CSVs and Tabular Data

LinkML can support both complex interlinked normalized relational data as well as flat/denormalized data as typically found in spreadsheets and in CSVs used by data scientists.

Our philosophy is “always have a schema” even when working with simple tabular data


the linkml-convert script can be used to convert between CSVs/TSVs and other formats like JSON/RDF. The same tooling for validating-data operate in the same way.

On the fly denormalization

See https://github.com/cmungall/json-flattener/

Inference of schemas from tabular data

Use tsvs2linkml in the enrichment toolkit