Data guidelines for checklists - inbo/vlaams-biodiversiteitsportaal GitHub Wiki
Note: these recommendations are mostly for thematic and regional checklists, not taxonomic descriptions.
Terms
| Term | Status |
|---|---|
| taxonID | Required |
| scientificNameID | Share if available * |
| acceptedNameUsageID | Do not use |
| parentNameUsageID | Do not use |
| originalNameUsageID | Do not use |
| nameAccordingToID | Do not use |
| namePublishedInID | Do not use |
| taxonConceptID | Do not use |
| scientificName | Required |
| acceptedNameUsage | Do not use |
| parentNameUsage | Do not use |
| originalNameUsage | Do not use |
| nameAccordingTo | Do not use |
| namePublishedIn | Do not use |
| namePublishedInYear | Do not use |
| higherClassification | Do not use |
| kingdom | Required |
| phylum | Share if available |
| class | Share if available |
| order | Share if available |
| family | Share if available |
| genus | Share if available |
| subgenus | Do not use |
| specificEpithet | Do not use |
| infraspecificEpithet | Do not use |
| taxonRank | Required |
| verbatimTaxonRank | Recommended * |
| identificationQualifier | Recommended * |
| verbatimIdentification | Recommended * |
| scientificNameAuthorship | Do not use |
| vernacularName | Share if available |
| nomenclaturalCode | Do not use |
| taxonomicStatus | Do not use |
| nomenclaturalStatus | Do not use |
| taxonRemarks | Do not use |
* Conditional, see Details section
Details
taxonID
Should be globally unique and preferably stable. GBIF uses the taxonID to assess if a (re)published taxon is a new one or one they already have. We therefore strongly recommend to choose a taxonID that is as globally unique and stable as possible. If such a taxon identifier is not present in the source data or the identifiers used there can easily change over time (e.g. numbered rows), we recommend generating taxonIDs in the mapping script.
Suggested components to combine as input for taxonID:
- dataset shortname
- scientific name
- kingdom
The scientific name and kingdom can be used as input for a hash function. This function creates a randomized code of fixed length from an input value. For a given input value, the code will always be the same and unique.
Some examples using the hash function:
alien-plants-belgium:taxon:0005624db3a63ca28d63626bbe47e520(input: shortnamealien_plants_belgium+ reference to taxon core (taxon) + randomized code using scientific nameAchillea filipendulina Lam.and kingdomplantaeas inputalien-fishes-checklist:taxon:dec8ee68b3fae146c056b4972e3e6b83(input: shortnamealien_fishes_checklist+ reference to taxon core (taxon) + randomized code using scientific nameAcipenser baeriand kingdomanimaliaas inputOther examples of globally unique identifiers:
urn:lsid:gbif.org:usages:32567http://species.gbif.org/abies_alba_1753
scientificNameID
If identified organism occurs in marine or brackish environment, it's relevant to technically facilitate uptake in OBIS by filling in its unique persistent identifier from the World Register of Marine Species (WoRMS) in urn format. For instance, for this occurrence of Ensis ensis (https://www.gbif.org/occurrence/3024789732), its WoRMS urn is filled in (cf. https://www.marinespecies.org/aphia.php?p=taxdetails&id=140733):
e.g. urn:lsid:marinespecies.org:taxname:140733
scientificName
The taxon name. For species and genera, we advise to include date and authorship information.
e.g. Pelophylax ridibundus (Pallas, 1771) e.g. Trachemys scripta troostii (Holbrook, 1836) e.g. Pogona (Storr, 1982)
kingdom
The full scientific name of the kingdom in which the taxon is classified.
e.g. Animalia, Plantae
phylum
The full scientific name of the phylum (or division) in which the taxon is classified.
e.g. Chordata, Bryophyta
class
The full scientific name of the class in which the taxon is classified.
e.g. Mammalia, Hepatisopsida
order
The full scientific name of the order in which the taxon is classified.
e.g. Carnivora, Monocleales
family
The full scientific name of the family in which the taxon is classified.
e.g. Felidae, Monoleaceae
genus
The full scientific name of the genus in which the taxon is classified, preferably including authorship information
taxonRank
Required. The taxonomic rank of the most specific name in the scientificName. Recommended vocabulary: http://rs.gbif.org/vocabulary/gbif/rank.xml
verbatimTaxonRank
Recommended if identification is a 'species aggregate' indicating some similar looking species, possibly within the same genus, for instance Weasel/Stoat Mustela nivalis/erminea (https://www.gbif.org/occurrence/5921138995)
e.g. species aggregate
identificationQualifier
Recommended if identification is a 'species aggregate' indicating some similar looking species, possibly within the same genus, for instance Weasel/Stoat Mustela nivalis/erminea (https://www.gbif.org/occurrence/5921138995)
e.g. species aggregate
verbatimIdentification
Recommended if identification is different than the taxon name mentioned in scientificName, especially in case of a 'species aggregate' indicating some similar looking species, possibly within the same genus, for instance Weasel/Stoat Mustela nivalis/erminea, if the genus name Mustela is filled in as the scientificName (https://www.gbif.org/occurrence/5921138995)
e.g. Mustela nivalis/erminea
vernacularName
Share if available, preferrably in Dutch (especially for Flemish data) or English, to enhance clarifying the identification for a wider audience.
e.g. Wezel/Hermelijn