odMLtablesForMNG

Introduction

Metadata is essential for sharing data according to FAIR principles. Standards are well established for most electrophysiological recording methods, but are still lacking in microneurography. We propose a standard for structuring and recording metadata based on odML and odML-tables by providing two templates for experimental properties adapted to microneurography recordings and installation guidelines to ensure usability. In addition, we present an extension to the odML-tables GUI, in which we integrate a new search functionality for a large database adapted to our needs. With our open-source repository, we encourage all microneurography labs to incorporate odML-based metadata into their lab routines. 

Templates

There are two templates. One for general experimental metadata and the other one for individual data recordings. Please take a look at the filled out example templates or check out the github wiki.

Installation

1. Get the most recent version of python from https://www.python.org, and download git from https://git-scm.com/downloads.
2. Start setup of python installation and make sure python.exe is added to the path by selecting the checkbox "Add python.exe to PATH".
   

3. Start setup of git installation.

4. Open the Command Line window for windows or Terminal for linux/macOS.

5. Install pipx - a program manager for python:

   • Type into command line or terminal and press enter: console python -m pip install pipx

6. Install odmltables: console pipx install odmltables

7. Now the standard version of odML-tables was installed. To add the new search functionality, certain files need to be downloaded and used as replacement for the old files.

   1. Download and save the python files in the same hierarchical structure. For example, click on green button <> Code and select "Download ZIP".
      
   2. Navigate to folder where pipx is installed and odmltables is located, for that write in command line or terminal console pipx list
   3. It should show: venvs are in YOURPATH\.local\pipx\venvs
      Navigate to the folder location in your file system by replacing YOURPATH with your actual path
      YOURPATH\.local\pipx\venvs\odmltables\Lib\site-packages\odmltables

8. Copy and replace files from Code folder

   1. Copy odml_table.py to folder YOURPATH\.local\pipx\venvs\odmltables\Lib\site-packages\odmltables
   2. Copy mainwindow.py to folder YOURPATH\.local\pipx\venvs\odmltables\Lib\site-packages\odmltables\gui (in gui folder).
   3. Copy searchpages.py to folder YOURPATH\.local\pipx\venvs\odmltables\Lib\site-packages\odmltables\gui (in gui folder).
   4. Copy searchwiz.py to folder YOURPATH\.local\pipx\venvs\odmltables\Lib\site-packages\odmltables\gui (in gui folder).
   5. Copy searchodml3.svg to folder YOURPATH\.local\pipx\venvs\odmltables\Lib\site-packages\odmltables\gui\graphics (in gui/graphics folder).

Problems or questions

If you observe any problems or questions in this extension of odML-tables please add a issue at the GitHub issue tracker.

Preprint