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fairgenomes / fairgenomes-semantic-model

FAIR Genomes semantic metadata model. The core is a YAML file, which is transformed into all other desired output formats.
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Investigate using LinkML to represent FAIR Genomes schema #128

Open joerivandervelde opened 2 years ago

joerivandervelde commented 2 years ago

"LinkML is a flexible modeling language that allows you to author schemas in YAML that describe the structure of your data". Perhaps we can represent the FAIR Genomes schema in LinkML to increase operability and visibility.

For instance, we would benefit from tools such as generators for many formats: https://linkml.io/linkml/generators/index.html

Automated model enhancement: https://github.com/linkml/linkml-model-enrichment

And join the LinkML Registry: https://linkml.io/linkml-registry/registry/

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The question is, how can we represent the content of the FAIR Genomes schema: https://github.com/fairgenomes/fairgenomes-semantic-model/blob/main/YamlFormat.md

In LinkML format: https://linkml.io/linkml/

deepakunni3 commented 2 years ago

Hi @joerivandervelde !

It is exciting to see the Fair Genomes team looking into LinkML to represent the FAIR Genomes Schema.

There are many features in LinkML that might help in representing the FAIR Genomes schema. And there may as well be features required by FAIR Genomes that may not yet be in LinkML.

It would be fantastic if we can combine efforts to see if we (the developers and collaborators LinkML) can improve LinkML such that your use-cases can be handled out of the box.

The LinkML repository (with loaders and generators) can be found here: https://github.com/linkml/linkml The LinkML metamodel can be found here: https://github.com/linkml/linkml-model