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Updating develop branch from last urgent fixes to main #169

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ca1297b
removing the validation directories
mbaudis Dec 22, 2022
2b12b23
Removing mentions to "aggregated" granularity in the code.
jrambla Mar 28, 2023
d553374
Merge pull request #64 from ga4gh-beacon/clean-up_remove_aggregated_r…
jrambla Mar 28, 2023
83c9bbb
Merge pull request #67 from ga4gh-beacon/clean-up_remove-validator-re…
costero-e Mar 29, 2023
d490eb7
missing object type fix
mbaudis May 24, 2023
634283d
Update CHANGELOG.md
mbaudis May 26, 2023
8065376
fix disease ageOfOnset examples
mbaudis Jun 1, 2023
11312cd
fixing the ontology term CUSTOM format
mbaudis Jun 10, 2023
5b47a87
Update entryTypeDefinition.yaml
mbaudis Jun 18, 2023
6aeb06f
Update entryTypeDefinition.json
mbaudis Jun 19, 2023
d3f7a92
removed ontologyTermForThisType requirement
mbaudis Jun 19, 2023
dd943ae
entry type as default instead entity
mbaudis Jun 19, 2023
94b7891
update entryType description
Jun 20, 2023
cb3b2ff
for templates the format must be "uri-template".
redmitry Sep 5, 2023
f4f8264
Merge branch 'main' into schema-urgent-fixes
costero-e Jan 16, 2024
13f8ac9
Merge pull request #133 from ga4gh-beacon/main
mbaudis Jul 6, 2024
971a2ad
Update requestParameters.yaml for at least 1 end value
mbaudis Jul 6, 2024
33d2228
Update requestParameters.json for at least 1 value in end
mbaudis Jul 6, 2024
9f9c96a
renaming endpoints for beaconMap
costero-e Jul 10, 2024
ae4214a
Merge pull request #134 from ga4gh-beacon/hotfix-beaconMap
costero-e Jul 10, 2024
de829f3
updated CNV term mapping table
mbaudis Jul 13, 2024
7b44cd5
Merge branch 'main' into schema-urgent-fixes
costero-e Jul 16, 2024
18eff1c
deleting aggregated from Granularity enum
costero-e Jul 16, 2024
556e5b5
deleting aggregated from Granularity description
costero-e Jul 16, 2024
731de0e
Merge pull request #146 from ga4gh-beacon/clean-up
costero-e Jul 16, 2024
de014e8
Merge pull request #82 from ga4gh-beacon/schema-urgent-fixes
costero-e Jul 16, 2024
0cfec9a
Merge branch 'main' into website-docs
costero-e Jul 16, 2024
f6f85c4
Merge pull request #147 from ga4gh-beacon/website-docs
costero-e Jul 16, 2024
bcec830
updated changelog of versions
costero-e Jul 18, 2024
fb34316
updated release date for version 2.1
costero-e Jul 18, 2024
65c2574
Merge pull request #149 from ga4gh-beacon/schema-urgent-fixes_update-…
costero-e Jul 18, 2024
85eb71e
Merge branch 'main' into schema-urgent-fixes
costero-e Jul 18, 2024
1686220
Merge pull request #150 from ga4gh-beacon/schema-urgent-fixes
costero-e Jul 18, 2024
690ee96
Merge branch 'main' into entry-type-definitions-cleanup
jrambla Oct 8, 2024
7e98b1e
Merge pull request #92 from ga4gh-beacon/entry-type-definitions-cleanup
costero-e Oct 8, 2024
1d4730a
Merge branch 'main' into uri-template
costero-e Oct 8, 2024
5ea17fb
Merge pull request #110 from redmitry/uri-template
costero-e Oct 8, 2024
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3 changes: 2 additions & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Fixed

* Fixed `POST`queries for `g_variant` (w/ examples)
* Removed 'json' references inside the yaml version (PR [#43] (https://github.com/ga4gh-beacon/beacon-v2/pull/43))
* Removed 'json' references inside the yaml version (PR [#43](https://github.com/ga4gh-beacon/beacon-v2/pull/43))
* added missing `type: object` to `ResultsetInstance` (PR [#82](https://github.com/ga4gh-beacon/beacon-v2/pull/82))

### Deprecated

Expand Down
24 changes: 23 additions & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,29 @@ As with other schema projects, here we separate between the schema source files

There is a set of tools in [`/bin`](./bin/) to facilitate the conversion. ATM, after editing `...yaml` schema files somewhere in the `/src` tree, a (local) run of `bin/yamlerRunner.sh` - which re-generates the `....json` files in the `/json` tree) has to be performed before pushing changes.

### Changes
### Changelog

## 2.1.0

*Released, July, 19, 2024*

* Relocated TypedQuantity required to proper level of the schema for complexValue
* Added end and start entities for ageRange and iso8601duration for age
* Filtering terms scopes changed from string to array of strings

## 2.0.1

*Released July, 16, 2024*

* Replaced ENSGLOSSARY for SO ontology family in documentation examples
* Moved CURIE to beaconCommonComponents
* Created filtering terms entity
* Removed validation directories
* Several fixes to entity types, typos and other non-breaking changes

## 2.0.0

*Released June, 21, 2022*

* change notes with respect to the repository & documentation are now in [docs.genomebeacons.org](https://docs.genomebeacons.org/changes-todo/)
* NOTE: on 2022-06-20 the previous development repositories have been archived:
Expand Down
33 changes: 17 additions & 16 deletions docs/variant-queries.md
Original file line number Diff line number Diff line change
Expand Up @@ -374,18 +374,19 @@ values to underlying genomic variations had not been precisely defined.

This table is maintained in parallel with the [hCNV community documentation](https://cnvar.org/resources/CNV-annotation-standards/#cnv-term-use-comparison-in-computational-fileschema-formats).

| [EFO](https://www.ebi.ac.uk/efo/EFO_0030063) | Beacon | [VCF](https://samtools.github.io/hts-specs/) | SO | GA4GH [VRS](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) &rArr;<br/>[VRS proposal](https://github.com/ga4gh/vrs/issues/404)[^1] | Notes |
| [EFO](http://www.ebi.ac.uk/efo/EFO_0030063) | Beacon | [VCF](https://samtools.github.io/hts-specs/) | SO | GA4GH [VRS](https://vrs.ga4gh.org/en/latest/terms_and_model.html#copynumberchange)[^1] | Notes |
| ------------------------------------------- | ------------------------------------------------------------------------------ | -------------------------------------------- | -------- | ------------------------------------------------------------------------------------------------------------------------------------------------- | ----- |
| <nobr>[`EFO:0030070`](https://www.ebi.ac.uk/efo/EFO_0030070)</nobr> copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030070`](https://www.ebi.ac.uk/efo/EFO_0030070)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`low-level gain`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) (implicit) &rArr; [`EFO:0030070`](https://www.ebi.ac.uk/efo/EFO_0030070) copy&nbsp;number&nbsp;gain | a sequence alteration whereby the copy number of a given genomic region is greater than the reference sequence |
| [`EFO:0030071`](https://www.ebi.ac.uk/efo/EFO_0030071) low-level copy number gain| `DUP`[^2] or<br/><nobr>[`EFO:0030071`](https://www.ebi.ac.uk/efo/EFO_0030071)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`low-level gain`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) &rArr; [`EFO:0030071`](https://www.ebi.ac.uk/efo/EFO_0030071) low-level copy number gain | |
| [`EFO:0030072`](https://www.ebi.ac.uk/efo/EFO_0030072) high-level copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030072`](https://www.ebi.ac.uk/efo/EFO_0030072)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`high-level gain`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) &rArr; [`EFO:0030072`](https://www.ebi.ac.uk/efo/EFO_0030072) high-level copy number gain | commonly but not consistently used for >=5 copies on a bi-allelic genome region |
| [`EFO:0030073`](https://www.ebi.ac.uk/efo/EFO_0030073) focal genome amplification | `DUP`[^2] or<br/><nobr>[`EFO:0030073`](https://www.ebi.ac.uk/efo/EFO_0030073)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`high-level gain`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) &rArr; [`EFO:0030073`](https://www.ebi.ac.uk/efo/EFO_0030073) focal genome amplification | commonly but not consistently used for >=5 copies on a bi-allelic genome region, of limited size (operationally max. 1-5Mb) |
| [`EFO:0030067`](https://www.ebi.ac.uk/efo/EFO_0030067) copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0030067`](https://www.ebi.ac.uk/efo/EFO_0030067)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`partial loss`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) (implicit) &rArr; [`EFO:0030067`](https://www.ebi.ac.uk/efo/EFO_0030067) copy number loss | a sequence alteration whereby the copy number of a given genomic region is smaller than the reference sequence |
| [`EFO:0030068`](https://www.ebi.ac.uk/efo/EFO_0030068) low-level copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0030068`](https://www.ebi.ac.uk/efo/EFO_0030068)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`partial loss`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) &rArr; [`EFO:0030068`](https://www.ebi.ac.uk/efo/EFO_0030068) low-level copy number loss | |
| [`EFO:0020073`](https://www.ebi.ac.uk/efo/EFO_0020073) high-level copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`partial loss`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) &rArr; [`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941) high-level copy number loss | a loss of several copies; also used in cases where a complete genomic deletion cannot be asserted |
| [`EFO:0030069`](https://www.ebi.ac.uk/efo/EFO_0030069) complete genomic deletion | `DEL`[^2] or<br/><nobr>[`EFO:0030069`](https://www.ebi.ac.uk/efo/EFO_0030069)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`complete loss`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) &rArr; [`EFO:0030069`](https://www.ebi.ac.uk/efo/EFO_0030069) complete genomic deletion | complete genomic deletion (e.g. homozygous deletion on a bi-allelic genome region) |

##### Last updated 2023-03-22 by @mbaudis (EFO:0020073)
| <nobr>[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070)</nobr> copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | <nobr>[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070) gain | a sequence alteration whereby the copy number of a given genomic region is greater than the reference sequence |
| [`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071) low-level copy number gain| `DUP`[^2] or<br/><nobr>[`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | <nobr>[`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071)</nobr> low-level gain | |
| [`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072) high-level copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | <nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr> high-level gain | commonly but not consistently used for >=5 copies on a bi-allelic genome region |
| [`EFO:0030073`](http://www.ebi.ac.uk/efo/EFO_0030073) focal genome amplification | `DUP`[^2] or<br/><nobr>[`EFO:0030073`](http://www.ebi.ac.uk/efo/EFO_0030073)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | <nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr> high-level gain[^4] | commonly but not consistently used for >=5 copies on a bi-allelic genome region, of limited size (operationally max. 1-5Mb) |
| [`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067) copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067)</nobr> loss | a sequence alteration whereby the copy number of a given genomic region is smaller than the reference sequence |
| [`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068) low-level copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068)</nobr> low-level loss | |
| [`EFO:0020073`](http://www.ebi.ac.uk/efo/EFO_0020073) high-level copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941)</nobr> high-level loss | a loss of several copies; also used in cases where a complete genomic deletion cannot be asserted |
| [`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069) complete genomic deletion | `DEL`[^2] or<br/><nobr>[`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069)</nobr> complete genomic loss | complete genomic deletion (e.g. homozygous deletion on a bi-allelic genome region) |


##### Last updated 2023-07-13 to align with 2023-03-22 hCNV documentation (VRS 1.3 adjustment) by @mbaudis
##### updated 2023-03-20 by @mbaudis (VRS proposal)

## Query Parameter Change Log
Expand Down Expand Up @@ -417,17 +418,17 @@ recommended for query forms
and `alternateBases`


[^1]: The VRS annotations refer to the status at v1.2 (2022). The GA4GH VRS team
is currently (Spring 2023) preparing an updated specification which will introduce
the new class `CopyNumberChange` ([discussion...](https://github.com/ga4gh/vrs/issues/404#issuecomment-1472599849)) with the use of the EFO terms (including a new term
for `high level deletion (EFO:0020073)` in the April 2023 EFO release).
[^1]: The VRS annotations refer to the status from v1.3 (2022) when
the new class `CopyNumberChange` ([discussion...](https://github.com/ga4gh/vrs/issues/404#issuecomment-1472599849))
with the use of the EFO terms.
[^2]: While the use of VCF derived (`DUP`, `DEL`) values had been introduced with
beacon v1, usage of these terms has always been a _recommendation_ rather than an integral part
of the API. We now encourage the support of more specific terms (particularly EFO)
by Beacon developers. As example, the Progentix Beacon API [uses EFO terms](https://progenetix.org/search/) but
by Beacon developers. As example, the Progentix Beacon API [uses EFO terms](http://progenetix.org/search/) but
provides an internal term expansion for legacy `DUP`, `DEL` support.
[^3]: VCFv4.4 introduces an `SVCLAIM` field to disambiguate between _in situ_ events (such as
tandem duplications; known _adjacency_/ _break junction_: `SVCLAIM=J`) and events where e.g. only the
change in _abundance_ / _read depth_ (`SVCLAIM=D`) has been determined. Both **J** and **D** flags can be combined.
[^4]: VRS did not adopt the "amplification" term due to possible inconsistencies


17 changes: 10 additions & 7 deletions framework/json/common/beaconCommonComponents.json
Original file line number Diff line number Diff line change
Expand Up @@ -76,11 +76,10 @@
},
"Granularity": {
"default": "boolean",
"description": "Level of detail of the response:\n* `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.:\n - keeping non-mandatory attributes empty\n - Beacon to provide a minimal record definition",
"description": "Level of detail of the response:\n* `boolean`: returns true/false' responses * `count`: adds the total number of positive results found * `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.:\n - keeping non-mandatory attributes empty\n - Beacon to provide a minimal record definition",
"enum": [
"boolean",
"count",
"aggregated",
"record"
],
"type": "string"
Expand Down Expand Up @@ -111,15 +110,19 @@
},
"HandoverType": {
"$ref": "./ontologyTerm.json",
"description": "Handover type, as an Ontology_term object with CURIE syntax for the `id` value. Use `CUSTOM` for the `id` when no ontology is available.",
"description": "Handover type, as an Ontology_term object with CURIE syntax for the `id` value. Use \"CUSTOM:123455\" CURIE-style `id` when no ontology is available.",
"examples": [
{
"id": "EFO:0004157",
"label": "BAM format"
"id": "EDAM:2572",
"label": "BAM"
},
{
"id": "CUSTOM",
"label": "download genomic variants in .pgxseg file format"
"id": "EDAM:3016",
"label": "VCF"
},
{
"id": "CUSTOM:pgxseg",
"label": "genomic variants in .pgxseg file format"
}
]
},
Expand Down
54 changes: 0 additions & 54 deletions framework/json/common/validation/beaconCommonComponents.json

This file was deleted.

6 changes: 3 additions & 3 deletions framework/json/configuration/beaconMapSchema.json
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
},
"filteringTermsUrl": {
"description": "Optional. Returns the list of filtering terms that could be applied to this entry type. It is added here for convenience of the Beacon clients, so they don't need to parse the OpenAPI endpoints definition to get that endpoint. Also, in very simple Beacons, that endpoint could be the one of the few implemented, together with \u00b4rootUrl` and \u00b4singleEntryUrl`, in which case the whole map of endpoints is found in the current Map.",
"format": "uri",
"format": "uri-template",
"type": "string"
},
"openAPIEndpointsDefinition": {
Expand All @@ -32,7 +32,7 @@
},
"singleEntryUrl": {
"description": "Optional, but recommended. Returns only one instance of this entry, identified by an `id`. It is added here for convenience of the Beacon clients, so they don't need to parse the OpenAPI endpoints definition to get that base endpoint. Also, in very simple Beacons, that endpoint could be the only one implemented, together with \u00b4rootUrl`, in which case the whole map of endpoints is found in the current Map.",
"format": "uri",
"format": "uri-template",
"type": "string"
}
},
Expand All @@ -50,7 +50,7 @@
},
"url": {
"description": "Endpoint URL",
"format": "uri",
"format": "uri-template",
"type": "string"
}
},
Expand Down
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