mapping-taxonomists

TETTRIs WP3, task 3.2: automatic mapping of taxonomic expertise

https://github.com/agentschapplantentuinmeise/mapping-taxonomists

Science Score: 44.0%

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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Scientific vocabulary similarity
Low similarity (6.6%) to scientific vocabulary

Last synced: 7 months ago · JSON representation ·

Repository

TETTRIs WP3, task 3.2: automatic mapping of taxonomic expertise

Basic Info

Host: GitHub
Owner: AgentschapPlantentuinMeise
License: mit
Language: Jupyter Notebook
Default Branch: main
Homepage:
Size: 77.4 MB

Statistics

Stars: 2
Watchers: 4
Forks: 2
Open Issues: 9
Releases: 1

Created about 3 years ago · Last pushed 8 months ago

Metadata Files

Readme License Citation

Automatic mapping of taxonomic expertise

This repository contains the scripts used to find European authors of taxonomic articles, identify the species they study, and compare their taxa of expertise to some demands for taxonomic expertise.

Prerequisites

Before starting you need to download the GBIF taxonomic backbone, unzip it and put the contents in the folder data/external/backbone You may also need to install SPARQLWrapper, geopandas and fiona to your Python installation, i.e. using pip install SPARQLWrapper

mappingTaxonomists.ipynb

It is possible to run the whole workflow one script after another. However, the Jupyter notebook mappingTaxonomists.ipynb allows you to run all the scripts in order.

Configuration

The dates between which the workflow will extract publications is set within the config.json file. The one and two word "keywords" are also set within the config file. The OpenAlex concept values are set within config.json The two letter country codes (ISO 3166-1 alpha-2) on which to conduct the analyis are listed in file included_countries.txt within the ./config/ directory

To reuse or repurpose this script these configutations may need changing. However, if the script is to be repurposed for a subject other than biological taxonomy then list_journals.py would need rewriting or replacing, because it is focused on taxonomic journals.

Owner

Name: Botanic Garden Meise
Login: AgentschapPlantentuinMeise
Kind: organization
Email: quentin.groom@plantentuinmeise.be
Location: Meise, Belgium

Website: http://www.plantentuinmeise.be/
Repositories: 11
Profile: https://github.com/AgentschapPlantentuinMeise

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: European taxonomy in profile
message: 'If you use this software, please cite it as below.'
type: software
authors:
  - given-names: Melanie
    family-names: De Nolf
    affiliation: Meise Botanic Garden
    orcid: 'https://orcid.org/0000-0001-6032-5198'
  - given-names: Sofie
    family-names: Meeus
    email: sofie.meeus@plantentuinmeise.be
    affiliation: Meise Botanic Garden
    orcid: 'https://orcid.org/0000-0003-0715-8647'
  - given-names: Quentin
    family-names: Groom
    email: quentin.groom@plantentuinmeise.be
    affiliation: Meise Botanic Garden
    orcid: 'https://orcid.org/0000-0002-0596-5376'
keywords:
  - taxonomy
  - bibliographic
  - scientific impact
  - research prioritization
license: MIT
version: 0.1.0
date-released: '2024-08-16'

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