This document discusses plans to integrate proteomics data repositories using resources from the EUDAT data infrastructure. It describes replicating data from the ELIXIR repository PRIDE to EUDAT data centers for backup and access. This will test using EUDAT services like B2SAFE for replication and assigning persistent identifiers (PIDs) to datasets and files. The current status describes installing necessary software at participating sites and initial testing of replication from PRIDE to the Swedish National Bioinformatics Infrastructure data center. Future plans include syncing data changes and exploring data push/pull models between repositories.

1. European Life Sciences Infrastructure for Biological Information
www.elixir-europe.org
Rafael C Jimenez
ELIXIR CTO
EDUAT conference, 25 September 2014
Proteomics repositories integration
using EUDAT resources

2. Data submissions
2
Submissions
raw data
processed data
metadata
Data
repository
Search
Integration

3. Noble WS, MacCoss MJ (2012) Computational and Statistical Analysis of Protein Mass Spectrometry Data. PLoS Comput Biol 8(1):
e1002296. doi:10.1371/journal.pcbi.1002296
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002296
Overview of shotgun proteomics data production
MKKKNIYSIRKLGVG
IASVTLGTLLISG
GVTPAANAAQHD
FYQVLNMPNLNADQ
RNGFIQSLK
DDPSQSANVKLN
4
Peptide sequences
Raw data Process data
Metadata

4. Data examples
4
Raw data Process data Metadata
DNA
Human
Liver
Mitochondria
W. Smith
…
Peptide
Mouse
Heart
Nucleus
J. Heinz
…
LPISASHSSK…
TTGTTATCCG…
… … …

5. Proteomics data in PRIDE
5
~85% raw data

6. ProteomeCentral
Metadata /
Manuscript
Raw Data*
Results
Journals
UniProt/
NeXtProt
Peptide Atlas
Other DBs
Receiving repositories
PASSEL
(SRM data)
PRIDE
(MS/MS data)
GPMDB
Researcher’s results Reprocessed results Raw data* Metadata
ProteomeXchange
Vizcaíno et al., Nature Biotechnology, 2014
• Framework to enable standard data submission and
dissemination pipelines between the main existing
proteomics resources.

7. 7 Martens et al., Proteomics, 2005
Vizcaíno et al., NAR, 2013
PRIDE (PRoteomics IDEntifications) database
Mass spectrometry

8. Origin:
152 USA
108 Germany
67 United Kingdom
53 Switzerland
48 Netherlands
42 China
42 Canada
41 France
36 Spain
33 Belgium
25 Australia
23 Sweden
17 Japan
16 Denmark
13 Norway
12 Finland
12 India
12 Taiwan
10 Italy
9 Republic of Korea
8 Austria
8 Ireland
8 Brazil
7 Singapore
5 Israel
5 Russia …
Type:
273 PRIDE complete
501 PRIDE partial
47 PeptideAtlas/PASSEL complete
Access:
38.3% PRIDE public
5.3% PASSEL public
56% PRIDE private
0.4% PASSEL private
Data volume:
Total: >40 TB
Number of all files: >120,000
PXD000320-324: ~ 5 TB
PXD000065: ~ 1.4TB
Top Species studied by at least 8
datasets:
381 Homo sapiens
100 Mus musculus
31 Arabidopsis thaliana
26 Saccharomyces cerevisiae
16 Escherichia coli
14 Rattus norvegicus
12 Mycobacterium tuberculosis
11 Drosophila melanogaster
~ 215 species in total
Submissions/year:
2012: 102
2013: 527
2014: 192

9. Pilot evolution
• Use EUDAT
• Replication of ELIXIR data in EUDAT data centers
• Delegation of ELIXIR data in EUDAT data centers
• Adopt EUDAT
• Replication of ELIXIR data in ELIXIR data centers using EUDAT
technology
9

10. Replication of ELIXIR data in EUDAT data
centers
10
Central repository Data storage centers
Meta
data
Raw
Data
Meta
data
Results
Raw
Data

11. ProteomeCentral
Metadata /
Manuscript
Raw Data*
Results
Journals
UniProt/
NeXtProt
Peptide Atlas
Other DBs
Receiving repositories
GPMDB
Researcher’s results Reprocessed results Raw data* Metadata
Vizcaíno et al., Nature Biotechnology, 2014
Raw Data*
PASSEL
(SRM data)
PRIDE
(MS/MS data)
Replication of ELIXIR data in EUDAT data
centers

12. Delegation of ELIXIR data in EUDAT data
centers
12
Central repository Data storage centers
Meta
data
Raw
Data
Meta
data
Results
Raw
Data

13. ProteomeCentral
Metadata /
Manuscript
Raw Data*
Results
Journals
UniProt/
NeXtProt
Peptide Atlas
Other DBs
Receiving repositories
GPMDB
Researcher’s results Reprocessed results Raw data* Metadata
Vizcaíno et al., Nature Biotechnology, 2014
Raw Data*
PRIDE
(MS/MS data)
PASSEL
(SRM data)
Delegation of ELIXIR data in EUDAT data
centers

14. Replication of ELIXIR data in ELIXIR data centers
using EUDAT technology
14
National proteomics centers
Meta
data
Results
Raw
Data
Central repository
Meta
data
Results
Raw
Data

15. Plans
15
National proteomics centers
Meta
data
Results
Raw
Data
Central repository
Meta
data
Results
Raw
Data
Data storage centers
Meta
data
Raw
Data
1.- ELXIR replication
2.- EUDAT replication

16. Plans
16
National proteomics centers
Meta
data
Results
Raw
Data
Central repository
Meta
data
Results
Raw
Data
Data storage centers
Meta
data
Raw
Data
3.- delegation

17. ELIXIR Pilot action
17

18. EUDAT services
18

19. File sharing model
19
CSC
BILS
Site B
Site C
EUDAT CDIELIXIR
B2SAFE
B2SAFE
B2SAFE
B2SAFE
PRIDE
EMBL-EBI

20. Pilot – EUDAT adoption: ELIXIR replication
20
CSC
BILS
Site B
Site C
EUDAT CDIELIXIR
B2SAFE
B2SAFE
B2SAFE
B2SAFE
PRIDE
EMBL-EBI
Central repositoryNational proteomics centers
Meta
data
Results
Raw
Data
Meta
data
Results
Raw
Data

21. PIDs
21
ELIXIR
community center
ELIXIR
Data center 1
EUDAT
Data center 1
CSCPRIDEBILS

22. Status
• BILS
• Migrating from existing Swestore dCache to iRODS
• Testing compatibility with B2SAFE
• Latest iRDOS not compatible with B2SAFE?
• PRIDE
• iRODS service installed
• B2SAFE module have been deployed at EMBL-EBI (PRIDE)
• Test B2SAFE replication PRIDE -> CSC
• DOI for datasets
• PID for dataset files
• Web service to associate datasets to dataset files
22

23. Status
In progress
• Handle System Registration
• Test requests of EPIC/EUDAT identifiers
Open questions
• BILS local PIDs?
• Sync back from PRIDE to BILS for modifications/additions at PRIDE?
• Data push or pull model?
• Replication of process data requires previous validation
23

24. Participants
EUDAT/CSC
• Jani Heikkinen
• Damien Lecarpentier
• Johannes Reetz
EMBL-EBI/systems
• Andy Jenkinson
• Steven Newhouse
24
BILS
• Mikael Borg
• Fredrik Levander
• Bengt Persson
EMBL-EBI/PRIDE
• JuanAntonioVizcaíno
• RuiWang
• Henning Hermjakob
ELIXIR Hub
• Rafael C Jimenez

25. European LifeSciences Infrastructure for Biological Information
www.elixir-europe.org
Thank you for your attention

26. Delegation of raw data
26
processed data
metadata
Data
repository
PID
Submissions
Search
Integration

27. 27
National proteomics centers
Meta
data
Results
Raw
Data
Central repository
Meta
data
Results
Raw
Data
Data storage centers
Meta
data
Raw
Data
National proteomics centers
Meta
data
Results
Raw
Data
Central repository
Meta
data
Results
Raw
Data
Data storage centers
Meta
data
Raw
Data