New term proposal: site

[cmungall]

Checklist

• [x] I have reviewed the existing MIxS checklists and extensions that the term does not exist.

Name

sample site

Title

sample_site

Description

A standardized identifier that references an environmental sampling or monitoring site. Examples could be NEON or LTER sites, or stable identifiers for individual plots that are the sites for multiple studies.

A non-exhaustive list of potential identifier systems that could be used:

• https://deims.org, e.g. NEON ABBY site: https://deims.org/0e39569d-ff81-4b78-9c34-b07309504d80
• GAZ (for higher level locations)

Note that DEIMS has extensive well-defined JSON metadata for each site e.g. https://deims.org/api/sites/0e39569d-ff81-4b78-9c34-b07309504d80

Note that where bounding boxes are provided it should be possible to do this from a lookup

More on site modeling and site registries here:

Wohner, C., Peterseil, J., Poursanidis, D., Kliment, T., Wilson, M., Mirtl, M., & Chrysoulakis, N. (2019). DEIMS-SDR – A web portal to document research sites and their associated data. Ecological Informatics, 51, 15–24. https://doi.org/10.1016/j.ecoinf.2019.01.005

· Wohner, C., Peterseil, J., Genazzio, M. A., Guru, S., Hugo, W., & Klug, H. (2020). Towards interoperable research site documentation – Recommendations for information models and data provision. Ecological Informatics, 101158. https://doi.org/10.1016/j.ecoinf.2020.101158

· Wohner, C., Ohnemus, T., Zacharias, S., Mollenhauer, H., Ellis, E. C., Klug, H., Shibata, H., & Mirtl, M. (2021). Assessing the biogeographical and socio-ecological representativeness of the ILTER site network. Ecological Indicators, 127, 107785. https://doi.org/10.1016/j.ecolind.2021.107785

· Wohner, C., Peterseil, J., & Klug, H. (2022). Designing and implementing a data model for describing environmental monitoring and research sites. In Ecological Informatics (Vol. 70, p. 101708). Elsevier BV. https://doi.org/10.1016/j.ecoinf.2022.101708

Short description of pattern or range.

CURIE

Pattern or range syntax

CURIE

Example

deims:0e39569d-ff81-4b78-9c34-b07309504d80

Unit

No response

Requirement

No response

Multivalued

No

Extensions(s)

all environmental

[cmungall]

bioregistry request for ID prefix for DEIMS: https://github.com/biopragmatics/bioregistry/issues/1381

[timalamenciak]

This is a good approach and solves a challenge we've run into with the research site property on Wikidata. Many ecological research sites in Canada are so remote that they would not have named locations. The approach here seems to be registering the sites with DEIMS then linking to the identifier, which is good. It may also be worth simply including the decimal degrees centroid of the research site as a permissible value.

I wonder if this should be multivalued? One study may involve multiple distinct research sites, and thus multiple DEIMS ids.

[only1chunts]

@timalamenciak the geo location decimal degrees should be included as values in the term "geographic location (latitude and longitude)" (aka "lat_lon"). The expected usage of MIxS is at the sample level rather than the project level, so we wouldn't usually expect multiple values for something like a sampling site, however, in order to make the term as useful as possible to everyone (even those wishing to apply it to a project level metadata object) I dont see any reason why it couldn't be multi-valued.

[jfy133]

I just saw this in passing:

I want to ask if this proposal would also account for e.g. an archaeological 'site'?

This would be very useful for the upcoming MInAS extension for ancient DNA samples, however the definition as proposed seems would exclude this.

If you you want to keep it specific to biological monitoring sites, I would suggest possibly renaming the term. site is extremely common terminology in anything 'archaeo-' or palaeo- so I fear it could be misinterpreted by archaeogeneticists.

Conversely, we could reduce the specificty of the term to more than just environmental sampling or monitoring site. However I'm not aware of any good identifier systems for archaeological sites (but I can ask around if it is of interest).

[only1chunts]

@pbuttigieg do you know if the observatory networks (omicBON etc) promote and/or use DEIMS?

[cmungall]

my intent was to be inclusive - if the sample is taken from a named location with shared properties then this could be used