Aligning TPT Collection Names with TPT Taxonomy

date 12 January 2023

Aligning names across collections help to integrate data across collections.

Many tools are available to help extract taxonomic names in collections and align them against some existing taxonomy.

This repository is an example of how to align names using Elton, and Nomer using make.sh, a bash script.

alternate workflow (with name scrubbing)

Some collection have yet to index names.

Name		Name	Last commit message	Last commit date
Latest commit History 12 Commits
README.md		README.md
collections_vs_collections_with_indexed_names.txt		collections_vs_collections_with_indexed_names.txt
make.sh		make.sh
names-aligned.tsv		names-aligned.tsv
names-collections.tsv		names-collections.tsv
names-hits.tsv		names-hits.tsv
names-miss.tsv		names-miss.tsv
names-parsed-and-aligned.tsv		names-parsed-and-aligned.tsv
names-parsed-hits.tsv		names-parsed-hits.tsv
names-parsed-miss.tsv		names-parsed-miss.tsv
names-parsed-total.tsv		names-parsed-total.tsv
names-parsed.tsv		names-parsed.tsv
names-total.tsv		names-total.tsv
names.tsv		names.tsv
names.tsv.gz		names.tsv.gz
nomer.properties		nomer.properties
parasitetracker.tsv		parasitetracker.tsv
parasitetracker_name_urls.txt		parasitetracker_name_urls.txt
parasitetracker_namespaces.tsv		parasitetracker_namespaces.tsv

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