# pymetadata

> Python utilities for working with metadata and COMBINE archives

The links below point to the markdown source of the documentation. [llms-full.txt](https://matthiaskoenig.github.io/pymetadata/llms-full.txt) contains all of it in a single file.

## Documentation

- [Home](https://matthiaskoenig.github.io/pymetadata/index.md): `pymetadata` is a collection of python utilities for working with metadata in the context of COMBINE standards.
- [Installation](https://matthiaskoenig.github.io/pymetadata/installation.md): `pymetadata` requires python >= 3.11 and is available from pypi.
- [Contributing](https://matthiaskoenig.github.io/pymetadata/development.md): Contributions are welcome.

## User guide

- [COMBINE archives](https://matthiaskoenig.github.io/pymetadata/omex.md): A COMBINE archive (OMEX, *Open Modeling EXchange format*) bundles everything belonging to a modeling study into a single ZIP file: models, simulation experiments, data, figures and documentation.
- [Annotations](https://matthiaskoenig.github.io/pymetadata/annotations.md): A model element on its own carries no meaning a machine can use.

## API reference

- [Overview](https://matthiaskoenig.github.io/pymetadata/api/index.md): The API reference is generated from the docstrings of the package.
- [cache](https://matthiaskoenig.github.io/pymetadata/api/cache.md): Caching of web service responses.
- [console](https://matthiaskoenig.github.io/pymetadata/api/console.md): Shared rich console.
- [log](https://matthiaskoenig.github.io/pymetadata/api/log.md): Logging of the package.
- [omex](https://matthiaskoenig.github.io/pymetadata/api/omex.md): COMBINE archive (OMEX) support.
- [annotation](https://matthiaskoenig.github.io/pymetadata/api/core.annotation.md): MIRIAM annotations.
- [creator](https://matthiaskoenig.github.io/pymetadata/api/core.creator.md): Creator information for models and archives.
- [miriam](https://matthiaskoenig.github.io/pymetadata/api/core.miriam.md): MIRIAM qualifiers.
- [xref](https://matthiaskoenig.github.io/pymetadata/api/core.xref.md): Cross references to database entries.
- [term](https://matthiaskoenig.github.io/pymetadata/api/ontologies.term.md): Ontology terms with the information of the ontology release.
- [chebi](https://matthiaskoenig.github.io/pymetadata/api/webservices.chebi.md): Substance information from ChEBI.
- [ols](https://matthiaskoenig.github.io/pymetadata/api/webservices.ols.md): Lookup of ontology terms in the Ontology Lookup Service (OLS).
- [registry](https://matthiaskoenig.github.io/pymetadata/api/webservices.registry.md): The identifiers.org registry.
- [unichem](https://matthiaskoenig.github.io/pymetadata/api/webservices.unichem.md): Substance cross references from UniChem.
- [webservice](https://matthiaskoenig.github.io/pymetadata/api/webservices.webservice.md): HTTP access to the web services.

## Optional

- [Repository](https://github.com/matthiaskoenig/pymetadata): source code, issues and releases.
- [Sitemap](https://matthiaskoenig.github.io/pymetadata/sitemap.xml): all pages of the rendered site.
- [objects.inv](https://matthiaskoenig.github.io/pymetadata/objects.inv): the API objects of the reference as a sphinx inventory.