1. The Web Services Game

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

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… 3

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

5. SOAP Web Services 5 GET WSDL WSDL 1 2 3 Reads SOAP Request SOAP Response 4 5 Method / ParametersData 45 WSDL

6. 6

7. SOAP vs. REST Based on Standards, Only accessed by software, Allow description of complex data structure in request and response, 7 Geared to simplicity, A browser can be a client, Request as complex as a URL can be,

8. Playing the REST Game 8

9. The Actors The user The client application The REST Service Mr Internet 9

10. 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 10

11. 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

12. 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 … 12 IDFORMAT fasta embl …

13. The REST URL http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=_____&id=_________&format=____&style=raw 13

14. The Data – Protein sequence 14

15. The Data – Gene sequence 15

16. Playing the SOAP Game 16

17. The Actors The user The client application The SOAP Service Mr Internet 17

18. 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 18

19. 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

20. Dbfetch WSDL Where is the WSDL file ? http://www.ebi.ac.uk/ws/services/WSDbfetchDoclit?wsdl Methods available getSupportedDbs getSupportedFormats getDbFormats db 20 fetchData query (i.e. db:id) format style

21. A SOAP Request Method name: _____________________ Parameters: 21 NameValue

22. The Data – Protein sequence 22

23. The Data – Gene sequence 23

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