standardization of terms

[timadriaens]

we finished standardization of fields invasionStage, introductionPathway, habitat, nativeRange and presence https://docs.google.com/spreadsheets/d/1KJX6QBhv2xmDffYtXGt6FHV41Pm_eQjcUrDqxZxouvQ/edit#gid=0

[timadriaens]

Some explanations of our way of working/assumptions/choices we made:

| = AND The recommended best practice is to separate the values with a vertical bar (' | '). A | B = B | A we use | because it’s the common value denominator in dwca

to be determined by experts = preferably to be complemented and adjusted in the source dataset, or more pragmatically to ask the dataset owner to create a new field with the corresponding standardized terms on top of the fields in their dataset; considering low numbers of records and presumably low effort to complement the data we took this approach sometimes

[timadriaens]

habitat

marine estuarine terrestrial freshwater combinations

if macroinverts = brackish, we assumed they are estuarine (--> based on sampling protocols described in boets et al)

Pathways

based on cbd framework (CBD, 2014. Pathways of introduction of invasive species, their prioritization and management.) . Attention: it's a hierarchical framework.

I attached it in excel format pathways_CBD.xlsx (sorry) in the register, we want to see level 1 and level 2 in one field e.g. “Release - Biocontrol“

fish: AQ, aquaculture; BW, ballast water; AM, active migration; OR, ornamental; AN, angling or bait fish; BC, biological control; UN, unintentional; A, acclimatized; N, naturalized; A*, acclimatized only in restricted areas at cooling water discharges of power plants)

plants [(catalogue):] urban weed → “Transport - stowaway” without further subcategory “etc.” not taken into account “?” → unknown “pathway y?” → not kept “pathway y, pathway x?” → only kept "pathway y" no data (empty) → to be determined by experts wool aliens: Transport - contaminant, Contaminant on animals (except parasites, species transported by host/vector) based on definition of this pathway in catalogue of neophytes in Belgium order or pathways: not taken into account salt: probably not pathway information but rather halophitic character so not taken into account fish → not clear, could be contaminant on fish or rather stowaway in water with fish lots → to be determined by experts Hybridization → considered this not a pathway, should be checked by experts what this is for the 47 spp. concerned (for what purpose/by which means were these hybrids introduced?)

InvasionStage

the 64 spp from MAP noted “inv.”: (definition Manual) Inv. (invasive): naturalized taxa that penetrate and proliferate in (semi-) natural habitats, not necessarily causing damage. Taxa that are found only occasionally or temporarily in (semi-) natural habitats are not considered as such (for instance Coronopus didymus) for some species this seems not correct (e.g. Egeria) for Belgium → we chose established to be correct

fish: "A" & "A*" considered established, even if in secluded warmer water of power plants (cf nile tilapia) → some non-native spp can only maintain populations due to human intervention

macroinvertebrates → considered all species established as they come from live samples in running waters

presence

if present in one region --> present in Belgium (idem marine areas) For the marine, we should cross-check with habitat --> If species is ESTUARINE | MARINE --> present in Flanders

origin (--> change to Native range)

field term: native range, to discriminate between natural range expansion and alien is important, and we don’t want to lose the information on where they naturally occur e.g. species where it is unknown whether they had natural range expansion or were introduced. Therefore, we can have EU in the area of origin (e.g. pontocaspian species, central european spp).

we don’t follow the gisin terms here since they in our opinion represent status there seems to be no corresponding controlled vocabulary in GRIIS for origin

we mapped onto the NOBANIS technical manual terms idea is to link origin with status and to distinguish primarily between species native to other parts of the EU from species from other continents

mapping combinations: “or” → Unknown "and" → Combine

Continents Africa The African continent Antarctica The Antarctic continent Asia Divides Asia from Europe along Ural/Kazakhstan, Black Sea Europe Divides Europe from Asia along Ural/Kazakhstan N. America Canada, USA and Mexico Oceania Australia, New Zealand, Tasmania and a number of small islands S. America All countries on the S. American continent south of Mexico

Oceans Arctic Ocean The ocean surrounding the North Pole Indian Ocean The Ocean south of India to the southern tip of Africa and to the northern tip of Australia N. Atlantic Ocean Upper part of the Atlantic Ocean divided by the equator S. Atlantic Ocean The lower part of the Atlantic Ocean divided by the equator N. Pacific Ocean The upper part of the Pacific Ocean divided by the equator S. Pacific Ocean The lower part of the Pacific ocean divided by the equator Southern Oceans The ocean surrounding the South Pole combinations (also across continents | oceans)

E AF AS-Te --> to be determined by experts (manual of alien plants: mediterranean) E AF AS-Te NAM --> to be determined by experts (manual of alien plants: mediterranean)

Verloove (catalogue of neophytes): For the interpretation of the various areas of origin the continental scheme (level 1) of Brummitt (2001) was followed. The following units are distinguished: Europe (E), Africa (AF), temperate Asia (AS-Te), tropical Asia (AS-Tr), Australasia (AUS), Northern America (NAM) and Southern America (SAM). Some taxa are originally native in more than one continental unit; Mediterranean taxa, for instance, are indicated as “E AF AS-Te”, or pan-American taxa as “AM”, etc. Other taxa are represented in the (sub-) tropics of both the Old and New World; they are indicated as “Trop.”. Still others are of unknown origin (“?”) or arose in cultivation (“Cult.”, for taxa that are of artificial origin). For taxa of presumed spontaneous hybrid origin, no area of origin is provided; they are indicated as “Hybr.”

[peterdesmet]

I have copied the mapping from Google Spreadsheet to this repo: https://github.com/inbo/alien-species-checklist/tree/master/mapping. I made the values lowercase and made sure B | A was changed to A | B. Please no longer update the spreadsheet!

I still have to:

• [x] add presence (as that seems more complicated)
• [x] do the AB=BA check for introductionPathway

[peterdesmet]

All vocabs and mappings have been added to https://github.com/inbo/alien-species-checklist/tree/master/vocabularies

Regarding indicating "Flanders" for estuarine species in WRIMS:

1. The habitat info is not listed in WRIMS, so we have to rely on outside information: what do we choose then?
2. The species could be listed in the other datasets
3. We don't populate coast, BEEZ or BPNS either for marine species potentially not listed in WRIMS.

So, I would leave this as is and keep it to what we have in the sources.