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1 EBI patent related services 4 th Annual Forum for SMEs October th 2010 Jennifer McDowall Senior Scientist, EMBL-EBI EBI is an Outstation of the European Molecular Biology Laboratory.

2 Overview Patent sequence data Sequence archives Sequence searches 2

3 Overview Patent sequence data Sequence archives Sequence searches 3

4 Sequence data from patent literature USPTO GenBank DDBJ JPO EPO policy: data released to public (and to EMBL) 18 months After patent application date, independent of whether patent has been granted. ENA EPO September 2010 nucl > 17.5m sequences prot > 4.9m sequences 4

5 Patent Sequence records European Nucleotide Archive (ENA, formerly EMBL-Bank) Universal Protein Resource (UniProt) Non-redundant Patent Sequence Databases 5

6 ENA ENA old EMBL-Bank + raw data archives ENA-Annotation Sequence Read Archive Trace Archive ENA-Annotation >124m sequences Includes patent class (PAT): EPO, USTPO, JPO, KIPO Dates include: date sequence went public, date of last revision 6

7 Patent sequence record in ENA Sequence version Navigate to related data e.g. Version archive Download data Dates (first public and last updated) Graphical viewer DNA source Patent reference Navigate to external data sources e.g. UniProt Sequence 7

8 UniProt Composed of 4 sections UniParc Non-redundant archive UniProtKB SwissProt / TrEMBL UniMES Metagenomic UniRef Sequence clusters UniParc >23m sequences Includes patent class (PRT): EPO, USTPO, JPO, KIPO Dates include: date sequence went public, date of last revision 8

9 Patent sequence record in UniProt Accession Download data List of databases containing sequence Navigate to individual entries REMTREMBL (deprecated database) Sequence 9

10 Non-redundant patent databases ENA (redundant) Remove sequence redundancy Level-1 NR Remove patent family redundancy Additional annotation, including priority dates for patent family Level-2 NR 10

11 Bulk Downloads Patent proteins Patent nucleotides Non-redundant sequences 11

12 Overview Patent sequence data Sequence archives Sequence searches 12

13 Sequence archives ENA nucleotide sequence version archive (SVA) /embl/sva UniSave Search by UniProt date sequence/annotation Search by accession version archive /uniprot/unisave get specific record only get all records 13

14 Provides complete version list Compare different versions View old entries 14

15 View old entries 15

16 Compare different versions 16

17 Overview Patent sequence data Sequence archives Sequence searches 17

18 Fast, easy to use EB-eye: text search Search for patent WO Lists all entries associated with WO Lists sequences associated with WO

19 For more complex searches SRS: advanced text search Select resources to search Create query Patent literature then Patent DNA Patent proteins

20 Sequence Similarity & Analysis Search for patent sequence Iterative searches BLAST Fragment searches FASTA 20

21 FASTA nucleotide patent search Search ENA patent class or non-redundant patent datasets 21

22 FASTA protein patent search Search individual patent offices or non-redundant patent datasets 22

23 Results: patent protein v UniProt Provide UniProt records Provide additional annotation 23

24 Additional annotation (protein searches) Nucleotide sequences Structures Molecular interactions GO mapping Enzyme data Literature Gene expression Genome information Chemical information Reactions & pathways 24 Domain/family classification

25 Functional predictions (protein searches) Visual comparison InterPro classification Helps identify mis- or partial matches 25

26 Functional predictions (protein searches) Extract information Prioritize results 100% ID Matches: family signature 4 domain signatures 34% ID Matches: family signature 3 domain signatures 28% ID Matches: 1 domain signature 26 24% ID Matches: No signatures

27 Summary Broad patent sequence coverage Protein/nucleotides: EPO, USTPO, JPO, KIPO Comprehensive sequence databases ENA & UniParc (PAT / PRT class data) Non-redundant patent sequences enriched Sequence archives ENA SVA & UniSave track changes Multiple search engines EB-eye text search >40 databases SRS advanced text searching >100 databases Multiple sequence search tools annotation-enhanced 27

28 QUESTIONS? Contacts: EBI is an Outstation of the European Molecular Biology Laboratory.

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