent sequence database fewer results to analyze, less chance of missing important results 8

9 Searching patent sequences NR patent Level-1 Example: Search patent protein sequence NR patent level-1 9

10 Results from level-1 database Each hit unique 10

11 Results from level-1 database List of all patents containing the sequence Earliest publication date Fifth Link level to sequence entry Link to patent documentation 11

12 Patent families Simple Patent Family is a group of patents that relate to the same invention, and are based on the same originating application They arise when an invention is patented in multiple countries Grouping patents into families reduces multi-national results down to a representative member 12

13 Patent families patent family Invention A second patent family ADA42650 HB GM CS ACQ13114 DI AAR79155 DD % identical sequences Invention B EP WO US US JP Same sequence can appear multiple times in a database due to: Same invention filed multiple times in different offices (same patent family) Different inventors use the same sequence in different contexts (different 13 patent families)

14 NR patent sequence databases LEVEL2 NR patent sequence database groups identical sequences by patent family provides earliest priority date for family 14

15 Searching patent sequences NR patent Level-2 Example: Search patent protein sequence NR patent level

16 Results from level-2 database Each hit = one family 16

17 Results from level-2 database patents in same family Earliest Second publication level (priority) date in family Fifth Link level to sequence entry Link to patent documentation 17

18 Non-redundant patent databases Level-1 Patent Patent Click nucleotides to edit Master proteins text styles NRNL1 NRPL1 (Non-redundant (Non-redundant nucleotide level-1) Fourth protein level-1) level Groups together 100% identical patent sequences Level-2 NRNL2 (Non-redundant nucleotide level-2) NRPL2 (Non-redundant protein level-2) Groups together identical sequences by patent family 18

19 Non-redundant patent databases ENA (redundant) Remove sequence redundancy Level-1 NR Group by patent families Additional annotation, including priority dates for patent families Level-2 NR 19

20 Patent sequence records at EBI Nucleotide Protein ENA ~22.3 M PAT sequences NRNL1 Second ~11.5 M level sequences NRNL2 Fourth ~16.7 level M sequences Patent Proteins ~6.0 M PRT sequences NRPL1 ~2.3 M sequences 20 NRPL2 ~3.8 M sequences

21 SRS advanced text search

22 SRS: advanced text search 1 st : Select resources to search 2 nd : Create query 22

23 SRS: advanced text search Select library tab 23

24 SRS: advanced text search Select library tab Search >100 databases NR patent DNA (NRNL1 & NRNL2) NR patent proteins (NRPL1 & NRPL2) 24

25 SRS: advanced text search Select library tab Example: Selected to search NR level-1 patent DNA database Search >100 databases 25

26 SRS: advanced text search Select library tab Select resources to search 26

27 SRS: advanced text search Select library tab Select Second resources level to search 27 1) Select field 2) Type in text

28 SRS: advanced text search Select library tab Select Second resources level to search 28 Here, selected patent number

29 SRS: advanced text search Select library tab Select Second resources level to search Create query 29

30 SRS: advanced text search Select library tab Select Second resources level to search Create query Lists non-redundant nucleotide sequences from WO

31 SRS: advanced text search Select library tab Select Second resources level to search Create query WO sequences 31

32 SRS: advanced text search Select library tab WO nucleotide sequence record in NRNL1 Select Second resources level to search Create query WO sequences 32 Details which other patents also claim this sequence (with NRNL2, would see family grouping)

33 SRS: advanced text search Select library tab Select Second resources level to search Create query NRNL1 sequence record WO sequences 33

34 SRS: advanced text search Select library tab Select Second resources level to search Create query WO literature WO sequences NRNL1 sequence record 34

35 Summary NR patent databases Searches against a non-redundant database are faster and ensures all entries are identified 35 Non-redundant Patent family classification Publication Fifth data level corrections Take family concepts into consideration; earliest priority date Correction of publication numbers and kind codes significantly improves data quality Annotation The collation of all biological features in a single record provides a significant improvement for understanding the biological context in which the sequence is being used

36 Help Contacts: 36