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1. EBI is an Outstation of the European Molecular Biology Laboratory.
EBI patent related services
Jennifer McDowall
Senior Scientist, EMBL-EBI
4th Annual
Forum for SMEs
October 18-19th 2010

2. • Patent sequence data
• Sequence archives
• Sequence searches
Overview
2 www.ebi.ac.uk

3. • Patent sequence data
• Sequence archives
• Sequence searches
Overview
3 www.ebi.ac.uk

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

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

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

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

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

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

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

11. Bulk Downloads
www.ebi.ac.uk
11
http://www.ebi.ac.uk/patentdata/
Patent proteins
Patent nucleotides
Non-redundant sequences

12. www.ebi.ac.uk
12
• Patent sequence data
• Sequence archives
• Sequence searches
Overview

13. Sequence archives
www.ebi.ac.uk
13
• ENA nucleotide sequence version archive (SVA)
www.ebi.ac.uk/embl/sva
• UniSave – UniProt sequence/annotation version archive
www.ebi.ac.uk/uniprot/unisave
Search by date 
get specific record
Search by accession
only  get all records

14. Provides complete version list
www.ebi.ac.uk
14
View old
entries
Compare
different versions

15. www.ebi.ac.uk
15
View old entries

16. Compare different versions
www.ebi.ac.uk
16

17. www.ebi.ac.uk
17 www.ebi.ac.uk
17
• Patent sequence data
• Sequence archives
• Sequence searches
Overview

18. EB-eye: text search
www.ebi.ac.uk
18
Fast, easy to use
Search for patent
WO0146262
Lists sequences
associated with
WO0146262
Lists all entries
associated with
WO0146262

19. www.ebi.ac.uk
www.ebi.ac.uk
SRS: advanced text search
For more complex searches
http://srs.ebi.ac.uk/
Select resources to search
Create query
then
Patent literature
Patent DNA
Patent proteins

20. 20 www.ebi.ac.uk
20 www.ebi.ac.uk
Sequence Similarity & Analysis
Search for patent
sequence
BLAST
FASTA
Iterative
searches
Fragment
searches

21. 21 www.ebi.ac.uk
FASTA nucleotide patent search
Search ENA
patent class
or
non-redundant
patent datasets

22. 22 www.ebi.ac.uk
FASTA protein patent search
Search individual
patent offices
or
non-redundant
patent datasets

23. 23 www.ebi.ac.uk
Results: patent protein v UniProt
Provide UniProt
records
Provide additional
annotation

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

25. 25 www.ebi.ac.uk
Functional predictions (protein searches)
• Visual comparison
• InterPro classification
• Helps identify mis- or
partial matches

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

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

28. EBI is an Outstation of the European Molecular Biology Laboratory.
Contacts:
http://www.ebi.ac.uk/support/
04.09.08
QUESTIONS?