Using SADI services – installing the plugin<br />Click on Advanced and then Updates and plugins.<br />
Using SADI services – installing the plugin<br />Click Find New Plugins.<br />
Using SADI services – installing the plugin<br />Select  SADI activity plugin 0.2.0<br />Click on Install.<br />
Using SADI services – installing the plugin<br />The plugin is being installed.<br />
Using SADI services – installing the plugin<br />When the plugin is installed a warning about restarting Taverna will be d...
Using SADI services – installing the plugin<br />Click on Close and then RESTART Taverna.<br />
Using SADI services – installing the plugin<br />When Taverna has restarted the Service panel will show a list of SADI ser...
Using SADI services<br />Now that we have SADI service available in Taverna we’re going to build a workflow to answer the ...
Using SADI services – building a workflow<br />Type sadikegg pathway genes into the Service panel Filter.<br />
Using SADI services – building a workflow<br />Right click on the getKEGGGenesByPathwayservice and click Add to workflow.<...
Using SADI services – building a workflow<br />The getKEGGGenesByPathwayservice is added to the Workflow diagram.<br />Cli...
Using SADI services – building a workflow<br />The service input and output ports are now shown in the diagram.<br />
Using SADI services – building a workflow<br />To add an output to the workflow right-click on the workflow diagram and cl...
Using SADI services – building a workflow<br />Name the output port gene and click OK.<br />
Using SADI services – building a workflow<br />Drag a link from the service output port to workflow output gene.<br />
Using SADI services – building a workflow<br />The next step in the workflow is to find a SADI service that takes the gene...
Using SADI services – building a workflow<br />Right-click on the service output port and click Find services that consume...
Using SADI services – building a workflow<br />Select getUniprotByKeggGene from the list of SADI services and click Connec...
Using SADI services – building a workflow<br />The getUniprotByKeggGene service is added to the workflow and automatically...
Using SADI services – building a workflow<br />Add a new workflow output called protein and connect the output from the ge...
Using SADI services – building a workflow<br />The next step in the workflow is to find a SADI service that takes the prot...
Using SADI services – building a workflow<br />The UniProt info service attaches the property hasSequenceso select this se...
Using SADI services – building a workflow<br />The UniProt info service is added to the workflow and automatically connect...
Using SADI services – building a workflow<br />Add a new workflow output called sequence and connect the output from the h...
Using SADI services – building a workflow<br />The KEGG pathway were interested in is "hsa00232”, so we’ll add it as a con...
Using SADI services – building a workflow<br />Enter the value hsa00232 and click OK.<br />
Using SADI services – building a workflow<br />The workflow is now complete and ready to run.<br />
Using SADI services – running the workflow<br />To run the workflow click on the green arrow in the tool bar. Taverna will...
Using SADI services – running the workflow<br />The progress of the workflow is shown in the diagram while the workflow is...
Using SADI services – viewing the results<br />To see the all the results for an output click on the output tab for that o...
Using SADI services – viewing the results<br />The output from a SADI service is an RDF node so Taverna displays the resul...
Using SADI services – viewing the results<br />When the value type is set to Text just the URL for the protein is displaye...
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SADI in Taverna Tutorial

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SADI in Taverna Tutorial

  1. 1. Using SADI services – installing the plugin<br />Click on Advanced and then Updates and plugins.<br />
  2. 2. Using SADI services – installing the plugin<br />Click Find New Plugins.<br />
  3. 3. Using SADI services – installing the plugin<br />Select SADI activity plugin 0.2.0<br />Click on Install.<br />
  4. 4. Using SADI services – installing the plugin<br />The plugin is being installed.<br />
  5. 5. Using SADI services – installing the plugin<br />When the plugin is installed a warning about restarting Taverna will be displayed. Click OK.<br />
  6. 6. Using SADI services – installing the plugin<br />Click on Close and then RESTART Taverna.<br />
  7. 7. Using SADI services – installing the plugin<br />When Taverna has restarted the Service panel will show a list of SADI services.<br />
  8. 8. Using SADI services<br />Now that we have SADI service available in Taverna we’re going to build a workflow to answer the questions:<br />What genes are involved in KEGG pathway "hsa00232"? What proteins do those genes code for? What are the sequences of those proteins?<br />The first step is to find a SADI service that will return the genes involved in a KEGG pathway.<br />
  9. 9. Using SADI services – building a workflow<br />Type sadikegg pathway genes into the Service panel Filter.<br />
  10. 10. Using SADI services – building a workflow<br />Right click on the getKEGGGenesByPathwayservice and click Add to workflow.<br />
  11. 11. Using SADI services – building a workflow<br />The getKEGGGenesByPathwayservice is added to the Workflow diagram.<br />Click on the Display all service ports button to show the service inputs and outputs.<br />
  12. 12. Using SADI services – building a workflow<br />The service input and output ports are now shown in the diagram.<br />
  13. 13. Using SADI services – building a workflow<br />To add an output to the workflow right-click on the workflow diagram and click Workflow output port.<br />
  14. 14. Using SADI services – building a workflow<br />Name the output port gene and click OK.<br />
  15. 15. Using SADI services – building a workflow<br />Drag a link from the service output port to workflow output gene.<br />
  16. 16. Using SADI services – building a workflow<br />The next step in the workflow is to find a SADI service that takes the genes from getKEGGGenesByPathwayand returns the proteins that those genes code for.<br />
  17. 17. Using SADI services – building a workflow<br />Right-click on the service output port and click Find services that consume KEGG_Record…<br />
  18. 18. Using SADI services – building a workflow<br />Select getUniprotByKeggGene from the list of SADI services and click Connect.<br />
  19. 19. Using SADI services – building a workflow<br />The getUniprotByKeggGene service is added to the workflow and automatically connected to the output from getKEGGGenesByPathway.<br />
  20. 20. Using SADI services – building a workflow<br />Add a new workflow output called protein and connect the output from the getUniprotByKeggGene service to it.<br />
  21. 21. Using SADI services – building a workflow<br />The next step in the workflow is to find a SADI service that takes the proteins and returns sequences of those proteins. Right-click on the encodes output port and click Find services that consume UniProt_Record…<br />
  22. 22. Using SADI services – building a workflow<br />The UniProt info service attaches the property hasSequenceso select this service and click Connect.<br />
  23. 23. Using SADI services – building a workflow<br />The UniProt info service is added to the workflow and automatically connected to the output from getUniprotByKeggGene .<br />
  24. 24. Using SADI services – building a workflow<br />Add a new workflow output called sequence and connect the output from the hasSequenceoutput from the UniProt info service to it.<br />
  25. 25. Using SADI services – building a workflow<br />The KEGG pathway were interested in is "hsa00232”, so we’ll add it as a constant value. Right-click on the KEGG_PATHWAY_Record input port and click Constant value.<br />
  26. 26. Using SADI services – building a workflow<br />Enter the value hsa00232 and click OK.<br />
  27. 27. Using SADI services – building a workflow<br />The workflow is now complete and ready to run.<br />
  28. 28. Using SADI services – running the workflow<br />To run the workflow click on the green arrow in the tool bar. Taverna will switch to the results view and start running the workflow.<br />
  29. 29. Using SADI services – running the workflow<br />The progress of the workflow is shown in the diagram while the workflow is running.<br />
  30. 30. Using SADI services – viewing the results<br />To see the all the results for an output click on the output tab for that output. To see an individual result click on the value in the result list.<br />Output tab<br />Result list<br />
  31. 31. Using SADI services – viewing the results<br />The output from a SADI service is an RDF node so Taverna displays the result as RDF by default. To change to a text display click on the Value type and select Text.<br />
  32. 32. Using SADI services – viewing the results<br />When the value type is set to Text just the URL for the protein is displayed.<br />
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