Features
n/a
Improvements
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 catwith 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 catas 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
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 catprovidedExternalId
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
Contributors
dimus and zedomel