It gives me immense pleasure to announce that WikiPathways Client Plugin version 0.2 is now available for download. This version has a new feature (i.e) Upload Pathways from Pathvisio.

Features:

Search Pathways (Basic and Advanced)
Browse Pathways
Upload Pathways (Create and update)

Additional Features:

Open pathway for pathway node that is annotated with pathway identifier
Open pathways which contain similar element as of the selected DataNode
For additional info:

Please Refer:http://plugins.pathvisio.org/wp-client/documentation/

It gives me a immense pleasure to bring into notice that, we have now a feature in WikiPathways Client Plugin which would enable the user to Upload (create/update) Pathways from PathVisio.

Step by step demonstration:

1. Create a Pathway-

  • Select Plugins>>WikiPathways>>Upload>> Create Pathway 

(If their is no Pathway to Upload, the options are disabled)

up1

 

  • Create a Pathway in PathVisio, then click on Create Pathway. A Login Panel appears – Fill the User Credentials.

LOGIN

  • If you don’t  have an account on WikiPathways or you have entered wrong User Credentials.

Loginerror

  • If the User Credentials are valid, then a Description Panel appears, where you have to fill the description to be added to the Pathway.

description

 

  • Now the Pathwasy will be created and uploaded to WikiPathways with Default Curation Tag -’ Under Construction’.

 

success

2. Upload Pathway

  • Search the Pathway From WikiPathways Client Plugin- to be updated .

 

SEARCHNOW

 

  •  Select Plugins>>WikiPathways>>Update>> UploadPathway  -Description Panel appears

(Login Panel appears if you haven’t logged in)

update

 

 

  • If their are no new revisions available online for the Pathway to be updated, then the Pathway will be updated.

 

update success

Today I’m delighted  to announce that WikiPathways Client Plugin  version 0.1  is now available for download. This version has a lot features.

Features:

  • Search Pathways  (Basic and Advanced)
  • Browse Pathways

Additional Features:

  • Open pathway for pathway node that is annotated with pathway identifier
  • Open pathways which contain similar element as of the selected DataNode

For additional info:

Please Refer:http://plugins.pathvisio.org/wp-client/documentation/

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