TaxonoPy

A Python package for efficiently aligning organismal taxonomic hierarchies using the Global Names Verifier.
https://github.com/imageomics/taxonopy

Category: Biosphere
Sub Category: Biodiversity Analysis and Metrics

Keywords

alignment hierarchy taxonomic-resolution taxonomy tree-of-life

Last synced: about 5 hours ago
JSON representation

Repository metadata

A Python package for efficiently aligning organismal taxonomic hierarchies using the Global Names Verifier

Host: GitHub
URL: https://github.com/imageomics/taxonopy
Owner: Imageomics
License: mit
Created: 2024-04-19T15:37:30.000Z (almost 2 years ago)
Default Branch: main
Last Pushed: 2026-02-27T01:39:34.000Z (28 days ago)
Last Synced: 2026-03-21T14:11:33.902Z (6 days ago)
Topics: alignment, hierarchy, taxonomic-resolution, taxonomy, tree-of-life
Language: Python
Homepage: https://imageomics.github.io/TaxonoPy/
Size: 1.25 MB
Stars: 14
Watchers: 5
Forks: 0
Open Issues: 14
Releases: 2
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
- Agents: AGENTS.md

TaxonoPy: Reproducible, Traceable, and Scalable Biological Taxonomy Alignment

TaxonoPy (taxon-o-pie) is a command-line tool for harmonizing large biodiversity datasets into a consistent taxonomy ready for AI applications. Built on the Global Names Verifier (GNVerifier), it provides complete provenance tracking, flexible resolution strategies, and batch processing of 100M+ records to address challenges in reproducibility and scale in massive multi-source taxonomy alignment.

Documentaion

See https://imageomics.github.io/TaxonoPy for documentation on installation, usage, and more.

Development

See the Wiki Development Page for development instructions.

Citation (CITATION.cff)

abstract: "A Python package for efficiently aligning organismal taxonomic hierarchies using the Global Names Verifier."
authors:
- family-names: "Thompson"
  given-names: "Matthew J."
  orcid: "https://orcid.org/0000-0003-0583-8585"
- family-names: "Campolongo"
  given-names: "Elizabeth G."
  orcid: "https://orcid.org/0000-0003-0846-2413"
- family-names: "Lapp"
  given-names: "Hilmar"
  orcid: "https://orcid.org/0000-0001-9107-0714"
- family-names: "Gu"
  given-names: "Jianyang"
  orcid: "https://orcid.org/0000-0002-4060-7427"
cff-version: 1.2.0
date-released: "2026-02-13"
identifiers:
  - description: "The GitHub release URL of tag v0.2.0."
    type: url
    value: "https://github.com/Imageomics/TaxonoPy/releases/tag/v0.2.0"
  - description: "The GitHub URL of the commit tagged with v0.2.0"
    type: url
    value: "https://github.com/Imageomics/TaxonoPy/tree/<update-after-release>"
keywords:
  - imageomics
  - taxonomy
  - "taxonomic resolution"
  - "tree of life"
  - alignment
  - hierarchy
references:
  - type: software
    title: "GNverifier -- a reconciler and resolver of scientific names against more than 100 data sources."
    version: "v1.2.5"
    authors:
      - family-names: "Mozzherin"
        given-names: "Dmitry"
        orcid: "https://orcid.org/0000-0003-1593-1417"
    repository-code: "https://github.com/gnames/gnverifier"
    date-released: "2025-04-02"
    doi: 10.5281/zenodo.5111542
    license: MIT
license: MIT
message: "If you use this software, please cite it using the metadata from this file."
repository-code: "https://github.com/Imageomics/TaxonoPy"
title: "TaxonoPy"
version: "0.2.0"
doi: "10.5281/zenodo.15499454"
type: software

Owner metadata

Name: Imageomics Institute
Login: Imageomics
Email:
Kind: organization
Description:
Website: https://imageomics.osu.edu
Location:
Twitter: imageomics
Company:
Icon url: https://avatars.githubusercontent.com/u/77468321?v=4
Repositories: 4
Last ynced at: 2023-03-05T05:05:36.574Z
Profile URL: https://github.com/Imageomics

GitHub Events

Total

Release event: 1
Delete event: 6
Member event: 2
Pull request event: 7
Issues event: 7
Watch event: 6
Issue comment event: 11
Public event: 1
Push event: 49
Gollum event: 1
Pull request review event: 12
Pull request review comment event: 21
Create event: 5

Last Year

Release event: 1
Delete event: 6
Member event: 2
Pull request event: 7
Issues event: 7
Watch event: 6
Issue comment event: 11
Public event: 1
Push event: 49
Gollum event: 1
Pull request review event: 12
Pull request review comment event: 21
Create event: 5

Committers metadata

Last synced: 2 days ago

Total Commits: 26
Total Committers: 3
Avg Commits per committer: 8.667
Development Distribution Score (DDS): 0.077

Commits in past year: 9
Committers in past year: 2
Avg Commits per committer in past year: 4.5
Development Distribution Score (DDS) in past year: 0.111

Name	Email	Commits
Matthew Thompson	t**9@o**u	24
Elizabeth Campolongo	3****9	1
Dahlializi	1****i	1

Committer domains:

osu.edu: 1

Issue and Pull Request metadata

Last synced: 6 days ago

Total issues: 9
Total pull requests: 13
Average time to close issues: 1 day
Average time to close pull requests: 28 days
Total issue authors: 2
Total pull request authors: 5
Average comments per issue: 0.33
Average comments per pull request: 1.54
Merged pull request: 7
Bot issues: 0
Bot pull requests: 0

Past year issues: 7
Past year pull requests: 10
Past year average time to close issues: 1 day
Past year average time to close pull requests: 2 days
Past year issue authors: 2
Past year pull request authors: 4
Past year average comments per issue: 0.29
Past year average comments per pull request: 1.8
Past year merged pull request: 5
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/imageomics/taxonopy

Top Issue Authors

thompsonmj (8)
Dahlializi (1)

Top Pull Request Authors

thompsonmj (9)
Copilot (1)
Dahlializi (1)
egrace479 (1)
vimar-gu (1)

Top Issue Labels

bug (3)
enhancement (2)
edge case (2)

Top Pull Request Labels

documentation (1)

Package metadata

Total packages: 1
Total downloads:
- pypi: 44 last-month
Total dependent packages: 0
Total dependent repositories: 0
Total versions: 3

pypi.org: taxonopy

A Python package for resolving taxonomic hierarchies using the Global Names Verifier API.

Homepage:
Documentation: https://github.com/Imageomics/TaxonoPy
Licenses: MIT License Copyright (c) 2025 Imageomics Institute Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Latest release: 0.2.0 (published about 1 month ago)
Last Synced: 2026-03-25T03:00:21.159Z (2 days ago)
Versions: 3
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 44 Last month
Rankings:
- Dependent packages count: 9.096%
- Average: 30.172%
- Dependent repos count: 51.248%

Dependencies

.github/workflows/publish-to-pypi.yaml actions

actions/checkout v4 composite
actions/setup-python v5 composite
pypa/gh-action-pypi-publish release/v1 composite

pyproject.toml pypi

pandas *
polars *
pyarrow *
pydantic *
requests *
tqdm *

Score: 8.215006432761575

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