Update distribution extension with newly adopted terms

[peterdesmet]

This PR updates the distribution extension with the new term concepts as introduced in https://doi.org/10.3897/biss.3.38084 (see also https://github.com/tdwg/dwc/pull/290). They have long been published and people are waiting for them (see e.g. https://github.com/gbif/ipt/issues/1532, also for TrIAS). IMO the current public review of Darwin Core is unlikely to affect the distribution extension, so we should not wait.

TODO once accepted

These are mainly questions for GBIF (@timrobertson100 @MattBlissett)

• [x] To allow for easier review, the changes are currently made without changing the distribution_2020-07-15 file name. Once accepted, a separate file should be made.
• [x] establishmentMeans still has http://rs.gbif.org/vocabulary/gbif/establishment_means.xml as thesaurus. It should be http://rs.tdwg.org/dwc/doc/em/ Will changing this break things?
• [x] degreeOfEstablishment has no thesaurus. It should be http://rs.tdwg.org/dwc/doc/doe/ Will adding this break things?
• [x] pathway has no thesaurus. It should be http://rs.tdwg.org/dwc/doc/pw/ Will adding this break things?
• [x] Remove trailing space in lifeStage definition, eventDate example
• [x] Use single quotes for thesaurus (consistency) in lifeStage, `threatStatus, appendixCITES
• [x] End definition with period (consistency) in endDayOfYear, occurrenceRemarks

Changes

These are mainly of interest to @qgroom @mdoering and @tucotuco

I have slightly adapted the new Darwin Core definitions to fit in the context of the distribution extension. This was also the case for the old definitions.

occurrenceStatus (updated)

old dist: Term describing the status of the organism in the given area based on how frequently the species occurs.

new dist: Statement about the presence or absence of the taxon in the given area.

dwc: A statement about the presence or absence of a Taxon at a Location.

I have dropped the "based on how frequently the species occurs" since we want to nudge people into using present or absent. The linked thesaurus (http://rs.gbif.org/vocabulary/gbif/distribution_status_2020-07-15.xml) still allows all terms (including present and absent). I would leave this as such for now (especially in light of all the discussions regarding occurrenceStatus)

establishmentMeans (updated)

old dist: Term describing whether the organism occurs natively, is introduced or cultivated.

new dist: Statement about whether the taxon has been introduced to the given area and time through the direct or indirect activity of modern humans. Recommended best practice is to use controlled value strings from the controlled vocabulary designated for use with this term, listed at http://rs.tdwg.org/dwc/doc/em/. For details, refer to https://doi.org/10.3897/biss.3.38084

dwc: Statement about whether an organism or organisms have been introduced to a given place and time through the direct or indirect activity of modern humans. Recommended best practice is to use controlled value strings from the controlled vocabulary designated for use with this term, listed at http://rs.tdwg.org/dwc/doc/em/. For details, refer to https://doi.org/10.3897/biss.3.38084

As mentioned, the linked thesaurus is still the old one. Ideally it should be http://rs.tdwg.org/dwc/doc/em/.

degreeOfEstablishment (new)

old dist: -

new dist: The degree to which the taxon survives, reproduces, and expands its range at the given area and time. Recommended best practice is to use controlled value strings from the controlled vocabulary designated for use with this term, listed at http://rs.tdwg.org/dwc/doc/doe/. For details, refer to https://doi.org/10.3897/biss.3.38084

dwc: The degree to which an Organism survives, reproduces, and expands its range at the given place and time. Recommended best practice is to use controlled value strings from the controlled vocabulary designated for use with this term, listed at http://rs.tdwg.org/dwc/doc/doe/. For details, refer to https://doi.org/10.3897/biss.3.38084

pathway (new)

old dist: -

new dist: The process by which the taxon came to be in the given area at the given time. Recommended best practice is to use controlled value strings from the controlled vocabulary designated for use with this term, listed at http://rs.tdwg.org/dwc/doc/pw/. For details, refer to https://doi.org/10.3897/biss.3.38084

dwc: The process by which an Organism came to be in a given place at a given time. Recommended best practice is to use controlled value strings from the controlled vocabulary designated for use with this term, listed at http://rs.tdwg.org/dwc/doc/pw/. For details, refer to https://doi.org/10.3897/biss.3.38084

The example list is non-exhaustive

[MattBlissett]

Thanks Peter. I applied the remaining changes (most importantly, the new vocabularies).

This is now in the sandbox, and can be used by IPTs in test mode.

[peterdesmet]

Excellent, any projection on when this would be available for production IPTs?

[MattBlissett]

https://github.com/gbif/rs.gbif.org/issues/21 is the issue to follow, plus the linked ones. We'll need to update our interpretation to recognize the moved terms (recordedByID etc) before we can make the changes available to production IPTs. I'm not sure what the plan is for that.