fred-metadata 2.0.3

Metadata generation, validation, search and visualization.

FRED

Introduction

Scientific research relies on transparent dissemination of data and its associated interpretations. This task encompasses accessibility of raw data, its metadata, details concerning experimental design, along with parameters and tools employed for data interpretation. Production and handling of these data represents an ongoing challenge, extending beyond publication into individual facilities, institutes and research groups, often termed Research Data Management (RDM). It is foundational to scientific discovery and innovation, and can be paraphrased as Findability, Accessibility, Interoperability and Reusability (FAIR). Although the majority of peer-reviewed journals require the deposition of raw data in public repositories in alignment with FAIR principles, metadata frequently lacks full standardization. This critical gap in data management practices hinders effective utilization of research findings and complicates sharing of scientific knowledge. Here we present a flexible design of a machine-readable metadata format to store experimental metadata, along with an implementation of a generalized tool named FRED (FaiR Experimental Designs). It enables i) dialog based creation of metadata files, ii) structured semantic validation, iii) logical search, iv) an external programming interface (API), and v) a standalone web-front end. The tool is intended to be used by non-computational scientists as well as specialized facilities, and can be seamlessly integrated in existing RDM infrastructure.

For more information about FRED, please see the documentation.

Quick start

# 1. Generate a metadata file
fred generate -p /my/project/folder -id dst123

# 2. Validate it
fred validate -p /my/project/folder/dst123_metadata.yaml

# 3. Search across a directory
fred find -p /my/project/folder -s 'organism_name:"Homo_sapiens"'

# 4. Export to MAGE-TAB (ArrayExpress) or GEO
fred export -p /my/project/folder/dst123_metadata.yaml --format mage-tab
fred export -p /my/project/folder/dst123_metadata.yaml --format geo

Available commands

Command	Description
fred generate	Create a new metadata file via interactive dialog
fred validate	Validate a metadata file or all files in a directory
fred edit	Edit an existing metadata file
fred find	Search for metadata files using a query string
fred export	Export metadata to MAGE-TAB (ArrayExpress) or GEO format
fred plot	Visualize the experimental design as a heatmap

Pass -h to any command for a full list of arguments, e.g. fred generate -h.

How to install

Via Python package

---

FRED is published in the Python Package Index (PyPI) under the name fred-metadata. It can be installed with the following command:

pip install fred-metadata

Via Repository

You can install FRED directly from the repository with the following commands:

1. Clone the repository

git clone https://github.com/loosolab/FRED.git

2. Move to the new repository directory

cd FRED

3. (Optional) Create and activate a pip environment

python3 -m venv .venv
source .venv/bin/activate

4. Install the package

pip install .

Standalone Version

The standalone web-frontend is provided in a separate Repository. You can find it here:

https://github.com/loosolab/FRED_standalone