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fair-convergence-matrix

Basic code to create FAIR convergence matrix from nanodash nanopublications

https://github.com/eu-parc/fair-convergence-matrix

Science Score: 75.0%

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Repository

Basic code to create FAIR convergence matrix from nanodash nanopublications

Basic Info
  • Host: GitHub
  • Owner: eu-parc
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 407 KB
Statistics
  • Stars: 3
  • Watchers: 3
  • Forks: 1
  • Open Issues: 1
  • Releases: 1
Created over 2 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Citation

README.md

DOI

FAIR-convergence-matrix

Basic code to create FAIR convergence matrix from nanodash nanopublications

Prerequisites

  • Basic knowledge on how to run r/python code
  • Filtering data using pandas (python) or tidyverse (r)

How to use

Change the input and output paths to your liking. The source for the newmatrix.csv in this repository is: https://github.com/peta-pico/dsw-nanopub-api/blob/main/tables/newmatrix.csv

Python

The Python code is available in the python folder. There are two ways to run the code.

  1. Run main.py
  2. Run create_FAIR_convergence_matrix.ipynb

In both cases you will have to change the selection of the data manually, to fit your needs. You can do this in many ways using python and pandas. Some of the methods are described here: https://pandas.pydata.org/docs/user_guide/indexing.html

The lines to change are indicated in both files respectively.

The current implementation selects all communities with an A in their name.

R

The R code is available in the r folder. You can run the code in the Quarto document fcm.qmd

You will have to change the selection of the data manually, to fit your needs. Currently this is done using the tidyverse, selecting data from all FICs that have "ENVRI" as supercommunity. More information on filtering using the information in the excellent "R for Data Science" book: https://r4ds.had.co.nz/transform.html?q=filter#filter-rows-with-filter.

Contact

Please use this GitHub repository's Issue tracker to report any issues or ask for requests.

Owner

  • Name: PARC, Partnership for the Assessment of Risks from Chemicals
  • Login: eu-parc
  • Kind: organization

Partnership for the Assessment of Risks from Chemicals aims to develop next-generation chemical risk assessment to protect human health and the environment. It

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Peeters
    given-names: Ruben
    orcid: https://orcid.org/0000-0002-0905-7033
  - family-names: Burger
    given-names: Gerhard
    orcid: https://orcid.org/0000-0003-1062-5576
title: "FCM-pyr: Python and R FAIR Convergence Matrix"
version: 0.1.0
identifiers:
  - type: doi
    value: 10.5281/zenodo.10556249
date-released: 2024.01.23

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Dependencies

python/poetry.lock pypi
  • appnope 0.1.3
  • asttokens 2.2.1
  • backcall 0.2.0
  • certifi 2023.7.22
  • cffi 1.15.1
  • charset-normalizer 3.2.0
  • colorama 0.4.6
  • comm 0.1.4
  • contourpy 1.1.0
  • cycler 0.11.0
  • debugpy 1.6.7.post1
  • decorator 5.1.1
  • et-xmlfile 1.1.0
  • executing 1.2.0
  • fonttools 4.42.1
  • idna 3.4
  • importlib-metadata 6.8.0
  • importlib-resources 6.0.1
  • ipykernel 6.25.1
  • ipython 8.14.0
  • isodate 0.6.1
  • jedi 0.19.0
  • jupyter-client 8.3.0
  • jupyter-core 5.3.1
  • kiwisolver 1.4.5
  • matplotlib 3.7.2
  • matplotlib-inline 0.1.6
  • nest-asyncio 1.5.7
  • networkx 3.1
  • numpy 1.25.2
  • openpyxl 3.1.2
  • packaging 23.1
  • pandas 2.0.3
  • parso 0.8.3
  • pexpect 4.8.0
  • pickleshare 0.7.5
  • pillow 10.0.0
  • platformdirs 3.10.0
  • prompt-toolkit 3.0.39
  • psutil 5.9.5
  • ptyprocess 0.7.0
  • pure-eval 0.2.2
  • pycparser 2.21
  • pygments 2.16.1
  • pyparsing 3.0.9
  • python-dateutil 2.8.2
  • pytz 2023.3
  • pywin32 306
  • pyzmq 25.1.1
  • rdflib 7.0.0
  • requests 2.31.0
  • seaborn 0.12.2
  • six 1.16.0
  • sparqlwrapper 2.0.0
  • stack-data 0.6.2
  • tornado 6.3.3
  • traitlets 5.9.0
  • typing-extensions 4.7.1
  • tzdata 2023.3
  • urllib3 2.0.4
  • wcwidth 0.2.6
  • zipp 3.16.2
python/pyproject.toml pypi
  • ipykernel ^6.25.1
  • matplotlib ^3.7.2
  • networkx ^3.1
  • numpy ^1.25.2
  • openpyxl ^3.1.2
  • pandas ^2.0.3
  • python ^3.9
  • requests ^2.31.0
  • seaborn ^0.12.2
  • sparqlwrapper ^2.0.0