Dynamic linkage of public proteomics data in Ensembl using TrackHubs

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.

http://www.ebi.ac.uk/pride

http://www.ensembl.org/



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



ProteoAnnotator pipeline workflow

Ghali et al., Proteomics, 2014



PRIDE-Ensembl pipeline workflow ProteoAnnotator

mzIdentML



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.



Acknowledgements

Tobias TernentHenning HermjakobThe rest of the PRIDE team

Andy YatesAllessandro VulloPaul Flicek

Andy JonesSimon ParkinsFawaz Ghalli

BBSRC ProteoGenomics grant

[BB/L024225/1]

Dynamic linkage of public proteomics data in Ensembl using TrackHubs

Science