Database Integration to Improve Accessibility to Public High-throughput Sequencing Data

A Presentation at National Institute of Genetics, Japan Retreat 2014

Transcript

1. Database Integration to Improve Accessibility to High-Throughput Seq Data
2. TAZRO OHTA @inutano
4. What do you imagine with a term “Database”?
8. Knowledge Scientific data Experimental data
9. Knowledge base Database Raw Data repository
10. Knowledge base Database Raw Data repository
11. What kind of data? Next-generation is already out there…
12. We all need Raw data repo for NGS
13. We’ve already seen WHY WE NEED
15. Reproducibility is what makes science fair.
16. 2 things required for data repository is…
17. 1: Reliability Data should be archived correctly, with explicit metadata 2: Accessibility Data should be able to be accessed by anyone, without special trick
18. 1: Reliability needs curation Data should be archived correctly, with explicit metadata 2: Accessibility needs good interface Data should be able to be accessed by anyone, without special trick
19. 1: Reliability needs curation Data should be archived correctly, with explicit metadata 2: Accessibility needs good interface Data should be able to be accessed by anyone, without special trick
20. 1: Reliability needs curation Data should be archived correctly, with explicit metadata 2: Accessibility needs good interface Data should be able to be accessed by anyone, without special trick
21. Current Web-interface for DRA http://trace.ddbj.nig.ac.jp/DRASearch
22. Good: Simple, Fast, and no bugs (!) Challenge: Lack of metadata caused “NOT FOUND”
23. PROBLEM:
24. ???
25. DRASearch can NOT find Data without metadata …but they definitely exist in the repo.
26. Too many to ask submitters; then we implemented a system to make metadata rich enough
27. 2 sources into DRA DDBJ Read Archive
28. Publications can have details of seq process, Seq Read Quality can be a source of data quality. DDBJ Read Archive PubMed PMC Extracted Read Quality
29. And then: integration enables to implement Efficient Data Search
30. Available via DBCLS SRA http://sra.dbcls.jp/
31. Available via DBCLS SRA http://sra.dbcls.jp/
32. Available via DBCLS SRA http://sra.dbcls.jp/
33. Power of Integration: Metadata Search http://sra.dbcls.jp/search
34. Power of Integration: Metadata Search http://sra.dbcls.jp/search
35. Power of Integration: Metadata Search http://sra.dbcls.jp/search
36. 83% seq reads satisfied average quality over 30 0.03% of seq reads fall into over 50% N content
37. 1: Reliability from paper/data qual more description brings more proof. 2: Accessibility from text-search Search included publication brings flexibility.
38. 2.20% of submitted projects has at least one publication 4429 / 201558 PROBLEM:
39. NIH Data sharing Guideline http://www.niaid.nih.gov/LabsAndResources/resources/dmid/Pages/data.aspx
40. NIH Data sharing Guideline http://www.niaid.nih.gov/LabsAndResources/resources/dmid/Pages/data.aspx
41. What is Next-step to carry on?
42. 1: Beyond Raw Data Archive is going to handle alignment data. 2: Analysis Reproducibility Public repo for analysis pipeline is required.
43. 1: Beyond Raw Data Archive is going to handle alignment data. 2: Analysis Reproducibility Public repo for analysis pipeline is required.
44. Database is for Biologists not for developers.
45. Thank you! t.ohta@dbcls.rois.ac.jp http://speakerdeck.com/inutano