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

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

0.5.9

Features

• n/a

Improvements

• upgrade to v0.24 of the Nomer Corpus of Taxonomic Resource [1].
• DiscoverLife bee checklist name matching now includes subgenus (among other higher taxonomic names), as well as higher order name matching related to #161 #167 #176 in collaboration with @seltmann

Bug Fixes

• n/a

References

[1] Poelen, J. H. (ed . ) . (2024). Nomer Corpus of Taxonomic Resources hash://sha256/83617875e84bb8ae7ac2a257ad50eb8e82d8935d975f465b8ee8f3a803f72b48 hash://md5/c639d7e3fcd5603f6c48e9d5e6c49672 (0.24) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.11105453

0.5.8

Features

• n/a

Improvements

• upgrade to globi-libs v0.25.18 related to globalbioticinteractions/name-alignment-template#18 as suggested by @whitfarnum
• update taxon resource indexes to include authorship of higher order taxa
• add support for including columns containing authorship of specific taxonomic ranks using "dot" notation:

To specify output schema with authorship of specific rank (e.g., kingdom), you can say:

nomer.append.schema.output=[{"column":0,"type":"path.kingdom.id"},{"column": 1,"type":"path.kingdom.name"},{"column": 2,"type":"path.kingdom.authorship"}]

and run

echo -e "\tEnhydra lutris"\
 | nomer append --properties my.properties --include-header pbdb\
 | mlr --itsvlite --oxtab cat

to produce:

providedExternalId              
providedName                    Enhydra lutris
relationName                    HAS_ACCEPTED_NAME
resolvedPath.kingdom.id         PBDB:1
resolvedPath.kingdom.name       Eukaryota
resolvedPath.kingdom.authorship É. Chatton 1925

Bug Fixes

• n/a

0.5.7

Features

• n/a

Improvements

• upgrade to Poelen, J. H. (ed . ) . (2024). Nomer Corpus of Taxonomic Resources hash://sha256/d2903d0384a8b8193819b8061c8c4e6fec8cc2f7fe72dc0e91c90c07ba2fe15e hash://md5/70645090fdecba640b50577e2a6f2342 (0.23) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10810821 related to @zedomel #86
• make specifying matcher mandatory, removing default matcher related to @mielliott #173
• update Relation Ontology mappings to incorporate https://github.com/oborel/obo-relations/releases/tag/v2024-02-13 by @anitacaron

Bug Fixes

• n/a

0.5.6

Features

• n/a

Improvements

• upgrade to Poelen, J. H. (ed . ) . (2023). Nomer Corpus of Taxonomic Resources hash://sha256/05d79ed0c00e07032d053663a8cfdcf24ba7b5aed651721d5e99659e4db94131 hash://md5/ad1d8ce1800e536f4a205ec47167c6ad (0.19) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10037817

Bug Fixes

• n/a