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Extension to include BridgeDB #1

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danielabutano opened this issue Nov 21, 2019 · 0 comments
Open

Extension to include BridgeDB #1

danielabutano opened this issue Nov 21, 2019 · 0 comments
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enhancement New feature or request

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@danielabutano
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danielabutano commented Nov 21, 2019

BridgeDB provides some mappings. It's based on Identifers.org (however it uses only the primary resource and not the alternative resources).
If we included in the widget, we might generate more links.

Widget input:
taxonId (e.g. 9606) or organism name (at least initially), if it's easier
LUI (e.g. ensembl:400500)
type (Gene or Protein)

Here the endpoint to call in bridgedb
It can be called for Protein and Gene. The organism in input is the organism name (not the taxonId :()
Here all the system codes. As system code, we will only use L (for genes) and S (for proteins).

Example: curl -X GET --header 'Accept: /' 'https://webservice.bridgedb.org/Homo%20sapiens/xrefs/L/400500'

The endpoint doesn't return the urls :( but only the identifiers.
In the bridgedb github repo, in the datasources.xml file, we can retrieve the URL pattern.

@danielabutano danielabutano added the enhancement New feature or request label Nov 21, 2019
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