The Web Services Game

• This game is intended for a non technical audience;

• We have purposely simplified technical aspect.

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What is a Web Service

• 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…

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REST Web Services

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URL

Data / Status

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2

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Rea

dsWADL

SOAP Web Services

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GET WSDL

WSDL

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Rea

ds

SOAP Request

SOAP Response

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Method / Parameters

Data

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WSDL

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SOAP vs. REST

• Based on Standards,

• Only accessed by software,

• Allow description of complex data structure in request and response,

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• Geared to simplicity,

• A browser can be a client,

• Request as complex as a URL can be,

Playing the REST Game

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The Actors

• The user

• The client application

• The REST Service

• Mr Internet

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How to play the REST game

1. Choose the actors

2. Get the User to ask a question to the Client Application

3. Get the Client Application to format a URL with user parameters

4. The Client Application invoked the Web Service with the URL

5. The Web Service processes the request and sends the data back to the Client Application (with the help of Mr Internet)

1. The Client application processed the data and shows to the User

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The REST Service

• Name: Dbfetch

• Purpose: To serve sequence of biological entities

• Documentation: http://www.ebi.ac.uk/Tools/dbfetch

• Query Example:• Get sequence of protein Q07812 from UniProt• Get Gene sequence for Ensembl Transcript: ENST00000345358

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Dbfetch Documentation

How to build a URL ?

http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=${DB}&id=${ID}&format=${FORMAT}&style=raw

URL Parameters

• DB• uniprotkb• ensembl• embl• …

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• ID • FORMAT• fasta• embl• …

The REST URL

http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=_____&id=_________&format=____&style=raw

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The Data – Protein sequence

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The Data – Gene sequence

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Playing the SOAP Game

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The Actors

• The user

• The client application

• The SOAP Service

• Mr Internet

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How to play the SOAP game

1. Choose the actors

2. Get the User to ask a question to the Client Application

3. Get the Client Application to retrieve the WSDL from the Web Service (with the help of Mr Internet)

4. The Client Application chooses the method and parameters

5. The Client Application sends the SOAP request to the Web Service (with the help of Mr Internet)

6. Web Service process the request and generate data, wraps it in a SOAP Response and send it back to the Client Application

7. The Client application processed the data and shows to the User

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The SOAP Service

• Name: Dbfetch

• Purpose: To serve sequence of biological entities

• Documentation: http://www.ebi.ac.uk/Tools/webservices/services/dbfetch

• Query Example:• Get sequence of protein Q07812 from UniProt• Get Gene sequence for Ensembl Transcript: ENST00000345358

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Dbfetch WSDL

Where is the WSDL file ?

http://www.ebi.ac.uk/ws/services/WSDbfetchDoclit?wsdl

Methods available

• getSupportedDbs

• getSupportedFormats

• getDbFormats• db

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• fetchData• query (i.e. db:id)• format• style

A SOAP Request

Method name: _____________________

Parameters:

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Name Value

The Data – Protein sequence

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The Data – Gene sequence

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Rafael Jimenez

Samuel Kerrien

You for being such good actors ;)

Acknowledgments