1. 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

2. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Overview … Introduction to the BioMart interface PRIDE BioMart Presentation of the PRIDE centric exercise (focused in data mining)

3. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk BIOMART INTERFACE

4. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@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

5. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk PRIDE BioMart

6. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk PRIDE BioMart

7. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk PRIDE BioMart

8. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@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

9. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk PRIDE CENTRIC EXERCISE

10. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk PRIDE centric exercise

11. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@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)

12. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@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)

13. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@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)

14. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@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).

15. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@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 …

16. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@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

17. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@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

18. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Time to Work on it…

19. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@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

20. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk The PRIDE Team: Who we are Attila Csordas David Ovelleiro Richard Côté Rui Wang Daniel Ríos Florian Reisinger Joe Foster Johannes Griss Jose A. Dianes Antonio Fabregat Yasset Perez-Riverol Juan Antonio Vizcaíno Henning Hermjakob

21. EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Questions?