LeibnizDSMZ/microbial-data-standard

Please note that this project is still in development

Microbial Data Standard

This project defines a new microbial data standard for culture collection strain data. The new microbial data standard is part of the work of WP6 of the Bioindustry 4.0 project.

Technical information

First there is a data model written in pydantic.

Also included in the project is the JSON-schema file of the new data standard. You find the JSON schema in schema/microbe_schema.json.

If you want to report a bug, contribute to the project or suggest new features, please contact the project owner.

How to use

The provided data model and schema are for data validation.

Examples for using the pydantic data model:

Import:

from microbial_strain_data_model.microbe import Microbe

Generate JSON schema:

import json
from microbial_strain_data_model.microbe import Microbe

mi = Microbe.model_json_schema()
print(json.dumps(mi, indent=2))

Validate a JSON against the pydantic model:

from microbial_strain_data_model.microbe import Microbe

with open("PATH_TO_FILE", "r") as f_in:
        file_content = f_in.read()

Microbe.model_validate_json(file_content)

Validate a JSON against the JSON schema:

import jsonschema
import json

with open("PATH_TO_SCHEMA", "r") as schema_file:
        schema = json.load(schema_file)

with open("PATH_TO_FILE", "r") as f_in:
        json_content = json.loads(f_in)

jsonschema.validate(json_content, schema)