reactome pathway viewer CURIE expansion support prefix

[sierra-moxon]

Prefix

reactome.pathway

Name

Reactome

Homepage

https://reactome.org/

Source Code Repository

https://github.com/reactome

Description

REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Founded in 2003, the Reactome project is led by Lincoln Stein of OICR, Peter D’Eustachio of NYU Langone Health, Henning Hermjakob of EMBL-EBI, and Guanming Wu of OHSU.

License

https://github.com/reactome/reactome2py/blob/master/LICENSE

Publications

https://reactome.org/cite

Example Local Unique Identifier

R-MMU-5655466

Regular Expression Pattern for Local Unique Identifier

R-[A-Z]{3}-\d+

URI Format String

https://reactome.org/PathwayBrowser/#/$1

Wikidata Property

[No response]

Contributor Name

Sierra Moxon

Contributor GitHub

sierra-moxon

Contributor ORCiD

0000-0002-8719-7760

Contributor Email

smoxon@lbl.gov

Contact Name

Peter D’Eustachio

Contact ORCiD

0000-0002-5494-626X

Contact GitHub

deustp01

Contact Email

deustp01@med.nyu.edu

Additional Comments

reactome already has a prefix reactome that refers to a specific detail page at reactome, e.g. https://www.reactome.org/content/detail/R-MMU-5655466

using the same identifier, you can get a different view, e.g. https://reactome.org/PathwayBrowser/#/R-MMU-5655466

this request is to add a "dot extension" to provide the secondary expansion for the same "source". e.g. reactome.pathway - expands_to -> "pathway page" vs. reactome - expands_to -> "detail page".

I am not sure if this means we need to edit the basic reactome prefix to support "dot extension" syntax? (e.g. does reactome need to change to reactome.detail to be consistent? - preference is that it does not change).

[cthoyt]

This isn't the right way to accomplish this - each Bioregistry prefix corresponds to a semantic space, not to a type of resolution. The way to add multiple different kinds of resolution is to curate in the "providers" slot. For example, see the "Extra Providers" section for ChEBI: https://bioregistry.io/chebi. The chebi-img provider lets you redirect to an image based on the molecule, so

• https://bioregistry.io/chebi:138488 redirects to the main page
• https://bioregistry.io/chebi:138488?provider=chebi-img redirects to the image

I can update the PR to accomplish this

[cthoyt]

See the updates in the PR, you can decide what the provider code is. Now the Reactome page's providers will look like this:

[sierra-moxon]

Thanks! this reminds me of the Alliance "page" approach in their resource_descriptor file.