How to describe target species?

[niconoe]

In GitLab by @peterdesmet on Sep 8, 2020, 14:04

This issue pivoted to a discussion on how to indicate target species

The current definition of taxonomic coverage is:

Taxonomic coverage for this data package. It is based on a set of unique values from scientific_name field in observations.csv table.

Could this be broadened to allow the inclusion of species that were available for determination (e.g. in a project defined species list) or were considered target species, but did not result in observations? Or should we consider another way to allow the inclusion of target species?

[niconoe]

In GitLab by @kbubnicki on Nov 30, 2020, 11:09

If I understand you correctly you would like to preserve the information about "real zeros" i.e. not recorded species confirmed before to be present in the study area, right? Very good point I would say, but I am not convinced that this should be mixed with the idea of taxonomic coverage. Mainly because this can be confusing for people searching for datasets containing images/videos of particular species or for algorithms doing an automatic data aggregation/harmonization etc For this reason I would not mix these two things. I think this needs more thinking and probably community:feedback?

[niconoe]

In GitLab by @peterdesmet on Nov 30, 2020, 16:30

Ok to keep taxonomic coverage to only those taxa that are included in dataset. :+1: Target species can be mentioned in dataset description anyway. Fine to close this issue.

[niconoe]

In GitLab by @kbubnicki on Nov 30, 2020, 17:48

What about not closing this but leaving marked as community:feedback? I see this as an interesting topic in general.

[niconoe]

In GitLab by @peterdesmet on Nov 30, 2020, 17:51

Ok, but best to update the title of this issue then

[niconoe]

In GitLab by @peterdesmet on Dec 1, 2020, 12:55

changed title from {-Broaden scope of taxonomic coverage to include target species-} to {+How to describe target species?+}

[niconoe]

In GitLab by @kbubnicki on Dec 1, 2020, 15:09

Perfect!

[peterdesmet]

Picking this one up again. Taxonomic scope is intended to list all species in the observations, but that doesn't really tell us much regarding:

1. What species were targeted (if any) and which ones were by catch
2. To what level classifications were made (only target species, sex, life stages, etc.).

I think the latter one is quite difficult to standardize and for publishers to assess at project level. The target species however could be indicated by adding an optional property target=TRUE to taxa in taxonomic coverage. The R package camtraptor could then e.g. include a target column to the observations based on the taxonomic coverage, just like it already does for vernacular names (ping @damianooldoni).

{
      "taxonID": "RQPW",
      "taxonIDReference": "https://www.checklistbank.org/dataset/3LR",
      "scientificName": "Castor fiber",
      "taxonRank": "species",
      "target": true, <--
      "vernacularNames": {
        "en": "Eurasian beaver",
        "nl": "bever"
      }
    },
    {
      "taxonID": "6MB3T",
      "taxonIDReference": "https://www.checklistbank.org/dataset/3LR",
      "scientificName": "Homo sapiens",
      "taxonRank": "species",
      "target": false, <--
      "vernacularNames": {
        "en": "human",
        "nl": "mens"
      }
    },

[damianooldoni]

I agree with you @peterdesmet: it's something to be specified in the taxonomic coverage (metadata) and can be indeed picked up by a package like camtraptor while reading this information from the camtrap datapackage. Indeed, something we do already with some other fields like vernacular names.

[peterdesmet]

Discussed with @kbubnicki. The problem with adding a target=TRUE is twofold:

• It only addresses a small aspect of sampling intend. There's also the spatial and temporal intend and other things that are best described in separate terms borrowed from Humboldt Extension (see #276)
• What do you do when a target=TRUE taxon was not observed. Do you add it to taxonomic scope? In that case, your taxonomic scope no longer describes the data (it's bigger than the data).

When there is a demand for it, it will likely be better to describe targetTaxa in a separate term, listing all target taxa (whether observed or not). That term will then align well with https://tdwg.github.io/hc/terms/#hc:targetTaxonomicScope. For now (1.0), we refer to the free text project description to indicate target taxa.