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Dr. Juan Antonio Vizcaíno
PRIDE Group CoordinatorProteomics Services TeamEMBL-EBIHinxton, Cambridge, UK
Dynamic linkage of public proteomics data in Ensembl using TrackHubs
Juan A. Vizcaí[email protected]
HUPO World Conference 2015Vancouver, 30 September 2015
Introduction• We aim to provide dynamic integration between the
public-domain proteomics data available in the PRIDE (PRoteomics IDEntifications) database (http://www.ebi.ac.uk/pride) and the genome information available through the Ensembl genome browser (http://www.ensembl.org).
• Joint project between PRIDE, Ensembl (EMBL-EBI), and (U. Liverpool (Andy Jones).
• Poster No CS29.08.
Juan A. Vizcaí[email protected]
HUPO World Conference 2015Vancouver, 30 September 2015
Data workflow
ProteoAnnotator
Public datasets in PRIDE are reprocessed using the ProteoAnnotator analysis pipeline
(input: MGF files)
mzIdentML
pepBED |BigBed
Different proteomics data TrackHubs
will be made availablein the Ensembl web
interface
Juan A. Vizcaí[email protected]
HUPO World Conference 2015Vancouver, 30 September 2015
ProteoAnnotator pipeline workflow
Ghali et al., Proteomics, 2014
Juan A. Vizcaí[email protected]
HUPO World Conference 2015Vancouver, 30 September 2015
PRIDE-Ensembl pipeline workflow ProteoAnnotator
mzIdentML
Juan A. Vizcaí[email protected]
HUPO World Conference 2015Vancouver, 30 September 2015
TrackHubs• Need to display the results from the new pipeline into the
Ensembl genome browser via TrackHubs.• TrackHubs replaces DAS, for efficient integration for
additional data sources.• This also requires setup of a new Registry to keep an up-
to-date listing of TrackHubs, again by Ensembl.• A new format called pepBED is being developed to add
proteomics information to the existing BED format.• The pepBED format is converted to BigBed, which is the
format used by the TrackHubs.
Juan A. Vizcaí[email protected]
HUPO World Conference 2015Vancouver, 30 September 2015
Acknowledgements
Tobias TernentHenning HermjakobThe rest of the PRIDE team
Andy YatesAllessandro VulloPaul Flicek
Andy JonesSimon ParkinsFawaz Ghalli
BBSRC ProteoGenomics grant
[BB/L024225/1]