BEDhost API guide
You can find the formal OpenAPI documentation and interactive interface at http://api.bedbase.org/docs. This document provides more conceptual introduction and explanations to how to use the API effectively.
General API organization
BEDbase stores two types of data, which we call records. They are 1. BEDs, and 2. BEDsets. BEDsets are simply collections of BEDs. Each record in the database is either a BED or a BEDset.
The endpoints are divided into 3 groups:
/bedendpoints are used to interact with metadata for BED records.
/bedsetendpoints are used to interact with metadata for BEDset records.
/objectsendpoints are used to download metadata and get URLs to retrieve the underlying data itself. These endpoints implement the GA4GH DRS standard.
Therefore, to get information and statistics about BED or BEDset records, or what is contained in the database, look through the
/bedset endpoints. But if you need to write a tool that gets the actual underlying files, then you'll need to use the
/objects endpoints. The type of identifiers used in each case differ.
Record identifiers vs. object identifiers
Each record has an identifier. For example,
eaf9ee97241f300f1c7e76e1f945141f is a BED identifier. You can use this identifier for the metadata endpoints. To download files, you'll need something slightly different -- you need an object identifier. This is because each BED record includes multiple files, such as the original BED file, the BigBed file, analysis plots, and so on. To download a file, you will construct what we call the
object_id, which identifies the specific file.
How to construct object identifiers
Object IDs take the form
<record_type>.<record_identifier>.<result_id>. An example of an object_id for a BED file is
So, you can get information about this object like this:
Or, you can get a URL to download the actual file with: