Hi Gabe,
The LabKey Server documentation for client APIs is located here:
https://www.labkey.org/home/Documentation/wiki-page.view?name=viewApis
Hopefully, an API exists for the programming language of your choice. If not, you could use the "HTTP interface" and write a wrapper around it.
To query the data you need to be somewhat familiar with the database schema. If you are the administrator of your own LabKey Server installation, or you have admin privileges for a project on PanoramaWeb or your own instance of LabKey Server, you can browse the schema via: Admin > Go To Module > Query. Look at the details of the 'targetedms' schema.
The "SelectRows" API is probably the most useful. Here is an example of getting a list of Skyline documents in a folder using the JavaScript API:
LABKEY.Query.selectRows({
containerPath: 'path_to_folder, // Folder of interest
schemaName: 'targetedms',
queryName: 'runs', // Name of table that stores an entry for each Skyline document uploaded to the folder
success: onSuccess,
failure: onFailure
});
Please let me know if you have any further questions, or if I can help you with any specific queries.
Thanks,
Vagisha