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trias-project / unified-checklist

🇧🇪 Global Register of Introduced and Invasive Species - Belgium
https://trias-project.github.io/unified-checklist/
MIT License
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How to add more WRIMS distributions #37

Closed peterdesmet closed 5 years ago

peterdesmet commented 5 years ago

WRIMS distributions need a combination of:

"country": "BE",
"status": "PRESENT"
"establishmentMeans": "INTRODUCED",

... to be selected. Ideally they have temporal information:

"temporal": "2000",

I notice many distributions only have part of the information: e.g. year, but not status. Search for example for "BE" in https://api.gbif.org/v1/species/157131005/distributions: there are 8 distributions for Belgium, but none have all 3 properties and year.

I wonder if we should drop the status field in our selection.

peterdesmet commented 5 years ago

Dropping filter on status present adds 2592 -> 2638 = 46 new taxa overall

qgroom commented 5 years ago

Or perhaps NOT ABSENT would be more future proof.

peterdesmet commented 5 years ago

Brilliant!! Requires an update of the gbif_has_distribution() function, so cannot test right away. Would you also exclude distributions that are defined as DOUBTFUL?

qgroom commented 5 years ago

Yes, ignore DOUBTFUL

peterdesmet commented 5 years ago

Implemented in #39. It's an improvement overall, the only negative effect is that two distributions now lost their years (they had it in RINSE pathways, but not in WRIMS and WRIMS takes precedence).

peterdesmet commented 5 years ago

From https://github.com/trias-project/wrims-checklist/issues/2#issuecomment-483296534, these are the values WRIMS has for:

occurrenceStatus

WRiMS value interpretation by GBIF in unified
Absent ABSENT excluded by filter 👍
Detected in invasion pathway - included 👍
Detected in the wild - included 👍
doubtful DOUBTFUL excluded by filter 👍
Eradicated - should be excluded 👎, but no records for Belgium 👍
Established - included 👍
Established and expanding - included 👍
Established and stable - included 👍
excluded EXCLUDED excluded by filter 👍
In captivity/cultivated -  included 👍
Not specified - (https://github.com/gbif/parsers/issues/16: DOUBTFUL) should be excluded 👎, but no records for Belgium 👍
present PRESENT included 👍
Recorded in error - (https://github.com/gbif/parsers/issues/15: DOUBTFUL) should be excluded 👎, but no records for Belgium 👍
Reported EXCLUDED (https://github.com/gbif/parsers/issues/15: PRESENT) excluded by filter 👎
Sometimes present - included 👍
Uncertain - (https://github.com/gbif/parsers/issues/16: DOUBTFUL) should be excluded 👎

establishmentMeans

WRIMS value GBIF interpretation in unified
Origin unknown  UNCERTAIN not included 👍
Origin uncertain UNCERTAIN not included 👍
Alien INTRODUCED  included 👍
Native  NATIVE not included 👍
Native Endemic - (https://github.com/gbif/parsers/issues/17: ENDEMIC) not included 👍
Native Non-endemic - (https://github.com/gbif/parsers/issues/17: NATIVE) not included 👍
peterdesmet commented 5 years ago

So most of it good, but will report the bold ones to GBIF for better mapping.

peterdesmet commented 5 years ago

@qgroom, are there any other values in https://github.com/trias-project/unified-checklist/issues/37#issuecomment-493006247 that you would map to GBIF vocab (those with a - in column 2)? E.g.:

Eradicated -> ABSENT ?
Established -> ??

If so, I will report them to GBIF

qgroom commented 5 years ago

I'm not total clear on the question, but here is my response anyway...

detected in wild -> PRESENT Established -> PRESENT Established and expanding -> PRESENT Established and stable -> PRESENT

Sometimes present -> IRREGULAR

In captivity/cultivated -> dwc:degreeOfEstablishment category B

peterdesmet commented 5 years ago

https://github.com/gbif/parsers/issues/15 is now resolved, so taxa that are "reported" are now longer excluded. Will rerun pipeline.

@qgroom, your suggestions seem ok, but less important to report to GBIF as they don't effect the pipeline.

peterdesmet commented 5 years ago

Done in https://github.com/trias-project/unified-checklist/commit/7384c21544f80dfbff6d5f01f38ed995227b47f3: 4 taxa added