Features

• add initial support for offline matching against World Register of Marine Species [1,2] #148 made possible by Checklist Bank @mdoering and WoRMS @bart-v and many many others.

Example usage:

 echo -e "\tAriopsis felis"\
 | nomer append worms

yields

	Ariopsis felis	HAS_ACCEPTED_NAME	WORMS:158709	Ariopsis felis	(Linnaeus, 1766)	species		Biota | Animalia | Chordata | Vertebrata | Gnathostomata | Osteichthyes | Actinopterygii | Actinopteri | Teleostei | Siluriformes | Ariidae | Ariopsis | Ariopsis felis	WORMS:1 | WORMS:2 | WORMS:1821 | WORMS:146419 | WORMS:1828 | WORMS:152352 | WORMS:10194 | WORMS:843664 | WORMS:293496 | WORMS:154157 | WORMS:154659 | WORMS:158708 | WORMS:158709	| kingdom | phylum | subphylum | infraphylum | parvphylum | gigaclass | superclass | class | order | family | genus | species	|  | Haeckel, 1874 |  | von Zittel, 1879 |  |  |  |  |  | Bleeker, 1858 | Gill, 1861 | (Linnaeus, 1766)	https://www.marinespecies.org/aphia.php?p=taxdetails&id=158709

or via

 echo -e "\tAriopsis felis"\
 | nomer append --include-header worms\
 | mlr --itsvlite --oxtab cat

providedExternalId      
providedName            Ariopsis felis
relationName            HAS_ACCEPTED_NAME
resolvedExternalId      WORMS:158709
resolvedName            Ariopsis felis
resolvedAuthorship      (Linnaeus, 1766)
resolvedRank            species
resolvedCommonNames     
resolvedPath            Biota | Animalia | Chordata | Vertebrata | Gnathostomata | Osteichthyes | Actinopterygii | Actinopteri | Teleostei | Siluriformes | Ariidae | Ariopsis | Ariopsis felis
resolvedPathIds         WORMS:1 | WORMS:2 | WORMS:1821 | WORMS:146419 | WORMS:1828 | WORMS:152352 | WORMS:10194 | WORMS:843664 | WORMS:293496 | WORMS:154157 | WORMS:154659 | WORMS:158708 | WORMS:158709
resolvedPathNames       | kingdom | phylum | subphylum | infraphylum | parvphylum | gigaclass | superclass | class | order | family | genus | species
resolvedPathAuthorships |  | Haeckel, 1874 |  | von Zittel, 1879 |  |  |  |  |  | Bleeker, 1858 | Gill, 1861 | (Linnaeus, 1766)
resolvedExternalUrl     https://www.marinespecies.org/aphia.php?p=taxdetails&id=158709

Improvements

• upgrade to v0.25 of the Nomer Corpus of Taxonomic Resource [3]
• add man doc examples as suggested by @seltmann in https://github.com/globalbioticinteractions/nomer/issues/81
• upgrade to globi-lib v0.25.19
• attempt to upgrade to GBIF name-parser 3.12.0; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/968

Bug Fixes

• allow for schema column type [path.kingdom.name] to populate value ev… …en though no path ids are available; related to https://github.com/globalbioticinteractions/nomer/issues/177

References

[1] WoRMS Editorial Board. (2024). World Register of Marine Species (S. Ahyong, C. Boyko, N. Bailly, J. Bernot, R. Bieler, S. Brandão, M. Daly, S. De Grave, S. Gofas, F. Hernandez, L. Hughes, T. A. Neubauer, & G. Paulay, Eds.; Version 2024-06-01). WoRMS Editorial Board, Belgium. https://doi.org/10.14284/170

[2] Poelen, J. H. (2024). World Register of Marine Species (WoRMS) Repackaged hash://sha256/4e969a1c8243b523b093d3a05fd5f7683479c2919e7d83e8b1383c5e5ef1d4e5 hash://md5/fb7559ce707d11f96a878d8a8a79a661 (0.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.12112610

[3] Poelen, J. H. (ed . ) . (2024). Nomer Corpus of Taxonomic Resources hash://sha256/3361f03229301a339b86779df0d74ed9ab564b1ef98dda4556ed0a0cafc28700 hash://md5/970d771ac2ff45e42a30b5cf88bf6a1b (0.25) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.12117955