0.5.5

Features

• n/a

Improvements

• add https://linker.bio as preston remote to offload calls to Zenodo and avoid hitting Zenodo API rate limits ; 0b05678
• add support for relations beyond SAME_AS when using nomer replace command #163

Bug Fixes

• remove doubles quotes from World of Flora Online species name indexes; related to #164 @seltmann
• add genus in taxonomic path of DiscoverLife Bee checklist; related to #165 @seltmann

0.5.4

Features

• n/a

Improvements

• upgrade to:

Poelen, Jorrit H. (ed.). (2023). Nomer Corpus of Taxonomic Resources hash://sha256/12051b8aa59930d6561a3ed46b7cf3f67a31a98445a457d78894f6b8a8e81641 hash://md5/1ff6b3628d7afc15b882cc0c9b1c3815 (0.18) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8326175

• update configuration to enable faster indexing of Catalog of Life to help facilitate workflows like those described in #162 by @whitfarnum

Bug Fixes

n/a

0.5.3

Features

• n/a

Improvements

• n/a

Bug Fixes

• allow for re-use of "old" catalogue of life pre-processed indexes #162 @whitfarnum - newer catalogue of life indexes support a prefix that accounts for the version of the catalogue of life: catalogue of life taxon ids are only defined in the context of a specific version, even though they may appear to be consistent across versions.

0.5.2

Features

• n/a

Improvements

• support TSN prefix for ITIS taxon ids to support their usage in https://github.com/mammalbase/database of @karilint . See also globalbioticinteractions/globalbioticinteractions#915

Example 1.

echo "tsn:946010"\
 | nomer append --include-header itis\
| mlr --itsvlite --oxtab cat

yields

providedExternalId      tsn:946010
relationName            HAS_ACCEPTED_NAME
resolvedExternalId      ITIS:946010
resolvedName            Rhinolophus sinicus
resolvedAuthorship      K. Andersen, 1905
resolvedRank            species
resolvedCommonNames     
resolvedPath            Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Chiroptera | Yinpterochiroptera | Rhinolophoidea | Rhinolophidae | Rhinolophus | Rhinolophus sinicus
resolvedPathIds         ITIS:202423 | ITIS:914154 | ITIS:914156 | ITIS:158852 | ITIS:331030 | ITIS:914179 | ITIS:914181 | ITIS:179913 | ITIS:179916 | ITIS:179925 | ITIS:179985 | ITIS:945840 | ITIS:945842 | ITIS:631242 | ITIS:631260 | ITIS:946010
resolvedPathNames       kingdom | subkingdom | infrakingdom | phylum | subphylum | infraphylum | superclass | class | subclass | infraclass | order | suborder | superfamily | family | genus | species
resolvedPathAuthorships 
resolvedExternalUrl     http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=946010

Bug Fixes

• n/a

0.5.1

Features

• n/a

Improvements

• upgrade to GloBI libs v0.25.7 https://github.com/globalbioticinteractions/globalbioticinteractions/releases/tag/0.25.7
• upgrade discoverlife bee checklist via [1] as suggested by @seltmann
• prefix Catalogue of Life ids with their datasetKey as suggested by @mdoering in CatalogueOfLife/general#98; see also #159

Bug Fixes

• n/a

References

[1] Poelen, Jorrit H. (2023). Nomer Corpus of Taxonomic Resources hash://sha256/ed9f35887419d44ad294b4225fed0a9113ac68ca5314c4b6b009709fc1698898 hash://md5/cd316b81c3a6626cc9c9c07c8b8b3872 (0.17) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8290342

0.5.0

Features

n/a

Improvements

*upgrade to Preston lib v0.7.1

Bug fixes

• update wfo endpoint configuration
• allow content retrieval via most recent alias through anchored preston achives bio-guoda/preston#252

0.4.12

Features

n/a

Improvements

• for now, use existing name relation has_unchecked_name when taxon status is [unchecked]; related to #100 (comment) ; fyi @jtmiller28
• upgrade discoverlife bee checklist
• make WFO label matching case insensitive
• update batname external urls
• update WFO backbone endpoint as suggested by @WUlate in #100
• upgrade to:

Poelen, Jorrit H. (2023). Nomer Corpus of Taxonomic Resources hash://sha256/0e9bc57bc082b58a2c7a509bb73362b258ec8ddfc6664898e25c639786413fda hash://md5/91dd844e787ffae8f0a2bbb8c1f29192 (0.15) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8124478

Bug fixes

• prevent configuration error in offline ITIS service (ef19ed2)

0.4.11

Features

n/a

Improvements

n/a

Bug fixes

• match discoverlife species names when subgenus is not specified, but provided by discoverlife (#149) @jtmiller28

0.4.10

Features

n/a

Improvements

• upgrade to Nomer Corpus to: Poelen, Jorrit H. (2023). Nomer Corpus of Taxonomic Resources hash://sha256/6dc0ab2adbba30dd9bb430f317d0a050585e5c2ebb4e8a932331d3c9f0428d17 hash://md5/296e40ecc206af0a5972009e226544db (0.13) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7693423
• upgrade to recent version of Ascher, J. S. and J. Pickering. 2022. Discover Life bee species guide and world checklist (Hymenoptera: Apoidea: Anthophila). http://www.discoverlife.org/mp/20q?guide=Apoidea_species. cc @jtmiller28 related to #149 .
• make Discover Life support configurable and accessible via Nomer's Corpus of Taxonomic Resources (#80)
• use sha256 hash anchor to integrate Nomer's Corpus of Taxonomic Resources
• use matcher names / provenance to indicate the name source globalbioticinteractions/name-alignment-template#6 .
• include 2023-01-30 copy of https://github.com/plazi/treatments-rdf

Bug fixes

n/a

0.4.9

Features

• add initial support for Paleobiology Database via pbdb matcher. globalbioticinteractions/name-alignment-template#9 @ljwalker @tkarim @markuhen

Example usage:

echo -e "\tTyrannosaurus rex"\
| nomer append --include-header pbdb\
| cut -f1-6

produced:

providedExternalId	providedName	relationName	resolvedExternalId	resolvedName	resolvedAuthorship
	Tyrannosaurus rex	HAS_ACCEPTED_NAME	PBDB:54833	Tyrannosaurus rex	H. F. Osborn 1905

• add initial support for Mammal Diversity Database via mdd matcher. (#141) @n8upham
  Example usage:

echo -e "\tHomo sapiens" \
| nomer append --include-header mdd\
 | cut -f1-6\
 | mlr --itsvlite --omd cat

providedExternalId	providedName	relationName	resolvedExternalId	resolvedName	resolvedAuthorship
	Homo sapiens	HAS_ACCEPTED_NAME	https://www.mammaldiversity.org/explore.html#genus=Homo&species=sapiens&id=1000718	Homo sapiens	Linnaeus, 1758

Improvements

• upgrade to GloBI lib 0.25.5
• upgrade to Nomer Corpus to:
  Poelen, Jorrit H. (2023). Nomer Corpus of Taxonomic Resources hash://sha256/b42923293cebab084517099670cf0b50ad1cce3066286c959644d950b43d7e1b hash://md5/70cbe32ac5ae87c4f70bc5277626cf8c (0.11) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7574586

Bug fixes

n/a