Help:WikiPathways Webservice
From WikiPathways
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| - | WikiPathways can be accessed programmatically through a | + | WikiPathways can be accessed programmatically through a REST web service. These services provide powerful means to query, access and interact with the pathway content at WikiPathways. |
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== API Reference == | == API Reference == | ||
| - | See the [ | + | See the [https://webservice.wikipathways.org Swagger] page for a list of available web service functions and data structures. |
=== Java libraries === | === Java libraries === | ||
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Below is a short list of libraries for popular programming languages that might help you work with the WikiPathways web service. | Below is a short list of libraries for popular programming languages that might help you work with the WikiPathways web service. | ||
| + | * R: The rWikiPathways package with vignettes at [https://bioconductor.org/packages/release/bioc/html/rWikiPathways.html bioconductor]. | ||
* Java: Java API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-java github]. | * Java: Java API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-java github]. | ||
* Perl: Perl API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-perl github]. | * Perl: Perl API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-perl github]. | ||
* Php: Example scripts at [https://github.com/wikipathways/scripts/ github]. | * Php: Example scripts at [https://github.com/wikipathways/scripts/ github]. | ||
* Python: Python API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-py github]. | * Python: Python API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-py github]. | ||
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== Other Examples == | == Other Examples == | ||
Current revision
Web Services for WikiPathways
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WikiPathways can be accessed programmatically through a REST web service. These services provide powerful means to query, access and interact with the pathway content at WikiPathways. |
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API ReferenceSee the Swagger page for a list of available web service functions and data structures. Java librariesYou can get a high-level API to the WikiPathways web service here: source compiled binaries (choose the most recent wikipathways_client_bin-*). Working with GPMLThe pathways on WikiPathways are stored in the GPML format. This is an XML format and can be processed in any programming language. See here for the GPML specification. If you are developing in Java, we recommend using our Java libraries. LibrariesBelow is a short list of libraries for popular programming languages that might help you work with the WikiPathways web service.
Other ExamplesGroovyThis blog post contains an example of how to use the WikiPathways webservice in Groovy. How to citeKelder T, Pico AR, Hanspers K, van Iersel MP, Evelo C, Conklin BR. (2009) Mining Biological Pathways Using WikiPathways Web Services. PLoS ONE 4(7): doi:10.1371/journal.pone.0006447 |
