Initial commit & first content

.github/workflows/mkdocs-build.yaml

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+name: mk-docs 
+on:
+  push:
+    branches:
+      - main
+      - master
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.x
+      - run: pip install mkdocs-material 
+      - run: pip install mkdocs-macros-plugin
+      - run: pip install pymdown-extensions
+      - run: pip install mkdocs-mermaid2-plugin
+      - run: pip install mdx_gh_links
+      - run: pip install mkdocs-with-pdf
+      - run: mkdocs gh-deploy --force

LICENSE

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README.md

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+# variant-query-types
+Schemas for genomic / molecular variation queries over the Beacon protocol and beyond

docs/index.md

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+# Beacon Variant Scouts
+
+**Variant Query Types and Components**
+
+The Beacon protocol has demonstrated the general feasibility of federated queries and aggregated responses for genomic sequence variations, over distributed and disparate resources when supporting a common protocol. The final Beacon v1 standard added the option to query some for some types of structural variations - notably CNVs; and during the design of the Beacon v2 standard a "Variant Scouts" group documented an extended set of supported query patterns, while the development team implemented the necessary parameters (such as aminoacidAlteration, variantMaxLength, geneId…)  into the Beacon default data model. However, several aspects had to be left open or have arisen since the original definitions - frequently not concerning necessary query parameter extensions but rather definition of standardized vocabularies and usage practices.
+
+The Beacon Varians Scouts work will focus on:
+
+* Establishing an extended set of use case driven variant query needs and document how to express them through current Beacon parameters
+* Suggesting extensions to the current specification where use cases, after triage against borderline scenarios and with a conservative view towards extending the vocabulary
+* Develop use cases into typed queries (e.g. deletion, fusion, translocation request) implemented through schema documents, following the previous points
+* Evaluate solutions for scenarios requiring identification of compound variants
+
+The outcome of this scout would be a document summarising points 1-3, and building on the previous Genomic variants document. It could, for example, take the form of a submitted article. Importantly, we envision that the group - in coordination with other standards groups from GA4GH and beyond - will provide solid "variant query standard blocks" - not necessarily limited to Beacon implementations; thereby providing an overarching harmonization of federated variant discovery tools and implementations.

mkdocs.yml

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+site_name: 'GA4GH Beacon Genomic Variation Query Standards'
+site_description: 'Development Site of the GA4GH Beacon community'
+site_author: Michael Baudis
+copyright: '© Copyright 2024 GA4GH and Beacon Contributors'
+repo-name: variant-query-types
+repo_url: https://github.com/ga4gh-beacon/variant-query-types
+edit_uri: edit/main/docs/
+
+###############################################################################
+
+nav:
+  - 'Home': index.md
+  - Variation Types: variant-types.md
+  - Query Types: query-types.md
+  - Query Schema Source Files: https://github.com/ga4gh-beacon/variant-query-types/tree/main/schemas
+
+###############################################################################
+
+theme:
+  name: material
+  palette:
+      primary: teal
+  logo: img/GA-logo.png
+  favicon: img/ga4gh_circle.ico
+  icon:
+    repo: fontawesome/brands/github-alt 
+  features:
+    - content.tabs.link
+    - search.highlight
+    - search.share
+    - navigation.instant
+    - navigation.tracking
+    - navigation.sections
+    # - toc.integrate
+
+plugins:
+  - search
+  - macros
+
+extra:
+  excerpt_separator: <!--more-->

query-types.md

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+# Query Types
+
+Genomic variation queries can be implemented through combinations of different parameters,
+as available through the given data model. Beacon v2's variation query parameters
+are defined in the `genomicVariations` default model's
+[requestParameters schema](https://github.com/ga4gh-beacon/beacon-v2/blob/main/models/src/beacon-v2-default-model/genomicVariations/requestParameters.yaml).
+As part of the 2024 Beacon Variant Scouts we work on a revison and potential
+extension of the available parameters, as well as on the definition of canonical
+_Query Types_ tailored to the retrieval of defined [_Variant Types_](variant-types).
+
+## _Sequence Queries_: `VariantSequenceRequest`[^1]
+
+_Sequence Queries_ query for the existence of a specified sequence at a given genomic
+position. Such queries roughly correspond to Beacon v1 queries and are used to match
+short, precisely defined genomic variants such as SNVs, MNVs and INDELs.
+
+## _Range Queries_: `VariantRangeRequest`[^1]
+
+Beacon _Range Queries_ are supposed to return matches of any variant with at least
+partial overlap of the sequence range specified by `referenceName`, `start` and `end`
+parameters.
+
+## _Bracket Queries_ ("CNV queries"): `VariantBracketRequest`[^1]
+
+_Bracket Queries_ allow the specification of sequence ranges for both start and end
+positions of a genomic variation. The typical example here is the query for similar
+structural variants - particularly CNVs - affecting a genomic region but potentially
+differing in their exact extents.
+
+## _GeneId Queries_: `GeneRequest`[^1]
+
+_GeneId Queries_ are in essence a variation of _Range Queries_ in which the coordinates
+are replaced by the [HGNC](https://www.genenames.org) gene symbol. It is left to the
+implementation if the matching is done on variants annotated for the gene symbol or if
+a positional translation is being applied.
+
+## ==TBC==
+
+
+[^1:] The names of the request type schemas should be considered "malleable".
+
+
+
+

schemas/VariantRangeRequest.yaml

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+"$schema": http://json-schema.org/draft-07/schema#
+"$id": https://beacon-project.io/schemas/beacon/BeaconRangeRequest/v1.1.0
+title: VariantRangeRequest
+description: >-
+  A request for matching variants in a genomic range.
+type: object
+required:
+  - referenceName
+  - start
+  - end
+
+properties:
+  referenceName:
+    $ref: variantRequestParameters.yaml#/definitions/referenceName
+
+  start:
+    $ref: variantRequestParameters.yaml#/definitions/start
+
+  end:
+    $ref: variantRequestParameters.yaml#/definitions/end
+
+  alternateBases:
+    $ref: variantRequestParameters.yaml#/definitions/alternateBases
+
+  variantType:
+    $ref: variantRequestParameters.yaml#/definitions/variantType
+
+  assemblyId:
+    $ref: variantRequestParameters.yaml#/definitions/assemblyId
+
+examples:
+  - referenceName: 17
+    start: 7572826
+    end: 7579005