trias-project/rinse-registry-checklist

🐞 RINSE - Registry of non-native species in the Two Seas region countries

rinse-registry-checklist's Issues

Wrong dates in biological invasions paper

The dates for records of Rhododendron ponticum Linnaeus in the Zieritz et al. (2016) dataset need cleaning: for observance in GB the date is 17634, and for Belgium it is 19204. I assume the latter should be 1904, as this is the date of observance in the Netherlands. However, for GB, I have no clue --> I will contact the authors for this and take 1763 for now.

How to handle infraspecificEpithets

As mentioned in #3, infraspecificEpithet is combined with specificEpithet in species in the source data. Together with the genus, this creates a scientific name we can submit to GBIF for parsing.

The resulting name is fine for animal names, which are written as:

Genus specificEpithet infraspecificEpithet

but not for plant names, where the infraspecific rank has to be known and included in the scientific name

Genus specificEpithet subsp. infraspecificEpithet
Genus specificEpithet var. infraspecificEpithet

Since we do not have the rank of the taxa in this checklist, it is impossible to build proper scientific names for the plants. The best course of action would be:

• To write the names as Genus specificEpithet infraspecificEpithet, even for plants
• To not provide a taxonRank for (plant) infraspecific names
• To not provide a nomenclaturalCode
• To hope that the name matching at GBIF will match with something valid
• To indicate this issue in the metadata

Add eventDate for non-DAISIE records?

The article states:

3. Period of study

Data was collected from 01/06/2012 to 27/02/2014. Collected data correspond to contemporary species records.

I think we should use those dates (maybe years only) for the eventDate? @qgroom @timadriaens?

Add source "data based solely on DAISIE portal" to distribution

For records with the note:

data based solely on DAISIE portal

Add that exact phrasing as source in the distribution extension. It will allow to differentiate between distributions for the same taxon or to exclude those for the unified checklist. Even though it is not the best way to write a source (i.e. not a proper citation), it is referenced as such in the paper (search on "solely") and thus more easily findable. Alternatively, we could use the proper citation:

DAISIE European Invasive Alien Species Gateway (http://www.europe-aliens.org/)

But that doesn't clarify that that it was solely based on those or use the field occurrenceRemarks, but is seems to fit better with source. @qgroom preferences?

nomenclatural code

This field is obligatory, but not available in the raw data. As the raw dataset is a compilation of different datasets and phyla/kingdoms, I would be surprised that one single nomenclatural code could be used. Suggestions?

Add scientific name

The scientific name of a species in RINSE is a compilation of the columns genus and species. To generate the taxonID, we need the full scientific name. However, when I paste genus and species into scientificName, some of the species are rather odd:

Brachyglottis x 'Sunshine'
Cotoneaster x 'Hybridus pendulus'
Triticosecale x
Hosta agg.
Medicago x varia
Larix x marschlinsii hyb.

Just to be sure that I'm generating scientificName correctly by pasting genus and species together. I don't think we should change the content, unless it is horribly wrong.

Extend README

Phylum vs Division

There's this column phylum_devision. As I am an ecologist and not an taxonomist, I kind of forgot what a division exactly is (although I knew that it's a higher level of classification 😅 ). A quick search gave me this answer:

Phylum vs Division Phylum and division are two taxonomic levels that are used in the biological classification of organisms. Both phylum and division occur below kingdom and above class. The main difference between phylum and division is that phylum is a classification level of the animal kingdom whereas division is the alternative classification level to the phylum in the kingdom Plantae and Fungi. Sometimes the term division is used as the lower classification level of the kingdom Protista and kingdom Monera. The kingdom Animalia comprises 36 phyla. The kingdom Plantae comprises 12 phyla, and the kingdom Fungi comprises 7 phyla.

So, can I put all devisions under the Darwin Core term phylum?

Taxon in distribution, not in core

According to the data validator, rinse-checklist:taxon:75b819e73a6106c9e9bc146bda773399 is present in the distribution (with 4 rows), but not in taxon core.

Duplicates in scientific name

It appears that some taxa in the checklist appear twice 😒 (see table bellow for a summary of all duplicated taxa). This is because:

• most duplicated species have contrasting presence information for one country (e.g. Anchusa arvensis). For some of these species, one record has the note "data based solely on DAISIE portal", while the other records lacks this note. In the main article, I found this:

data based solely on DAISIE portal - taxon listed as present by the DAISIE portal but not by any of the other databases consulted; no additional portal was consulted regarding geographical distribution (also see Methods section)

So, does this mean that, in the one case, only the DAISIE portal was consulted, and in the others, all portals were consulted? Which distribution information do we use then? I see that this also affects species presence for Belgium.

• Some duplicated species are assigned to two kingdoms, i.e. Elachista and Acrophyllum dentatum. I can find information that verifies both cases...So if this is information is in fact true, then we will get the same taxonID for both species, which is problematic.

In case of the first problem, I think it is best to contact the authors for advice. In the second problem, I'm not sure what to do. I can generate a taxonID based on the combination of phylum and scientifc name in this case?

phylum_division	class	genus	species	great_britain	france	belgium	netherlands	environment	notes	scientificName
Angiospermae	Eudicotyledoneae	Acrophyllum	dentatum	present	not confirmed	not confirmed	not confirmed	terrestrial	NA	Acrophyllum dentatum
Angiospermae	Eudicotyledoneae	Anchusa	arvensis	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Anchusa arvensis
Angiospermae	Eudicotyledoneae	Anchusa	arvensis	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Anchusa arvensis
Angiospermae	Monocotyledoneae	Avena	sterilis	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Avena sterilis
Angiospermae	Monocotyledoneae	Avena	sterilis	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Avena sterilis
Angiospermae	Monocotyledoneae	Avena	strigosa	present	present	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Avena strigosa
Angiospermae	Monocotyledoneae	Avena	strigosa	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Avena strigosa
Angiospermae	NA	Beta	vulgaris	not confirmed	present	not confirmed	not confirmed	terrestrial	NA	Beta vulgaris
Angiospermae	NA	Beta	vulgaris	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Beta vulgaris
Angiospermae	NA	Brassica	elongata	present	present	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Brassica elongata
Angiospermae	NA	Brassica	elongata	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Brassica elongata
Angiospermae	NA	Chenopodium	berlandieri	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Chenopodium berlandieri
Angiospermae	NA	Chenopodium	berlandieri	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Chenopodium berlandieri
Angiospermae	NA	Chenopodium	strictum	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Chenopodium strictum
Angiospermae	NA	Chenopodium	strictum	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Chenopodium strictum
Angiospermae	Monocotyledoneae	Cynodon	incompletus	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Cynodon incompletus
Angiospermae	Monocotyledoneae	Cynodon	incompletus	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Cynodon incompletus
Angiospermae	Eudicotyledoneae	Epilobium	x novae-civitatis	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Epilobium x novae-civitatis
Angiospermae	Eudicotyledoneae	Epilobium	x novae-civitatis	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Epilobium x novae-civitatis
Angiospermae	NA	Hypericum	hircinum	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Hypericum hircinum
Angiospermae	NA	Hypericum	hircinum	not confirmed	present	not confirmed	not confirmed	terrestrial	NA	Hypericum hircinum
Angiospermae	NA	Lythrum	junceum	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Lythrum junceum
Angiospermae	NA	Lythrum	junceum	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Lythrum junceum
Angiospermae	NA	Mentha	x piperita	present	not confirmed	present	not confirmed	terrestrial	data based solely on DAISIE portal	Mentha x piperita
Angiospermae	NA	Mentha	x piperita	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Mentha x piperita
Angiospermae	Monocotyledoneae	Papaver	atlanticum	present	not confirmed	present	not confirmed	terrestrial	data based solely on DAISIE portal	Papaver atlanticum
Angiospermae	Monocotyledoneae	Papaver	atlanticum	present	not confirmed	present	present	terrestrial	NA	Papaver atlanticum
Angiospermae	NA	Populus	nigra	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Populus nigra
Angiospermae	NA	Populus	nigra	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Populus nigra
Angiospermae	NA	Salix	x sepulcralis	present	present	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Salix x sepulcralis
Angiospermae	NA	Salix	x sepulcralis	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Salix x sepulcralis
Arthropoda	Insecta	Cinara	pini	present	present	not confirmed	present	terrestrial	NA	Cinara pini
Arthropoda	Insecta	Cinara	pini	present	not confirmed	not confirmed	not confirmed	terrestrial	NA	Cinara pini
Arthropoda	Insecta	Elachista	sp.	present	present	present	present	marine	NA	Elachista sp.
Bryophyta	Eudicotyledoneae	Acrophyllum	dentatum	present	not confirmed	not confirmed	not confirmed	terrestrial	NA	Acrophyllum dentatum
Heterokontophyta	Phaeophyceae	Elachista	sp.	not confirmed	not confirmed	not confirmed	present	marine	NA	Elachista sp.
Nematoda	Adenophorea	Xiphinema	rivesi	not confirmed	present	not confirmed	not confirmed	terrestrial	NA	Xiphinema rivesi
Nematoda	Adenophorea	Xiphinema	rivesi	not confirmed	present	not confirmed	not confirmed	terrestrial	NA	Xiphinema rivesi
Pteridophyta	Pteridopsida	Dicksonia	antarctica	present	not confirmed	not confirmed	not confirmed	terrestrial	NA	Dicksonia antarctica
Pteridophyta	Pteridopsida	Dicksonia	antarctica	present	not confirmed	not confirmed	not confirmed	terrestrial	NA	Dicksonia antarctica

Update hybrid taxonRank

All taxa with taxonRank hybrid are hybrid formulas (unlike those in the MAP: trias-project/alien-plants-belgium#39), although they are not all written out as full hybrid formulas. hybrid is not recognized as a taxonRank however. Once we have guidance on how to populate the taxonRank for hybrid formulas we should update this in this dataset.

Taxa:

scientificName
Acaena anserinifolia x inermis
Aconitum napellus x variegatum
Agrostis gigantea x stolonifera
Artemisia verlotiorum x vulgaris
Avena sativa x sterilis
Chenopodium album x amaranticolor
Chenopodium album x hircinum
Chenopodium album x missouriense
Chenopodium album x probstii
Corylus avellana x maxima
Crataegus heterophylla x monogyna
Crocosmia aurea x pottsii
Crocus tommasinianus x vernus
Dianthus caryophyllus x gratianopolitanus
Dianthus gratianopolitanus x plumarius
Dipsacus fullonum x sativus
Epilobium ciliatum x lanceolatum
Festuca arundinacea x Lolium multiflorum
Festuca rubra x Vulpia myuros
Fumaria densiflora x officinalis
Fumaria officinalis x parviflora
Galanthus elwesii x nivalis
Galanthus elwesii x plicatus
Galanthus nivalis x plicatus
Helianthus rigidus x tuberosus
Heracleum mantegazzianum x sphondylium
Juncus inflexus x pallidus
Lupinus arboreus x nootkatensis x polyphyllus
Lysichiton americanus x camtschatcensis
Nothofagus nervosa x obliqua
Oenothera biennis x cambrica
Populus canadensis x jackii
Populus jackii x nigra
Quercus cerris x robur
Rumex conglomeratus x patientia
Rumex cristatus x palustris
Sorbus aucuparia x intermedia
Tripleurospermum inodorum x maritimum
Verbascum blattaria x phoeniceum
Verbascum nigrum x pyramidatum
Verbascum pyramidatum x thapsus

Cleaning steps references

Some feedback needed:

The Zieritz et al. (2016) checklist has a reference column containing numbers. Two things with respect to that:

1. The numbers are separated by comma's and hyphens. The hyphen is used to indicate a sequence, i.e. 1-4 refers to references 1, 2, 3 and 4. We need the latter. I didn't figure out yet how I can generate these sequences in an way that makes the code readable. Thus, I suggest to generate the sequences in the raw data file, rather than performing the cleaning in the R script (which makes it more messy). As this is a dead dataset, I think the cleaning step won't harm.

2. For some species, about 12 reference numbers are provided, which is a lot. Just to be sure, is it really necessary to integrate the full reference? The fields will be full of text, but I guess there's no other way around that right?

Publish under University of Cambridge

The three main authors of the original paper on which this dataset is based, are affiliated with:

Department of Zoology, University of Cambridge, Cambridge, United Kingdom
University of Cambridge, Cambridge, United Kingdom

Which is why we also opted to use University of Cambridge in institutionCode (see #9).

The university is not yet registered with GBIF as a data publisher, but University Museum of Zoology Cambridge is: https://www.gbif.org/publisher/d9ccac00-9bc7-11de-a329-b8a03c50a862

I would:

1. Ask @dbloom and @tucotuco (to ask their contacts) if it would be OK to update https://www.gbif.org/publisher/d9ccac00-9bc7-11de-a329-b8a03c50a862 to the higher level University of Cambridge itself. It won't affect any existing dataset, because none have been published.
2. If 1 doesn't work, ask the authors if it is OK to register under the zoology museum at cam
3. If that is not OK, see if we can make a new University of Cambridge publisher, confusing matters at GBIF
4. If that doesn't work, give up and publish under INBO, which is incorrect

license, rightsHolder and institutionCode

The Neobiota paper is published under the CC BY 4.0 license (https://neobiota.pensoft.net/article/4007/list/8/)

With respect to the data in supplementary material I found the following:

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.

So use http://opendatacommons.org/licenses/odbl/1.0/ for accessRights and license?

change taxonID

Ideally, the taxonID for this checklist should be rinse-registry-checklist:taxon:hash. Now, it's still the old version rinse-checklist:taxon:hash.