Aligning taxonomic names is a common task in biodiversity informatics.
This template repository offers an automated method to align any text file with names against common taxonomic name lists like Catalogue of Life, NCBI Taxonomy, Integrated Taxonomic Information System (ITIS), and GBIF Backbone taxonomy.
To re-use:
- create your own repository using this repository as a template
- add/replace your own name list in a file with .txt extension
- commit the changes to github
- inspect results of name alignment in "Github Actions" (e.g., sample results Download the name alignment results with the single-use, and expiring, file.io link at: https://file.io/IllemEVSEfXa )
- download results from provided single-use https://file.io link (e.g., look for
Download the name alignment results with the single-use, and expiring, file.io link at: https://file.io/[something]in alignment report) - to re-create results, change your name list in github or select "re-run jobs" in Github Actions.
This repository was conceived on 2022-03-08 during the Alien CSI Hack-a-thon in Romania by Christina, Quentin, Jorrit, Jasmijn, .... For more information see https://github.com/alien-csi/alien-csi-hackathon .
| name | affiliation | orcid |
|---|---|---|
| Jorrit Poelen | GloBI; Ronin Institute | https://orcid.org/0000-0003-3138-4118 |
| your name | your affiliation | your orcid |
This repository uses scripts in https://github.com/globalbioticinteractions/globinizer. These script use commandline tools like GloBI's nomer, cut, sed, etc.
install nomer java8 / java11 -
https://github.com/globalbioticinteractions/nomer
e.g., Carl Boettiger taxondb R package
Print names and add a tab in front, to prepare for nomer.
cat foodorganisms.txt | sed 's/^/\t/g' > foodorganisms.tsv
Nomer expects the format to be:
[id][tab][name]
e.g., id\tname NCBI:9606\tHomo sapiens
Print names to screen and append itis taxonomic interpretation, and write/redirect to a file 'name-itis.tsv'
cat foodorganisms.tsv | nomer append itis > name-itis.tsv
open in LibreOffice Calc
Repeat with 'gbif' instead of 'itis'