PSIMEx Workshop Interactions and Pathways. 6-7 October 2011

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

2. Table of contents
• Data integration
– Data integration approaches
• Warehousing vs. Federation
• Dataset integration
– Query interfaces
• Web Services
– SOAP vs. REST
• PSICQUIC
– Registry
– Services
• REST queries
• MIQL
– PSICQUIC view
– PSISCORE
• Registry
• Client
• Workflows
– myGrid tools
– PSICQUIC workflows
• myExperiment
• Taverna

3. 1 3
5
Popular data integration approaches
4
6
2
...
Data centralization Data warehousing Dataset integration Hyperlinks
Federated databases View integration

4. 13.12.2018 4
Warehousing vs. Federation
Database Query InterfaceQI User
Data warehousing Federated databases
S
i
S i
i
S
integration
standardization

5. Data warehousing
Examples:
• Pathway Commons
• String
• Atlas

6. ….….
….....
….….
….....
….….
….....
PSICQUIC PSICQUIC PSICQUIC
Federated databases
PSICQUIC
Examples:
• DAS
• PSICQUIC
• EnCore
• RDF

7. Warehousing vs. Federation
• Data warehousing
– Pull data from several resources into one resource.
– Main features:
• Data centralization
• High maintenance
• Data out of date
• Modifications (schema, format, content, …)
• Federated databases
– Data residing in different sources with a common standard
protocol and query system.
– Main features:
• Fresh data (original)
• Data redundancy
• Data inconsistency

8. QI
i
3
Dataset integration
Curators / Annotators
Original data sources
Third party implementations
Users
Examples:
• Your own script
• Workflows
i
S
integration
standardization

9. 3
Dataset integration
Examples:
• Your own script
• Workflows

10. Query Interfaces
Graphical User Interface (GUI)
leverage
1
2
Software
engineers
Bioinformaticians
Programmatic interface
• API (application programming interface)
• WS (web services)
Biologists
<xml>
…
</xml>
Custom
workflows & analysis

11. Web Services
• It is a piece of software that runs remotely
• It is accessible over a network (e.g. Internet)
• It is meant for machine to machine communication
• Independent from programming languages
• It can be operated following specific rules (i.e. protocol)
• There are 2 main protocols in use:
– REST
– SOAP
This introduction is intended for a non technical
audience with purposely simplified technical concepts.

12. Web Services
How should I invoke you?
Documentation
Make a request
Results
Web serverClient
describes the methods and variables to query the service
1
2
3
4
2

13. SOAP vs. REST
13
REST
• Geared to simplicity
• A browser can be a client
• Request as complex as a URL can be
http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/P99999?format=xml25
SOAP
• Based on Standards
• Only accessed by software
• Allow description of complex data structure in request and response
SOAP REST

14. PSICQUIC
• Proteomics Standards Initiative Common QUery InterfaCe.
• Community effort to standardise the way to access and retrieve data
from Molecular Interaction databases.
• Widely implemented by independent interaction data resources.
• Based on the PSI standard formats (PSI-MI XML and MITAB)
• Not limited to protein-protein interactions, also e.g.
• Drug-target interactions
• Simplified pathway data
• A registry listing resources implementing PSICQUIC
• Documentation: http://psicquic.googlecode.com

15. PSICQUIC
http://www.ncbi.nlm.nih.gov/pubmed/21716279

16. • Services (SOAP/REST web services)
• IntAct
• Biogrid
• String
• ...
• Registry
• Clients
• PSICQUIC view
• Citoscape
• Envision2
• …
13.12.201816
Service
broker
Service
consumer
Service
provider
query
PublishFind
Service Oriented Architecture
PSI-MI
PSICQUIC
Registry
DAS ClientsDAS ClientsPSICQUIC
Clients
Format
PSICQUIC
sources
PSICQUIC
sources
PSICQUIC
Services
PSICQUIC
MIQL

17. PSICQUIC
Query Interactions
PSICQUIC
Registry
PSI-MIMIQL
Input Output
PSICQUIC
Service A
PSICQUIC
Service B
PSICQUIC
Service C
User View
Web Service System
Data Provenance
PSICQUIC

18. PSICQUIC Registry
• It contains a list of the PSICQUIC services from different
providers.
• It is a web service itself, and it can be accessed remotely
using REST.
• Information can be found about the services, such as the
URLs to use, number of interactions provided, versioning,
tags, etc.

19. PSICQUIC Registry
• 16 sources
• 16,358,233 interactions
http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS

20. PSICQUIC Registry
Tagging
Content
protein-protein
small molecule-protein
nucleic acid-protein
Interaction representation
evidence
clustered
Curation standards
mimix curation
imex curation
rapid curation
Source
internally curated
text mining
predicted
imported
Complex expansion
spoke
matrix
bipartite

21. • PSICQUIC services are Web Services
• SOAP
• REST
• The same methods to query several services
• Results from different sources following the same PSI-MI standards
• Results in two standard formats: PSI-MI XML or PSI-MI TAB.
PSICQUIC services

22. PSICQUIC SOAP service
species:trypanosoma AND detmethod:’two hybrid’

23. PSICQUIC REST queries
Bruno Aranda (baranda@ebi.ac.uk)
http://mint.bio.uniroma2.it/mint/psicquic/webservices/current/search/query/p53
http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/p53
http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/p53
1
2
3

24. MIQL
Bruno Aranda (baranda@ebi.ac.uk)
• Molecular Interaction Query Language

25. MIQL
…/query/specie:rat
…/query/brca AND rpa1
• Terms
• Fields
• Operands

26. PSICQUIC view
• Simple and complex queries
• Link back to the original source for more details
• Clustering of queries across providers
• Visualization of graphical network
http://www.ebi.ac.uk/Tools/webservices/psicquic/view/

27. 27
PSICQUIC view
source interactions

28. 28
PSICQUIC view
clustering

29. PSICQUIC View
graphical network

30. 0.90
0.380.25
—0.63
0.45
0.71
0.40
0.11
PSICQUIC PSISCORE
Query Interactions
PSI-MI
0.90
0.380.25
—0.63
0.45
0.71
0.40
0.11
PSICQUIC
Registry
Confidence Scores
PSI-MIMIQL
PSISCORE
Registry
client
Input Input
Output Output
PSICQUIC
Service A
PSICQUIC
Service B
PSISCORE
Service D
PSISCORE
Service E
PSICQUIC
Service C
User View
Web Service System
PSISCORE

31. PSISCORE registry
• 4 sources
• 14 scoring methods

32. PSISCORE client

33. EnVision: a PSICQUIC & PSISCORE client

34. Introduction to Web Services at EBI
Workflow
• Workflow
– Sequence of tasks that produces
a result of observable value
• Workflow management
system
– Computer system to compose
and execute workflows.
• Workflow components
– Input
– Service
– Output
– Shims
Service A
Service B

35. Create and run workflows
Share, discover and reuse workflows
Discover and reuse services
myGrid tools

36. PSICQUIC workflows in myExperiment

37. PSICQUIC workflow in Taverna
http://www.myexperiment.org/workflows/2274.html
tab25 0 1000 P99999
http://ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search

38. PSICQUIC workflow in Taverna

39. Thank you!
Questions?
ProteomicsServicesTeam