0.6.2

Features

n/a

Improvements

• support a 2026 copy of Catalogue of Life; [upgrade to Nomer Corpus of Taxonomic Resources v0.31; Poelen, J. H. (ed . ) . (2026). Nomer Corpus of Taxonomic Resources hash://sha256/f52b268bbabb342bb3e6312bc54e2f6ebe9ef6d2e745a42ee890e9d05537a77b hash://md5/f20ee16f88fa50ec2bc20660896376b6 (0.31) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.18717269 ; related to https://github.com//issues/209 .

Bug Fixes

n/a

0.6.1

Features

• add support for Moure Catalogue by @zedomel via Salim, J. A. (2026). Moure Neotropical Bees Cataogue [Data set]. Zenodo. https://doi.org/10.5281/zenodo.18379586

Improvements

• upgrade to Nomer Corpus of Taxonomic Resources v0.30; Nomer Corpus of… … Taxonomic Resources hash://sha256/bb066cdfa70a4c871fa33c3077d65debcfe1b515826a8d1c2d550afa72d419c1 hash://md5/23de6028974a8c729b4ac21ae87b96a2; fyi @zedomel
• align with most recent RO
• add homebrew install instructions

Bug Fixes

n/a

0.6.0

Features

n/a

Improvements

• generate man pages for subcommands also
• towards supporting homebrew install; similar to bio-guoda/preston#348
• upgrade to globi libs 0.28.8; related to #202

Bug Fixes

n/a

0.5.17

Features

n/a

Improvements

• upgrade Nomer Corpus of Taxonomic Resources v0.28 #200 @KatjaSchulz . See also:

Schulz, K. (2025). EOL Dynamic Hierarchy version 2.2.6 [Data set]. Zenodo. https://doi.org/10.5281/zenodo.15399237

and

Poelen, J. H. (ed . ) . (2025). Nomer Corpus of Taxonomic Resources hash://sha256/43450c358a666eb5cba6a16aed4e855887bb36b61dd6360b713529fd3d7a1f75 hash://md5/cba513e77093c9cc46312126bcb193e6 (0.28) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.15596413

Bug Fixes

n/a

0.5.16

Features

• add rpm packaging in addition to deb and standalone jar.

Improvements

• allow for multiple matchers to be used in a single append command (big thanks to @zedomel !)

echo -e "\tEnhydra lutris"\
 | nomer append col itis\
 | mlr --itsvlite --oxtab cat

now produces both col and itis matches, whereas previously, only the first (e.g., col) match was listed

providedExternalId      
providedName            Enhydra lutris
relationName            HAS_ACCEPTED_NAME
resolvedExternalId      COL:39TWB
resolvedName            Enhydra lutris
resolvedAuthorship      (Linnaeus, 1758)
resolvedRank            species
resolvedCommonNames     
resolvedPath            Biota | Animalia | Chordata | Vertebrata | Gnathostomata | Osteichthyes | Sarcopterygii | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Carnivora | Caniformia | Mustelidae | Lutrinae | Enhydra | Enhydra lutris
resolvedPathIds         COL:5T6MX | COL:N | COL:CH2 | COL:8V4V3 | COL:8V4V5 | COL:8VVWB | COL:8VSMX | COL:9CK8W | COL:8VLBH | COL:6224G | COL:924GT | COL:LG | COL:B6L7F | COL:4CT | COL:CZT | COL:628LJ | COL:62RW6 | COL:39TWB
resolvedPathNames       unranked | kingdom | phylum | subphylum | infraphylum | parvphylum | gigaclass | megaclass | superclass | class | subclass | infraclass | order | suborder | family | subfamily | genus | species
resolvedPathAuthorships |  |  |  |  |  |  |  |  | Linnaeus, 1758 | Parker & Haswell, 1897 | Gill, 1872 | Bowdich, 1821 | Kretzoi, 1938 | Fischer, 1817 | Bonaparte, 1838 | Fleming, 1822 | (Linnaeus, 1758)
resolvedExternalUrl     https://www.catalogueoflife.org/data/taxon/39TWB

providedExternalId      
providedName            Enhydra lutris
relationName            HAS_ACCEPTED_NAME
resolvedExternalId      ITIS:180547
resolvedName            Enhydra lutris
resolvedAuthorship      (Linnaeus, 1758)
resolvedRank            species
resolvedCommonNames     
resolvedPath            Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Carnivora | Caniformia | Mustelidae | Lutrinae | Enhydra | Enhydra lutris
resolvedPathIds         ITIS:202423 | ITIS:914154 | ITIS:914156 | ITIS:158852 | ITIS:331030 | ITIS:914179 | ITIS:914181 | ITIS:179913 | ITIS:179916 | ITIS:179925 | ITIS:180539 | ITIS:552303 | ITIS:180545 | ITIS:552326 | ITIS:180546 | ITIS:180547
resolvedPathNames       kingdom | subkingdom | infrakingdom | phylum | subphylum | infraphylum | superclass | class | subclass | infraclass | order | suborder | family | subfamily | genus | species
resolvedPathAuthorships |  |  |  |  |  |  | Linnaeus, 1758 | Parker and Haswell, 1897 | Gill, 1872 | Bowdich, 1821 | Kretzoi, 1938 | Fischer, 1817 | Bonaparte, 1838 | Fleming, 1822 | (Linnaeus, 1758)
resolvedExternalUrl     http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180547

• update RO mappings

Bug Fixes

n/a

0.5.15

Features

n/a

Improvements

• enable hierarchical matching when providing name and path (part); #197 (comment) via @zedomel

Example of selecting Agathis montana the plant, but not Agathis montana the insect -

echo -e "\tAgathis montana\tPlantae"\
 | nomer append --properties nomer.properties --include-header col\
 | mlr --itsvlite --oxtab cat

with nomer.properties being

nomer.schema.input=[{"column":0,"type":"externalId"},{"column": 1,"type":"name"},{"column": 2,"type":"path"}]

produces a NONE match for the insect, and a HAS_ACCEPTED_NAME for the plant with same name Agathis montana

providedExternalId      
providedName            Agathis montana
providedPath            Plantae
relationName            HAS_ACCEPTED_NAME
resolvedExternalId      COL:662TS
resolvedName            Agathis montana
resolvedAuthorship      de Laub.
resolvedRank            species
resolvedCommonNames     
resolvedPath            Biota | Plantae | Tracheophyta | Pinopsida | Pinales | Araucariaceae | Agathis | Agathis montana
resolvedPathIds         COL:5T6MX | COL:P | COL:TP | COL:GG | COL:623FD | COL:6MH | COL:BDV7Y | COL:662TS
resolvedPathNames       unranked | kingdom | phylum | class | order | family | genus | species
resolvedPathAuthorships |  |  |  |  |  |  | de Laub.
resolvedExternalUrl     https://www.catalogueoflife.org/data/taxon/662TS

providedExternalId      
providedName            Agathis montana
providedPath            Plantae
relationName            NONE
resolvedExternalId      COL:6635S
resolvedName            Agathis montana
resolvedAuthorship      Shestakov, 1932
resolvedRank            species
resolvedCommonNames     
resolvedPath            Biota | Animalia | Arthropoda | Insecta | Hymenoptera | Ichneumonoidea | Braconidae | Agathis | Agathis montana
resolvedPathIds         COL:5T6MX | COL:N | COL:RT | COL:H6 | COL:HYM | COL:62255 | COL:7D4 | COL:BJ5YH | COL:6635S
resolvedPathNames       unranked | kingdom | phylum | class | order | superfamily | family | genus | species
resolvedPathAuthorships |  |  |  |  |  |  |  | Shestakov, 1932
resolvedExternalUrl     https://www.catalogueoflife.org/data/taxon/6635S

• upgrade to taxon-graph v0.5.4 Also see

Poelen, J. H. (2025). Global Biotic Interactions: Taxon Graph hash://sha256/0b58753e4ff5519442689d866c0f1d19ffa7d97f917144df1d1cd56ea756921d hash://md5/b23bd0210c88ca10c3e3253091f4fdfa (0.5.4) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.14861926

• update custom patches for batnames for html associated with 2025 version

• implement support @dimus globalnames most recent api; related to #196

Example of getting names associated with Enhydra lutris (sea otter)

echo -e "\tEnhydra lutris"\
 | nomer append --include-header globalnames\
 | head -3\
 | mlr --itsvlite --oxtab cat

as executed on 2025-02-19, resulted in:

providedExternalId      
providedName            Enhydra lutris
relationName            HAS_ACCEPTED_NAME
resolvedExternalId      COL:39TWB
resolvedName            Enhydra lutris
resolvedAuthorship      
resolvedRank            species
resolvedCommonNames     
resolvedPath            Animalia | Chordata | Vertebrata | Gnathostomata | Osteichthyes | Tetrapoda | Mammalia | Theria | Eutheria | Carnivora | Caniformia | Mustelidae | Lutrinae | Enhydra | Enhydra lutris
resolvedPathIds         COL:N | COL:CH2 | COL:8V4V3 | COL:8V4V5 | COL:8VVWB | COL:9CK8W | COL:BMGVD | COL:924GT | COL:LG | COL:B6L7F | COL:4CT | COL:CZT | COL:628LJ | COL:62RW6 | COL:39TWB
resolvedPathNames       kingdom | phylum | subphylum | infraphylum | parvphylum | megaclass | class | subclass | infraclass | order | suborder | family | subfamily | genus | species
resolvedPathAuthorships 
resolvedExternalUrl     https://www.catalogueoflife.org/data/taxon/39TWB

providedExternalId      
providedName            Enhydra lutris
relationName            HAS_ACCEPTED_NAME
resolvedExternalId      ITIS:180547
resolvedName            Enhydra lutris
resolvedAuthorship      
resolvedRank            species
resolvedCommonNames     
resolvedPath            Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Carnivora | Caniformia | Mustelidae | Lutrinae | Enhydra | Enhydra lutris
resolvedPathIds         ITIS:914154 | ITIS:914156 | ITIS:158852 | ITIS:331030 | ITIS:914179 | ITIS:914181 | ITIS:179913 | ITIS:179916 | ITIS:179925 | ITIS:180539 | ITIS:552303 | ITIS:180545 | ITIS:552326 | ITIS:180546 | ITIS:180547
resolvedPathNames       subkingdom | infrakingdom | phylum | subphylum | infraphylum | superclass | class | subclass | infraclass | order | suborder | family | subfamily | genus | species
resolvedPathAuthorships 
resolvedExternalUrl     http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180547

Bug Fixes

• fix regression (bug) preventing higher order matching; related to #197

Example of matching Agathis montana the plant, but not Agathis montana the insect by prefixing the name to be match with Plantae | , the desired higher order taxonomic name.

echo -e "\tPlantae | Agathis montana"\
 | nomer append --include-header col\
 | mlr --itsvlite --oxtab cat

providedExternalId      
providedName            Plantae | Agathis montana
relationName            HAS_ACCEPTED_NAME
resolvedExternalId      COL:662TS
resolvedName            Agathis montana
resolvedAuthorship      de Laub.
resolvedRank            species
resolvedCommonNames     
resolvedPath            Biota | Plantae | Tracheophyta | Pinopsida | Pinales | Araucariaceae | Agathis | Agathis montana
resolvedPathIds         COL:5T6MX | COL:P | COL:TP | COL:GG | COL:623FD | COL:6MH | COL:BDV7Y | COL:662TS
resolvedPathNames       unranked | kingdom | phylum | class | order | family | genus | species
resolvedPathAuthorships |  |  |  |  |  |  | de Laub.
resolvedExternalUrl     https://www.catalogueoflife.org/data/taxon/662TS

providedExternalId      
providedName            Plantae | Agathis montana
relationName            NONE
resolvedExternalId      COL:6635S
resolvedName            Agathis montana
resolvedAuthorship      Shestakov, 1932
resolvedRank            species
resolvedCommonNames     
resolvedPath            Biota | Animalia | Arthropoda | Insecta | Hymenoptera | Ichneumonoidea | Braconidae | Agathis | Agathis montana
resolvedPathIds         COL:5T6MX | COL:N | COL:RT | COL:H6 | COL:HYM | COL:62255 | COL:7D4 | COL:BJ5YH | COL:6635S
resolvedPathNames       unranked | kingdom | phylum | class | order | superfamily | family | genus | species
resolvedPathAuthorships |  |  |  |  |  |  |  | Shestakov, 1932
resolvedExternalUrl     https://www.catalogueoflife.org/data/taxon/6635S

0.5.14

Features

n/a

Improvements

• fix typo as found by @zygoballus in #191 (comment)
• update usage description as inspired by #191
• update examples as suggested by @zygoballus
• add more description of offline enabled taxonomic resources as sugges… …ted by @zygoballus in #191

Bug Fixes

• avoid splitting arguments on whitespaces bio-guoda/preston@d226274
• only attempt to rematch synonyms if alternates are generated; related… … to #188 thanks to @nleguillarme

0.5.13

Features

n/a

Improvements

• make caching more resilient against parallel processed; related to #183
• working towards name-based alignments for EOL; related to #184
• upgrade to Poelen, J. H. (ed . ) . (2024). Nomer Corpus of Taxonomic Resources hash://sha256/b60c0d25a16ae77b24305782017b1a270b79b5d1746f832650f2027ba536e276 hash://md5/17f1363a277ee0e4ecaf1b91c665e47e (0.27) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.12695629

Bug Fixes

n/a

0.5.12

Features

• implement synonymizer using -i/-ii (and similar) suffix permutations for context, see #143 . Big thanks to @n8upham @KatjaSchulz @mdoering and @JelleZijlstra for contributing to this feature.

With this, Plecotus christii is recognized as a synonym of Plecotus christiei even though the matching taxonomy (in this case Wikidata) does not have an explicit mention of this synonym_of relation.

providedExternalId      https://www.mammaldiversity.org/taxon/1005665
providedName            Plecotus christii
relationName            SYNONYM_OF
resolvedExternalId      WD:Q2472925
resolvedName            Plecotus christiei
resolvedAuthorship      
resolvedRank            WD:Q7432
resolvedCommonNames     
resolvedPath            Boreoeutheria | Laurasiatheria | Scrotifera | Apo-Chiroptera | Chiroptera | Microchiroptera | Vespertilionidae | Vespertilioninae | Plecotus | Plecotus christiei
resolvedPathIds         WD:Q132666 | WD:Q27379 | WD:Q7439311 | WD:Q123986694 | WD:Q28425 | WD:Q971343 | WD:Q210358 | WD:Q642437 | WD:Q279869 | WD:Q2472925
resolvedPathNames       WD:Q6054237 | WD:Q5868144 |  | WD:Q713623 | WD:Q36602 | WD:Q5867959 | WD:Q35409 | WD:Q164280 | WD:Q34740 | WD:Q7432
resolvedPathAuthorships |  |  |  |  |  |  |  |  |
resolvedExternalUrl     https://www.wikidata.org/wiki/Q2472925

Improvements

• workaround performance issue with StringUtils.capitalize() as described in #182 .

Bug Fixes

n/a

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