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

1. Introduction to Web Services
Programmatic Access To Biological Databases (Perl)
1 – 4 October 2012
Rafael C. Jimenez
rafael@ebi.ac.uk

2. Query interfaces
13/12/2018
2
Graphical
User
Interface
(GUI)
FTP
access
Database
access
Application
Programmatic
Interface
(API)
Data
Web
Services
Biologist Bioinformaticians Developers
remote resource

3. Query interfaces
13/12/2018
3
Graphical
User
Interface
(GUI)
FTP
access
Database
access
Application
Programmatic
Interface
(API)
Data
Web
Services
Interface: A program that allows users to interact with a system
API: An interface that can be accessed using a specific
programing language
Web service: A web API available for multiple programming languages
This introduction is intended for a non technical
audience with purposely simplified technical concepts.
remote resource

4. Web Services
• It is a piece of software to interact with a remote system
• It is accessible over a network (Internet)
• It is meant for machine to machine communication
• Independent from programming languages
• It can be operated following specific rules (protocols: REST
or SOAP)
This introduction is intended for a non technical
audience with purposely simplified technical concepts.

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

6. REST Web Services
How should I invoke you?
Documentation
Make a request ( GET or POST)
Results (data + status)
Web server
Sometimes a WADL file is available in the server to describe
the service
1
2
3
4
2
WADLor
Informal
Description
Formal
Description
Application
Developer

7. SOAP Web Services
How should I invoke you?
Documentation (WSDL)
Make a SOAP request
Web server1
2
3
WSDL
Method / Parameters Data
4
3 4SOAP request SOAP response
and
Informal
Description
Formal
Description
Results (SOAP response)
Application
Developer

8. SOAP vs. REST
8
REST
• Geared to simplicity.
• A browser can be a client.
• Request as complex as a URL can be.
REST query: http://www.ebi.ac.uk/…/query/P99999?format=xml25
WADL: http://www.ebi.ac.uk/…/current?_wadl
SOAP
• Based on Standards.
• Only accessed by software.
• Allow description of complex data structure in request and response.
SOAP REST
WSDL: http://www.ebi.ac.uk/…/psicquic?wsdl

9. Thank you!
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9
ProteomicsServicesTeam