https://github.com/neotomadb/taxoninsertion

A package to bulk upload taxonomic data (beetles in this case) from Family/genus/species info.
https://github.com/neotomadb/taxoninsertion

Last synced: 11 months ago
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A package to bulk upload taxonomic data (beetles in this case) from Family/genus/species info.

• Host: GitHub
• URL: https://github.com/neotomadb/taxoninsertion
• Owner: NeotomaDB
• License: mit
• Created: 2025-02-26T23:00:10.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2025-05-21T21:31:23.000Z (about 1 year ago)
• Last Synced: 2025-05-21T21:36:47.000Z (about 1 year ago)
• Language: Python
• Size: 38.1 KB
• Stars: 0
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Code of conduct: code_of_conduct.md

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# Taxon Insertion in Neotoma

This is a package intended to help support both bulk and individual taxon insertion in Neotoma.

What the package does:

1. Connects to the Neotoma Paleoecology Database (both main and tank).

2. Takes a taxon name and checks the name with GBIF and NCBI.

3. Finds the appropriate insertion point within Neotoma for insertion.

4. Returns a set of rows to be inserted into Neotoma to support the new taxonname.

5. Inserts new rows into Neotoma.

6. Supports rollback and commit features.

## Contributors

* [Simon Goring](http://goring.org): University of Wisconsin - Madison [![orcid](https://img.shields.io/badge/orcid-0000--0002--2700--4605-brightgreen.svg)](https://orcid.org/0000-0002-2700-4605)

## Using this Repository

Secrets to connect to the database are in an "ignored" file named `.env`. It should have the format:

```bash

DBAUTH={"host":"localhost","port":5432,"user":"postgres","password":"postgres","dbname":"neotoma"}

```

The repository uses the `uv` package manager to help manage dependencies and ensure a stable development platform. To use this repository, first clone the repository locally, and then, run `uv init` to install all neccessary packages. Once the packages are installed, the script `testing_beetles.py` can be run using `uv run testing_beetles.py`.

The script may be slow to run because it must interact with the Neotoma database (and could interact with GBIF and NCBI if wanted).

## Current Expected Input and Output

The script in this repository is designed to work with a CSV file provided by the [BUGSCep](https://bugscep.com/) research data group. That CSV has the format:

```csv

CODE,FAMILY,GENUS,SPECIES,AUTHORITY,epithet,neotoma_path,gbifid,ncbi_id,taxonRank,taxonomicStatus,ncbi_lineage_names

```

The `testing_beetles.py` file parses this document row by row and returns a similar CSV, with the additional columns `familyid`, `genusid`, and `speciesid`, with the associated Neotoma taxon IDs.