odMLtables (Extended Version)

An interface to convert odML structures to and from table-like representations, such as spreadsheets.

This repository is a fork of the original odMLtables project: https://github.com/INM-6/python-odmltables

It extends the original functionality with additional graphical user interface tools to facilitate metadata exploration and search.

odMLtables provides a set of functions to simplify the setup, maintenance and usage of a metadata management structure using odML. In addition to the Python API, odMLtables provides its main functionality via a graphical user interface.

New Features in this Fork

Search Wizard

This fork introduces a graphical Search Wizard that allows users to search metadata stored in odML files more efficiently.

The wizard enables users to:

• Search for specific words within metadata entries
• Search for property–value pairs

This functionality is intended to simplify metadata findability and exploration when working with experimental datasets.

Microneurography Metadata Workflow

The modifications in this fork were developed in the context of building a metadata management workflow for microneurography recordings.

The metadata templates, workflow description, and user manual for this application are maintained in a separate repository:

Repository for microneurography metadata workflow and templates: https://github.com/Digital-C-Fiber/odMLtablesForMNG

Dependencies

odMLtables is based on odML. A complete list of dependencies is available in the odMLtables documentation at Read the Docs.

Installation

Since this version is not released on the Python Package Index (PyPI), it must be installed directly from this GitHub repository.

Install the latest version using pip:

pip install git+https://github.com/YOUR-USERNAME/python-odmltables.git

To install with graphical user interface support:

pip install git+https://github.com/YOUR-USERNAME/python-odmltables.git#egg=odmltables[gui]

Alternatively, clone the repository and install locally:

git clone https://github.com/YOUR-USERNAME/python-odmltables.git
cd python-odmltables
pip install .

To install with GUI support locally:

pip install .[gui]

Documentation

The odMLtables documentation is available on Read the Docs.

It is based on Sphinx and can also be built locally. To build the HTML documentation:

cd doc
make html

The generated documentation will be available in:

doc/_build/html/index.html

All available output formats can be listed using:

make -n

Original Project

This repository is based on the original odMLtables project developed at:

INM-6, Forschungszentrum Jülich

Original repository: https://github.com/INM-6/python-odmltables

If you use odMLtables in scientific work, please cite the original project accordingly.

The extensions implemented in this fork were developed in the context of microneurography data analysis and metadata management. A scientific publication describing the related methodology and application is available:

Troglio A, Nickerson A, Schlebusch F, Röhrig R, Dunham J, Namer B, Kutafina E. odML-Tables as a Metadata Standard in Microneurography. Stud Health Technol Inform. 2023 Sep 12;307:3-11. doi: 10.3233/SHTI230687. PMID: 37697832. https://pubmed.ncbi.nlm.nih.gov/37697832/

Bugs and Issues

If you observe a bug or encounter issues, please report them via the GitHub issue tracker of this repository.

License

This project follows the same license as the original odMLtables project. Please refer to the LICENSE file for details.

Contact

Email: alina.troglio@rwth-aachen.de