Advanced Search will  enables user to

  • search for pathways by identifier/Title
  • search for pathways by pathway element identifier
  • search for pathways by publication reference

Details:

  • search for pathways by identifier

http://www.wikipathways.org/wpi/webservice/webservice.php/getPathway?pwId=WP

  • search for pathways by pathway element identifiers

          By pathway element identifiers:

http://www.wikipathways.org/wpi/webservice/webservice.php/findPathwaysByXref?ids=1234&codes=L

  •   search for pathways by publication reference

         By Pubmed ID:  Eg: Pubmed ID:22096230

http://www.wikipathways.org/wpi/webservice/webservice.php/findPathwaysByLiterature?query=22096230

         By Title: Eg:Selenoproteins

 http://www.wikipathways.org/wpi/webservice/webservice.php/findPathwaysByLiterature?query=Selenoproteins

Step by step demonstration of task:

  • search for pathways by Pathway identifier

ps1

  • search for pathways by Pathway Title

ps2

  • search for pathways by publication reference

                  By Pubmed ID:  Eg: Pubmed ID:18651794

SR2

By Publication Title

SR

  • search for pathways by pathway element identifier

SI

->With pathway element being highlighted

SI2

 

 

Now we can directly open pathway from WikiPathways on right click of Data Node that is well  annotated .

Considering an example pathways – WP434 ,when we import  it or get it loaded into PathVisio after searching  on Wikpathways through WikipathwaysClient Plugin. We can see that “Acetyl-CoA” (Metabolite) is annotated with Pathway Identifier (HMDB01206) and Datasource (‘HMDB’).

 

OPENXREF3

 

On Right Click of the “Acetyl-CoA” (Metabolite) an option “Open pathways From Wikipathways”  will exist on choosing it  we get the  Dialog with list of all th e pathways which contain element- “Acetyl-CoA” (Metabolite)

OPENXREF2

 

 

As of  now only one Data Node  can be selected . I would extend the Feature to open pathway from WikiPathways on selection of set Data Nodes

 

 

 

A new Tab “Advanced Search” have been appended to provide the Advanced search functionality.

 

 

advanced

 

Advanced Search:

  • Search by pathway identifier, title, curator

Step by step demonstration of task:

  1. Search by pathway identifier

advanced1

2. Search by pathway Title:

advanced3

3.Search by pathway curator Tag:

advanced2

I am working on other Advanced Search use cases. I will keep updating this corner of blog.

“Wikipathways” Menu is been added under “Plugins” menu of WikiPathways.

Now we have

1

 

Basic Browse Functionality which enables user to

  • Browse pathways by species
  • Browse pathways by Collections
  • Browse pathways by Curation tags

Details 

1.    Browse pathways by species

http://www.wikipathways.org/wpi/webservice/webservice.php/findPathwaysByText?query=%22%22&species=Homo%20sapiens

2.Browse pathways by curation tags

http://www.wikipathways.org/wpi/webservice/webservice.php/getCurationTagsByName?tagName=Curation:FeaturedPathway

Collections List includes: Curated pathways (default), Featured pathways, GenMAPP pathways, CIRM pathways, Reactome pathways, Open Access pathways, WormBase pathways , Wikipedia pathways ,All pathways(inlcudes all  the pathways present in Collection List)

Curation Tags List includes: Not specified (default), missing annotations,unconnected lines,under construction, stub, needs work

Step by step demonstration of task:

  • Browse pathways by Collections and Species:

2

  •   Browse pathways by Curation tags and Species:

3

  •  Browse by Collections:

4

  • Browse By CurationTags:

 5