Towards Long-lived Specimens, Data, and Increased Impact
26 May 2023 - Tommy McElrath, Deborah Paul
Insights from our first Vouchering and Digital Data Management Workshop.
Authors (all workshop participants)
- (Lead) Tommy McElrath, INHS Insect Collection, Researcher, Collection Manager, https://orcid.org/0000-0003-0390-4227, Email
- (Lead) Deborah Paul, INHS Species File Group Biodiversity Informatics Liaison, https://orcid.org/0000-0003-2639-7520,Email
- Enrique Santoyo-Brito, INHS NIZ Collections, Fluid Collections Manager, https://orcid.org/0000-0003-3997-3232
- Valeria Trivellone, INHS, PostDoctoral researcher, https://orcid.org/0000-0003-1415-4097
- Sreelakshmi Suresh, Entomology, Graduate Student
- Elizabeth Hrycyna, INHS, Research Technician
- Virginia Roberts, Entomology, Research Technician
- Alison Stodola, INHS Malacology Collection, https://orcid.org/0000-0002-3942-8712
- Ember Clodfelter, Entomology, Graduate Student
- Phillip Hogan, Entomology, Graduate Student, https://orcid.org/0000-0002-6546-272X
- Susan McIntyre, INHS, Assistant Research Scientist
- Kim Drager, INHS, Entomology Department
- Juliana Soto Patiño, INHS Research Assistant, Graduate Student
- Chris Stone, INHS, Entomology Department, Researcher
- Lily Hart, INHS, Entomology, Species File Group
Why this workshop?
With insights and skills gained as a participant at a 4-day iDigBio Workshop: Field to Database in 2015, Tommy McElrath, INHS Insects Collection Manager and researcher, was inspired to create a similar event here (Paul et al 2015). Fast forward to 2023, with Species File Group Informatics Liaison, Deborah Paul as a collaborator, we worked together to design a one-day version highlighting key topics of best (or at least better) practices for vouchering specimens and creating, stewarding, and using data. Additionally, we wanted to engage everyone in an informal needs assessement. We get to discover we have many similar knowledge / skills needs and think about how we can address these strategically as part of capacity development here at PRI and UIUC and with our students, colleagues, and administrators.
Our Vouchering and Data Workshop One Cohort - Front row: (left to right) Valeria Trivellone, Eric Schauber, Daniel Swanson, Virginia Roberts, Lauren Urie, Lily Hart, Elizabeth Hrycyna, Alison Stodola, Kim Drager, Susan McIntyre Back row: Enrique Santoyo-Brito, Dominic Evangelista, Mark Wetzel, the Bison, Chris Stone, Aidan Garrett, Ember Clodfelter, Sreelakshmi Suresh, Deborah Paul, Jason Karakehian, Tommy McElrath, Phillip Hogan. (Not in picture: Juliana Soto)
Many folks from different departments, especially the UIUC Entomology Department and from the Illinois Natural History Survey across disciplines and career stages from student to retired. Folks who attended collect all sorts, including plants, fungi, insects, fish, annelids, ticks, mollusks, and more … and willingly shared their expert insights with everyone. We were pleased to have Eric Schauber, Director of INHS, attend for part of the day to both listen and contribute his insights.
What did we experience?
You can see the broad topics we covered and even see the slides on our workshop repository on GitHub. Intrigued? We are repeating this event on 18 August 2023 and there are still some slots. Now’s the time to sign up so you are sure to get a spot. [See the repository for a link to the sign up sheet - 10 spots left at this writing].
We asked and discussed questions like:
- What does the future you need (for data, for vouchers)?
- Are we collecting and sharing the data that will make our future selves and future researchers like us happy?
- What software are we all using and what software would we like to learn?
- Where do we get these skills and knowledge (i.e. capacity development) that we’re discovering in this workshop?
- What do we know presents challenges and that we need to watch out for when caring for specimens (and related data) to ensure they have a long(er) life? (flat, pinned, or wet!).
Photos by Tommy McElrath and Sreelakshmi Suresh.
What did we learn?
- In the first half of our day, we learned about better ways to collect data in the field, as well as best practices for vouchering, data standards, labeling, and preparing specimens.
- In the second half, over half of attendees were blown away by the usefulness and potential of OpenRefine, a data cleaning and visualizing tool.
- Throughout the day, attendees and presenters alike presented their expertise about all topics covered, showing how much of this day was about sharing experience and knowledge.
- What might come next? What are our needs? Lots of attendees want to learn more about data manipulation tools, especially R, OpenRefine, versioning (e. g. using GitHub), data standards, and relational databases. There was serious energy about doing another Carpentries workshop very soon! (Organizers note that UIUC is a Carpentries member and this gives our university some unique opportunities and a willing and pedagogically-trained group ready to help meet some of these skills / knowledge needs across all departments).
Photos by Tommy McElrath.
From the participant’s point of view
Want to know more about what you can expect? Presentations from Tommy and Debbie were interspersed with hands-on activities. If you check out our shared notes (see the workshop repository for links) you can also learn more. Next, we asked our workshop attendees to share with you what they found compelling / useful..
- It was a great opportunity to think about how I can more effectively collect data in the field and have that preserved along with my specimen data. Most of the participants used similar field labeling methods, but none of us did things exactly the same. I think we all came out of it taking away something new that will improve our science.
- This was a great experience and opportunity to learn more about best practices concerning data collection and specimens preservation. No matter the biological collection similar conservation standards and methods may be applied. Learning directly from experts in the matter was, of course, a plus!
- It was a very useful opportunity to share experiences with colleagues that handle big data in different fields of biological research. This workshop stimulated me to revise the data workflow for my research program. Studying biological interactions, I handle big and high-dimensional data which require the use of established ontologies, shared standards, selected software to share and use data from multiple sources. Finally, my goal is to optimize/minimize human transcription time and error. – Valeria Trivellone.
- Having been a curatorial assistant in an herbarium before, I never quite got the database training I had hoped. This workshop was a great introduction on biological databases and tools. I wish I had known much of the information before, but I’ll make the most of it now! – Sreelakshmi Suresh
- I came away from this workshop better prepared to design and execute field data collection to make it more efficient and complete. I also feel more equipped to clean and merge large datasets that I or others created. This workshop was particularly great because I learned general strategies for data management and insect vouchering that I can apply to a wide variety of research, as well as specific tips that I have already implemented in my work! While the workshop is centered around insects, it is a great learning opportunity for anyone working with biological specimens and data.
- This was a rare opportunity for an early career scientist to discuss the finer details of data collection and management with more experienced professionals. While I usually dread data cleaning, leaving this workshop I was excited to get to work using new tools and ideas brought by both the organizers and fellow attendees. – Virginia Roberts
- This was a well-designed workshop that met each participant where they were and provided useful tools for data success. I loved learning how each of us gather, store, organize, and use data, and I found the refinement software OpenRefine to be particularly helpful.
- My favorite conversation topic from the workshop was about how to make your specimens useful 100+ years in the future. Thinking about what data to collect in the field and how to make specimens useful across disciplines was very interesting and will certainly be useful going forward. As someone who has worked in a few entomological collections, I wish I’d known some of this information before, especially some of the tools to help streamline tedious processes (OpenRefine!), but I look forward to using them in the future. – Ember Clodfelter
- Absolutely a blast taking this workshop. I am convinced that this workshop should be a requirement for entomology students to take some time during their career here at UIUC because of how useful the information was. The crash course on a wide variety of subjects was well structured. – Phillip Hogan
- Coming from a non-entomology background, it was helpful to hear how other researchers collect and use data, even 100 years later. The format of the workshop was also interesting, with plenty of time for group participation, sharing knowledge and experience. I learned about many resources available to me as I embark on my own collections and best practices to make my specimens useful for future researchers.
Your thoughts on these topics?
For what might resonate with you in this post, we would love to know. Please feel free to send Tommy and/or Debbie an email or better yet, post your ideas to our GitHub repository as a “New issue.”
Paul D (formerly at iDigBio, now INHS), Seltmann K (TTD-TCN, AMNH), Michonneau F (FLMNH - iDigBio), Masaki D (USGS - BISON), Soltis P (FLMNH - iDigBio PI), Ellis S (iDigBio), Love K (iDigBio) 2015. Field to Database: Biodiversity Informatics and Data Management Skills for Specimen Based Research Workshop. iDigBio host 2015 March 9 - 12. https://www.idigbio.org/wiki/index.php?title=Field_to_Database
- Shout out to all who helped with collaborative note taking, especially Sreelakshmi Suresh.
- A tasty thanks to INHS’s own Cathy Bialeschki and Eric Shauber. With their input, participation, and some funding, not only did we eat well, our event space, logistics, and overall impact benefitted from their expert help.
- And to Virginia Roberts, workshop participant and artist giving us permission to share this cool image she was inspired to draw at this event.