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EBI services

EBI services. Jennifer McDowall EMBL-EBI. Overview. Introduction EBI Databases Searching for sequences NEW: simple EBI search Advanced SRS text search Sequence search tools Accessing Old entries Sequence archives Chemoinformatics. Thematic index. Website:. http://www.ebi.ac.uk/.

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EBI services

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  1. EBI services Jennifer McDowall EMBL-EBI

  2. Overview • Introduction • EBI Databases • Searching for sequences • NEW: simple EBI search • Advanced SRS text search • Sequence search tools • Accessing Old entries • Sequence archives • Chemoinformatics

  3. Thematic index Website: http://www.ebi.ac.uk/ EBI Search Search all databases and literature in one go

  4. Website: Databases Tools • Patent resources • Sequences • Genomes • Chemistry • Structures • Gene expression • Reactions & pathways • Literature • Sequence searching • Sequence analysis • Structural analysis • Functional analysis Training Industry programme • eLearning • Workshops • 2Can education resource • Industry support • SME Support www.ebi.ac.uk

  5. EBI databases patent-related resources...

  6. USPTO JPO + KIPO GenBank DDBJ ENA EPO Sequence data from patent literature EPO policy: Data publically released 18 monthsafter patent application date (whether patent granted or not) INSDC agreement: • Free unrestricted access • Permanently accessible • All data exchanged daily October 2010 patent nucleotides > 17.5m sequencespatent proteins > 4.9m sequences

  7. Patent resources at EBI www.ebi.ac.uk/patentdata

  8. Patent sequence records at EBI • >124 million sequences • patent + non-patent nucleotides • redundant ENA (formerly EMBL-Bank) non-patent sequence prior art searches • >24 million sequences • patent + non-patent proteins • non-redundant UniParc (division of UniProt) patent sequence prior art searches • patent proteins and nucleotides • non-redundant • additional patent annotation NR patent sequences

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

  10. Sequence submissions Not accepted Submit claim to EPO Step 1 Generate sequence Step 2 Submit to journal Submit to ENA Submit to journal Submission guides at www.ebi.ac.uk

  11. Searching for sequences simple EBI search...

  12. EBI-Search by patent number Follow link to NEW EBI Search www.ebi.ac.uk

  13. EBI-Search by patent number Link to NEW EBI Search

  14. EBI-Search by patent number • Getting started • How it works • Gene & protein summaries NEW EBI Search Link to NEW EBI Search Training video

  15. EBI-Search by patent number Search for patent WO0146262 Link to NEW EBI Search

  16. EBI-Search by patent number Link to NEW EBI Search Search for WO0146262

  17. EBI-Search by patent number Sequence data for WO0146262 Link to NEW EBI Search Search for WO0146262 Literature for WO0146262

  18. EBI-Search by patent number Link to NEW EBI Search Search for WO0146262 Link to full patent paper

  19. EBI-Search by patent number Link to NEW EBI Search Search for WO0146262 WO0146262 literature and sequence databases

  20. EBI-Search by patent number Link to NEW EBI Search Search for WO0146262 WO0146262 literature and sequence databases WO0146262 in CiteXplore

  21. EBI-Search by patent number Link to NEW EBI Search Search for WO0146262 WO0146262 literature and sequence databases WO0146262 in CiteXplore

  22. EBI-Search by patent number Link to NEW EBI Search Search for WO0146262 WO0146262 literature and sequence databases WO0146262 in CiteXplore WO0146262 in Esp@cenet

  23. EBI-Search by patent number Link to NEW EBI Search Search for WO0146262 WO0146262 literature and sequence databases WO0146262 in CiteXplore WO0146262 in Esp@cenet

  24. EBI-Search by patent number Link to NEW EBI Search Search for WO0146262 WO0146262 literature and sequence databases WO0146262 in CiteXplore WO0146262 in Patent Lens WO0146262 in Esp@cenet

  25. EBI-Search by patent number Link to NEW EBI Search Search for WO0146262 WO0146262 literature and sequence databases WO0146262 in CiteXplore WO0146262 in Patent Lens WO0146262 in Esp@cenet

  26. EBI-Search by patent number Lists nucleotide sequences from WO0146262 Link to NEW EBI Search Search for WO0146262 WO0146262 literature and sequence databases WO0146262 in CiteXplore Additional annotation WO0146262 in Patent Lens WO0146262 in Esp@cenet

  27. EBI-Search by patent number Link to NEW EBI Search WO0146262 nucleotide sequence record in ENA Search for WO0146262 WO0146262 literature and sequence databases WO0146262 in CiteXplore WO0146262 in Patent Lens WO0146262 in Esp@cenet

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

  29. EBI-Search by patent number Link to NEW EBI Search Search for WO0146262 WO0146262 literature and sequence databases WO0146262 in CiteXplore ENA sequence record WO0146262 in Patent Lens WO0146262 in Esp@cenet

  30. EBI-Search by gene name Search for src gene Link to NEW EBI Search

  31. EBI-Search by gene name Link to NEW EBI Search Search for src

  32. EBI-Search by gene name Gene & protein summaries Link to NEW EBI Search Search for src Genome information

  33. EBI-Search by gene name Let’s select src in humans Link to NEW EBI Search Search for src

  34. EBI-Search by gene name Link to NEW EBI Search Search for src src gene & protein summary

  35. EBI-Search by gene name Species selector Link to NEW EBI Search Search for src src gene & protein summary

  36. EBI-Search by gene name • Gene sequence • Location • Sequence variations • Orthologs Gene tab Gene structure (forward & reverse strand) Link to NEW EBI Search Search for src src gene & protein summary Data source (Ensembl)

  37. EBI-Search by gene name Link to NEW EBI Search Search for src src gene & protein summary Gene & protein summary gene tab

  38. EBI-Search by gene name Expression tab Link to NEW EBI Search Search for src src gene & protein summary Gene & protein summary gene tab Data source (Expression Atlas) Expression studies

  39. EBI-Search by gene name Gene Atlas Link to NEW EBI Search Search for src src gene & protein summary Gene & protein summary gene tab See expression in cell type

  40. EBI-Search by gene name Link to NEW EBI Search Search for src Gene & protein summary expression tab src gene & protein summary Gene & protein summary gene tab

  41. EBI-Search by gene name Protein tab • Function • Isoforms • Sequence • Classification • Interactions Link to NEW EBI Search Search for src Gene & protein summary expression tab src gene & protein summary Gene & protein summary gene tab Data sources (UniProt, InterPro, IntAct)

  42. EBI-Search by gene name Link to NEW EBI Search Search for src Gene & protein summary expression tab src gene & protein summary Gene & protein summary gene tab Gene & protein summary protein tab

  43. EBI-Search by gene name Citation Structure tab Link to NEW EBI Search Search for src Gene & protein summary expression tab src gene & protein summary Gene & protein summary gene tab Structural domains 47 additional structures Data source (PDBe) Gene & protein summary protein tab

  44. EBI-Search by gene name Link to NEW EBI Search Search for src Gene & protein summary structure tab Gene & protein summary expression tab src gene & protein summary Gene & protein summary gene tab Gene & protein summary protein tab

  45. EBI-Search by gene name • Search results taken from: • PubMed • PubMedUK • Agricola • EPO Literature tab Divided into categories Description of categories Link to NEW EBI Search Search for src Gene & protein summary structure tab Gene & protein summary expression tab src gene & protein summary Gene & protein summary gene tab Gene & protein summary protein tab

  46. EBI-Search by gene name Literature tab Curator-selected articles Patents Link to NEW EBI Search Search for src Gene & protein summary structure tab Gene & protein summary expression tab src gene & protein summary Gene & protein summary gene tab Gene & protein summary protein tab

  47. EBI-Search by gene name Gene & protein summary literature tab Link to NEW EBI Search Search for src Gene & protein summary structure tab Gene & protein summary expression tab src gene & protein summary Gene & protein summary gene tab Gene & protein summary protein tab

  48. EBI-Search by gene name Reporting view  print full summary page Link to NEW EBI Search Search for src Gene & protein summary structure tab Gene & protein summary expression tab src gene & protein summary Gene & protein summary gene tab Gene & protein summary protein tab

  49. EBI-Search by gene name Print report Gene & protein summary literature tab Link to NEW EBI Search Search for src Gene & protein summary structure tab Gene & protein summary expression tab src gene & protein summary Gene & protein summary gene tab Gene & protein summary protein tab

  50. Searching for sequences advanced SRS text search...

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