Post on 20-Jan-2016
EBI is an Outstation of the European Molecular Biology Laboratory.
PRIDE centric exercise:BioMart interface
PRIDE team, Proteomics Services Group
PANDA group
European Bioinformatics Institute
Hinxton, Cambridge
United Kingdom
Juan Antonio VIZCAINO
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
Overview …
• Introduction to the BioMart interface
• PRIDE BioMart
• Presentation of the PRIDE centric exercise (focused in data mining)
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
BIOMART INTERFACE
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
Introduction to BioMart …
• Interface developed originally at the EBI to access data at EBI resources. It is another way to access the data…
• Suitable for making more complex data queries that the web interface.
• Very powerful: suitable for wet lab scientists without being experts in bioinformatics
• You can search and integrate data from two resources simultaneously…
www.biomart.org
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
PRIDE BioMart
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
PRIDE BioMart
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
PRIDE BioMart
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
The spectacular bit: across-BioMart queries!Question: “Which proteins, identified in PRIDE, in blood plasma,
are transcribed from genes located in chromosome 11”PRIDE
Ensembl
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
PRIDE CENTRIC EXERCISE
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
PRIDE centric exercise
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
In this exercise…
• You will learn how to use PRIDE for data mining purposes…
• You will learn how to retrieve data from the PRIDE database using the PRIDE BioMart
• You will also browse the PRIDE web interface, and learn how to make use of the PICR protein mappings
• You will learn how to search data combining the PRIDE (Proteomics) and the Ensembl BioMarts (Genomics)
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
In this exercise…
• Let’s suppose that you are particularly interested in one protein you obtained in your results after the search with OMSSA:
Protein accession O76094 (Signal recognition particle 72 kDa protein)
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
You will use PRIDE to find out…
• If this same protein (O76094) has been detected by MS before.
• If so, how was/were the experiment(s) done?
• Information about the peptide sequences identified and possible protein modifications (PTMs)
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
Don’t forget…
• You need to consider all possible mappings of the protein. If there are equivalent protein accessions in other DBs (IPI, Ensembl protein, etc)
• You will use the PRIDE BioMart (easy way to retrieve data for biologists without bioinformatics/ programming knowledge).
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
Make proteomics results comparable
No direct comparison can be done if the different submitters use different databases to perform the searches
Protein list A
(DB Search vs. IPI)
IPI000001
IPI000002
IPI000003
…
Protein list B
(DB Search vs. UniProt)
P00001
P00002
P00003
…
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
Make proteomics results comparable
Protein list A
(DB Search vs. IPI)
IPI000001
IPI000002
IPI000003
…
Protein list B
(DB Search vs. UniProt)
P00001
P00002
P00003
…
No direct comparison can be done if the different submitters use different databases to perform the searches
We will use the PICR tool to be able to make protein identifiers comparable
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
…and also, across-BioMart queries!You will need to combine the PRIDE and Ensembl BioMarts:
easy way to perform data mining using proteomics and genomics data
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
Time to Work on it…
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
Conclusions
• You have learnt how to use PRIDE for data mining purposes
• You have learnt to use the BioMart interface (available not only for PRIDE)
• Hopefully, you have learnt the need to use the PICR service to make proteomics experiments comparable
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
The PRIDE Team: Who we areAttila CsordasDavid OvelleiroRichard CôtéRui WangDaniel RíosFlorian Reisinger
Joe FosterJohannes GrissJose A. DianesAntonio FabregatYasset Perez-Riverol
Juan Antonio VizcaínoHenning Hermjakob
EBI RoadshowRotterdam, 12 June 2012
Juan A. Vizcaínojuan@ebi.ac.uk
Questions?