Beacon api
A beacon is a gateway to your data. By creating a beacon and pointing at specific data sets within the MOLGENIS database, you allow people to query multiple data sets via one entry point.
Read more about beacons here.
The MOLGENIS Beacons are meant to be used with genetic data sets containing at least the following column types:
Chromosome
Start position
Reference allele(s)
Alternative allele(s)
A MOLGENIS beacon only exposes whether a specific variant exists. Nothing more.
Organization
An organization can be used to organize one or more beacons. An organization is the business card for your beacons. When hooking up your beacon to the global https://beacon-network.org, the organization information is shown when your beacons respond to queries.
Creating your first beacon
When you have uploaded some genetic data sets in the form of an EMX or VCF, you can go to the Dataexplorer to start creating your first beacon.
The following examples work with this data.
Select the Beacon table in the dropdown, and add a new row.
The beacon created here has only one data set, namely beacon_set. Note that the Organization is still empty, we will come back to that later.
Now that we have created a beacon, we can actually already query for variants.
Seeing a list of all the beacons
http://localhost:8080/beacon/list
produces
See the info of one beacon
http://localhost:8080/beacon/MyFirstBeacon
produces
Query the beacon for a variant via GET or POST
http://localhost:8080/beacon/MyFirstBeacon/query?referenceName=7&start=130148888&referenceBases=A&alternateBases=C
http://localhost:8080/beacon/MyFirstBeacon/query
produces
When querying goes wrong When an exception occurs, we return a response containing a BeaconError
Creating an organization
For your beacon to look nice to the world, we will add it to an organization.
In the dataexplorer, go to the dropdown in the top right, select the BeaconOrganization table, and add a new row
Configure dataset as Beacon
And now we can link to this organization and dataset by editing the Beacon row we created before
And by requesting info on our beacon again
http://localhost:8080/beacon/MyFirstBeacon
We now get information on our organization
Specifications
The complete specification can be found on ga4gh-beacon/specification
Within MOLGENIS we decided on a subset of the API. Due to the dynamic nature of our data, we can not always supply all fields.
Last updated