For the Basic search implementation part I have reused the code of  Wikipathways  Client Plugin created by Thomas Kelder (code repository: https://github.com/thomaskelder/pathvisio-wikipathways-client).

The task for this first week is to :

  • Implement the GUI for Basic Search

Basic Search:

Search by query as on http://www.wikipathways.org itself.

  1. Search for pathways by name, pathway element labels

  2. Search by text but for specific species

I have used the findPathwaysByText method of  WikiPathways web service

Details

1. Search for pathways by name, pathway element labels

By name: e.g.  Asparagine degradation

 http://www.wikipathways.org/wpi/webservice/webservice.php/findPathwaysByText?query=Asparagine%20degradation

By pathway element label: e.g. pathway element label:   ASP3-4

http://www.wikipathways.org/wpi/webservice/webservice.php/findPathwaysByText?query=ASP3-4

2. search for pathways by species/organism: e.g.  Homo Sapeins

http://www.wikipathways.org/wpi/webservice/webservice.php/findPathwaysByText?query=cancer&species=Homo%20sapiens

From the above queries we get a number of  pathways,  which are displayed in a Table .Then the user can select any one and the selected pathway gets loaded (opened)  in PathVisio Tool.

Step by step demonstration of task:

When the Wikipathway Client Plugin is loaded into PathVisio –  “Wikipathways” menu with submenus- ‘Search’, ‘Browse’, ‘Update’ gets registered

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When the ‘Search’ option is chosen – Search WikiPathways Dialog popsout

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Then user can search pathways , based on any query text like –

Pathway Name: Asparagine degradation

Pathway element Label: ASP3-4

Search by text but for specific species

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Finding pathways using a textual search on the description and text labels of the pathway objects. The query syntax can have several options:

  • Combine terms with AND and OR. Combining terms with a space is equal to using OR (‘p53 OR apoptosis’ gives the same result as ‘p53 apoptosis’).
  • Group terms with parentheses, e.g. ‘(apoptosis OR mapk) AND p53’
  • You can use wildcards * and ?. * searches for one or more characters, ? searchers for only one character.
  • Use quotes to escape special characters. E.g. ‘”apoptosis*”‘ will include the * in the search and not use it as wildcard.

Then the list of pathways is shown, user can select anyone of the pathway

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Then on the double click of the selected pathways from list of pathways, the pathway gets loaded into pathvisio

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