Appreciating TaxonWorks Together 2022

07 Oct 2022 - Deborah Paul, Matt Yoder

twt2022 logo139 people joined our 3rd TaxonWorks Together Event. Part conference, part community roundtable, part choose-your-own-adventure unconference, for three days we explored, shared, and learned about TaxonWorks (TW) and from each other as collaborators, all working to make it possible to describe life.

To delve deeper into what topics we covered, please peruse the agenda. Links to meeting minutes are included there. New this year, we’ve uploaded a good portion of the content on to YouTube!

A huge thank you! to all involved in planning, speaking, and engaging – in all the activities. And of course, join us on Wednesdays with your followup-up questions, all topics are welcome.

Getting started.

One never quite knows how many people will register for any event. With the magic of social media and one particular Facebook post, we extended our reach far into the Latin American world. Muchas gracias! With the help of several Species File Group (SFG) members and Jennifer Girón, our participants could ask questions in Spanish and we could answer them (in English and Spanish too). While some who participated know TW well, others joined as first-time explorers. We also noted a richly diverse audience when we asked about the roles they engage in. (see screenshots)

Software AND Community.

Embodied in the philosophy and vision of the Species File Group, and evidenced in the building of the TaxonWorks workbench software, is our goal to serve, support, and engage with those who use the software and those who collaborate in the building of the software. Our TWT2022 sessions highlight our efforts to do this – together.

The Big Picture. Day One.

We started with an Introduction and State of All Things SFG: highlights of 2021+ (Youtube). A great place to start for experienced users and our new folks. From there, we experienced a very quick (fun!) tour of just what’s inside TaxonWorks, see for yourself with the Quick hits video. A blitz of features new and old, including those you might have missed. With all of us now up-to-date, we enjoyed our TaxonWorks Community Speaks session where various community members share their individual/community use cases, their progress, their dreams for TW. With their presentations, you can listen-in too or review their slides. Thanks very much to:

  • Jim Woolley - representing the Universal Chalcidoidea Database
  • Davide Dal Pos - wasps (specifically, Ichneumoninae)
  • Emily Struckhoff - of ticks and interactive keys
  • Brian Fisher - AntWeb
  • Belén Cabrera - Orthoptera Species File
  • Donald Hobern - The Global Lep Index

The TaxonWorks Ecosystem. Day Two.

For a community gathering around a software suite to thrive, they need a system indexed for searching documentation, in which they can both contribute and edit. Framing documentation as a collaborative, we selected software that makes possible. It’s a work-in-progress now developed to the point the whole community (anyone) can add / edit / explore /search / link and we’ve had our first community-committed changes made at TWT2022 just after our quick tour.

For the data and our community to thrive and grow, the information in the database (and related objects like images) need to get out of TaxonWorks. Insect Collections Manager, Tommy McElrath took us on a journey from a TW Collection Object, to getting over 1M records from INHS to GBIF to highlight the local to global process of digitization (Youtube).

Next we explored “Spinoffs”, that is, tools emerging out of the Species File Group connected to but distinct from TaxonWorks itself. In a very exciting moment, we saw the demonstration (and later the same afternoon, use) of our TaxonPages software. What does it do? It provides you with a way to create, customize, and extend your own “Pages” for public view, sharing the data stored inside your TW project database. We discovered we can make public-facing interactive Keys in TW (generated almost magically!) from TW Matrices. We learned it is now possible to generate Taxonomic Catalogs for your TW captured data, and researcher Kojun Kanda shared how he has learned to write / edit existing API scripts that support him getting the data he needs – in the format he needs it in – from his own instance of TW.

poll about writing code n8n software screenshot If you say, “I don’t know how to code”, we learned about “no code” / “low code” tools, specifically n8n. Using this tool, SFG software developer, Geoff Ower shared “Linking it all: A practical exploration of linking Biodiversity Informatics APIs using n8n.” At the SFG we are very excited to note Geoff also submitted this work for the GBIF Ebbe Nielsen Prize 2022. (Oh my goodness Debbie, What’s an API? That’s Application Programming Interface). Notice how our poll shows why tools like these are quite important.

character statesmatrix hub screenshotWe wrapped up day two with our first choose-your-own-adventure (aka TaxonWorks Unconference I). Participants provided topics, then voted on them, and off we went to engage in creating TaxonPages, creating a Matrix in TaxonWorks and then, creating a Key using “distinguish” to publish that key.

Community curation, Growing TaxonWorks. Day 3.

Curious about future TW plans? We started our third day with an overview from Matt about “What’s Next for TaxonWorks in 2023+”. This transitioned into an open session where we collaboratively worked on a prioritization list.

Next, what does a community do to move from one person gathering all related nomenclature and related publications for over 20 years to a community-based sustainable model designed to share expertise and tacit knowledge? Here we learned from the folks collaboratively curating the Universal Chalcidoidea Database (UCD@TW). They shared their experience using the “barbeque” (BBQ) strategy and TW to work on-a-regular-basis both “alone” and “together” to speed up their community collective efforts to catch up (and then keep up) with databasing relevant chalcid nomenclatural data as they prepare for publication. In the recording and through the slides, find out “What’s a BBQ anyway and how is this working for the UCD?”

In the presentation “The 3i Experience: focus on Matrices”, Ph D student Saad A. El-Sonbati offered in-depth insights into his ideas for functions to add to the matrix software. We eagerly gathered many of these ideas in our GitHub repository. Saad is an enthusiastic user of TaxonWorks and we learned more about his efforts in the next event …

With The Student’s View section, Davide Dal Pos, Emily Struckoff, and Saad A. El-Sonbati walked us through their research use cases. We want to know and share where TW supports or could support their work (and where it cannot, too). We were treated to three fabulous examples of TW-in-action.

In 3 Minutes 1 Slide anyone participating in TWT2022 got the chance to share whatever TW-related ideas they wished. Three people put their hand up. First, Megan McCuller, Marine Invertebrate (non-molluscan) Collection Manager, is also a bryophyte researcher. Her use case centers around being able to use TW collaboratively in conjunction with the Specify database at the North Carolina Museum of Natural Sciences in support of her research use case. In “one” slide, she clearly communicated the complexity of what she wants to be able to do given the fact that epibiota are very common in marine invertebrate collections. Sharing and studying these relationships and taxa requires tools making it possible to easily communicate hosts / substrates / and relationships between these taxa for a given specimen.

megan's one slide showing epibiota

Researcher Heidi Hopkins studies the Blattodea. She knows TaxonWorks and Species File software and manages data in 8 Species Files. Her use case highlights what is possible when the researcher can work directly with collections and inside the software for those collections. With a loan of 10 INHS drawers of pinned Blattodea, over the course of year, Heidi imaged and identified specimens, added taxon names needed, and discovered a new species – all while working directly inside TW. Next she’s going to work on the specimens in alcohol. She is excited to note how empowering it is to work in this new, integrated, collaborative: collections + researchers in one workbench. Thanks to both Heidi and to Tommy McElrath, INHS Insect Collection Manager for exemplifying what this collaboration can accomplish.

heidi's slide showing blattodea and images in taxonworks

From Jennifer Girón, Ph D student, we listened as she described an imagined future in which those studying the Entiminae (14K species) work collaboratively in TW to gather literature and specimens in a working community. She envisions harmonization of characters and character-state descriptions via depictions to produce matrices and associated keys. In addition, she sees this TW workbench and community as a way to train and empower students (from anywhere on the planet to codify, to identify, to collaborate and share expertise. Jennifer, like Heidi, stresses how having the tool set up, and showing it in use, can encourage others to join and close the gap between research and collections. jennifer's slide showing her wishes for the Entiminae community and taxonworks

A huge thank you to all the students and those who did “3 minutes 1 slide” to share their work and their vision for both their own research and for their respective communities. These stories help the Species File Group, TW, and the community-at-large to understand where we are, where you want to go, so we can figure out how we might get there!

We wrapped up day 3 with the Species File Group Business Meeting to review our collaboration model and vision for new and existing partners using TaxonWorks and other SFG efforts. Then, we stepped into TaxonWorks Unconference II: where the two topics selected by participants included a Novice Tour of TaxonWorks lead by Deborah Paul, Tommy McElrath, Dmitry Dmitriev, and Using the TaxonWorks API.

So what’s next?

The TWT2022 events and conversations give us a lot of material to review to help guide our prioritization list and enhance our community and software-building engagement. Some ideas that came out of TWT2022 to explore include: - offering a “novice” break-out room at each of our Wednesday meetings (compared to honing in on specific topics such as nomenclature, digitization, or matrices). - engage even more students next year. Their stellar presentations this year inspired all of us, and give us those aha moments for what TW offers them, or could offer them. - documenting our various key use cases so that those considering various software tools can see themselves in a given group (or not) - developing a sort of ambassador system to match experienced users with those whose use-case matches, but they need a mentor, and - encourage people to contribute to the documentation when asked a question, rather than (or in addition to) sending a 1:1 email

We welcome all of you to explore and join our TaxonWorks community and please join us next year for TWT2023. Please see the events page to find out how.