diff --git a/README.md b/README.md index 114a698..4170ff5 100644 --- a/README.md +++ b/README.md @@ -1,21 +1,35 @@ # LinkML Schema Automator -This is a toolkit that assists with: +This is a toolkit that assists with the generation and enhancement of [LinkML](https://linkml.io/linkml) schemas -1. Bootstrapping LinkML models from instance data - - TSVs and spreadsheets - - SQLite databases - - RDF instance graphs -2. Bootstrapping a LinkML model from a different schema representation (i.e. opposite of a linkml.generator) - - OWL (RDFS-like subset) - - TODO: JSON-Schema, XSD, ShEx, SHACL, SQL DDL, FHIR, Python dataclasses/pydantic, etc -3. Using automated methods to enhance a model - - Using text mining and concept annotator APIs to enrich semantic enums - - TODO: querying sparql endpoints to retrieve additional metadata +## Install -These can be composed together. For example, run `tsvs2linkml` followed by `annotate-enums` +```bash +pip install schema-automator +``` -The toolkit is still experimental. It is intended as an aid to schema creation rather than as a formal conversion -tool. +## Command Line -[Full Documentation](https://linkml.io/schema-automator/) +See [CLI docs](https://linkml.io/schema-automator/cli) + +Generalizing: + +```bash +schemauto generalize-tsv my-data.tsv > my-schema.yaml +``` + +Importing: + +```bash +schemauto import-json-schema their.schema.json > my-schema.yaml +``` + +Annotating: + +```bash +schemauto annotate-schema my-schema.yaml +``` + +## Full Documentation + +[linkml.io/schema-automator](https://linkml.io/schema-automator/) diff --git a/pyproject.toml b/pyproject.toml index 1b9c7df..f91ecd8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,6 +4,7 @@ version = "0.0.0" description = "Infer models, enrich with meaning for terms including enum permissible values" authors = ["Chris Mungall", "Mark Miller", "Sierra Moxon", "Harshad Hegde"] license = "BSD 3-Clause" +readme = "README.md" packages = [ { include = "schema_automator" }