0.5.11

Features

• add initial support for offline matching against Wikidata Taxon Items [1] by upgrading to a newer version of Nomer's Corpus of Taxonomic Resources [2] #181 fyi @Daniel-Mietchen

Example usage:

echo -e "\tElymus repens"\
 | nomer append\
 --include-header wikidata\
 | mlr --itsvlite --oxtab cat

yields

providedExternalId      
providedName            Elymus repens
relationName            HAS_ACCEPTED_NAME
resolvedExternalId      WD:Q276262
resolvedName            Elymus repens
resolvedAuthorship      
resolvedRank            WD:Q7432
resolvedCommonNames     Gewöhnliche Quecke @de | quackgrass @en | niittyjuola @fi | 偃麦草 @zh
resolvedPath            Spermatophytes | Magnoliophyta | Liliopsida | Commelinidae | Cyperales | Poaceae | Pooideae | Triticeae | Elymus | Elymus repens
resolvedPathIds         WD:Q25814 | WD:Q14562931 | WD:Q1147601 | WD:Q1115272 | WD:Q1860104 | WD:Q43238 | WD:Q4662262 | WD:Q148694 | WD:Q1072892 | WD:Q276262
resolvedPathNames       WD:Q3491997 | WD:Q38348 | WD:Q37517 | WD:Q5867051 | WD:Q36602 | WD:Q35409 | WD:Q164280 | WD:Q227936 | WD:Q34740 | WD:Q7432
resolvedPathAuthorships |  |  |  |  |  |  |  |  |
resolvedExternalUrl     https://www.wikidata.org/wiki/Q276262

or via a Wikidata supported taxonomic scheme like ITIS -

echo -e "ITIS:512839"\
  | nomer append --include-header wikidata\
 | mlr --itsvlite --oxtab cat

providedExternalId      ITIS:512839
relationName            SYNONYM_OF
resolvedExternalId      WD:Q276262
resolvedName            Elymus repens
resolvedAuthorship      
resolvedRank            WD:Q7432
resolvedCommonNames     Gewöhnliche Quecke @de | quackgrass @en | niittyjuola @fi | 偃麦草 @zh
resolvedPath            Spermatophytes | Magnoliophyta | Liliopsida | Commelinidae | Cyperales | Poaceae | Pooideae | Triticeae | Elymus | Elymus repens
resolvedPathIds         WD:Q25814 | WD:Q14562931 | WD:Q1147601 | WD:Q1115272 | WD:Q1860104 | WD:Q43238 | WD:Q4662262 | WD:Q148694 | WD:Q1072892 | WD:Q276262
resolvedPathNames       WD:Q3491997 | WD:Q38348 | WD:Q37517 | WD:Q5867051 | WD:Q36602 | WD:Q35409 | WD:Q164280 | WD:Q227936 | WD:Q34740 | WD:Q7432
resolvedPathAuthorships |  |  |  |  |  |  |  |  |
resolvedExternalUrl     https://www.wikidata.org/wiki/Q276262

Improvements

• add support for NCBI Taxonomy equivalent name associations; related to #180
• undo quoting introduced by gbif-parser for now; globalbioticinteractions/globalbioticinteractions#968
• capitalize all lowercase phrases: [homo sapiens] -> [Homo sapiens]

Bug Fixes

n/a

References

[1] Wikidata Community, & Poelen, J. H. (2024). Wikidata Taxon Items in JSON Lines Format hash://sha256/e76276c283090381fc4b3efe28fc61c28f5bf03db0f3743f7178b999ebccada2 hash://md5/967c79ea605fda781129273a9f229eac (0.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.12535891

[2] Poelen, J. H. (ed . ) . (2024). Nomer Corpus of Taxonomic Resources hash://sha256/b959e969ddf4114bd590ec1cdcf7ec572076bd46e2e28e2fee038a3f6d41b9fd hash://md5/8df50c05e1801b526c6cf43535b9ab0b [Data set]. Zenodo. https://doi.org/10.5281/zenodo.12536844