beacon_operations.post_search
POST /g_variants
Search for variants
Request Body
Schema for the Beacon request. It is named RequestBody
to keep the same nomenclature used by OpenAPI v3, but it actually contains the definition of the whole HTTP POST request payload.
object
Meta section of the Beacon request. It includes request context details relevant for the Beacon server when processing the request.
object
Version of API, e.g. in request or response. Beacon uses a Github-style, “v”-prefixed semantic versioning format.
Set of schemas to be used in the response to a request.
Schema to be used for the requested entry type in the response.
object
Parameters to limit the list of returned results.
object
Indicator of whether responses from every Resultset should be included in the response to this request or just the ones with positive, negative results or no details at all. If null (not specified), the default value of ‘HIT’ is assumed. This parameter allows for returning boolean/counting results although the Beacon instance is capable to return record level details.
Pagination to apply or that has been applied on the results.
object
A hash or similar that allows the server to retrieve a “page”, e.g. (a subset of) a query response.
Size of the page. Use 0
to return all the results or the maximum allowed by the Beacon, if there is any.
A hash or similar that allows the server to retrieve a “page”, e.g. (a subset of) a query response.
A hash or similar that allows the server to retrieve a “page”, e.g. (a subset of) a query response.
- In the request: number of pages to skip * In the response: number of pages that has been skipped
object
Alternate bases for this variant (starting from start
). * Accepted values: [ACGTN]*
* N is a wildcard, that denotes the position of any base,
and can be used as a standalone base of any type or within a partially known
sequence. As example, a query of ANNT
the Ns can take take any form of [ACGT]
and will match ANNT
, ACNT
, ACCT
, ACGT
… and so forth.
- an empty value is used in the case of deletions with the maximally trimmed,
deleted sequence being indicated in
ReferenceBases
- Categorical variant queries, e.g. such not being represented through
sequence & position, make use of the
variantType
parameter. - either
alternateBases
orvariantType
is required.
Aminoacid alteration of interest. Format 1 letter, e.g. “V600E”
Genomic assembly accession and version as RefSqeq assembly accession (e.g. “GCF_000001405.39”) or a versioned assembly name or synonym such as UCSC Genome Browser assembly (e.g. “hg38”) or Genome Reference Consortium Human (e.g. “GRCh38.p13”) names.
Precise or bracketing the end of the variants of interest: * (0-based, exclusive) - see start
* for bracket queries, provide 2 values (e.g. [111,222]).”
- A gene identifier * It is strongly suggested to use a symbol following the HGNC (https://www.genenames.org) nomenclature.
HGVSId descriptor, e.g. NC_000017.11:g.43057063G>A
Reference bases for this variant (starting from start
). * Accepted values: [ACGTN]*
* N is a wildcard, that denotes the position of any base,
and can be used as a standalone base of any type or within a partially known
sequence. As example, a query of ANNT
the Ns can take take any form of [ACGT]
and will match ANNT
, ACNT
, ACCT
, ACGT
… and so forth.
- an empty value is used in the case of insertions with the maximally trimmed, inserted
sequence being indicated in
AlternateBases
Reference sequence id for genomic reference sequence in which variant coordinates are given, e.g. “refseq:NC_000009.12” for human chromosome 9 in the GRCh38 assembly. The use of the assembly specific RefSeqId is recommended although alternatively names, synonymous or aliases e.g. “chr9” could be used in conjunction with an Assembly
parameter.
Precise or fuzzy start coordinate position(s), allele locus (0-based, inclusive). * start
only:
- for single positions, e.g. the start of a specified sequence
alteration where the size is given through the specified
alternateBases
- typical use are queries for SNV and small InDels
- the use of
start
without anend
parameter requires the use ofalternateBases
start
andend
:- for searching any variant falling fully or partially within the range
between
start
andend
(a.k.a. “range query”) - additional use of
variantType
ORalternateBases
can limit the scope of the query - by convention, partial overlaps of variants with the indicated genomic range are accepted; for specific overlap requirements the 4-parameter “Bracket Queries” should be employed
- for searching any variant falling fully or partially within the range
between
- 2 values in both
start
andend
for constructing a “Bracket Query”:- can be used to match any contiguous genomic interval, e.g. for querying imprecise positions
- identifies all structural variants starting between
start[0]
andstart[1]
, and ending betweenend[0]
<->end[1]
- single or double sided precise matches can be achieved by setting
start[1]=start[0]+1
andend[1]=end[0]+1
- Maximum length in bases of a genomic variant. * This is an optional parameter without prescribed use. While a length is commonly available for structural variants such as copy number variations, it is recommended that length based queries should also be supported for variants with indicated referenceBases and alternateBases, to enable length-specific wildcard queries.
- Minimum length in bases of a genomic variant * This is an optional parameter without prescribed use. While a length is commonly available for structural variants such as copy number variations, it is recommended that length based queries should also be supported for variants with indicated referenceBases and alternateBases, to enable length-specific wildcard queries.
The variantType
is used to query variants which are not defined through a sequence of one or more bases using the alternateBases
parameter. Examples here are e.g. structural variants: * DUP
- increased allelic count of material from the genomic region between
start
andend
positions - no assumption about the placement of the additional sequences is being made (i.e. no in situ requirement as tandem duplications)
- DEL: deletion of sequence following
start
The Beacon model is not prescriptive with regard to the values allowed forvariantType
with use of extended types (such as fromEFO:0030063
) being possible. However, a support for the basic CNV types above - where represented in the data - is recommended. EitheralternateBases
orvariantType
is required, with the exception of range queries (singlestart
andend
parameters).
Level of detail of the response:
boolean
: returns true/false’ responses *count
: adds the total number of positive results found *aggregated
: returns summary, aggregated or distribution like responses *record
: returns details for every row. In cases where a Beacon prefers to return records with fewer than allattributes, different strategies have to be considered w/o adding them to the current design, e.g.:- keeping non-mandatory attributes empty
- Beacon to provide a minimal record definition
Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE testMode
parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When true
the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.
Responses
200
Successful operation.
Complete definition for a minimal response that provides only a Boolean
exists true|false answer.
object
Set of handovers to be added in one section the response.
A handover is a typed link for attaching actionable links to results, non purely informational, requests. The goal of the handovers is to list the different actions available, e.g.:
- a link to a request access page * linking to a file for download, e.g. a VCF file Another common scenario is to provide a fast summary response (e.g. BeconCountResponse) and to provide access to different endpoints for the entities matched by the query using temporary access tokens in the handover URLs.
object
In our context, only htsget urls should be returned
object
An optional text including considerations on the handover link provided.
URL endpoint to where the handover process could progress, in RFC3986 format
Placeholder to allow the Beacon to return any additional information that is necessary or could be of interest in relation to the query or the entry returned. It is recommended to encapsulate additional informations in this attribute instead of directly adding attributes at the same level than the others in order to avoid collision in the names of attributes in future versions of the specification.
object
Information about the response that could be relevant for the Beacon client in order to interpret the results.
object
Version of API, e.g. in request or response. Beacon uses a Github-style, “v”-prefixed semantic versioning format.
The Id of a Beacon. Usually a reversed domain string, but any URI is acceptable. The purpose of this attribute is, in the context of a Beacon network, to disambiguate responses coming from different Beacons.
Section of the response that summarize the request received as it has been interpreted by the Beacon server. This summary can help to identify differences between the incoming request and its interpretation or processing, e.g. in the response granularity or pagination. The required properties include those that should be part of every request.
object
Version of API, e.g. in request or response. Beacon uses a Github-style, “v”-prefixed semantic versioning format.
Set of schemas to be used in the response to a request.
Schema to be used for the requested entry type in the response.
object
Ontology based filters. A CURIE syntax is encouraged to be used.
object
Alternate bases for this variant (starting from start
). * Accepted values: [ACGTN]*
* N is a wildcard, that denotes the position of any base,
and can be used as a standalone base of any type or within a partially known
sequence. As example, a query of ANNT
the Ns can take take any form of [ACGT]
and will match ANNT
, ACNT
, ACCT
, ACGT
… and so forth.
- an empty value is used in the case of deletions with the maximally trimmed,
deleted sequence being indicated in
ReferenceBases
- Categorical variant queries, e.g. such not being represented through
sequence & position, make use of the
variantType
parameter. - either
alternateBases
orvariantType
is required.
Aminoacid alteration of interest. Format 1 letter, e.g. “V600E”
Genomic assembly accession and version as RefSqeq assembly accession (e.g. “GCF_000001405.39”) or a versioned assembly name or synonym such as UCSC Genome Browser assembly (e.g. “hg38”) or Genome Reference Consortium Human (e.g. “GRCh38.p13”) names.
Precise or bracketing the end of the variants of interest: * (0-based, exclusive) - see start
* for bracket queries, provide 2 values (e.g. [111,222]).”
- A gene identifier * It is strongly suggested to use a symbol following the HGNC (https://www.genenames.org) nomenclature.
HGVSId descriptor, e.g. NC_000017.11:g.43057063G>A
Reference bases for this variant (starting from start
). * Accepted values: [ACGTN]*
* N is a wildcard, that denotes the position of any base,
and can be used as a standalone base of any type or within a partially known
sequence. As example, a query of ANNT
the Ns can take take any form of [ACGT]
and will match ANNT
, ACNT
, ACCT
, ACGT
… and so forth.
- an empty value is used in the case of insertions with the maximally trimmed, inserted
sequence being indicated in
AlternateBases
Reference sequence id for genomic reference sequence in which variant coordinates are given, e.g. “refseq:NC_000009.12” for human chromosome 9 in the GRCh38 assembly. The use of the assembly specific RefSeqId is recommended although alternatively names, synonymous or aliases e.g. “chr9” could be used in conjunction with an Assembly
parameter.
Precise or fuzzy start coordinate position(s), allele locus (0-based, inclusive). * start
only:
- for single positions, e.g. the start of a specified sequence
alteration where the size is given through the specified
alternateBases
- typical use are queries for SNV and small InDels
- the use of
start
without anend
parameter requires the use ofalternateBases
start
andend
:- for searching any variant falling fully or partially within the range
between
start
andend
(a.k.a. “range query”) - additional use of
variantType
ORalternateBases
can limit the scope of the query - by convention, partial overlaps of variants with the indicated genomic range are accepted; for specific overlap requirements the 4-parameter “Bracket Queries” should be employed
- for searching any variant falling fully or partially within the range
between
- 2 values in both
start
andend
for constructing a “Bracket Query”:- can be used to match any contiguous genomic interval, e.g. for querying imprecise positions
- identifies all structural variants starting between
start[0]
andstart[1]
, and ending betweenend[0]
<->end[1]
- single or double sided precise matches can be achieved by setting
start[1]=start[0]+1
andend[1]=end[0]+1
- Maximum length in bases of a genomic variant. * This is an optional parameter without prescribed use. While a length is commonly available for structural variants such as copy number variations, it is recommended that length based queries should also be supported for variants with indicated referenceBases and alternateBases, to enable length-specific wildcard queries.
- Minimum length in bases of a genomic variant * This is an optional parameter without prescribed use. While a length is commonly available for structural variants such as copy number variations, it is recommended that length based queries should also be supported for variants with indicated referenceBases and alternateBases, to enable length-specific wildcard queries.
The variantType
is used to query variants which are not defined through a sequence of one or more bases using the alternateBases
parameter. Examples here are e.g. structural variants: * DUP
- increased allelic count of material from the genomic region between
start
andend
positions - no assumption about the placement of the additional sequences is being made (i.e. no in situ requirement as tandem duplications)
- DEL: deletion of sequence following
start
The Beacon model is not prescriptive with regard to the values allowed forvariantType
with use of extended types (such as fromEFO:0030063
) being possible. However, a support for the basic CNV types above - where represented in the data - is recommended. EitheralternateBases
orvariantType
is required, with the exception of range queries (singlestart
andend
parameters).
Indicator of whether responses from every Resultset should be included in the response to this request or just the ones with positive, negative results or no details at all. If null (not specified), the default value of ‘HIT’ is assumed. This parameter allows for returning boolean/counting results although the Beacon instance is capable to return record level details.
Pagination to apply or that has been applied on the results.
object
A hash or similar that allows the server to retrieve a “page”, e.g. (a subset of) a query response.
Size of the page. Use 0
to return all the results or the maximum allowed by the Beacon, if there is any.
A hash or similar that allows the server to retrieve a “page”, e.g. (a subset of) a query response.
A hash or similar that allows the server to retrieve a “page”, e.g. (a subset of) a query response.
- In the request: number of pages to skip * In the response: number of pages that has been skipped
Level of detail of the response:
boolean
: returns true/false’ responses *count
: adds the total number of positive results found *aggregated
: returns summary, aggregated or distribution like responses *record
: returns details for every row. In cases where a Beacon prefers to return records with fewer than allattributes, different strategies have to be considered w/o adding them to the current design, e.g.:- keeping non-mandatory attributes empty
- Beacon to provide a minimal record definition
Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE testMode
parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When true
the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.
Level of detail of the response:
boolean
: returns true/false’ responses *count
: adds the total number of positive results found *aggregated
: returns summary, aggregated or distribution like responses *record
: returns details for every row. In cases where a Beacon prefers to return records with fewer than allattributes, different strategies have to be considered w/o adding them to the current design, e.g.:- keeping non-mandatory attributes empty
- Beacon to provide a minimal record definition
Set of schemas to be used in the response to a request.
Schema to be used for the requested entry type in the response.
object
Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE testMode
parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When true
the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.
Boolean (true/false) response section.
object
Indicator of whether any record was observed in any of the collections queried. This should be non-null.
Complete definition for a response that does not include record level details but provides Boolean
and count
information.
object
Set of handovers to be added in one section the response.
A handover is a typed link for attaching actionable links to results, non purely informational, requests. The goal of the handovers is to list the different actions available, e.g.:
- a link to a request access page * linking to a file for download, e.g. a VCF file Another common scenario is to provide a fast summary response (e.g. BeconCountResponse) and to provide access to different endpoints for the entities matched by the query using temporary access tokens in the handover URLs.
object
In our context, only htsget urls should be returned
object
An optional text including considerations on the handover link provided.
URL endpoint to where the handover process could progress, in RFC3986 format
Placeholder to allow the Beacon to return any additional information that is necessary or could be of interest in relation to the query or the entry returned. It is recommended to encapsulate additional informations in this attribute instead of directly adding attributes at the same level than the others in order to avoid collision in the names of attributes in future versions of the specification.
object
Information about the response that could be relevant for the Beacon client in order to interpret the results.
object
Version of API, e.g. in request or response. Beacon uses a Github-style, “v”-prefixed semantic versioning format.
The Id of a Beacon. Usually a reversed domain string, but any URI is acceptable. The purpose of this attribute is, in the context of a Beacon network, to disambiguate responses coming from different Beacons.
Section of the response that summarize the request received as it has been interpreted by the Beacon server. This summary can help to identify differences between the incoming request and its interpretation or processing, e.g. in the response granularity or pagination. The required properties include those that should be part of every request.
object
Version of API, e.g. in request or response. Beacon uses a Github-style, “v”-prefixed semantic versioning format.
Set of schemas to be used in the response to a request.
Schema to be used for the requested entry type in the response.
object
Ontology based filters. A CURIE syntax is encouraged to be used.
object
Alternate bases for this variant (starting from start
). * Accepted values: [ACGTN]*
* N is a wildcard, that denotes the position of any base,
and can be used as a standalone base of any type or within a partially known
sequence. As example, a query of ANNT
the Ns can take take any form of [ACGT]
and will match ANNT
, ACNT
, ACCT
, ACGT
… and so forth.
- an empty value is used in the case of deletions with the maximally trimmed,
deleted sequence being indicated in
ReferenceBases
- Categorical variant queries, e.g. such not being represented through
sequence & position, make use of the
variantType
parameter. - either
alternateBases
orvariantType
is required.
Aminoacid alteration of interest. Format 1 letter, e.g. “V600E”
Genomic assembly accession and version as RefSqeq assembly accession (e.g. “GCF_000001405.39”) or a versioned assembly name or synonym such as UCSC Genome Browser assembly (e.g. “hg38”) or Genome Reference Consortium Human (e.g. “GRCh38.p13”) names.
Precise or bracketing the end of the variants of interest: * (0-based, exclusive) - see start
* for bracket queries, provide 2 values (e.g. [111,222]).”
- A gene identifier * It is strongly suggested to use a symbol following the HGNC (https://www.genenames.org) nomenclature.
HGVSId descriptor, e.g. NC_000017.11:g.43057063G>A
Reference bases for this variant (starting from start
). * Accepted values: [ACGTN]*
* N is a wildcard, that denotes the position of any base,
and can be used as a standalone base of any type or within a partially known
sequence. As example, a query of ANNT
the Ns can take take any form of [ACGT]
and will match ANNT
, ACNT
, ACCT
, ACGT
… and so forth.
- an empty value is used in the case of insertions with the maximally trimmed, inserted
sequence being indicated in
AlternateBases
Reference sequence id for genomic reference sequence in which variant coordinates are given, e.g. “refseq:NC_000009.12” for human chromosome 9 in the GRCh38 assembly. The use of the assembly specific RefSeqId is recommended although alternatively names, synonymous or aliases e.g. “chr9” could be used in conjunction with an Assembly
parameter.
Precise or fuzzy start coordinate position(s), allele locus (0-based, inclusive). * start
only:
- for single positions, e.g. the start of a specified sequence
alteration where the size is given through the specified
alternateBases
- typical use are queries for SNV and small InDels
- the use of
start
without anend
parameter requires the use ofalternateBases
start
andend
:- for searching any variant falling fully or partially within the range
between
start
andend
(a.k.a. “range query”) - additional use of
variantType
ORalternateBases
can limit the scope of the query - by convention, partial overlaps of variants with the indicated genomic range are accepted; for specific overlap requirements the 4-parameter “Bracket Queries” should be employed
- for searching any variant falling fully or partially within the range
between
- 2 values in both
start
andend
for constructing a “Bracket Query”:- can be used to match any contiguous genomic interval, e.g. for querying imprecise positions
- identifies all structural variants starting between
start[0]
andstart[1]
, and ending betweenend[0]
<->end[1]
- single or double sided precise matches can be achieved by setting
start[1]=start[0]+1
andend[1]=end[0]+1
- Maximum length in bases of a genomic variant. * This is an optional parameter without prescribed use. While a length is commonly available for structural variants such as copy number variations, it is recommended that length based queries should also be supported for variants with indicated referenceBases and alternateBases, to enable length-specific wildcard queries.
- Minimum length in bases of a genomic variant * This is an optional parameter without prescribed use. While a length is commonly available for structural variants such as copy number variations, it is recommended that length based queries should also be supported for variants with indicated referenceBases and alternateBases, to enable length-specific wildcard queries.
The variantType
is used to query variants which are not defined through a sequence of one or more bases using the alternateBases
parameter. Examples here are e.g. structural variants: * DUP
- increased allelic count of material from the genomic region between
start
andend
positions - no assumption about the placement of the additional sequences is being made (i.e. no in situ requirement as tandem duplications)
- DEL: deletion of sequence following
start
The Beacon model is not prescriptive with regard to the values allowed forvariantType
with use of extended types (such as fromEFO:0030063
) being possible. However, a support for the basic CNV types above - where represented in the data - is recommended. EitheralternateBases
orvariantType
is required, with the exception of range queries (singlestart
andend
parameters).
Indicator of whether responses from every Resultset should be included in the response to this request or just the ones with positive, negative results or no details at all. If null (not specified), the default value of ‘HIT’ is assumed. This parameter allows for returning boolean/counting results although the Beacon instance is capable to return record level details.
Pagination to apply or that has been applied on the results.
object
A hash or similar that allows the server to retrieve a “page”, e.g. (a subset of) a query response.
Size of the page. Use 0
to return all the results or the maximum allowed by the Beacon, if there is any.
A hash or similar that allows the server to retrieve a “page”, e.g. (a subset of) a query response.
A hash or similar that allows the server to retrieve a “page”, e.g. (a subset of) a query response.
- In the request: number of pages to skip * In the response: number of pages that has been skipped
Level of detail of the response:
boolean
: returns true/false’ responses *count
: adds the total number of positive results found *aggregated
: returns summary, aggregated or distribution like responses *record
: returns details for every row. In cases where a Beacon prefers to return records with fewer than allattributes, different strategies have to be considered w/o adding them to the current design, e.g.:- keeping non-mandatory attributes empty
- Beacon to provide a minimal record definition
Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE testMode
parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When true
the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.
Level of detail of the response:
boolean
: returns true/false’ responses *count
: adds the total number of positive results found *aggregated
: returns summary, aggregated or distribution like responses *record
: returns details for every row. In cases where a Beacon prefers to return records with fewer than allattributes, different strategies have to be considered w/o adding them to the current design, e.g.:- keeping non-mandatory attributes empty
- Beacon to provide a minimal record definition
Set of schemas to be used in the response to a request.
Schema to be used for the requested entry type in the response.
object
Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE testMode
parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When true
the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.
Payload definition for the “count” response.
object
Indicator of whether any record was observed in any of the collections queried. This should be non-null.
Total number of results. NOT the number of results returned in this batch (after pagination) but the total obtained by the query.
Beacon response that includes record level details, grouped in Resultsets.
object
Set of handovers to be added in one section the response.
A handover is a typed link for attaching actionable links to results, non purely informational, requests. The goal of the handovers is to list the different actions available, e.g.:
- a link to a request access page * linking to a file for download, e.g. a VCF file Another common scenario is to provide a fast summary response (e.g. BeconCountResponse) and to provide access to different endpoints for the entities matched by the query using temporary access tokens in the handover URLs.
object
In our context, only htsget urls should be returned
object
An optional text including considerations on the handover link provided.
URL endpoint to where the handover process could progress, in RFC3986 format
Placeholder to allow the Beacon to return any additional information that is necessary or could be of interest in relation to the query or the entry returned. It is recommended to encapsulate additional informations in this attribute instead of directly adding attributes at the same level than the others in order to avoid collision in the names of attributes in future versions of the specification.
object
Information about the response that could be relevant for the Beacon client in order to interpret the results.
object
Version of API, e.g. in request or response. Beacon uses a Github-style, “v”-prefixed semantic versioning format.
The Id of a Beacon. Usually a reversed domain string, but any URI is acceptable. The purpose of this attribute is, in the context of a Beacon network, to disambiguate responses coming from different Beacons.
Section of the response that summarize the request received as it has been interpreted by the Beacon server. This summary can help to identify differences between the incoming request and its interpretation or processing, e.g. in the response granularity or pagination. The required properties include those that should be part of every request.
object
Version of API, e.g. in request or response. Beacon uses a Github-style, “v”-prefixed semantic versioning format.
Set of schemas to be used in the response to a request.
Schema to be used for the requested entry type in the response.
object
Ontology based filters. A CURIE syntax is encouraged to be used.
object
Alternate bases for this variant (starting from start
). * Accepted values: [ACGTN]*
* N is a wildcard, that denotes the position of any base,
and can be used as a standalone base of any type or within a partially known
sequence. As example, a query of ANNT
the Ns can take take any form of [ACGT]
and will match ANNT
, ACNT
, ACCT
, ACGT
… and so forth.
- an empty value is used in the case of deletions with the maximally trimmed,
deleted sequence being indicated in
ReferenceBases
- Categorical variant queries, e.g. such not being represented through
sequence & position, make use of the
variantType
parameter. - either
alternateBases
orvariantType
is required.
Aminoacid alteration of interest. Format 1 letter, e.g. “V600E”
Genomic assembly accession and version as RefSqeq assembly accession (e.g. “GCF_000001405.39”) or a versioned assembly name or synonym such as UCSC Genome Browser assembly (e.g. “hg38”) or Genome Reference Consortium Human (e.g. “GRCh38.p13”) names.
Precise or bracketing the end of the variants of interest: * (0-based, exclusive) - see start
* for bracket queries, provide 2 values (e.g. [111,222]).”
- A gene identifier * It is strongly suggested to use a symbol following the HGNC (https://www.genenames.org) nomenclature.
HGVSId descriptor, e.g. NC_000017.11:g.43057063G>A
Reference bases for this variant (starting from start
). * Accepted values: [ACGTN]*
* N is a wildcard, that denotes the position of any base,
and can be used as a standalone base of any type or within a partially known
sequence. As example, a query of ANNT
the Ns can take take any form of [ACGT]
and will match ANNT
, ACNT
, ACCT
, ACGT
… and so forth.
- an empty value is used in the case of insertions with the maximally trimmed, inserted
sequence being indicated in
AlternateBases
Reference sequence id for genomic reference sequence in which variant coordinates are given, e.g. “refseq:NC_000009.12” for human chromosome 9 in the GRCh38 assembly. The use of the assembly specific RefSeqId is recommended although alternatively names, synonymous or aliases e.g. “chr9” could be used in conjunction with an Assembly
parameter.
Precise or fuzzy start coordinate position(s), allele locus (0-based, inclusive). * start
only:
- for single positions, e.g. the start of a specified sequence
alteration where the size is given through the specified
alternateBases
- typical use are queries for SNV and small InDels
- the use of
start
without anend
parameter requires the use ofalternateBases
start
andend
:- for searching any variant falling fully or partially within the range
between
start
andend
(a.k.a. “range query”) - additional use of
variantType
ORalternateBases
can limit the scope of the query - by convention, partial overlaps of variants with the indicated genomic range are accepted; for specific overlap requirements the 4-parameter “Bracket Queries” should be employed
- for searching any variant falling fully or partially within the range
between
- 2 values in both
start
andend
for constructing a “Bracket Query”:- can be used to match any contiguous genomic interval, e.g. for querying imprecise positions
- identifies all structural variants starting between
start[0]
andstart[1]
, and ending betweenend[0]
<->end[1]
- single or double sided precise matches can be achieved by setting
start[1]=start[0]+1
andend[1]=end[0]+1
- Maximum length in bases of a genomic variant. * This is an optional parameter without prescribed use. While a length is commonly available for structural variants such as copy number variations, it is recommended that length based queries should also be supported for variants with indicated referenceBases and alternateBases, to enable length-specific wildcard queries.
- Minimum length in bases of a genomic variant * This is an optional parameter without prescribed use. While a length is commonly available for structural variants such as copy number variations, it is recommended that length based queries should also be supported for variants with indicated referenceBases and alternateBases, to enable length-specific wildcard queries.
The variantType
is used to query variants which are not defined through a sequence of one or more bases using the alternateBases
parameter. Examples here are e.g. structural variants: * DUP
- increased allelic count of material from the genomic region between
start
andend
positions - no assumption about the placement of the additional sequences is being made (i.e. no in situ requirement as tandem duplications)
- DEL: deletion of sequence following
start
The Beacon model is not prescriptive with regard to the values allowed forvariantType
with use of extended types (such as fromEFO:0030063
) being possible. However, a support for the basic CNV types above - where represented in the data - is recommended. EitheralternateBases
orvariantType
is required, with the exception of range queries (singlestart
andend
parameters).
Indicator of whether responses from every Resultset should be included in the response to this request or just the ones with positive, negative results or no details at all. If null (not specified), the default value of ‘HIT’ is assumed. This parameter allows for returning boolean/counting results although the Beacon instance is capable to return record level details.
Pagination to apply or that has been applied on the results.
object
A hash or similar that allows the server to retrieve a “page”, e.g. (a subset of) a query response.
Size of the page. Use 0
to return all the results or the maximum allowed by the Beacon, if there is any.
A hash or similar that allows the server to retrieve a “page”, e.g. (a subset of) a query response.
A hash or similar that allows the server to retrieve a “page”, e.g. (a subset of) a query response.
- In the request: number of pages to skip * In the response: number of pages that has been skipped
Level of detail of the response:
boolean
: returns true/false’ responses *count
: adds the total number of positive results found *aggregated
: returns summary, aggregated or distribution like responses *record
: returns details for every row. In cases where a Beacon prefers to return records with fewer than allattributes, different strategies have to be considered w/o adding them to the current design, e.g.:- keeping non-mandatory attributes empty
- Beacon to provide a minimal record definition
Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE testMode
parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When true
the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.
Level of detail of the response:
boolean
: returns true/false’ responses *count
: adds the total number of positive results found *aggregated
: returns summary, aggregated or distribution like responses *record
: returns details for every row. In cases where a Beacon prefers to return records with fewer than allattributes, different strategies have to be considered w/o adding them to the current design, e.g.:- keeping non-mandatory attributes empty
- Beacon to provide a minimal record definition
Set of schemas to be used in the response to a request.
Schema to be used for the requested entry type in the response.
object
Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE testMode
parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When true
the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.
Sets of results to be returned as query response.
object
object
Id of the resultset
Additional details that could be of interest about the Resultset. Provided to clearly enclose any attribute that is not part of the Beacon specification.
object
Schema for a genomic variant entry. In this case, each GenomicVariant represents a single alternate allele, with the reference allele assumed from the reference sequence.
object
CaseLevelData reports about the variation instances observed in individual analyses.
object
Ontology value for allele origin of variant in sample from the Variant Origin (SO:0001762). Categories are somatic variant
, germline variant
, maternal variant
, paternal variant
, de novo variant
, pedigree specific variant
, population specific variant
. Corresponds to Variant Inheritance in FHIR.
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
Reference to the bioinformatics analysis ID (analysis.id
)
Reference to biosample ID (biosample.id
). For MoH, this will be {program_id}~{submitter_sample_id}
, delimited with a tilde. If this is not available, it will be the name of the sample as listed in the variant file.
List of annotated effects on disease or phenotypes.
object
object
Name of the tool.
References to the tool
object
Version used.
Ontology term for the type of disease, condition, phenotypic measurement, etc.
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
Indication of the clinical relevance of the variant Recommended: A value from the five-tiered classification from the American College of Medical Genetics (ACMG) designed to describe the likelihood that a genomic sequence variant is causative of an inherited disease. (NCIT:C168798).
Internal identifier of the phenotype or clinical effect.
Ontology term for the phenotypic or clinical effect
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
Ontology term for the type of evidence supporting variant-disease association Recommended: values from the Evidence & Conclusion Ontology (ECO)
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
Internal id of this case level instance of the variant. This is an optional housekeeping parameter and should not be confused with the identifier of the variant (variantInternalId
).
Reference to individual ID (individual.id
)
List of annotated effects on disease or phenotypes.
object
object
Name of the tool.
References to the tool
object
Version used.
Ontology term for the type of disease, condition, phenotypic measurement, etc.
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
Indication of the clinical relevance of the variant Recommended: A value from the five-tiered classification from the American College of Medical Genetics (ACMG) designed to describe the likelihood that a genomic sequence variant is causative of an inherited disease. (NCIT:C168798).
Internal identifier of the phenotype or clinical effect.
Ontology term for the phenotypic or clinical effect
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
Ontology term for the type of evidence supporting variant-disease association Recommended: values from the Evidence & Conclusion Ontology (ECO)
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
Reference to the experimental run ID (run.id
)
object
Ontology term for zygosity in which variant is present in the sample from the Zygosity Ontology (GENO:0000391) , e.g heterozygous
(GENO:0000135)
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
VCF GT-style value, e.g. 0/0, 1|2
VariantInternalIds of the other allele(s) present in this genotype
object
ClinVar variant id. Other id values used by ClinVar can be added to variantAlternativeIds
HGVSId descriptor.
List of HGVSId descriptor(s) at protein level (for protein-altering variants).
List of HGVSId descriptor(s) at transcript level.
List of cross-referencing ID(s), for the variant in other databases (e.g. dbSNP, ClinVar, ClinGen, COSMIC), as externalReferences
with CURIE(s).
object
object
List of change(s) at aminoacid level for protein affecting variants.
Genomic feature(s) related to the variant. NOTE: Although genes could also be referenced using these attributes, they have an independent section to allow direct queries.
object
Ontology term that describes the class of genomic feature affected by the variant. Values from SO (Sequence ontology) are recommended, e.g. SO:0001623: 5 prime UTR variant
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
Where applicable, ID/accession/name of genomic feature related to the featureClass
, preferably in CURIE format. If the value is a gene id or name, it points to the gene related to the featureClass
, e.g. the 5 prime UTR upstream of TP53
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
Ontology term that includes describes the class of molecular consequence generated by the variant. Values from SO (Sequence Ontology) are recommended, e.g. SO:0001583: missense variant
.
Definition of an ontology term.
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
Reference to the internal variant ID. This represents the primary key/identifier of that variant inside a given Beacon instance. Different Beacon instances may use identical id values, referring to unrelated variants. Public identifiers such as the GA4GH Variant Representation Id (VRSid) MUST be returned in the identifiers
section. A Beacon instance can, of course, use the VRSid as their own internal id but still MUST represent this then in the identifiers
section.
object
List of annotated effects on disease or phenotypes.
object
object
Name of the tool.
References to the tool
object
Version used.
Ontology term for the type of disease, condition, phenotypic measurement, etc.
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
Indication of the clinical relevance of the variant Recommended: A value from the five-tiered classification from the American College of Medical Genetics (ACMG) designed to describe the likelihood that a genomic sequence variant is causative of an inherited disease. (NCIT:C168798).
Internal identifier of the phenotype or clinical effect.
Ontology term for the phenotypic or clinical effect
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
Ontology term for the type of evidence supporting variant-disease association Recommended: values from the Evidence & Conclusion Ontology (ECO)
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
List of annotated effects on disease or phenotypes.
object
object
Name of the tool.
References to the tool
object
Version used.
Ontology term for the type of disease, condition, phenotypic measurement, etc.
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
Indication of the clinical relevance of the variant Recommended: A value from the five-tiered classification from the American College of Medical Genetics (ACMG) designed to describe the likelihood that a genomic sequence variant is causative of an inherited disease. (NCIT:C168798).
Internal identifier of the phenotype or clinical effect.
Ontology term for the phenotypic or clinical effect
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
Ontology term for the type of evidence supporting variant-disease association Recommended: values from the Evidence & Conclusion Ontology (ECO)
object
A W3C Compact URI formatted string. A CURIE string has the structure prefix
:reference
, as defined by the W3C syntax.
The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.
A variation on a contiguous molecule.
object
MUST be “Allele”
A Location defined by an interval on a referenced Sequence.
object
MUST be “SequenceLocation”
A VRS Computed Identifier for the reference Sequence.
A SequenceInterval represents a span on a Sequence. Positions are always represented by contiguous spans using interbase coordinates or coordinate ranges.
object
MUST be “SequenceInterval”
A bounded, inclusive range of numbers.
object
MUST be “DefiniteRange”
The minimum value; inclusive
The maximum value; inclusive
A half-bounded range of numbers represented as a number bound and associated comparator. The bound operator is interpreted as follows: ’>=’ are all numbers greater than and including value
, ’<=’ are all numbers less than and including value
.
object
MUST be “IndefiniteRange”
The bounded value; inclusive
MUST be one of ”<=” or ”>=”, indicating which direction the range is indefinite
A simple integer value as a VRS class.
object
MUST be “Number”
The value represented by Number
A bounded, inclusive range of numbers.
object
MUST be “DefiniteRange”
The minimum value; inclusive
The maximum value; inclusive
A half-bounded range of numbers represented as a number bound and associated comparator. The bound operator is interpreted as follows: ’>=’ are all numbers greater than and including value
, ’<=’ are all numbers less than and including value
.
object
MUST be “IndefiniteRange”
The bounded value; inclusive
MUST be one of ”<=” or ”>=”, indicating which direction the range is indefinite
A simple integer value as a VRS class.
object
MUST be “Number”
The value represented by Number
object
MUST be “LiteralSequenceExpression”
The literal Sequence expressed
Number of results in this Resultset.
Set of handovers to be added in one section the response.
A handover is a typed link for attaching actionable links to results, non purely informational, requests. The goal of the handovers is to list the different actions available, e.g.:
- a link to a request access page * linking to a file for download, e.g. a VCF file Another common scenario is to provide a fast summary response (e.g. BeconCountResponse) and to provide access to different endpoints for the entities matched by the query using temporary access tokens in the handover URLs.
object
In our context, only htsget urls should be returned
object
An optional text including considerations on the handover link provided.
URL endpoint to where the handover process could progress, in RFC3986 format
Entry type of resultSet. It SHOULD MATCH an entry type declared as collection in the Beacon configuration.
Beacon results summary section.
object
Indicator of whether any record was observed in any of the collections queried. This should be non-null.
Total number of results. NOT the number of results returned in this batch (after pagination) but the total obtained by the query.
default
An unsuccessful operation.
object
Beacon-specific error.
object
Entry not found
Information about the response that could be relevant for the Beacon client in order to interpret the results.
object
Version of API, e.g. in request or response. Beacon uses a Github-style, “v”-prefixed semantic versioning format.
The Id of a Beacon. Usually a reversed domain string, but any URI is acceptable. The purpose of this attribute is, in the context of a Beacon network, to disambiguate responses coming from different Beacons.
Section of the response that summarize the request received as it has been interpreted by the Beacon server. This summary can help to identify differences between the incoming request and its interpretation or processing, e.g. in the response granularity or pagination. The required properties include those that should be part of every request.
object
Version of API, e.g. in request or response. Beacon uses a Github-style, “v”-prefixed semantic versioning format.
Set of schemas to be used in the response to a request.
Schema to be used for the requested entry type in the response.
object
Ontology based filters. A CURIE syntax is encouraged to be used.
object
Alternate bases for this variant (starting from start
). * Accepted values: [ACGTN]*
* N is a wildcard, that denotes the position of any base,
and can be used as a standalone base of any type or within a partially known
sequence. As example, a query of ANNT
the Ns can take take any form of [ACGT]
and will match ANNT
, ACNT
, ACCT
, ACGT
… and so forth.
- an empty value is used in the case of deletions with the maximally trimmed,
deleted sequence being indicated in
ReferenceBases
- Categorical variant queries, e.g. such not being represented through
sequence & position, make use of the
variantType
parameter. - either
alternateBases
orvariantType
is required.
Aminoacid alteration of interest. Format 1 letter, e.g. “V600E”
Genomic assembly accession and version as RefSqeq assembly accession (e.g. “GCF_000001405.39”) or a versioned assembly name or synonym such as UCSC Genome Browser assembly (e.g. “hg38”) or Genome Reference Consortium Human (e.g. “GRCh38.p13”) names.
Precise or bracketing the end of the variants of interest: * (0-based, exclusive) - see start
* for bracket queries, provide 2 values (e.g. [111,222]).”
- A gene identifier * It is strongly suggested to use a symbol following the HGNC (https://www.genenames.org) nomenclature.
HGVSId descriptor, e.g. NC_000017.11:g.43057063G>A
Reference bases for this variant (starting from start
). * Accepted values: [ACGTN]*
* N is a wildcard, that denotes the position of any base,
and can be used as a standalone base of any type or within a partially known
sequence. As example, a query of ANNT
the Ns can take take any form of [ACGT]
and will match ANNT
, ACNT
, ACCT
, ACGT
… and so forth.
- an empty value is used in the case of insertions with the maximally trimmed, inserted
sequence being indicated in
AlternateBases
Reference sequence id for genomic reference sequence in which variant coordinates are given, e.g. “refseq:NC_000009.12” for human chromosome 9 in the GRCh38 assembly. The use of the assembly specific RefSeqId is recommended although alternatively names, synonymous or aliases e.g. “chr9” could be used in conjunction with an Assembly
parameter.
Precise or fuzzy start coordinate position(s), allele locus (0-based, inclusive). * start
only:
- for single positions, e.g. the start of a specified sequence
alteration where the size is given through the specified
alternateBases
- typical use are queries for SNV and small InDels
- the use of
start
without anend
parameter requires the use ofalternateBases
start
andend
:- for searching any variant falling fully or partially within the range
between
start
andend
(a.k.a. “range query”) - additional use of
variantType
ORalternateBases
can limit the scope of the query - by convention, partial overlaps of variants with the indicated genomic range are accepted; for specific overlap requirements the 4-parameter “Bracket Queries” should be employed
- for searching any variant falling fully or partially within the range
between
- 2 values in both
start
andend
for constructing a “Bracket Query”:- can be used to match any contiguous genomic interval, e.g. for querying imprecise positions
- identifies all structural variants starting between
start[0]
andstart[1]
, and ending betweenend[0]
<->end[1]
- single or double sided precise matches can be achieved by setting
start[1]=start[0]+1
andend[1]=end[0]+1
- Maximum length in bases of a genomic variant. * This is an optional parameter without prescribed use. While a length is commonly available for structural variants such as copy number variations, it is recommended that length based queries should also be supported for variants with indicated referenceBases and alternateBases, to enable length-specific wildcard queries.
- Minimum length in bases of a genomic variant * This is an optional parameter without prescribed use. While a length is commonly available for structural variants such as copy number variations, it is recommended that length based queries should also be supported for variants with indicated referenceBases and alternateBases, to enable length-specific wildcard queries.
The variantType
is used to query variants which are not defined through a sequence of one or more bases using the alternateBases
parameter. Examples here are e.g. structural variants: * DUP
- increased allelic count of material from the genomic region between
start
andend
positions - no assumption about the placement of the additional sequences is being made (i.e. no in situ requirement as tandem duplications)
- DEL: deletion of sequence following
start
The Beacon model is not prescriptive with regard to the values allowed forvariantType
with use of extended types (such as fromEFO:0030063
) being possible. However, a support for the basic CNV types above - where represented in the data - is recommended. EitheralternateBases
orvariantType
is required, with the exception of range queries (singlestart
andend
parameters).
Indicator of whether responses from every Resultset should be included in the response to this request or just the ones with positive, negative results or no details at all. If null (not specified), the default value of ‘HIT’ is assumed. This parameter allows for returning boolean/counting results although the Beacon instance is capable to return record level details.
Pagination to apply or that has been applied on the results.
object
A hash or similar that allows the server to retrieve a “page”, e.g. (a subset of) a query response.
Size of the page. Use 0
to return all the results or the maximum allowed by the Beacon, if there is any.
A hash or similar that allows the server to retrieve a “page”, e.g. (a subset of) a query response.
A hash or similar that allows the server to retrieve a “page”, e.g. (a subset of) a query response.
- In the request: number of pages to skip * In the response: number of pages that has been skipped
Level of detail of the response:
boolean
: returns true/false’ responses *count
: adds the total number of positive results found *aggregated
: returns summary, aggregated or distribution like responses *record
: returns details for every row. In cases where a Beacon prefers to return records with fewer than allattributes, different strategies have to be considered w/o adding them to the current design, e.g.:- keeping non-mandatory attributes empty
- Beacon to provide a minimal record definition
Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE testMode
parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When true
the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.
Level of detail of the response:
boolean
: returns true/false’ responses *count
: adds the total number of positive results found *aggregated
: returns summary, aggregated or distribution like responses *record
: returns details for every row. In cases where a Beacon prefers to return records with fewer than allattributes, different strategies have to be considered w/o adding them to the current design, e.g.:- keeping non-mandatory attributes empty
- Beacon to provide a minimal record definition
Set of schemas to be used in the response to a request.
Schema to be used for the requested entry type in the response.
object
Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE testMode
parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When true
the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.