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Minimum Information about any (X) Sequence” (MIxS) specification
https://w3id.org/mixs
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Geo location usage guidance #17

Open only1chunts opened 6 years ago

only1chunts commented 6 years ago

The current description of the geo-location variable is

The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ)

This is fine but... do we (GSC or DarwinCore) supply any advice/guidance on which location should be used for things that have been moved. e.g. plants originally collected in the wild but been grown for many years in a botanical garden somewhere, or zoo animals originally from the wild, or wild fish/coral now kept in aquariums? For metagenome sequences I can see that the current location is appropriate, but for the genome of the sample should we use the original or the transplanted location? Do we need a way to specify which has been given?

pyilmaz commented 6 years ago

We don't have any guidance so far. I remember that this issue was discussed in the context of occurrences in GBIF (tigers in UK). I'm not sure what the outcome of that is. Perhaps @jdeck88 or @tucotuco could comment what their guidance is and we can try to adopt that.

jdeck88 commented 6 years ago

Bob Robbins liked to ask: what is the difference between an ant transporting a leaf to an underground hole and a monkey putting a cat in a box?

Philosophical ponderings aside, Darwin Core has a useful term establishmentMeans (http://rs.tdwg.org/dwc/terms/#establishmentMeans) that indicates how the occurrence (or in our case, sample) became established at the location that is marked by the country, location, or coordinates.

John

On Thu, Jun 21, 2018 at 7:32 AM pyilmaz notifications@github.com wrote:

We don't have any guidance so far. I remember that this issue was discussed in the context of occurrences in GBIF (tigers in UK). I'm not sure what the outcome of that is. Perhaps @jdeck88 https://github.com/jdeck88 or @tucotuco https://github.com/tucotuco could comment what their guidance is and we can try to adopt that.

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ramonawalls commented 5 years ago

If this is still an important term, I suggest adopting the new DwC terms for research and management of alien species. The manuscript is currently under review, but when finalized, the new changes will be:

  1. Introducing a controlled vocabulary for the existing Darwin Core term dwc:establishmentMeans

  2. Promoting the pathway term from the Darwin Core Invasive Species Pathways extension as a new Darwin Core term dwc:pathway

  3. Adopting a new Darwin Core term dwc:degreeOfEstablishment with an associated controlled vocabulary

A lot of effort and community input went into this, so no reason for GSC to reinvent the wheel.

I will update here when the paper is accepted and the standard is updated.

ramonawalls commented 3 years ago

For MIxS 6, we can leave this as is, but work with the MIxS/DwC coordination group to clarify location terms.

This terms is for a place name. We have lat and long terms.

Will need to clarify between where original sample was taken in the wild and where a sample was taken in a lab (if that info is relevant).

@pbuttigieg