Society for the Preservation of Natural History Collections: "Taking the Long View"

Talks

echinopscis will be presented in two sessions at the forthcoming Society for the Preservation of Natural History Collections (SPNHC) 38th annual meeting hosted by the California Academy of Sciences in San Francisco, US (www.calacademy.org/spnhc-2023).

“Narrowing the gaps” symposium

Logistics

  • Session: Narrowing the Gaps: The role of digital infrastructure in shortening the distance between physical collections and their derivative research products
  • Title: Researchers as digital infrastructure creators: maximising use of digitised specimen data in taxonomic research
  • Authors Nicky Nicolson (K), Eve Lucas (K), Elspeth Haston (E)
  • Session link (for registered participants): virtual.oxfordabstracts.com/#/event/3926/submission/172
  • Location / time (PDT): Hilton: Imperial A 10:30-12:00 Thursday, 1 June, 2023
  • Talk materials: github.com/echinopscis/spnhc-2023-symposium-abstract
  • Cite as: Nicolson, Nicky; Lucas, Eve; Haston, Elspeth (2023): Researchers as digital infrastructure creators: maximising use of digitised specimen data in taxonomic research (SPNHC 2023). figshare. Conference contribution. doi:10.6084/m9.figshare.22922729.v1

Researchers as digital infrastructure creators (SPNHC 2023 presentation) from nickynicolson on Vimeo.

Abstract

Following large scale specimen digitisation initiatives, more specimen-oriented activities (such as grouping, annotation, determination) are likely to transition online. We need to develop collaborative prototypes to enable informed discussion and to properly understand the potential of this move. It is important that the changes we make to speed transmission of information do not have any unintended effects which may inhibit valuable contributions.

We have been developing a prototype system (echinopscis.github.io) to inform discussions between technologists and taxonomic researchers. We propose to discuss topics regarding the transition of activity online with reference to this system, including:

  1. What can we learn from the built environment developed in dedicated specimen collection working spaces? These provide a model for how we need to develop virtual working environments to enable researchers to sort and group specimen images. These groupings reflect hypotheses and are valuable data - so we will need to consider what kinds of visibility and stages of release that we would need to support.
  2. Expert generated links between specimens such as those between duplicates which share a collecting event or specimens which are co-cited in a treatment could be captured and used to seed the network of relationships necessary to deliver the “digital extended specimen” concept. This has great potential but we will need to understand how to enable the creation of these data without overloading already busy people.
  3. How the transition to digital may affect researcher behaviour with specimen artifacts. With physical specimen sheets, researchers are free to make “notes to self” (determinations of the species represented) which remain on the sheet and are subsequently used by others. As we transition to digital working practices, could researchers be inhibited about making these labels immediately world readable? What stages of release might we need to support?
  4. The kinds of information network topologies which could best enable the digital curation of the global corpus of botanical specimens. Whilst biodiversity hotspots tend to be in the global south, historical specimen collections are most often held in the global north. We will outline the potential for the use of federated technologies (aka the “fediverse”) to help mobilise curation events attached to digitised representations of specimens. Could such a system diversify curation and strengthen local networks of expertise?

Democamp

Abstract

In biodiversity informatics, we use technology to mobilise data from sources like field studies, specimens and literature. One key effort is the work that supports species description - an on-going process, as in plants roughly two thousand new species are described each year. These often have narrow distributions and therefore face conservation threats. Accelerating the descriptive process is central to addressing the biodiversity crisis and is a truly global effort - it is therefore essential that we develop tools in open and participatory projects.

This demonstration will showcase work towards “an extensible notebook for open science on specimens” (echinopscis.github.io) based on freely available personal knowledge management software, allowing an expert user to collate the materials necessary to describe new species. The prototype system uses open APIs (application programming interfaces) to access data from digital repositories. The researcher can develop their theories through side by side comparison of multiple specimen images and published descriptions, enabling the comparison and drafting of new species descriptions from linked components in revision controlled markdown documents. These can be passed into rapid data publication pipelines to mobilise data.

We will live demo the tool integrated with an open access bibliographic reference manager (Zotero), retrieving specimen metadata and images from GBIF, marking up material examined sections from published literature, translating complex technical terms using a dictionary and drafting new treatments by referencing specimens.

We aim to open a discussion on lightweight alternatives to traditional species treatment, dataset and document production, building on tools and practices covered by training resources aimed at researchers, such as software, data and author carpentry. Our project aims to support open science, using open access to the data needed to support a researchers areas of study and enabling open publishing of results. We also feel it is important to empower researchers to be “open to choose” how they organise their work - recognising that research is a creative process.