GA4GH Schema

GA4GH

The Global Alliance for Genomics and Health 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: Linked data modeling language that allows you to specify and author schemas or data models as YAML files
2. 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:

poetry run sheets2linkml --output src/linkml/ga4gh-va-schema.yaml src/data/spreadsheets/ga4gh_schemasheets.tsv

Results

1. ga4gh_schemasheets.tsv: schemasheets specific tsv which contains the GA4GH source data model as a spreadsheet
2. ga4gh-va-schema.yaml: LinkML model generated from the above spreadsheet specification file