Programmatic Access To Biological Databases (Perl). 1 October 2012

1. Tutorial
PSICQUIC
Programmatic Access To Biological Databases (Perl)
1 – 4 October 2012
Marine Dumousseau, Noemi Del Toro Ayllon and Rafael C. Jimenez
marine@ebi.ac.uk, ntoro@ebi.ac.uk and rafael@ebi.ac.uk

2. 1
Exercise: Find available PSICQUIC services
• Aim: Connect to the PSICQUIC Registry and collect a list of services
• Requirements: Internet connection
• Script: 1-read-registry.pl
• Documentation:
• REST specification
• http://code.google.com/p/psicquic/wiki/Registry
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3. Solution: Find available PSICQUIC services
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1

4. Exercise: Query a PSICQUIC Service
• Aim: Query a PSICQUIC service using a MIQL query
• Requirements: Internet connection
• Script: 2-read-single-psicquic.pl
• Documentation:
• REST specification
• http://code.google.com/p/psicquic/wiki/PsicquicSpec_1_2_Rest
• MIQL reference
• http://code.google.com/p/psicquic/wiki/MiqlReference
• PSI-MI TAB 2.5 format
• http://code.google.com/p/psicquic/wiki/MITAB25Format
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5. Solution: Query a PSICQUIC service
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6. Exercise: Query multiple PSICQUIC Service
• Aim: Query all the curated PSICQUIC services and present the data
• Requirements: Internet connection
• Script: 3-read-curated-psicquic.pl
• Algorithm
– Read services from the Registry tagged as “internally-curated”
– Iterate and get ALL data for each service
• Warning
– URLs returned by the registry are not REST, make sure you read
the PSICQUIC REST specification to find out how to modify the
URLs to search.
• Documentation:
• REST specification
• http://code.google.com/p/psicquic/wiki/PsicquicSpec_1_2_Rest
• MIQL reference
• http://code.google.com/p/psicquic/wiki/MiqlReference
• PSI-MI TAB 2.5 format
• http://code.google.com/p/psicquic/wiki/MITAB25Format
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3

7. Solution: Query multiple PSICQUIC services (1/2)
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8. Solution: Query multiple PSICQUIC services (2/2)
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3

9. Exercise: Load PSICQUIC data in Cytoscape
• Aim: Modify previous script to export a Tab separated file (.tsv) that we can
then try to load into Cytoscape to display the aggregated network.
• Requirements: Internet connection
• Script: 4-export-cytoscape.pl
• Columns in the File:
– Molecule 1
– Molecule 2
– Properties of the interaction (PMID, experimental method…)
•
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10. Solution: Export PSICQUIC to Cytoscape
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11. 4
Loading our data into Cytoscape (1/9)
• Make sure you run your script and output the result into a
file. (i.e. perl export-cytoscape.pl LSM7 > lsm7.tsv)
• Start Cytoscape
• Load the File
• Map the column to the Cytoscape Model
• Import the data
• Apply a layout to beautify the network
• Highlight properties of the network (e.g. originating publication)

12. 4
IntAct And PSICQUIC
Loading our data into Cytoscape (2/9)
• Load the data file

13. 4
IntAct And PSICQUICSamuel Kerrien (skerrien@ebi.ac.uk)
Bruno Aranda (baranda@ebi.ac.uk)
Loading our data into Cytoscape (3/9)
• Loading File & Mapping of columns

14. 4
IntAct And PSICQUIC
Loading our data into Cytoscape (4/9)
• Import data as a Network

15. 4
IntAct And PSICQUIC
Loading our data into Cytoscape (5/9)
• Improve readability by selecting a network Layout

16. 4
IntAct And PSICQUIC
Loading our data into Cytoscape (6/9)
• Beautified network

17. 4
IntAct And PSICQUIC
Loading our data into Cytoscape (7/9)
• Highlight interaction properties

18. 4
IntAct And PSICQUIC
Loading our data into Cytoscape (8/9)
• Highlight interaction properties

19. 4
IntAct And PSICQUIC
Loading our data into Cytoscape (9/9)
• Highlight interaction properties

20. Thank you!
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ProteomicsServicesTeam