proteomics repositories integration using eudat resources · proteomics repositories integration...

European Life Sciences Infrastructure for Biological Informationwww.elixir-europe.org

Rafael C JimenezELIXIR CTO

25 September 2014

Proteomics repositories integration using EUDAT resources

Data submissions

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Integration

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

http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002296

Data examples

4

Raw data Process data Metadata

DNA

Human

Liver

Mitochondria

W. Smith

…

Peptide

Mouse

Heart

Nucleus

J. Heinz

…

LPISASHSSK…

TTGTTATCCG…

… … …

Proteomics data in PRIDE

5

~85% raw data

ProteomeCentralMetadata /

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 Martens et al., Proteomics, 2005

Vizcaíno et al., NAR, 2013

PRIDE (PRoteomics IDEntifications) database

Mass spectrometry

Origin: 152 USA108 Germany67 United Kingdom53 Switzerland48 Netherlands42 China42 Canada41 France36 Spain33 Belgium25 Australia23 Sweden17 Japan16 Denmark13 Norway12 Finland12 India12 Taiwan10 Italy9 Republic of Korea8 Austria8 Ireland8 Brazil7 Singapore5 Israel5 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

Pilot evolution

• Use EUDAT• Replication of ELIXIR data in EUDAT data centers

• Delegation of ELIXIR data in EUDAT data centers

• Adopt EDUAT• Replication of ELIXIR data in ELIXIR data centers using EUDAT

technology

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Replication of ELIXIR data in EUDAT data centers

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Central repository Data storage centers

Meta

data

Raw

Data

Meta

data

ResultsRaw

Data


Manuscript

Raw Data*

Results

Journals

UniProt/

NeXtProt

Peptide Atlas

Other DBs


GPMDB



Raw Data*

PASSEL

(SRM data)

PRIDE

(MS/MS data)

Replication of ELIXIR data in EUDAT data centers

Delegation of ELIXIR data in EUDAT data centers

12

Central repository Data storage centers

Meta

data

Raw

Data

Meta

data

ResultsRaw

Data


Manuscript

Raw Data*

Results

Journals

UniProt/

NeXtProt

Peptide Atlas

Other DBs


GPMDB



Raw Data*

PRIDE

(MS/MS data)

PASSEL

(SRM data)

Delegation of ELIXIR data in EUDAT data centers

Replication of ELIXIR data in ELIXIR data centers using EUDAT technology

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National proteomics centers

Meta

data

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Data

Central repository

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data

ResultsRaw

Data

Plans

15


Meta

data

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Central repository

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Data storage centers

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Data

1.- ELXIR replication

2.- EUDAT replication

Plans

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Meta

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Central repository

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3.- delegation

ELIXIR Pilot action

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EUDAT services

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File sharing model

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CSC

BILS

Site B

Site C

EUDAT CDIELIXIR

B2SAFE

B2SAFE

B2SAFE

B2SAFE

PRIDEEMBL-EBI

Pilot – EUDAT adoption: ELIXIR replication

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CSC

BILS

Site B

Site C

EUDAT CDIELIXIR

B2SAFE

B2SAFE

B2SAFE

B2SAFE

PRIDEEMBL-EBI

Central repositoryNational proteomics centers

Meta

data

ResultsRaw

Data

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ResultsRaw

Data

PIDs

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ELIXIR

community centerELIXIR

Data center 1

EUDAT

Data center 1

CSCPRIDEBILS

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

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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

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Participants

EUDAT/CSC

• Jani Heikkinen

• Damien Lecarpentier

EMBL-EBI/systems

• Andy Jenkinson

• Steven Newhouse

EMBL-EBI/PRIDE

• Juan Antonio Vizcaíno

• Henning Hermjakob

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BILS

• Mikael Borg

• Fredrik Levander

• Bengt Persson

ELIXIR Hub

• Rafael C Jimenez

European Life Sciences Infrastructure for Biological Information

www.elixir-europe.org

Thank you for your attention

Delegation of raw data

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processed data

metadata

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Integration

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proteomics repositories integration using eudat resources · proteomics repositories integration...

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