EBI patent related services · Non-redundant patent sequences enriched. Sequence archives ENA SVA &...
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EBI is an Outstation of the European Molecular Biology Laboratory. EBI patent related services Jennifer McDowall Senior Scientist, EMBL-EBI 4 th Annual Forum for SMEs October 18-19 th 2010
Transcript of 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
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• Patent sequence data
• Sequence archives
• Sequence searches
Overview
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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)
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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
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Sequence Similarity & AnalysisSearch for patent
sequence
BLAST
FASTA
Iterativesearches
Fragmentsearches
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FASTA nucleotide patent search
Search ENA patent class
ornon-redundant patent datasets
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FASTA protein patent search
Search individual patent offices
ornon-redundant patent datasets
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Results: patent protein v UniProt
Provide UniProt records
Provide additional annotation
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Additional annotation (protein searches)Nucleotide sequences
Structures
GOmapping
Literature
Genome information
Domain/family classification
Reactions & pathways
Chemical information
Gene expression
Enzyme data
Molecular interactions
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Functional predictions (protein searches)
• Visual comparison• InterPro classification• Helps identify mis- or
partial matches
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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
Presenter
Presentation Notes
Compare InterPro coverage to find mis- or partial matches
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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
QUESTIONS?
