https://github.com/sujaypatil96/ga4gh-va
LinkML schema for GA4GH variant annotation
https://github.com/sujaypatil96/ga4gh-va
ga4gh linkml schema
Last synced: 7 months ago
JSON representation
LinkML schema for GA4GH variant annotation
- Host: GitHub
- URL: https://github.com/sujaypatil96/ga4gh-va
- Owner: sujaypatil96
- License: mit
- Created: 2022-04-28T08:38:41.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2022-05-06T12:48:28.000Z (over 3 years ago)
- Last Synced: 2025-03-29T12:12:31.258Z (7 months ago)
- Topics: ga4gh, linkml, schema
- Language: Jinja
- Homepage: https://sujaypatil96.github.io/ga4gh-va/
- Size: 1.67 MB
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
# GA4GH Schema
## GA4GH
The [Global Alliance for Genomics and Health](https://www.ga4gh.org/) is an international coalition, formed to enable the sharing of genomic and clinical data.
## Schema
### Toolchain
The tools used to build a data model for GA4GH variant annotation are:
1. [LinkML](https://linkml.io/linkml/): Linked data modeling language that allows you to specify and author schemas or data models as YAML files
2. [schemasheets](https://linkml.io/schemasheets/): A tool built on top of LinkML that allows data modelers to specify schemas in a spreadsheet format, which can be compiled down to LinkML
###
Run the following command to auto generate a LinkML model from the schemasheets specification of the GA4GH model:
```bash
poetry run sheets2linkml --output src/linkml/ga4gh-va-schema.yaml src/data/spreadsheets/ga4gh_schemasheets.tsv
```
### Results
1. [ga4gh_schemasheets.tsv](src/data/spreadsheets/ga4gh_schemasheets.tsv): schemasheets specific tsv which contains the GA4GH source data model as a spreadsheet
2. [ga4gh-va-schema.yaml](src/linkml/ga4gh-va-schema.yaml): LinkML model generated from the above spreadsheet specification file