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talk · Thursday 24 September · 16:24–⁠16:36 · SAL A

Mobilizing rich, interoperable, and secure fossil data from underserved collections using Symbiota

Erica Krimmel · Solutions for Research Collection Management Systems Challenges

Recording time 8:50:03–9:01:53Open on Vimeo ↗

Summaries and key moments are machine-produced. Check the recording for the speaker’s exact words.

The short versionTargeted Symbiota enhancements around geological context, taxonomy and relationships make a low-barrier CMS viable for under-resourced fossil collections.

Overview

What this was about

Erika Krimmel described a project (started 2023) to make Symbiota work for fossil collections, which are underrepresented despite Symbiota's popularity with small, under-resourced collections. A new Paleo Data Portal serves as testbed. Enhancements released in Symbiota 3.4 include GBIF GeoTime–based chronostratigraphy entry with auto-populated hierarchy, and staging scripts for stratigraphic and morphology remarks. There is inclusive numerical-time search, a Macrostrat geology map layer (also in georeferencing), and taxonomy sourced from Catalogue of Life XR via ChecklistBank to trace errors. Other additions: default 'FossilSpecimen' basis of record, description fields for material type, and relationships such as part/counterpart and slab-with. Features are documented in Symbiota Docs and a new Paleodata Knowledge Hub, and collections are being onboarded.

Why it matters. It extends the benefits of a widely used, low-cost platform to paleontological collections and improves how geological time data reach GBIF.

Key ideas

In the room

  • Symbiota's pre-2023 paleo module had undocumented custom fields, and geological context was not searchable or exportable publicly.
  • Chronostratigraphic entry now uses a controlled vocabulary aligned with GBIF GeoTime and the International Chronostratigraphic Chart.
  • Search over geological time is inclusive using the vocabulary's numerical timescale, based on researcher feedback.
  • Macrostrat API geology layer is available in map search and georeferencing.
  • Taxonomy is sourced from Catalogue of Life Extended Release in ChecklistBank, allowing tracing and reporting of incorrect higher taxonomy.
  • Collections can set FossilSpecimen as the default basis of record.
  • Relationships document part/counterpart pairs and slab associations with uncatalogued material; links to MorphoSource, MorphoBank and BHL.
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Notable moments

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Transcript

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Programme abstract

Mobilizing rich, interoperable, and secure fossil data from underserved collections using Symbiota

Erica Krimmel

Symbiota software underlies over 70 data portals that are used as collections management systems and data aggregators. While U.S. federal funding catalyzed the use of Symbiota for the digitization of biological collections, Symbiota’s uptake by the paleontological community was previously limited by a lack of functionality for paleontological context data. To address these needs, new software enhancements for managing and publishing fossil specimen data are now available in Symbiota 3.4. Notably, these enhancements implement full functionality for Darwin Core GeologicalContext terms in Symbiota’s public interfaces, at the database level, and for data harvesting. Substantial development efforts have been leveraged to reconfigure the handling of chronostratigraphic information to align output data with GBIF’s GeoTime vocabulary and improve downstream interoperability. These features are complemented by revised documentation available in the Symbiota Docs user information resource and via a new Paleo Data Knowledge Hub. In addition to making these enhancements available to all Symbiota portals, a new Symbiota portal, the “Paleo Data Portal” (PDP), was launched to provide secure infrastructure to fossil collections that have not yet received support through U.S. federal digitization funding, allowing these collections to engage in the global paleo data ecosystem. The PDP currently serves as a testing ground to better understand gaps in existing data standards and digitally available taxonomy to inform a forthcoming “Paleo Roadmap” intended to guide future paleo-related cyberinfrastructure improvements. All Symbiota software enhancements are synergistic with greater community-wide efforts to improve the utility of existing cyberinfrastructure for paleontological research.

Submitted to the conference programme before the talk, so the talk itself may differ.