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The Web Services Game

The Web Services Game. This game is intended for a non technical audience ; We have purposely simplified technical aspect. What is a Web Service. It is a piece of software that runs remotely, It is accessible over a network (e.g. Internet),

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The Web Services Game

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  1. The Web Services Game

  2. This game is intended for a non technical audience; • We have purposely simplified technical aspect.

  3. 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…

  4. REST Web Services 2 1 3 WADL Reads URL Data / Status

  5. SOAP Web Services 2 4 4 1 WSDL 3 5 5 GET WSDL Reads WSDL SOAP Request SOAP Response Method / Parameters Data

  6. SOAP vs. REST • Based on Standards, • Only accessed by software, • Allow description of complex data structure in request and response, SOAP REST • Geared to simplicity, • A browser can be a client, • Request as complex as a URL can be,

  7. Playing the REST Game

  8. The Actors • The user • The client application • The REST Service • Mr Internet

  9. How to play the REST game • Choose the actors • Get the User to ask a question to the Client Application • Get the Client Application to format a URL with user parameters • The Client Application invoked the Web Service with the URL • The Web Service processes the request and sends the data back to the Client Application (with the help of Mr Internet) • The Client application processed the data and shows to the User

  10. 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

  11. 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 • … • ID • FORMAT • fasta • embl • …

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

  13. The Data – Protein sequence

  14. The Data – Gene sequence

  15. Playing the SOAP Game

  16. The Actors • The user • The client application • The SOAP Service • Mr Internet

  17. How to play the SOAP game • Choose the actors • Get the User to ask a question to the Client Application • Get the Client Application to retrieve the WSDL from the Web Service (with the help of Mr Internet) • The Client Application chooses the method and parameters • The Client Application sends the SOAP request to the Web Service (with the help of Mr Internet) • Web Service process the request and generate data, wraps it in a SOAP Response and send it back to the Client Application • The Client application processed the data and shows to the User

  18. 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

  19. Dbfetch WSDL Where is the WSDL file ? http://www.ebi.ac.uk/ws/services/WSDbfetchDoclit?wsdl Methods available • getSupportedDbs • getSupportedFormats • getDbFormats • db • fetchData • query (i.e. db:id) • format • style

  20. A SOAP Request Method name: _____________________ Parameters:

  21. The Data – Protein sequence

  22. The Data – Gene sequence

  23. Acknowledgments Rafael Jimenez Samuel Kerrien You for being such good actors ;)

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