EBI is an Outstation of the European Molecular Biology Laboratory. PRIDE centric exercise: BioMart...

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. Vizcaí[email protected]

Overview …

• Introduction to the BioMart interface

• PRIDE BioMart

• Presentation of the PRIDE centric exercise (focused in data mining)



BIOMART INTERFACE



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

http://www.biomart.org/



PRIDE BioMart



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



PRIDE CENTRIC EXERCISE



PRIDE centric exercise



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)



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)



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)



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).



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

…



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



…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



Time to Work on it…



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



The PRIDE Team: Who we areAttila CsordasDavid OvelleiroRichard CôtéRui WangDaniel RíosFlorian Reisinger

Joe FosterJohannes GrissJose A. DianesAntonio FabregatYasset Perez-Riverol

Juan Antonio VizcaínoHenning Hermjakob



Questions?

EBI is an Outstation of the European Molecular Biology Laboratory. PRIDE centric exercise: BioMart...

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