Some questions/comments regarding beacons

[Marc Hoeppner]

Hi,

I hope this is the right forum (this time) for some beacon-related questions/comments. I have started integrating beacon technologies into our local variant database infrastructure and will probably roll this out as a beacon and/or MME node at some point in the future. However, I do have some questions about the API.

Q: Assembly versions supported by a beacon and dataset?

I have installed a local beacon as well as written some simple code to query the BoB to check if variants in our dataset are present in any external databases. While I can specify the assembly version I wish to query, the beacon API does not seem to tell me in advance which assembly version it supports for any given dataset. So I may get a "false" as a response, but not because the variant is not present, but because it wasn't checking the correct assembly version (we do have some code that converts between assemblies on the fly to allow us to query as many beacons as possible for any given variant). This seems to be true for an individual beacon as well as the BoB. Is this something that could be added or is going to be added down the line?

Q: API support for frequency data

Apart from knowing if a given variant exists in an external database, it would be equally interesting to check at which frequency this variant has been observed. I have seen some remarks on github that this may be something that will be added to the API, but was wondering if that plan is still on the table and whether there is a time line for that?

Thanks!

Marc

[Miro Cupak]

Hi Marc,

sorry for the delayed response, I've been traveling for a while.
Comments inline:

On 10/29/2015 02:29 AM, Marc Hoeppner wrote:
> Hi,
>
> I hope this is the right forum (this time) for some beacon-related
> questions/comments. I have started integrating beacon technologies into our
> local variant database infrastructure and will probably roll this out as a
> beacon and/or MME node at some point in the future. However, I do have some
> questions about the API.
>
> Q: Assembly versions supported by a beacon and dataset?
>
> I have installed a local beacon as well as written some simple code to
> query the BoB to check if variants in our dataset are present in any
> external databases. While I can specify the assembly version I wish to
> query, the beacon API does not seem to tell me in advance which assembly
> version it supports for any given dataset.

This is a good feature request. I filed the following issue and will
implement it soon.

https://github.com/mcupak/beacon-of-beacons/issues/98

> So I may get a "false" as a
> response, but not because the variant is not present, but because it wasn't
> checking the correct assembly version (we do have some code that converts
> between assemblies on the fly to allow us to query as many beacons as
> possible for any given variant). This seems to be true for an individual
> beacon as well as the BoB. Is this something that could be added or is
> going to be added down the line?

Actually, you should never see false for references not supported by a
beacon. If we think the reference is not supported by a beacon, we
return null.

Compare e.g.:
-
https://beacon-network.org/api/responses/ega?chrom=14&pos=106833421&allele=A&ref=hg19
(supported reference, response = false)
-
https://beacon-network.org/api/responses/ega?chrom=14&pos=106833421&allele=A&ref=hg20
(unsupported reference, response = null)

If you're getting true or false for multiple reference, the beacon
you're querying supports multiple references, or at least we think it
does. Example: http://beacon.eecs.berkeley.edu/

If you don't specify a reference in the query, we automatically query
all the references we think the given beacon supports.

>
> Q: API support for frequency data
>
> Apart from knowing if a given variant exists in an external database, it
> would be equally interesting to check at which frequency this variant has
> been observed. I have seen some remarks on github that this may be
> something that will be added to the API, but was wondering if that plan is
> still on the table and whether there is a time line for that?

This already is in the Beacon API, see the following:

https://github.com/ga4gh/schemas/blob/beacon/src/main/resources/avro/beacon.avdl#L147

Beacon Network does not support frequency right now, partially because
very few beacons actually provide this data. It's on my TODO list though
and should be added as part of this issue:

https://github.com/mcupak/beacon-of-beacons/issues/33

Hope this helps,
Miro

>
> Thanks!
>
> Marc
>