Open LienReyserhove opened 6 years ago
in the Alien Plants Belgium list you use the term "invasion stage", but here you say "invasiveness". These are not the same thing. I assume invasiveness comes from WRIMS and TrIAS I is invasion stage. If this is the case then your mapping is fine.
Yes, invasiveness
applies to WRIMS and invasion stage
applies to TrIAS. I agree this is confusing in the table. I will change this.
This list will probably be longer. I filtered on the Belgian locations, but this by using the prefix "belg". This excludes locations like Westerschelde
, De Panne
, etc. (see #3 ). I will update this issue once we have the subset for all Belgian locations.
After selecting on the Belgian locations (country
= BE
), the issue remains more or less the same.
But: to generate the unified checklist, we make a selection based on the following criteria:
occurrenceStatus
=present
,common
,rare
,irregular
establishmentMeans
=introduced
,naturalized
,invasive
,assisted colonization
This has implications for our suggestions to map the WRIMS data to a controlled vocabulary. Some of the taxa in WRIMS will not be selected anyway (e.g. as they have an uncertain occurrenceStatus), even if we change the current WRIMS vocabulary. Other taxa however, should be integrated in the unified checklist but will not be selected unless we change the current WRIMS vocabulary. An overview:
WRIMS OS | WRIMS EM | WRIMS I | needed in unified checklist? | selected based on criteria? |
---|---|---|---|---|
uncertain | origin unknown | not specified | no | no |
uncertain | alien | uncertain | no | no |
doubtful | alien | NA | no | no |
doubtful | NA | NA | no | no |
excluded | alien | NA | no | no |
excluded | NA | NA | no | no |
present | alien | NA | yes | no |
present | origin uncertain | no | no | |
present | NA | NA | no? | no? |
established | alien | invasive | yes | no |
established | alien | not specifed | yes | no |
established | alien | uncertain | yes | no |
reported | alien | not invasive | yes | no |
reported | alien | not specified | yes | no |
reported | alien | of concern | yes | no |
reported | alien | uncertain | yes | no |
This means that we need to change the following vocabs:
occurrenceStatus established
--> present
occurrenceStatus reported
--> present
establishmentMeans alien
--> introduced
With respect to invasiveness: this field should be in description. I will make another issue for that
Perhaps you could explain the problem on Tuesday?
The required mapping I see is:
uncertain
--> doubtful
(or the alternative presence uncertain
)established
--> present
reported
--> present
alien
--> introduced
(or the alternative alien
=> no need to update)origin unknown
--> uncertain
(or the alternative unknown
)origin uncertain
--> uncertain
@bart-v --> what do you think about this suggestion?
I'm OK with this.
But it's a pity you loose so much valuable information, just to make GBIF happy... i.e. "established" says so much more than "present" ...
Thanks @bart-v, and I agree that we loose some information that way. @qgroom is leading a paper to suggest changes to Darwin Core to capture this information better. For established
it would have:
establishmentMeans
: introduced
(same as now)occurrenceStatus
: present
(same as now)degreeOfEstablishment
: established
(new term)I guess we can close this issue then Thanks for the discussion!
To summarize:
occurrenceStatus
in WRIMS to GBIF vocabulary:WRIMS | GBIF |
---|---|
uncertain | doubtful |
doubtful | doubtful |
excluded | excluded |
present | present |
established | present |
reported | present |
establishmentMeans
in WRIMS to GBIF vocabulary:WRIMS | GBIF |
---|---|
origin unknown | uncertain |
origin uncertain | uncertain |
alien | introduced |
This is a special case as we do not integrate this term in the distribution, but in the description extension.
But this is how we translate Invasiveness
in WRiMS to invasion stage
in the description extension on GBIF:
established
--> invasion stage = established
invasion stage
emptyThe latest update of WRiMS did not contain the suggested changes. Rather, it includes even more terms for occurrenceStatus
and some native taxa. @bart-v , could you please go through the suggestions, comment on this and integrate this in the next update of WRiMS?
New terms since the latest updates are indicated in bold
WRiMS | GBIF |
---|---|
Absent | absent |
Detected in invasion pathway | present |
Detected in the wild | present |
doubtful | doubtful |
Eradicated | absent |
Established | present |
Established and expanding | present |
Established and stable | present |
excluded | absent |
In captivity/cultivated | present |
Not specified | doubtful |
present | present |
Recorded in error | doubtful |
Reported | present |
Sometimes present | present |
Uncertain | doubtful |
No new terms for introduced species:
WRIMS | GBIF |
---|---|
origin unknown | uncertain |
origin uncertain | uncertain |
alien | introduced |
But: some taxa have status native
WRIMS | records |
---|---|
Native | 113 |
Native Endemic | 2 |
Native Non-endemic | 3 |
Unless I'm missing something these records should be removed for WRiMS
This term is not yet integrated into the description extension. This is the suggested content (with changes relating to the latest update in bold):
established
, Established and expanding
or Established and stable
--> invasion stage = established
invasion stage
emptyI think TrIAS should do (script) this mapping, if really wanted.
We cannot publish WRiMS data with a GBIF vocab that does not include all the important detailed information provided by our editors. DwC is made for this: extensible via vocabs: so better use them...
OK, we can do the scripting if we need the information.
These records will have a distribution:invalid
flag
This is how the information will look like on GBIF for Claviceps purpurea:
Input record:
term | value |
---|---|
eventDate | 1960 |
occurrenceStatus | Established |
locality | Irish part of the Irish Sea and St. George's Channel |
countryCode | IE |
establishmentMeans | Alien |
locationID | http://marineregions.org/mrgid/25211 |
Invasiveness | Of concern |
source | Nehring, S.; Boestfleisch, C.; Buhmann, A. (...) |
occurrenceRemarks | In the winter of 1960-1961 (...) |
Record on GBIF:
verbatim information:
term | value | |
---|---|---|
locationID | http://rs.tdwg.org/dwc/terms/locationID | http://marineregions.org/mrgid/25211 |
locality | Irish part of the Irish Sea and St. George's Channel | |
source | Nehring, S.; Boestfleisch, C.; Buhmann, A.; Papenbrock, J. (2012). The North American toxic fungal pathogen G3 Claviceps purpurea (Fries) Tulasne is established in the German Wadden Sea. BioInvasions Records. 1(1): 5-10. | |
establishmentMeans | Alien | |
occurrenceRemarks | In the winter of 1960-1961, C. purpurea was detected in Townsend's cord-grass at Dublin Sites | |
eventDate | 1960 | |
occurrenceStatus | Established | |
countryCode | IE | |
Invasiveness | Of concern |
interpreted information:
PRESENT IN IRELAND, HTTP://MARINEREGIONS.ORG/MRGID/25211, IRISH PART OF THE IRISH SEA AND ST. GEORGE'S CHANNEL
Record available though the API:
{ "http://rs.tdwg.org/dwc/terms/locationID": "http://marineregions.org/mrgid/25211", "http://rs.tdwg.org/dwc/terms/locality": "Irish part of the Irish Sea and St. George's Channel", "http://purl.org/dc/terms/source": "Nehring, S.; Boestfleisch, C.; Buhmann, A.; Papenbrock, J. (2012). The North American toxic fungal pathogen G3 Claviceps purpurea (Fries) Tulasne is established in the German Wadden Sea. BioInvasions Records. 1(1): 5-10.", "http://rs.tdwg.org/dwc/terms/establishmentMeans": "Alien", "http://rs.tdwg.org/dwc/terms/occurrenceRemarks": "In the winter of 1960-1961, C. purpurea was detected in Townsend's cord-grass at Dublin Sites", "http://rs.tdwg.org/dwc/terms/eventDate": "1960", "http://rs.tdwg.org/dwc/terms/occurrenceStatus": "Established", "http://rs.tdwg.org/dwc/terms/countryCode": "IE", "http://www.marinespecies.org/traits/Invasiveness": "Of concern" }
@LienReyserhove could you update your previous comment with actual data now that it is published?
approach WRIMS
Currently, the following information is available in the distribution extension of WRIMS (only specified for Belgian species!):
occurrenceStatus (not conform with GBIF vocabulary):
establishmentMeans (not conform with GBIF vocabulary):
Invasiveness (not a DwC term)
approach TrIAS
For occurrenceStatus and establishmentMeans, we strive to use GBIF vocabulary. Information on Invasiveness is integrated under
Invasion Stage
in the description extension (for more information, see https://github.com/trias-project/alien-plants-belgium/issues/60 and https://github.com/trias-project/alien-fishes-checklist/issues/6).Below, I give a full overview of all combinations of occurrenceStatus, establishmentMeans and Invasiveness in WRIMS, with an attempt to translate it to the TrIAS vocabulary:
(OS = occurrenceStatus, EM =establishmentMeans, I = invasiveness, IS = invasion stage)