https://github.com/kit-data-manager/nmr_fair-dos
This tool extracts metadata regarding NMR data from multiple repositories and creates FAIR-DOs for them.
https://github.com/kit-data-manager/nmr_fair-dos
chemotion cli elasticsearch extraction-tool fair-dos kit-data-manager nmrxiv
Last synced: about 1 month ago
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This tool extracts metadata regarding NMR data from multiple repositories and creates FAIR-DOs for them.
- Host: GitHub
- URL: https://github.com/kit-data-manager/nmr_fair-dos
- Owner: kit-data-manager
- License: apache-2.0
- Created: 2024-11-04T08:46:59.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-02-07T15:45:53.000Z (over 1 year ago)
- Last Synced: 2025-02-14T15:41:57.788Z (over 1 year ago)
- Topics: chemotion, cli, elasticsearch, extraction-tool, fair-dos, kit-data-manager, nmrxiv
- Language: Python
- Homepage: https://kit-data-manager.github.io/nmr_FAIR-DOs/
- Size: 1.68 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION.cff
- Authors: AUTHORS.md
- Codemeta: codemeta.json
Awesome Lists containing this project
README
[
](https://kit-data-manager.github.io/nmr_FAIR-DOs)
[
](https://github.com/kit-data-manager/nmr_FAIR-DOs/actions/workflows/ci.yml)
# nmr_FAIR-DOs
This project creates FAIR Digital Objects (FAIR-DOs) for multiple repositories, registers them with the [Typed PID-Maker](https://github.com/kit-data-manager/pit-service) and indexes them in an Elasticsearch instance.
Currently, these repositories are supported:
- [NMRXiv](https://nmrxiv.org)
- [Chemotion](https://chemotion-repository.net)
See the [created FAIR-DOs](https://bwsyncandshare.kit.edu/s/P6qt5ecGsDa2yan) of the project.
If you want to explore these FAIR-DOs in a user-friendly manner, please visit the [search interface](https://metarepo.nffa.eu/nep-search).
For more information, see the [documentation](https://kit-data-manager.github.io/nmr_FAIR-DOs/main).
## Installation
Clone this project and use [Poetry](https://python-poetry.org/) to install the dependencies.
```bash
git clone https://github.com/kit-data-manager/nmr_FAIR-DOs.git
cd nmr_FAIR-DOs
poetry install
```
This project works with Python > 3.8.
## Getting Started
Get started by running the command line interface (CLI) with the `nmr_FAIR-DOs` command. You can use the `--help` flag to see the available options.
```bash
poetry run nmr_FAIR-DOs-cli --help
```
To create FAIR-DOs for all NMR data in the repositories and log the output, run the following command:
```bash
poetry run nmr_FAIR-DOs-cli createallavailable 2>&1 | tee full.log
```
## Troubleshooting
### When I try installing the package, I get an `IndexError: list index out of range`
Make sure you have `pip` > 21.2 (see `pip --version`), older versions have a bug causing
this problem. If the installed version is older, you can upgrade it with
`pip install --upgrade pip` and then try again to install the package.
**You can find more information in the
[documentation](https://kit-data-manager.github.io/nmr_FAIR-DOs/).**
## How to Cite
If you want to cite this project in your scientific work,
please use the [citation file](https://citation-file-format.github.io/)
in the [repository](https://github.com/kit-data-manager/nmr_FAIR-DOs/blob/main/CITATION.cff).
## Acknowledgements
This is a Python project generated from the [fair-python-cookiecutter](https://github.com/Materials-Data-Science-and-Informatics/fair-python-cookiecutter) template.
We kindly thank all
[authors and contributors](https://kit-data-manager.github.io/nmr_FAIR-DOs/latest/credits).
This tool was created at [Karlsruhe Institute of Technology (KIT)](https://kit.edu) at the [Scientific Computing Center (SCC)](https://scc.kit.edu) in the department [Data Exploitation Methods (DEM)](https://www.scc.kit.edu/ueberuns/dem.php).
This work is supported by the consortium NFDI-MatWerk, funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI 38/1 – project number 460247524.
**TODO: relevant organizational acknowledgements (employers, funders)**