The document describes a tutorial on accessing molecular interaction data through the PSICQUIC web services using different methods. The tutorial covers: 1) exploring the PSICQUIC registry; 2) using the PSICQUIC View client to search interactions from multiple sources; 3) making REST and SOAP queries programmatically through web services; and 4) building workflows using Taverna to integrate PSICQUIC web services. The goal is to demonstrate how to access molecular interaction content in a standardized way across different sources and formats.

1. PSIMEx Workshop
Interactions and Pathways
6-7 October 2011
Rafael Jimenez
rafael@ebi.ac.uk
PSICQUIC tutorial

2. Tutorial scope
Data
Formats, ontologies, Minimum information guidelines
Web Services
SOAP & REST
Programmatic Access
Python, Java, Perl, ...
Software
Psicqcuic View, Cytoscape, Taverna, ...

3. Tutorial scope
Data
Web Services
Software
• PSI-MITAB format
• REST queries using your internet browser
• SOAP queries using SOAP-UI
• MIQL queries
• PSICQUIC registry
• PSIQCUIC view
• Taverna workflows

4. Tutorials
1. PSICQUIC Registry
2. PSICQUIC View
3. PSICQUIC REST service
4. PSICQUIC SOAP service
5. PSICQUIC workflows with Taverna

5. PSICQUIC Registry
1. Have a look to the PSICQUIC registry
– http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS
2. Spend few minutes getting familiar with the results table
3. How many sources do manual curation at the level of MIMIx?
– http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS&tags=mimix%20curation
4. How many resources provide predicted interactions?
– http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS&tags=predicted
5. How many resources provide interactions between small molecules and proteins?
– http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS&tags=smallmolecule-protein
6. How many annotations in total are provided by sources with experimental evidence
annotations?
– http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS&tags=evidence
7. What other parameters can you use to filter the registry?
– http://code.google.com/p/psicquic/wiki/Registry

6. PSICQUIC Registry

7. PSICQUIC View
1. Have a look to the PSICQUIC view
– http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml
2. Look at the interactions results from one of the services
1. IntAct for example has in total around 276.000 binary interactions
2. If you click on “IntAct”, a table will display the first 30 binary interactions
3. On the top right corner of the table you could find a link to see the next 30 interactions.
4. If you are interested in one interaction you could find the original source information by
clicking in the interaction accession (Interaction AC column).
3. What is the meaning of each column in the table?
– Each column is closely related to the fields defined for the PSI-MITAB format:
http://code.google.com/p/psicquic/wiki/MITAB25Format
4. Filter result by organism
1. Click on the “Fields” link next to the search box
2. Select the “organism” filed and input a specie name or tax Id, i.e. “trypanosoma”
5. Display a network graph with your filter result for one source
1. For instance click again on IntAct
2. And select the “Graph” view (link on the top left of the table)
6. Add more filters to display just interactions detected by a specific detection method.
1. Click on the “Fields” link next to the search box
2. Select the “Detection method” filed and input a detection method, i.e. “two hybrid”

8. PSICQUIC View

9. PSICQUIC View
6. Export table results
6. In the “Table” view click on the “PSI-MI TAB” icon to export result in a TSV format
(easy to open with excel).
7. Cluster interactions from all the services
1. Click on the “Cluster this query” button* (on the right side of the service list).
2. Wait few seconds until the cluster query gets completed
3. Click on the “View” link inside the Cluster table.
1. Originally you clustered interaction from 4 services, however the “Source
Database” column shows interactions just from 3 different services. This is
because “APID” and “iRefIndex” are integrated resources collecting
information from other databases. The “Source Database column just
displays the original database the interaction comes from” in this case
“IntAct”, “DIP” and “bind”.
2. Check the interaction between “Q387L4” and “Q4VHG6”. It has been
reported by two databases. This entry collects non redundant information
provided by DIP and IntAct
* Note:
PSICQUIC View allows you to cluster filtered results with less than 5000 interactions. The
cluster looks at merging redundancy to come up with unique interaction results.

10. PSICQUIC View

11. PSICQUIC REST service
1. Select a REST URL from the PSICQUIC registry
1. Go to the PSICQUIC registry
1. http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS
2. Copy a REST URL from one service into a new window of your web browser, i.e.
• http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/
2. Query a service
1. Add to the REST URL the word “query/”
• http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/
2. Copy one of the queries we have already used in the PSICQUIC client
• species:trypanosoma AND detmethod:"two hybrid“
3. Add to the REST URL your query
• http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/species:tryp
anosoma AND detmethod:"two hybrid“
3. Use the same query in a different service
– i.e. Copy the iRefIndex REST URL and add the same query parameters
• http://imex.mbi.ucla.edu/psicquic-ws/webservices/current/search/query/species:trypanosoma AND
detmethod:"two hybrid“
4. Make more complex queries
– You have already learnt how to use some of the MIQL fields to query PSICQUIC services.
Have a look to the complete MIQL list of fields and examples to make more complex queries.
i.e.
• http://code.google.com/p/psicquic/wiki/MiqlReference
• http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/(species:try
panosoma AND detmethod:"two hybrid") AND NOT pubid:12821657

12. PSICQUIC REST service

13. PSICQUIC SOAP service
1. Create a new project in soapUI
1. Download soapUI if not installed in you computer
• http://sourceforge.net/projects/soapui/files/soapui/4.0.1/
2. On the menu click on “File” and “New soapUI Project”
3. Enter a name for your project. i.e. “psicquic-intact”
4. Enter the WSDL URL for a psicquic service
1. Copy the SOAP URL for a PSICQUIC service from the registry. i.e.
1. http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/psicquic
2. Add “?wsdl” at the end of the SOAP URL. i.e.
1. http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/psicquic?wsdl
5. Click the “OK” button.
2. Query a service
Note: soapUI will display all the query methods available for a new project (service) on the left menu.
1. Open a method. i.e “getByQuery”
2. Double click on “Request 1”
This will display a new window to query the PSICQUIC service. SOAP services use the XML format to
perform a query.
3. Complete the query in the XML
1. In the “query” XML tag, substitute “?” by your query
species:trypanosoma AND detmethod:’two hybrid’ (careful, use simple quotes)
2. In the “resultsType” XML tag substitute “?” by the format you would like to see the results
psi-mi/tab25
4. Submit the query and get your results
1. Click on the play button (on the top left corner of your XML window)

14. PSICQUIC SOAP service

15. PSICQUIC workflows with Taverna
1. Find PSICQUIC workflows using Taverna
1. Download the Taverna Workbech 2.3 if not installed in you computer
• http://www.taverna.org.uk/download/workbench/2-3/
2. Open Taverna and click the “myExperiment” button.
myExperiment is a repository of workflow
3. In the “Query” field, type “psicquic”
2. Open one PSICQUIC workflow
1. Find the “Molecular Interactions from IntAct PSICQUIC service (REST)”
workflow and click on the “Open” button.
3. Run a PSICQUIC workflow
1. In the menu click on “File” and “Run workflow”
4. Define your query
1. Find and click the “Set value” button
2. Specify your MIQL query. i.e
• species:trypanosoma AND detmethod:”two hybrid”
3. Click on the button “Run workflow”
5. Check your results
1. In the bottom left corner, in the “MITAB” tab, click on “Value1”
6. Save results
1. Click on the “Save value” button on the bottom right corner.

16. PSICQUIC workflows with Taverna

17. More about PSICQUIC
• Programmatic access to Molecular Interactions
http://www.ebi.ac.uk/~skerrien/talks/2011.05-
IntAct_in_Java/Tutorial.pdf
• PSICQUIC wiki
http://code.google.com/p/psicquic/w/list
• Twitter
http://twitter.com/PSICQUIC
• Mailing list
http://groups.google.com/group/psicquic

18. PSICQUIC homehttp://code.google.com/p/psicquic/

19. Programmatic access
Python

20. Programmatic access
Java

21. Programmatic access
Perl