COS 119-2 - The Symbiota software project: Advancing the integration of biodiversity collections and long-term ecological research data

Abstract: We review new developments for the open source Symbiota software project (https://symbiota.org/ and https://github.com/Symbiota/). Symbiota is a popular platform for community-driven publishing and editing of biodiversity collections data, based on the Darwin Core (DwC) data standard. At present, 1,800 natural history collections manage their data, i.e. 90 million occurrences and 45 million images, in 55 variously themed, regionally to globally situated Symbiota portals. Since 2019, Symbiota is also the platform for publishing sample-based records for the National Ecological Observatory Network, NEON Biorepository (https://biorepo.neonscience.org/portal/). NEON produces 100,000 physical samples and specimens each year that pertain to 70 collections managed by the Biodiversity Knowledge Integration Center (BioKIC) at Arizona State University. Because NEON data are "born" in general alignment with the Ecological Metadata Language (EML), Symbiota's capabilities are being extended to facilitate an increasingly automated, reciprocal integration between two prevalent data standards and cultures related to biodiversity collections and long-term ecological research. The workflow begins with an EML-based manifest module to track shipments and check-in samples and specimens arriving daily, either directly from NEON domains or intermediary contractors. Once samples are checked in, the samples endpoint of the NEON Application Programming Interface (API) is called, and sample-associated metadata is pulled in from the Main NEON data portal (https://data.neonscience.org/) to create individual DwC occurrence records. For many sample types, more data-rich records ("Extended Specimens") can be published that include linkages to related samples (e.g., DNA samples or mammalian ectoparasites), images, field and lab measurements, citations to research products using the specimens, and more. The NEON Biorepository assigns International Generic Sample Numbers (IGSNs) to each sample or specimen, and registers them via the System for Earth Sample Registration (SESAR) API. These globally unique identifiers are then returned and ingested by the main NEON data portal to facilitate periodic sample data re-harvesting, thereby maintaining information synchrony between the NEON Main and Biorepository data portals. For end users, the NEON Biorepository data portal provides occurrence records that are both interoperable with global biodiversity datasets and closely connected to co-collected gene-to-ecosystem level data. These Symbiota extensions are novel and relevant to advancing the integration and interests of other projects and communities that lead sample- and collections-based ecological research, such as the Long-Term Ecological Research Network.