Transcript EGA: Accessing and submitting controlled access data

The European Genome-phenome Archive
Accessing and submitting controlled access data
Jeff Almeida-King
User Support & Outreach
EGA Session summary
• Introduction to the EGA
• Accessing data (+hands on)
• Submitting sequence (+hands on)
EBI: Open and Controlled access archives
Sequence
Variants
EVA
Phenotypes
Structural
variants
Open & public archives
Controlled access archive
What is EGA controlled access data anyway?
• Usually human, personally identifiable (Genetic,
phenotypic)
• Affiliated to medical research or consortium projects
• Requires secure storage and distribution
• Access determined by formal application procedure
• Informed consents specifying controlled release
requirements
EGA Overview
• Launched 14th July 2008
• 2500+ data access accounts; 125+ submission accounts
• 700Tb+ data archived (200,000 samples); 600 datasets in distribution
• Data access decisions made by a Data Access Committee (DAC)
Consortium data archived at the EGA
Guide to accessing data
EGA Distribution model for controlled access
Obtaining an EGA Account
Using Your EGA Account
•
•
•
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Download accounts require manual set-ups
Distribution requires data preparation
Download accounts expire in 14 days
Data must be decrypted using keys supplied offline
Secure EGA Downloader (Pilot stage)
Log in/select transfer protocol
Create key
Select destination directory
Filter and select files
Download!
Secure EGA Downloader (Pilot phase)
Specify key
Select directories
Select files
Decrypt!
Exercises: Accessing data (Hands-on)
www.ebi.ac.uk/ega/tutorials/accessing_data
1) Navigating to your study of interest
2) Using your EGA acount
3) Downloading data
Directory: [Shared_folder]/ESGI/EGA/downloading_data/<token_name>
(exercise 3)
Submitting sequence
Why Submit to the EGA?
Funders and journals increasingly require researchers to have
a data sharing plan.
1) Wellcome Trust "Policy on data management and sharing”
http://www.wellcome.ac.uk/About-us/Policy/Policy-and-position-statements/WTX035043.html
2) Nature "Availability of data and materials”
http://www.nature.com/authors/editorial_policies/availability.html
3) Public Library of Science (PloS) "Sharing of Materials,
Methods, and Data”
http://www.plosone.org/static/policies.action#sharing
Who is submitting to the EGA?
Additional requirements for an EGA submission
• Submission statements & DAC access policy
• File preparation: Data encryption
• Register DAC, Policy and Dataset
How to submit to the EGA?
1
[email protected]
2
EGA submission account details
3
Using EGA uploader (encrypts, generates md5sums
and uploads)
4
Provide submission metadata
EGA Webin data uploader
Log in/select transfer protocol
Select source directory
Select submission files
Encrypt and upload!
EGA sequencing metadata
EGA Webin
Study
STUDY (EGAS)
Samples
SAMPLES (EGAN)
Experiment
EXPERIMENT (EGAX)
Run
Accessioned XML objects
RUNS (EGAR)
Dataset
Policy
DAC
DATASET(E
GAD)
POLICY (EGAP)
DATA ACCESS
COMMITTEE(E submission
objects
GAC)
EGA Webin
EGA sequencing analysis submissions
EGA Webin
•
(EGAS)
Aligned BAM, Variant STUDY
Call Files
(VCF) and phenotype files
•
Study
Relatively
small data size
•
Submission of both raw
and analysis
files encouraged
SAMPLES
(EGAN)
• Data
upload process remains the same
Samples
ANALYSIS (EGAZ)
Analysis
Dataset
Accessioned XML objects
DATASET
(EGAD)
POLICY(EGAP)
Policy
DAC
DATA ACCESS
COMMITTEE
(EGAC)
XML
objects
Acknowledgments
Paul Flicek
Team Leader
Vertebrate Genomics
Saif Ur-Rehman
Scientific Programmer
Justin Paschall
Team Leader
Variation
Jag Kandasamy
Web Developer
Ilkka Lappalainen
Variation Archive
Project Leader
Alexander Senf
Scientific Programmer
Vasudev Kumanduri
Scientific Programmer
Exercises: Submitting sequence
www.ebi.ac.uk/ega/tutorials/submitting_sequence
1) Uploading your files using the EGA Webin Uploader
2) Registering study, samples, experiments and runs
3) Registering your Data Access Committee, Policy and creating your dataset
Directory: /[Shared_folder]/ESGI/EGA/submitting_sequence/<token_name>