aind-data-schema

aind-data-schema

A library that defines AIND data schema and validates JSON files.

User documentation available on readthedocs.

Overview

This repository contains the schemas needed to ingest and validate metadata that are essential to ensuring AIND data collection is completely reproducible. Our general approach is to semantically version core schema classes and include those version numbers in serialized metadata so that we can flexibly evolve the schemas over time without requiring difficult data migrations. In the future, we will provide a browsable list of these classes rendered to JSON Schema, including all historic versions.

Be aware that this package is still under heavy preliminary development. Expect breaking changes regularly, although we will communicate these through semantic versioning.

A simple example:

import datetime

from aind_data_schema.core.subject import BreedingInfo, Housing, Subject
from aind_data_schema_models.organizations import Organization
from aind_data_schema_models.species import Species

t = datetime.datetime(2022, 11, 22, 8, 43, 00)

s = Subject(
   species=Species.MUS_MUSCULUS,
   subject_id="12345",
   sex="Male",
   date_of_birth=t.date(),
   genotype="Emx1-IRES-Cre;Camk2a-tTA;Ai93(TITL-GCaMP6f)",
   housing=Housing(home_cage_enrichment=["Running wheel"], cage_id="123"),
   background_strain="C57BL/6J",
   source=Organization.AI,
   breeding_info=BreedingInfo(
         breeding_group="Emx1-IRES-Cre(ND)",
         maternal_id="546543",
         maternal_genotype="Emx1-IRES-Cre/wt; Camk2a-tTa/Camk2a-tTA",
         paternal_id="232323",
         paternal_genotype="Ai93(TITL-GCaMP6f)/wt",
   ),
)

s.write_standard_file() # writes subject.json

{
   "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/subject.py",
   "schema_version": "0.5.6",
   "subject_id": "12345",
   "sex": "Male",
   "date_of_birth": "2022-11-22",
   "genotype": "Emx1-IRES-Cre;Camk2a-tTA;Ai93(TITL-GCaMP6f)",
   "species": {
      "name": "Mus musculus",
      "abbreviation": null,
      "registry": {
         "name": "National Center for Biotechnology Information",
         "abbreviation": "NCBI"
      },
      "registry_identifier": "10090"
   },
   "alleles": [],
   "background_strain": "C57BL/6J",
   "breeding_info": {
      "breeding_group": "Emx1-IRES-Cre(ND)",
      "maternal_id": "546543",
      "maternal_genotype": "Emx1-IRES-Cre/wt; Camk2a-tTa/Camk2a-tTA",
      "paternal_id": "232323",
      "paternal_genotype": "Ai93(TITL-GCaMP6f)/wt"
   },
   "source": {
      "name": "Allen Institute",
      "abbreviation": "AI",
      "registry": {
         "name": "Research Organization Registry",
         "abbreviation": "ROR"
      },
      "registry_identifier": "03cpe7c52"
   },
   "rrid": null,
   "restrictions": null,
   "wellness_reports": [],
   "housing": {
      "cage_id": "123",
      "room_id": null,
      "light_cycle": null,
      "home_cage_enrichment": [
         "Running wheel"
      ],
      "cohoused_subjects": []
   },
   "notes": null
}

Installing and Upgrading

To install the latest version:

pip install aind-data-schema

Every merge to the main branch is automatically tagged with a new major/minor/patch version and uploaded to PyPI. To upgrade to the latest version:

pip install aind-data-schema --upgrade

Issues and Discussions

If you've found a bug in the schemas or would like to make a minor change, open an issue and please use the provided templates. If you'd like to propose a large change or addition, or generally have a question about how things work, head start a new Discussion!

Controlled Vocabularies

Controlled vocabularies and other enumerated lists are maintained in a separate repository: aind-data-schema-models. This allows us to specify these lists without changing aind-data-schema. Controlled vocabularies include lists of organizations, manufacturers, species, modalities, platforms, units, harp devices, and registries.

To upgrade to the latest data models version:

pip install aind-data-schema-models --upgrade

Contributing

Contributions are more than welcome for this project! If you'd like to develop the code, please follow the standards outlined in the contribution guide.

Documentation

To generate the rst files source files for documentation, run:

sphinx-apidoc -o docs/source/ src

Then to create the documentation html files, run:

sphinx-build -b html docs/source/ docs/build/html

More info on sphinx installation can be found here: https://www.sphinx-doc.org/en/master/usage/installation.html