0.5.10
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 like @ljwalker for suggesting Nomer's support for WoRMS.
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 #81
- upgrade to globi-lib v0.25.19
- attempt to upgrade to GBIF name-parser 3.12.0; related to globalbioticinteractions/globalbioticinteractions#968
Bug Fixes
- allow for schema column type [path.kingdom.name] to populate value ev…
…en though no path ids are available; related to #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
