ebi patent related services · non-redundant patent sequences enriched. sequence archives ena sva...

EBI is an Outstation of the European Molecular Biology Laboratory.

EBI patent related services

Jennifer McDowallSenior Scientist, EMBL-EBI

4th Annual Forum for SMEs

October 18-19th 2010

• Patent sequence data

• Sequence archives

• Sequence searches

Overview

2 www.ebi.ac.uk

• Patent sequence data

• Sequence archives

• Sequence searches

Overview

3 www.ebi.ac.uk

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September 2010nucl > 17.5m sequencesprot > 4.9m sequences

GenBank

ENA

DDBJ

EPO

USPTO JPO

EPO policy: data released topublic (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

Patent Sequence records

Universal Protein Resource

(UniProt)

Non-redundant Patent

Sequence Databases

European Nucleotide Archive

(ENA, formerly EMBL-Bank)

5 www.ebi.ac.uk

ENA

• ENA-Annotation >124m sequences

• Includes patent class (PAT): EPO, USTPO, JPO, KIPO

www.ebi.ac.uk6

• ENAold EMBL-Bank

raw data archives

ENA-Annotation

Trace ArchiveSequence Read Archive

+

• Dates include: date sequence went public, date of last revision

www.ebi.ac.uk

Patent sequence record in ENA

www.ebi.ac.uk7

Graphical viewer

Sequence

Patent reference

Navigate to related datae.g. Version

archive

Navigate to external data

sourcese.g. UniProt

Download data

DNA source

Dates (first public and last updated)

Sequence version

UniProt

www.ebi.ac.uk8

• 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 / TrEMBLNon-redundant archive

Metagenomic

Sequence clusters

Patent sequence record in UniProt

www.ebi.ac.uk9

Sequence

Navigate to individual entries

Download data

REMTREMBL(deprecated database)

Accession

List of databases containing sequence

www.ebi.ac.uk10

Non-redundant patent databases

www.ebi.ac.uk10

ENA(redundant)

Remove sequence redundancy

Level-1 NR

Remove patent family redundancy

Level-2 NR

Additional annotation, including priority dates

for patent family

Bulk Downloads

www.ebi.ac.uk11

http://www.ebi.ac.uk/patentdata/

Patent proteins

Patent nucleotides

Non-redundant sequences

www.ebi.ac.uk12

• Patent sequence data

• Sequence archives

• Sequence searches

Overview

Sequence archives

www.ebi.ac.uk13

• ENA nucleotide sequence version archive (SVA)www.ebi.ac.uk/embl/sva

• UniSave – UniProt sequence/annotation version archivewww.ebi.ac.uk/uniprot/unisave

Search by date get specific record

Search by accession only get all records

Provides complete version list

www.ebi.ac.uk14

View old entries

Compare different versions

www.ebi.ac.uk15

View old entries

Compare different versions

www.ebi.ac.uk16

www.ebi.ac.uk17 www.ebi.ac.uk17

• Patent sequence data

• Sequence archives

• Sequence searches

Overview

EB-eye: text search

www.ebi.ac.uk18

Fast, easy to use

Search for patent WO0146262

Lists sequences associated with

WO0146262

Lists all entries associated with

WO0146262

www.ebi.ac.ukwww.ebi.ac.uk

SRS: advanced text searchFor more complex searches

http://srs.ebi.ac.uk/

Select resources to search

Create query

thenPatent literature

Patent DNA

Patent proteins

20 www.ebi.ac.uk20 www.ebi.ac.uk

Sequence Similarity & AnalysisSearch for patent

sequence

BLAST

FASTA

Iterativesearches

Fragmentsearches

21 www.ebi.ac.uk

FASTA nucleotide patent search

Search ENA patent class

ornon-redundant patent datasets

22 www.ebi.ac.uk

FASTA protein patent search

Search individual patent offices

ornon-redundant patent datasets

23 www.ebi.ac.uk

Results: patent protein v UniProt

Provide UniProt records

Provide additional annotation

24 www.ebi.ac.uk24 www.ebi.ac.uk

Additional annotation (protein searches)Nucleotide sequences

Structures

GOmapping

Literature

Genome information

Domain/family classification

Reactions & pathways

Chemical information

Gene expression

Enzyme data

Molecular interactions

25 www.ebi.ac.uk

Functional predictions (protein searches)

• Visual comparison• InterPro classification• Helps identify mis- or

partial matches

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

Extractinformation

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

EBI is an Outstation of the European Molecular Biology Laboratory.

Contacts:http://www.ebi.ac.uk/support/

04.09.08

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