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.
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.
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Get the most recent version of python from https://www.python.org, and download git from https://git-scm.com/downloads.
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Start setup of python installation and make sure python.exe is added to the path by selecting the checkbox "Add python.exe to PATH".
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Start setup of git installation.
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Open the Command Line window for windows or Terminal for linux/macOS.
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Install pipx - a program manager for python:
- Type into command line or terminal and press enter:
python -m pip install pipx
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Install odmltables:
pipx install odmltables
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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.
- Download and save the python files in the same hierarchical structure. For example, click on green button <> Code and select "Download ZIP".
- Navigate to folder where pipx is installed and odmltables is located, for that write in command line or terminal
pipx list
- 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
- Download and save the python files in the same hierarchical structure. For example, click on green button <> Code and select "Download ZIP".
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Copy and replace files from Code folder
- Copy odml_table.py to folder
YOURPATH\.local\pipx\venvs\odmltables\Lib\site-packages\odmltables
- Copy mainwindow.py to folder
YOURPATH\.local\pipx\venvs\odmltables\Lib\site-packages\odmltables\gui
(in gui folder). - Copy searchpages.py to folder
YOURPATH\.local\pipx\venvs\odmltables\Lib\site-packages\odmltables\gui
(in gui folder). - Copy searchwiz.py to folder
YOURPATH\.local\pipx\venvs\odmltables\Lib\site-packages\odmltables\gui
(in gui folder). - Copy searchodml3.svg to folder
YOURPATH\.local\pipx\venvs\odmltables\Lib\site-packages\odmltables\gui\graphics
(in gui/graphics folder).
- Copy odml_table.py to folder
If you observe any problems or questions in this extension of odML-tables please add a issue at the GitHub issue tracker.