PathwayCommons / cpath2

Biological pathway data integration and access platform (Pathway Commons)
http://www.pathwaycommons.org/pc2/
MIT License
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Wikipathways filtering id is inconsistent #265

Closed mj3cheun closed 7 years ago

mj3cheun commented 7 years ago

The wikipathways identifier is wp. Yet, the only name which is accepted when filtering search results is wikipathways. In my opinion, the names accepted for search filtering should be changed to accept both tokens.

IgorRodchenkov commented 7 years ago

Hi Manfred, all,

Nope,

"wp" is just our internal metadata identifier (and we do not encourage anyone to use these via api, because there can be values, e.g.: 'intact', 'intact_complex', 'wp1', 'wp2', 'wp3', 'reactome_mouse' now or in the future - depends how we prepare and import data into PC...).

However, the /search query accepts absolute URIs as 'datasource' filter values as well, i.e.:

http://beta.pathwaycommons.org/pc2/search?q=*&type=pathway&datasource=http://pathwaycommons.org/pc2/wp

(note: URL query parameters after /search? must be URL-encoded, though it sometimes works as is in browsers); but then, if you'd filter by the 'intact' URI you'd miss 'intact_complex'...

Although filtering by URI works now for all sources but Intact the same way if you'd use corresponding standard name, I strongly do not recommend using URI there... (one can even do like datasource=w* but I would not recommend ;))

Therefore, we want users search by data provider's name, which every data portion/chunk behind the scene has, despite having different URIs.

Igor R.

On Tue, Apr 4, 2017 at 4:48 PM, Manfred notifications@github.com wrote:

The wikipathways identifier is wp. Yet, the only name which is accepted when filtering search results is wikipathways. In my opinion, the names accepted for search filtering should be changed to accept both tokens.

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IgorRodchenkov commented 7 years ago

On Tue, Apr 4, 2017 at 5:27 PM, Igo R rodche@gmail.com wrote:

datasource=w*

Correction: no, you cannot do: datasource=w* (wildcard filter values)

mj3cheun commented 7 years ago

Ok thanks, will switch from using id to name.