https://github.com/repronim/reproschema
A standardized form generation and data collection schema to harmonize results by design across projects.
https://github.com/repronim/reproschema
clinical-assessments interoperability schema standardizing-assessments
Last synced: about 1 year ago
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A standardized form generation and data collection schema to harmonize results by design across projects.
- Host: GitHub
- URL: https://github.com/repronim/reproschema
- Owner: ReproNim
- License: other
- Created: 2018-10-03T13:16:14.000Z (over 7 years ago)
- Default Branch: main
- Last Pushed: 2024-10-08T08:14:14.000Z (over 1 year ago)
- Last Synced: 2025-04-12T02:13:10.168Z (about 1 year ago)
- Topics: clinical-assessments, interoperability, schema, standardizing-assessments
- Language: Python
- Homepage: https://www.repronim.org/reproschema/
- Size: 22.2 MB
- Stars: 16
- Watchers: 12
- Forks: 22
- Open Issues: 16
-
Metadata Files:
- Readme: README.md
- Contributing: docs/CONTRIBUTING.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
[](https://doi.org/10.5281/zenodo.4064940)
# ReproSchema: Enhancing Research Reproducibility through Standardized Survey Data Collection
The ReproSchema project integrates five key components designed to standardize research protocols and enhance consistency across various stages of data collection.
- Foundational Schema ([reproschema](https://github.com/ReproNim/reproschema)): This core schema delineates the content and relationships of protocols, assessments, and items to ensure consistency and facilitate data harmonization across studies.
- Assessment Library ([reproschema-library](https://github.com/ReproNim/reproschema-library)): This library provides a comprehensive collection of standardized questionnaires, supporting the application of uniform assessments across time and different studies.
- Python-based CLI Tool ([reproschema-py](https://github.com/ReproNim/reproschema-py)): This command-line interface tool facilitates schema development and validation, aiding researchers in efficiently creating and refining data collection frameworks.
- User Interface ([reproschema-ui](https://github.com/ReproNim/reproschema-ui)): This intuitive user interface simplifies the visualization and interaction with data, enhancing the manageability of the data collection process for researchers.
- Protocol Template ([reproschema-protocol-cookiecutter](https://github.com/ReproNim/reproschema-protocol-cookiecutter)): This customizable template supports the design and implementation of research protocols tailored to specific study requirements.
This repository contains:
- the [different terms of the ReproSchema](./terms)
- the [corresponding context files](./contexts)
- a example of [a protocol based on the reproschema](./examples)
- the [documentation](./docs)
## Developing ReproSchema
### Updating the schema
As of release 1.0.0, a linked data modeling language, [LinkML](https://linkml.io/linkml/), is used to create
a [YAML file](linkml-schema/reproschema.yaml) with the schema.
The [context file](contexts/reproschema) was automatically generated using LinkML,
and then manually curated in order to support all the reproschema feature.
#### Style
This repo uses pre-commit to check styling.
- Install pre-commit with pip: `pip install pre-commit`
- In order to use it with the repository, you have to run `run pre-commit install` in the root directory the first time you use it.
### Release
Upon release, there are additional formats, `jsonsld`, `turtle`, `n-triples`
and `pydantic` that are created using `LinkML` tools, `reproschema-py`,
and [reproschema-specific script](./scripts/fix_pydantic.py) to "fix" the `pydantic` format.
The entire process is automated in the GitHub Action Workflow:
[Validate and Release](.github/workflows/validate_and_release.yml).
This workflow must be manually triggered by the core developers once a new release is ready.
All the releases can be found in [releases directory](./releases).
### Updating model in reproschema-py
Another GitHub Action Workflow: [ Create Pull Request to reproschema-py](.github/workflows/push_reproschema_py.yml)
is responsible for creating pull request to the `reproschema-py` Python library with
the new version of pydantic model and context.
The workflow is currently also triggered manually by the core developers.
## Licenses
### Code
The content of this repository is distributed under the [Apache 2.0 license](./LICENSE).
### Documentation
The corresponding documentation is licensed under a Creative Commons Attribution 4.0 International License.
## Contributors
https://github.com/ReproNim/reproschema/graphs/contributors