Augment WikiPathways OpenAPI info with `x-bte` information

[andrewsu]

WikiPathways is a valuable resource for information on biological pathways. We should annotate the API using the x-bte extensions so it can be called within BioThings Explorer.

These are example API calls:

• Disease -> Pathway: https://webservice.wikipathways.org/getPathwaysByParentOntologyTerm?term=DOID%3A10763&format=json
• Pathway -> Disease: https://webservice.wikipathways.org/getOntologyTermsByPathway?pwId=WP4863&format=json)
• Gene -> Pathway: https://webservice.wikipathways.org/findPathwaysByXref?ids=59272&codes=L&format=json
• Pathway -> Gene: https://webservice.wikipathways.org/getXrefList?pwId=WP4863&code=L&format=json
• Metabolite -> Pathway: https://webservice.wikipathways.org/findPathwaysByXref?ids=52931518&codes=Cpc&format=json (*)
• Pathway -> Metabolite: https://webservice.wikipathways.org/getXrefList?pwId=WP5064&code=Cpc&format=json (*)

(*) @ariutta I would have thought these two API calls would work based the pattern for gene mappings and the table of ID abbreviations you sent, but they are not currently returning results. Metabolites with Pubchem-compound IDs are found on https://www.wikipathways.org/index.php/Pathway:WP5064. Can you review please?

Presumably after the appropriate x-bte annotations are defined here, this issue would result in a PR to the Wikipathways code that generates that swagger / Open API content.

Relevant links:

• SmartAPI record for Wikipathways: https://smart-api.info/registry?q=45f6ce9f9f2072b581ab85771e2ab15b
• OpenAPI annotation: https://webservice.wikipathways.org/index.php?swagger

[colleenXu]

• Disease -> Pathway looks okay, if we can assume that the value of the id field in each record is always WIKIPATHWAYS. Small note: would be nice if the NCBITaxon ID was also provided for the species.
• Pathway -> Disease: is it possible to get only the DOID records? I'm unsure on whether BTE can handle this without some custom api-response-transform post-processing.
• Gene -> Pathway looks okay. Same small note as above for Disease -> Pathway.
• Pathway -> Gene: Probably okay. I'm a bit unsure since the IDs are in an array (not separate records for each). Can we assume that these are all Entrez gene IDs (Translator uses the prefix NCBIGene)?

I'll review the Metabolite -> Pathway and Pathway -> Metabolite links once we figure those out.

---

Some questions:

• these look like GET queries - so we'd have to provide 1 ID at a time, right?
• I see a "/findInteractions" endpoint in https://webservice.wikipathways.org/index.php?swagger .... is that gene-gene interactions? Is that interesting? However, based on the swagger annotation, it doesn't look like it takes gene IDs as input or gives them as output...

[colleenXu]

I'll also note that the current swagger link seems to be written in an older standard (2.0?) that I'm not familiar with.

I guess I'm familiar with OpenAPI 3.0, so I'd probably be more comfortable rewriting the file to OpenAPI 3.0 / SmartAPI before adding x-bte annotation...

[ariutta]

Our colleagues in the Netherlands are in the process of updating the webservice API. We can connect you with them if you think it’d be useful to discuss OpenAPI 3.0.

We also have an RDF endpoint that should be able to return everything needed, e.g., here's an example query for getting all pathways with a specific gene.

Alternatively, we’re happy to provide a monthly flat file. For just genes, the GMT is enough, but for ontology terms or metabolites, it'd probably make sense to create a new file.

[ariutta]

@colleenXu, I sent an update by email, but I'll copy it over here too:

I talked with Egon and some other folks from Maastricht today, and they said let's go ahead with the update based on the existing API. Egon created a GitHub repo for the current API definition here: https://github.com/wikipathways/openapi/blob/main/openapi.json

Colleen, if you want to make a pull request, you can feel free to add x-bte annotations and any other updates as required.

[colleenXu]

@ariutta Thank you, I've seen the email. I have a plan to review that link and make a fork to write a openapi v3 version with x-bte annotation.

Just need to get around to getting it done >.<