Annotation for all wikipathway#

[James Moon]

Hello! Wikipathway team.

I have a program that do some clustering analysis with a long list of wikipathway.

I am trying to find a big annotation table that would show all pathway's annotation like "Ontology Terms" or "Pathway Ontology".

For example, https://www.wikipathways.org/index.php/Pathway:WP165 will have WP165 on the first column and the second column will have "tryptophan biosynthetic pathway".

Any help is accpreciated!

Thank you!

James

[Martina Summer-Kutmon]

Dear James,

You can use the rWikiPathways package to get all pathways and then retrieve their ontology terms (getOntologyTermIds(pathway) or getOntologyTermNames(pathway)). 

That should allow you to create the annotation table.

If you want to use another programming language, you can use the REST webservice method to get the ontology terms for each pathway: https://webservice.wikipathways.org/ui/#!/Pathway_information/get_getOntologyTermsByPathway.

Let me know if you have any questions about those suggestions.

Best regards,

Tina

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Martina Summer-Kutmon, PhD
email: mku...@gmail.com