Schema for the Open Standards Community for Electron Microscopy (OSC-EM): Defining the electron microscopy-related fields required by the OSCEM standard.
The OSCEM schemas are designed to standardize metadata for electron microscopy, structured modularly to accommodate various methods and use cases. Each module can represent different aspects of an experiment, such as "sample", "instrument", "author" and "processing". These modules are combined into a comprehensive schema that defines the required metadata for a specific method. This standard ensures consistency in data collection, facilitates data validation, and enhances comparability between datasets.
To increase compatibility with different formats, we utilize LinkML, which allows us to export the schema to widely used formats.
- cryoEM:
- Single particle analysis
- Tomography:
- Subtomogram averaging
- Cellular tomography
- Environmental tomography
All schemas are available in YAML format under the directory src/oscem_schemas/schema. Files prefixed with oscem_* refer to collections of subschemas, such as those for single particle analysis. Schemas with more specific names, like "instrument," represent individual subschemas that can be modularly incorporated into oscem_* schemas. By using LinkML generator functions, these schemas can be exported to various formats such as JSON Schema, JSON-LD, OWL, CSV and RDF. For metadata validation, we recommend using the JSON Schema versions.
Current versions are a work in progress, details might change.
Here you can browse all our keywords for the different schemas with descriptions: https://osc-em.github.io/OSCEM_Schemas/
- examples/ - example data
- project/ - project files (do not edit these)
- src/ - source files (edit these)
- tests/ - Python tests
make setup: one-time setupmake all: make everythingmake deploy: deploys sitemake test: run tests and lintingmake serve: run docs locally on http://127.0.0.1:8000/oscem-schemas/make clean: remove generated files
Adaptations were made to the cookiecutters Makefile that change its template beahviour in the following ways:
- instead of targeting a single root schema, the cookiecutter searches for schemas following the oscem_schemas_$.yaml pattern in src/oscem_schemas/schema/ where $ corresponds to the name of your schema.
- generates an overall documentation webpage, with subpages for each of the individual schemas. If you add a new schema its subpage will be added automatically BUT you need to add a general description and an apropriate link in perm_docs/index.md to make it appear in the overall index page!
- example data for testing goes into src/data/examples/ and follows the pattern example_valid_$.yaml where $ corresponds to the same schema name as oscem_schemas_$.yaml.
- All LinkML output files for each of the schemas will still be generated into the projects directory, with a subfolder per schema e.g. projects/spa/
This project was made with linkml-project-cookiecutter.