TaxonWorks

Describe life.

TaxonWorks is an integrated web-based workbench for taxonomists and biodiversity scientists.

It allows you to capture, organize, and enrich your data; share it with collaborators; and package it for analysis and publication.

A digital companion for discovering biodiversity

Our vision

From observation to archive, TaxonWorks is there at every step of the taxonomic process.

Capture your early observations, images and notes. Collaboratively refine, validate, and grow your datasets. Turn your discoveries into polished conclusions faster. Integrate data across your career, and hand it off to your protégé. Spend more time researching, and less time with the mundane.

For scientists and developers

We seek to surround TaxonWorks with scientists who can effect change in the tools they use, and software carpenters who can effect change in science through their contributions.

The TaxonWorks community is built around an open software ecosystem that facilitates participation at many levels, and expertise from scientists at every stage in their careers.

Rich, fluid, customizable data

TaxonWorks is part of your research data pipeline.

Flow data in via batch loaders, wrappers on external providers, scripts, the TaxonWorks JSON API, and an ever improving optimized user interface.

Adapt core data with many customizable annotations that optionally reference external standards.

Improve your data with a wealth of non-constraining validators.

Export an ever growing number of formats directly to your analysis tools, manuscript-ready documents, and global archives.

Long-term development support

Endowed and maintained by the Species File Group. Supported by the National Science Foundation. Created in collaboration with partner universities and labs.

Like life, TaxonWorks is ever-evolving

TaxonWorks has over 50 years of collective experience behind it. From experimental features to highly refined workflows, TaxonWorks aims to balance innovation and tradition. Lend your voice to a growing community of adopters and help TaxonWorks adapt.

Explore feature in use, development, and discussion

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Describe taxa, specimens, and anatomy

Use a wide range of data to describe life.
Status:
In use
Available:
Now

Phylogenetic matrices

Create traditional qualitative or quantitative phylogenetic matrices. Annotate data throughout with notes, images, tags and confidence levels.
Status:
In use
Available:
Now

Free text notes and descriptions

Edit textual descriptions per topic for taxa. Cite, figure, and annotate them. Compare, clone, and copy from your own templates.
Status:
In use
Available:
Now

Biological relationships

Create and manage biological relationships between taxa, specimens or field occurrences, or some combination of both. For example host-parasites.
Status:
In use
Available:
Now

Anatomical reference systems

Use ontologies to annotate the morphology of taxa, specimens, or field occurrences. Use these systems to annotate, query, and organize your data by anatomy.
Status:
In development
Available:
This year

Manuscript and datasets export

Summarize data into taxonomic descriptions (e.g. nomenclatural history, descriptions, material examined sections) ready for publication. Export CSV, DWCA, Nexus, and many other data formats.
Status:
In development
Available:
Within the next three years

Multi-entry keys

Use a multiple-entry key interface, with support for multiple languages, to analyze, build, and refine your observations.
Status:
In use
Available:
Now

Traditional diagnostic keys

Create dichotomous keys, particularly useful for keeping past keys at your fingertips with enhanced navigation.
Status:
In use
Available:
Now

Advanced anatomical interfaces

Describe anatomical features using graphical interfaces. Drag, drop, and slide to measure, characterize, and qualify observations.
Status:
In discussion
Available:
Within the next three years

Landmark metadata

Create landmark data and tie it to anatomical ontologies for future use and organziation.
Status:
In discussion
Available:
Within the next three years

Sequences

Manage curated DNA sequences and metadata. Annotate them with protocols, and other sequence related metadata (e.g. extract and specimen, primers, or query sequences).
Status:
In discussion
Available:
Within the next three years

Specimens and collecting events

The best descriptions are those tied directly to specimens and collections. Capture these data at the personal or institutional level.
Status:
In use
Available:
Now

Digitization workflows

Capture detail for collecting events and specimens with features like customizable, fine grained attributes, lockable values, and varying levels of form complexity. Built in OCR and image processing.
Status:
In use
Available:
Now

Draw-to-digitize

Automatically stub collection objects by drawing a ROIs (regions of interest) within an image.
Status:
In use
Available:
Now

Grid digitization

Semi-automatic breakdown of images into grids each cell generating a new collection object. Add identifiers in sequence, and add metadata throughout all objects.
Status:
In use
Available:
Now

Integrated GIS

Search and return specimen, literature, and field-occurrence data spatially. Create georeferences of any shape. Also wraps GeoLocate.
Status:
In use
Available:
Now

Loans

Manage personal or institutional loans with many ways to add, annotate, and return collection objects.
Status:
In use
Available:
Now

Nomenclature

Curate all levels of nomenclature with specific reference to the governing codes of nomenclature, plants and animals are covered. Rich coverage of nomenclatural rules are included to ensure adequate metadata are provided.
Status:
In use
Available:
Now

Catalog exports

Summarize nomenclatural data in print and machine readable formats.
Status:
In use
Available:
Now

DwC Checklist

Export basic nomenclature data as a Darwin Core Checklist.
Status:
In discussion
Available:
Within the next three years

Catalog of Life

Export basic nomenclature data to the Catlog of Life format.
Status:
In use
Available:
Now

"Paper" formats

Export nomenclature and distribution data to a classic in-print catalog format for use in Markdown, HTML, e-books, or Word conversions.
Status:
In use
Available:
Now

TaxonPages public websites

Create publicly accessible websites in minutes wrapping TaxonWorks API with the TaxonPages framework.
Status:
In use
Available:
Now

Validation

Use well over a hundred non-constraining validations to ensure data meet plant, animal, and bacterial codes of nomeclature.
Status:
In use
Available:
Now

Import, annotate, and export

Handle data at all stages of the scientific pipeline. Batch load, annotated and refine, export via files or API.
Status:
In use
Available:
Now

Darwin Core (DwC) occurrence import and export

Import and export DwC occurence data validating it along the way.
Status:
In use
Available:
Now

Cite everything

Tie *all* your data to references that you can import from BibTeX.
Status:
In use
Available:
Now

Media and references

Load references, images, and other supporting documents. Link them as citations, depictions, or supporting data to all of the core data classes.
Status:
In use
Available:
Now

Data attributes, alternative value, notes

Add your own attributes that optionally reference external controlled vocabularies. Provide translations, abbreviations, misspellings for existing records.
Status:
In use
Available:
Now

Images, sounds, documents

Depict, convey, and document data throughout your project.
Status:
In use
Available:
Now

Images

Depict not just specimens, but collecting event, observations, and even data elements like taxon names.
Status:
In use
Available:
Now

Sounds

Convey the relationship between recorded sounds and observations, specimens, and collecting events.
Status:
In use
Available:
Now

Documents

Document where your data come from, not just PDFs for refrences, but but also lab protocols, field notes, and phylogenetic matrices.
Status:
In use
Available:
Now

Rich support for collaborating developers

A open-source code base with a community that facilates new collaborators and a long-term development process.
Status:
In use
Available:
Now

Get help

A growing number of developers support interactions throughout the TaxonWorks ecosystem.
Status:
In use
Available:
Now

Cross-platform docker and native development environments

Quickly initialize a local instance of TaxonWorks using Docker or native configurations.
Status:
In use
Available:
Now

JSON serving API

Work with the TaxonWorks back end through a token-based JSON serving API. Develop in your favourite framework, and integrate natively, or as a stand-alone tool.
Status:
In use
Available:
Now

Unit tests

TaxonWorks has thousands of unit tests. Tests minimize the likelihood of new features breaking existing functionality. They clarify intent, and when included in new code make code acceptance straightforward.
Status:
In use
Available:
Now

AI friendly code-base

Use LLMs to rapidly prototype then refine to add new features, data importers, and API wrappers.
Status:
In development
Available:
Within the next three years

Get started with

This is the logo of TaxonWorks

TaxonWorks is an open-source web application. Each installation of TaxonWorks supports multiple projects and users.
If you have the means you can install it on your own, or you can look to collaborate with those hosting an instance.

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See TaxonWorks data in public