Metadata access - REST API

[beatrizserrano]

Hi,

I need some metadata (gene, reagent, labels for controls, etc.) associated with a well that I couldn't find in the REST API. To get this extra metadata, I usually merge the data from the REST API that describes the layout and the annotations from the data provider (CSV format).

For instance, I can't find the gene, reagent or whether this is a control or not in this query. Could you give me an example of where to find this information using only the API?

Thanks!

[will-moore]

Hi,

I think all the data you want is on Map Annotations. You can get the Map Annotations for multiple objects via: http://idr.openmicroscopy.org/webclient/api/annotations/?type=map&well=67070&well=67069

NB: If you load annotations for more than 1 object at a time (e.g. 2 wells in that example) then you'll need to use the link.parent.id data to know which annotation is on which object. If just a single object (e.g. well=67070 then you know all the annotations are on that object.

These /webclient/api/ URLs are not well documented since we've generally treated these as for 'internal' usage by the webclient. But you can find them using the developer tools in your browser (look in Network tab under XHR). E.g. when you click on a Well at http://idr.openmicroscopy.org/webclient/?show=well-67070 you'll see the above URL being loaded.

Other /api/ URLs are documented at https://docs.openmicroscopy.org/omero/5.5.1/developers/json-api.html and /webgateway/ URLs are at https://docs.openmicroscopy.org/omero/5.5.1/developers/Web/WebGateway.html.

I don't know if you have a "JSON" plugin/extension for your browser, but the formatting of JSON in the browser makes it much easier to inspect what you're getting from those URLs.

Regards,
Will.

[beatrizserrano]

Thanks @will-moore! That's very useful.