Hey @mluerig -
Long form taxonomies are supported through Nomer (a tool that “maps identifiers and names to other identifiers and names”, GitHub - globalbioticinteractions/nomer: maps identifiers and names to other identifiers and names) out of the box.
To generate gbif long form - type the following in your terminal/command line -
nomer ls --include-header gbif
to produce stuff like -
| providedExternalId |
providedName |
relationName |
resolvedExternalId |
resolvedName |
resolvedAuthorship |
resolvedRank |
resolvedCommonNames |
resolvedPath |
resolvedPathIds |
resolvedPathNames |
resolvedPathAuthorships |
resolvedExternalUrl |
| GBIF:1423395 |
Ischnura elegans |
HAS_ACCEPTED_NAME |
GBIF:1423395 |
Ischnura elegans |
(Vander Linden, 1820) |
species |
|
Animalia | Arthropoda | Insecta | Odonata | Coenagrionidae | Ischnura | Ischnura elegans |
GBIF:1 | GBIF:54 | GBIF:216 | GBIF:789 | GBIF:8577 | GBIF:1423281 | GBIF:1423395 |
kingdom | phylum | class | order | family | genus | species |
| | | | | Charpentier, 1840 | (Vander Linden, 1820) |
Ischnura elegans (Vander Linden, 1820) |
other supported taxonomies include, but are not limited to, ITIS, World of Flora Online, Catalogue of Life, DiscoverLife, Paleobiology Database, Mammal Diversity Database and NCBI Taxonomy.
And . . . Nomer uses a versioned snapshots of taxonomic resources to reduce variability due to upgrades or internet outages [1].
See also GitHub - globalbioticinteractions/name-alignment-template: align names with known taxonomic resources and associated re-usable workshop at Big-Bee-Network: 18 January 2023 . The name alignment template is configured to produce name alignments like:
providedExternalId
providedName Adoretus
parseRelation SAME_AS
parsedExternalId
parsedName Adoretus
parsedAuthority
parsedRank
parsedCommonNames
parsedPath
parsedPathIds
parsedPathNames
parsedPathAuthorships
parsedNameSource gbif-parse
parsedNameSourceUrl https://linker.bio,https://zenodo.org/records/10810821/files,https://zenodo.org/records/10045382/files,https://zenodo.org/records/10037817/files,https://zenodo.org/records/8327611/files
parsedNameSourceAccessedAt hash://sha256/d2903d0384a8b8193819b8061c8c4e6fec8cc2f7fe72dc0e91c90c07ba2fe15e
alignRelation HAS_ACCEPTED_NAME
alignedCatalogName itis
alignedExternalId http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=187484
alignedName Adoretus
alignedAuthorship Dejean, 1833
alignedRank genus
alignedCommonNames
alignedKingdomName Animalia
alignedKingdomId ITIS:202423
alignedKingdomAuthorship
alignedPhylumName Arthropoda
alignedPhylumId ITIS:82696
alignedPhylumAuthorship
alignedClassName Insecta
alignedClassId ITIS:99208
alignedClassAuthorship
alignedOrderName Coleoptera
alignedOrderId ITIS:109216
alignedOrderAuthorship Linnaeus, 1758
alignedFamilyName Scarabaeidae
alignedFamilyId ITIS:114493
alignedFamilyAuthorship Latreille, 1802
alignedSubfamilyName Rutelinae
alignedSubfamilyId ITIS:678509
alignedSubfamilyAuthorship MacLeay, 1819
alignedTribeName Adoretini
alignedTribeId ITIS:926256
alignedTribeAuthorship Burmeister, 1844
alignedSubtribeName
alignedSubtribeId
alignedSubtribeAuthorship
alignedGenusName Adoretus
alignedGenusId ITIS:187484
alignedGenusAuthorship Dejean, 1833
alignedSubgenusName
alignedSubgenusId
alignedSubgenusAuthorship
alignedSpeciesName
alignedSpeciesId
alignedSpeciesAuthorship
alignedSubspeciesName
alignedSubspeciesId
alignedSubspeciesAuthorship
alignedPath Animalia | Bilateria | Protostomia | Ecdysozoa | Arthropoda | Hexapoda | Insecta | Pterygota | Neoptera | Holometabola | Coleoptera | Polyphaga | Scarabeiformia | Scarabaeoidea | Scarabaeidae | Rutelinae | Adoretini | Adoretus
alignedPathIds ITIS:202423 | ITIS:914154 | ITIS:914155 | ITIS:914158 | ITIS:82696 | ITIS:563886 | ITIS:99208 | ITIS:100500 | ITIS:563890 | ITIS:914213 | ITIS:109216 | ITIS:112747 | ITIS:678302 | ITIS:114486 | ITIS:114493 | ITIS:678509 | ITIS:926256 | ITIS:187484
alignedPathNames kingdom | subkingdom | infrakingdom | superphylum | phylum | subphylum | class | subclass | infraclass | superorder | order | suborder | infraorder | superfamily | family | subfamily | tribe | genus
alignedPathAuthorships | | | | | | | | | | Linnaeus, 1758 | Emery, 1886 | Crowson, 1960 | Latreille, 1802 | Latreille, 1802 | MacLeay, 1819 | Burmeister, 1844 | Dejean, 1833
alignedNameSource itis
alignedNameSourceUrl https://linker.bio,https://zenodo.org/records/10810821/files,https://zenodo.org/records/10045382/files,https://zenodo.org/records/10037817/files,https://zenodo.org/records/8327611/files
alignedNameSourceAccessedAt hash://sha256/d2903d0384a8b8193819b8061c8c4e6fec8cc2f7fe72dc0e91c90c07ba2fe15e
Big thanks to GBIF, ITIS, World of Flora Online, Catalogue of Life, DiscoverLife, Paleobiology Database, Mammal Diversity Database and NCBI Taxonomy and many other projects for making their taxonomic resource available for re-use online in bulk. With these comprehensive taxonomic structured resources, (fast!) tools like GitHub - globalbioticinteractions/nomer: maps identifiers and names to other identifiers and names, GitHub - ropensci/taxadb: 📦 Taxonomic Database [2], Global Names Resolver [3] can be developed independent of the specific tools and services provided by the taxonomic projects themselves.
Hope this helps provide some perspective,
-jorrit
References
[1] Poelen, J. H. (ed . ) . (2024). Nomer Corpus of Taxonomic Resources hash://sha256/83617875e84bb8ae7ac2a257ad50eb8e82d8935d975f465b8ee8f3a803f72b48 hash://md5/c639d7e3fcd5603f6c48e9d5e6c49672 (0.24) [Data set]. Zenodo. Nomer Corpus of Taxonomic Resources hash://sha256/83617875e84bb8ae7ac2a257ad50eb8e82d8935d975f465b8ee8f3a803f72b48 hash://md5/c639d7e3fcd5603f6c48e9d5e6c49672
[2] Norman KEA, Chamberlain S, Boettiger C. taxadb: A high-performance local taxonomic database interface. Methods Ecol Evol. 2020; 11: 1153–1159. https://doi.org/10.1111/2041-210X.13440
[3] Dmitry Mozzherin. (2023). gnames/gnverifier: v1.1.5 (v1.1.5). Zenodo. gnames/gnverifier: v1.1.5 . See also https://globalnames.org .