Name Alignment Workshop



18 January 2023

1:00 pm - 2:00 pm PST

Instructors: JT Miller, Jorrit Poelen, Katja C. Seltmann

General Information

A showcase of Global Biotic Interactions GloBI’s name-alignment-tool, used to align a list of taxonomic names against multiple catalogues. This workshop is directed towards assisting curators in standardizing their collections. The workshop will be one hour and will go through a step by step guide to using the name-alignment-tool including navigating github, editing arguments, and accessing outputs.

Our overall goal of this workshop is provide a tutorial on the usage of the name-alignment-tool in resolving large taxonomic lists as well as illustrate common issues one should be aware of when aligning names.


A special thanks to the following organizations and projects that made this work and tutorial possible: NSF for their support and funding of Big-Bee, Extending Anthophila research through image and trait digitilization. (NSF:DBI:2102006), Global Biotic Interactions GloBI for integration of Nomer for name alignment, and iDigBio for TCN support.


Note that this is not (yet) an official Carpentries workshop, but we are working towards becoming one.

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: 18 January 2023. Add to your Google Calendar.

Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email , or for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.


Before Participants are encouraged to follow setup instructions a day before the workshop
12:00 Pacific Introduction to Name Alignment
12:10 Pacific Navigating Github & the name-alignment-tool
12:20 Pacific Using the name-alignment-tool
12:40 Pacific What do these resolutions actually mean?
13:00 Pacific End


You can find a mp4 recording of the 2023-01-18 event via:

Jan192023-taxon-name-alignment.mp4 from Irene Moon on Vimeo.


To participate in a Data Carpentry workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

The setup instructions for the Data Carpentry Ecology workshops (with R) can be found at the workshop overview site.