MNXtools API

[marieBvr]

Hi MNX developers,
Is there a way to use the "MNXref ID mapper" via an API or program/language (python, R)?

Thanks,
Marie

[smoretti]

Hi
Sorry @marieBvr, we totally missed your issue. I think GitHub has changed the default for the watching/following behavior, and the owners of a repository don't get a notification for issues and pull requests unless they are specifically mentioned. I set it to watch/follow all now.

The SPARQL endpoint offers more possibilities, but it is possible to query the "MNXref ID mapper" directly.
This is not documented (yet).

Here is an example of query:
https://www.metanetx.org/cgi-bin/mnxweb/id-mapper?query_index=chem&output_format=JSON&query_list=MNXM4%20MNXM7

With those possible parameters:

• query_index to select the data category: chem for the compounds/chemicals, reac for the reactions, and comp for the compartments.
• output_format to select the output format: JSON for JSON, TSV for tab-delimited format, and HTML for an HTML table. JSON is parsable by all programming languages.
• query_list is the list of identifiers you want to map. This is a list separated by space characters you have to URL encode by %20

Hope this helps you.