linkml/schema-automator: v0.5.6

Zenodo (CERN European Organization for Nuclear Research)

Abstract

This release builds out a data dictionary adapter ecosystem (#202): a canonical data-dictionary format, adapters that translate between it and common external formats, a schema→DD projector, and a DD-driven schema enrichment step. It also modernizes the project's tooling and XML handling. Highlights Canonical data dictionary format — a documented, LinkML-modeled DD format that the new adapters translate to and from, giving a single hub representation for tabular metadata. New format adapters — Frictionless Table Schema, dbGaP variable digests, and REDCap data dictionaries, each convertible in both directions against the canonical DD. EML importer — import Ecological Metadata Language XML into LinkML (schemauto import-eml), one class per , one slot per . Schema enrichment from data dictionaries — overlay one or more canonical DDs onto an inferred schema (schemauto enrich) to add descriptions, labels, URIs, units, permissible values, and constraints (#192). New adapters & importers Frictionless Table Schema adapter — convert between a Frictionless Table Schema and the canonical DD in both directions. dbGaP variable digest adapter — ingest dbGaP variable digests as data dictionaries (import-side of the long-standing dbGaP request). REDCap data dictionary adapter — round-trip between a REDCap data dictionary CSV and the canonical DD (schemauto adapt-redcap, --reverse for the return direction) (#204). EML XML importer (schemauto import-eml) — with --schema-name / --schema-id overrides; the schema name and id default to the EML packageId. Data dictionary tooling Canonical DD format spec — prose spec plus the LinkML metamodel the adapters share. schemauto extract-dd — project a LinkML schema (including importer output: XSD, JSON Schema, OWL, RDFS, SQL DDL, EML) into the canonical DD format, per-class or in batch. Schema-driven XML loader — a reusable, annotation-driven XML→dict loader; the dbGaP adapter and EML importer are both built on it. Schema enrichment schemauto enrich — overlay canonical data dictionaries onto an inferred schema by slot name, flowing descriptions, titles, semantic URIs, units, permissible values, min/max, required, multivalued, and patterns into the schema, with conflicts surfaced as warnings. Multiple DDs can be layered in order (#192). Infrastructure & dependencies Migrated from Poetry to uv for dependency management and builds. Consolidated XML parsing on lxml and dropped the direct defusedxml dependency; parsing now uses a hardened lxml parser (no external/DTD entity resolution, no network). linkml-map ≥ 0.5.3 and linkml-runtime 1.11.x — trans-spec source_schema/target_schema now use the SchemaReference shape, and the REDCap/Frictionless code lists are derived via class_derivations rather than expression comprehensions. Python: 3.10–3.14 supported and tested in CI. Full changelog: https://github.com/linkml/schema-automator/compare/v0.5.5...v0.5.6

Authors 17

1. Chris J Mungall

   Lawrence Berkeley National Laboratory

   Affiliation as printed

   Lawrence Berkeley National Laboratory

2. Mark Andrew Miller

   Lawrence Berkeley National Laboratory

   Affiliation as printed

   Lawrence Berkeley National Laboratory

3. Sierra Moxon

   Lawrence Berkeley National Laboratory

   Affiliation as printed

   Lawrence Berkeley National Lab

4. Corey Cox
5. Michael
6. Harshad
7. Patrick Golden

   University of North Carolina at Chapel Hill

   Affiliation as printed

   UNC Chapel Hill

8. Charles Tapley Hoyt Aachen

   RWTH Aachen University

   Affiliation as printed

   RWTH Aachen University

9. David Linke

   Leibniz Institute for Catalysis

   Affiliation as printed

   Leibniz Institute for Catalysis (LIKAT)

10. Nicolas Matentzoglu
    Affiliation as printed

    semanticly.ai

11. Nomi Harris

    Lawrence Berkeley National Laboratory

    Affiliation as printed

    Lawrence Berkeley National Laboratory

12. Sigfried Gold
13. Trish Whetzel
14. Yaroslav Halchenko

    Dartmouth College

    Affiliation as printed

    Dartmouth College, @dandi, @Debian, @DataLad, @neurodebian, @PyMVPA, @fail2ban

15. epstein6
16. N
17. wb0206