Upgrade to Pro
— share decks privately, control downloads, hide ads and more …
Speaker Deck
Features
Speaker Deck
PRO
Sign in
Sign up for free
Search
Search
Database Integration to Improve Accessibility to Public High-throughput Sequencing Data
Search
Tazro Inutano Ohta
July 04, 2014
Science
0
140
Database Integration to Improve Accessibility to Public High-throughput Sequencing Data
A Presentation at National Institute of Genetics, Japan Retreat 2014
Tazro Inutano Ohta
July 04, 2014
Tweet
Share
More Decks by Tazro Inutano Ohta
See All by Tazro Inutano Ohta
Yevis: System to support building a workflow registry with automated quality control
inutano
0
95
Standardization of biological sample information database
inutano
0
38
Describe data analysis workflow with workflow languages
inutano
4
3.7k
Container virtualization technologies and workflow languages improve portability and reproducibility of data analysis environment
inutano
3
310
次世代シーケンサーによるメタゲノム解析:桜の花びらに付着した環境DNAを解析する
inutano
0
63
Workflows that run everywhere and where to run them
inutano
0
130
The Sequence Read Archive search system to make use of public high-throughput sequencing data
inutano
0
220
Improve portability of bioinformatics software across HPC and cloud infrastructures
inutano
1
83
Container, Cloud, and HPC
inutano
0
140
Other Decks in Science
See All in Science
Ph.D. defense "Convex Manifold Approximation for Tensors"
gkazunii
0
170
DEIM2024 チュートリアル ~AWSで生成AIのRAGを使ったチャットボットを作ってみよう~
yamahiro
2
570
Science of Scienceおよび科学計量学に関する研究論文の俯瞰可視化_LT版
hayataka88
0
400
Pandas 2 vs Polars vs Dask (PyDataGlobal 2023 December)
ianozsvald
0
410
qeMLパッケージの紹介
bob3bob3
0
960
LCG20
lcolladotor
0
190
Endocannabinology 101
drbonci
PRO
0
250
脳とAIは似ているか ― NeuroAI の挑戦
ykamit
9
6.8k
(Forkwell Library #48)『詳解 インシデントレスポンス』で学び倒すブルーチーム技術
scientia
2
880
『データ可視化学入門』を PythonからRに翻訳した話
bob3bob3
1
360
データで課題を解決する -因果関係を調べる統計的因果推論-
sshimizu2006
4
1.3k
Mastering Feature Engineering: Mining the Hidden Salary Formula with CakeResume
tlyu0419
0
130
Featured
See All Featured
Navigating Team Friction
lara
177
13k
Docker and Python
trallard
33
2.7k
Atom: Resistance is Futile
akmur
258
25k
Large-scale JavaScript Application Architecture
addyosmani
503
110k
Adopting Sorbet at Scale
ufuk
67
8.6k
Responsive Adventures: Dirty Tricks From The Dark Corners of Front-End
smashingmag
243
20k
The Language of Interfaces
destraynor
151
23k
Music & Morning Musume
bryan
41
5.6k
Building a Scalable Design System with Sketch
lauravandoore
455
32k
It's Worth the Effort
3n
180
27k
Bootstrapping a Software Product
garrettdimon
PRO
301
110k
Done Done
chrislema
178
15k
Transcript
Database Integration to Improve Accessibility to High-Throughput Seq Data
TAZRO OHTA @inutano
None
What do you imagine with a term “Database”?
None
None
None
Knowledge Scientific data Experimental data
Knowledge base Database Raw Data repository
Knowledge base Database Raw Data repository
What kind of data? Next-generation is already out there…
We all need Raw data repo for NGS
We’ve already seen WHY WE NEED
None
Reproducibility is what makes science fair.
2 things required for data repository is…
1: Reliability Data should be archived correctly, with explicit metadata
2: Accessibility Data should be able to be accessed by anyone, without special trick
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
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
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
Current Web-interface for DRA http://trace.ddbj.nig.ac.jp/DRASearch
Good: Simple, Fast, and no bugs (!) Challenge: Lack of
metadata caused “NOT FOUND”
PROBLEM:
???
DRASearch can NOT find Data without metadata …but they definitely
exist in the repo.
Too many to ask submitters; then we implemented a system
to make metadata rich enough
2 sources into DRA DDBJ Read Archive
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
And then: integration enables to implement Efficient Data Search
Available via DBCLS SRA http://sra.dbcls.jp/
Available via DBCLS SRA http://sra.dbcls.jp/
Available via DBCLS SRA http://sra.dbcls.jp/
Power of Integration: Metadata Search http://sra.dbcls.jp/search
Power of Integration: Metadata Search http://sra.dbcls.jp/search
Power of Integration: Metadata Search http://sra.dbcls.jp/search
83% seq reads satisfied average quality over 30 0.03% of
seq reads fall into over 50% N content
1: Reliability from paper/data qual more description brings more proof.
2: Accessibility from text-search Search included publication brings flexibility.
2.20% of submitted projects has at least one publication 4429
/ 201558 PROBLEM:
NIH Data sharing Guideline http://www.niaid.nih.gov/LabsAndResources/resources/dmid/Pages/data.aspx
NIH Data sharing Guideline http://www.niaid.nih.gov/LabsAndResources/resources/dmid/Pages/data.aspx
What is Next-step to carry on?
1: Beyond Raw Data Archive is going to handle alignment
data. 2: Analysis Reproducibility Public repo for analysis pipeline is required.
1: Beyond Raw Data Archive is going to handle alignment
data. 2: Analysis Reproducibility Public repo for analysis pipeline is required.
Database is for Biologists not for developers.
Thank you!
[email protected]
http://speakerdeck.com/inutano