Java library for the WikiPathways web service.
This library reimplements most of the methods from the original WikiPathways API client.
Instead of accessing the WikiPathways pathway database from Java through the REST web service API (http://webservice.wikipathways.org), the library now access the database via WikiPathways JSON File and WikiPathways GitHub assets for better performance and maintainability.
It provides nearly identical functionality to rWikiPathways, an R package in Bioconductor available to R programmers.
You need the following tools:
Compile the code and run the tests with:
cd org.wikipathways.client
mvn clean installThis library includes the following new methods:
- getCommunities
- getPathwaysByCommunity
- getCommunitiesByPathway
The method for maintaining a local cache of WikiPathways pathways is now deprecated. The following methods are also deprecated:
- getRecentChanges
- login
- updatePathway
- createPathway
- removeCurationTag
- saveCurationTag
- getCurationTags
- getCurationTagsByName
- getCurationTagHistory
- getColoredPathway
- findInteractions
- saveOntologyTag
- removeOntologyTag
- getUserByOrcid