Frequently Asked Questions¶
Citation
Beacon v2 and Beacon Networks: a "lingua franca" for federated data discovery in biomedical genomics, and beyond. Jordi Rambla, Michael Baudis, Tim Beck, Lauren A. Fromont, Arcadi Navarro, Manuel Rueda, Gary Saunders, Babita Singh, J.Dylan Spalding, Juha Tornroos, Claudia Vasallo, Colin D.Veal, Anthony J.Brookes. Human Mutation (2022) DOI.
How do I emulate Beacon v1 while supporting the v2 protocol?
The Beacon Framework describes the overall structure of the API requests, responses, parameters etc. One can implement e.g. a Boolean beacon (cf. the original protocol) without any use of the model, just by providing a well-formed JSON response upon a request very similar to the (pre-)v1 allele request.
Minimal Example Request¶
This example is for a minimal SNV-type variant query.
/beacon/g_variants/?referenceName=refseq:NC_000017.11&start=7577120&referenceBases=G&alternateBases=A
Example Boolean Response¶
In this minimal response to the query above the beacon indicates that its default
response is Boolean and that it could interpreted it against the genomicVariant
entity and in the context of the same Beacon version.
In principle one could launch a Beacon instance using the example response document as a template
in whatever server environment one has at hand. However, a proper Beacon v2
installation also has to provide informational endpoints (/info
, /map
...)
to allow it's integration through aggregators.
{
"meta": {
"apiVersion": "v2.0.0",
"beaconId": "org.progenetix.beacon",
"receivedRequestSummary": {
"apiVersion": "v2.0.0",
"pagination": {
"limit": 2000,
"skip": 0
},
"requestedGranularity": "boolean",
"requestedSchemas": [
{
"entityType": "genomicVariant",
"schema": "https://progenetix.org/services/schemas/genomicVariant/"
}
],
"requestParameters": {
"alternateBases": "A",
"referenceBases": "G",
"referenceName": "refseq:NC_000017.11",
"start": [
7577120
]
}
},
"returnedGranularity": "boolean",
"returnedSchemas": [
{
"entityType": "genomicVariant",
"schema": "https://progenetix.org/services/schemas/genomicVariant/"
}
]
},
"responseSummary": {
"exists": true
}
}
last change 2023-02-17 by Michael Baudis ¶
Is it Beacon
or beacon
?
The uppercase Beacon
is used to label API, framework or protocol and their
components - while lower case beacons
are instances of these, i.e. individual
resources using the protocol.
last change 2022-10-01 by Michael Baudis ¶
What types of genomic variants are supported in Beacon queries?
Beacon v2.0 does not provide a mechanism to detect what types of genomic variant queries are supported by a given instance.
Beacon had been originally designed to handle the "simplest" type of genomic
variant queries in which a position
, alternateBases
(i.e. one or more base
sequence of the variant at the position) and - sometimes optional - the reference
sequence at this position (necessary e.g. for small deletions).
Beacon v1.1 in principle supported "bracketed" queries and a variantType
parameter
(pointing to the VCF use) - see the current documentation for details. However, the support & interpretation was - and still is (2022-12-13) -
left to implementers. Similar for Beacon Range Queries.
However, the Beacon documentation
provides information about use and expected interpretation of variantType
values, specifically
for copy number variations.
last change 2022-12-14 by Michael Baudis ¶
How can I add e.g. an age limit to a query for a disease?
Ages are queried as ISO8601 durations
such as P65Y
(i.e. 65 years) with a comparator (=
, <=
, >
...). However,
the value needs an indication of what the duration refers to and resources
may provide different ways to indicate this (as then shown in their /filtering_terms
)
endpoint).
We recommend that all Beacon instances that support age queries support at
minimum the syntax of age:<=P65Y
and map such values to the internal datapoint
most relevant for the resource's context (in most cases probably corresponding
to "age at diagniosis").
However, different scenarios may be supported (e.g. EFO_0005056:<=P1Y6M
for
an "age at death" scenario).
last change 2023-05-31 by Michael Baudis ¶
How can I handle haplotype queries & representation in Beacon v2?"
Queries¶
The Beacon framework currently (v2.0 and earlier) considers genomic
variants to be allelic and does not support the query for multiple alleles
or "haplotype shorthand expressions" (e.g. C,T
).
Workarounds In case of a specific need for haplotype queries implementers of a given beacon with control of its data content in principle can extend their query model to support shorthand haploype expressions, as long as they support the standard format, too. However, such an approach may be superseeded or in conflict with future direct protocol support.
An approach in line with the current protocol would be to query for one allelic
variant with a record-level genomicVariation
response, and then query the
retrieved variants individually by their id
in combination with the second
allele.
Variant representation¶
As with queries the Beacon "legacy" format does not support haplotype representation but would represent each allelic variation separately. The same is true for the VRSified variant representation which for v2.0 corresponds to VRS v1.2. However, draft versions of the VRS standard (will) address haplotype and genotype representations and will be adopted by Beacon v2.n after reaching a release state.