Extended Specimens

in Symbiota Portals

Biodiversity specimens are more than just preserved organisms in physical places; they represent complex networks of interconnected data and, often, related specimens, samples, or concepts. This idea is recently referred to as the Extended Specimen concept (Webster 2017; Nelson and Ellis 2018; Lendemer et al. 2020), and a great challenge for the modern era of digitization remains to integrate specimens with all their related data in an accessible, interoperable way.

Symbiota supports management of extended specimens in several ways:

  • Traits – traits of individual specimen occurrences can be scored or codified in Symbiota portals using a suite of trait-scoring tools. A vocabulary of traits and states must be integrated into the portal by a portal administrator to be available for all users, which may require discussion within the portal community. See Trait Scoring Tools in Symbiota Docs. Example record: BSCA2305 (see “Traits” tab).
  • Genetic data – genetic resources derived from specimens can be added via the Linked Resources tab. It is highly recommended to include a stable URL to a genetic repository when reporting linked genetic resources. See Linked Resources in Symbiota Docs. Example record: NEON03SVQ (see “Genetic” tab). 
  • Linked occurrences (incl. duplicates) – samples, specimens, observations, or other occurrences can also be linked to occurrences via the Linked Resources tab. These occurrences can be located within the same Symbiota portal, another portal, or an entirely different resource. See Linked Resources in Symbiota Docs. For botanical specimens, linked occurrences often include specimen duplicates, which can be managed through several tools. See Duplicate Clustering Tools in Symbiota Docs. Example records: NEON03SVQ (linked resource) RSA0470725 (duplicate).
  • Associated taxa – taxa associated with a given occurrence can be linked, even if no physical specimen exists for that taxon (e.g. field observation, iNaturalist, etc.). This can be done through the Linked Resource tab or through the Associated Taxa field. See Linked Resources in Symbiota Docs. Example record: NEON02ZVQ. 
  • Checklists – specimens can be connected to one or many checklists, as vouchers of particular taxa found in particular regions. As of 2023, checklists can be parsed into derivative “children” checklists. See Checklists in Symbiota Docs. Example checklists: Arizona Flora.
  • Datasets – specimens can be linked to research datasets created by portal users. Datasets can be shared with other user groups under read-only or full administrative access. The dataset module can be used in various ways, such as to link specimens to a research project or publication, to request a loan, to print labels, or simply to define a custom Darwin Core Archive download for a research or educational use. See Creating Datasets in Symbiota Docs. Example dataset: Chapman, 2022.
  • Material Sample – specimen occurrences can be linked to subsamples derived from the same individual or specimen lot. Includes data normalization options with controlled vocabularies. See Material Sample in Symbiota Docs. Example record: NEON03SVQ. 
  • Alternative Identifiers – specimen occurrences can be associated with multiple identifiers (e.g. secondary barcodes, deprecated catalog numbers, etc.) beyond the primary identifier. See Additional Identifier Values in Symbiota Docs. Example record: NEON0113M.

Additional features available for use through the database’s backend:

  • Agent Names – disambiguation of collectors and identifiers using unique identifiers (e.g. ORCIDs, WikiData identifiers) using dwc:recordedByID. Complete indexing tools are yet to be developed. 
  • Associated References – ability to associate occurrence records with complete bibliographic information and associated identifiers. Example record: NEON02ZVQ.

Gallery

Select images from the gallery below to view different Symbiota features that support the Extended Specimen.

References

  • Lendemer J et al. 2020. The Extended Specimen Network: A Strategy to Enhance US Biodiversity Collections, Promote Research and Education, BioScience. 70(1):23–30. https://doi.org/10.1093/biosci/biz140
  • Nelson G, Ellis S. 2018. The history and impact of digitization and digital data mobilization on biodiversity research. Philosophical Transactions of the Royal Society B 374: 20170391. https://doi.org/10.1098/rstb.2017.0391
  • Webster, MS. 2017. The Extended Specimen: Emerging Frontiers in Collections-Based Ornithological Research, 1st ed. CRC Press.

Related Resources

Last updated: March 4, 2024