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globalbioticinteractions/nomer: 0.5.15

integration_instructionsResearch softwarekeyboard_double_arrow_right Software 19 Feb 2025Publisher:Zenodo

Authors: José Augusto Salim; Jorrit Poelen;

doi: 10.5281/zenodo.14893840

globalbioticinteractions/nomer: 0.5.15

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Abstract

Features n/a Improvements enable hierarchical matching when providing name and path (part); https://github.com/globalbioticinteractions/nomer/issues/197#issuecomment-2667122515 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 https://github.com/globalbioticinteractions/nomer/issues/196 Example of getting names associated with Enhydra lutris (sea otter) echo -e "\tEnhydra lutris"\ | nomer append --include-header globalnames\ | mlr --itsvlite --omd cat as executed on 2025-02-19, resulted in the table below: providedExternalId providedName relationName resolvedExternalId resolvedName resolvedAuthorship resolvedRank resolvedCommonNames resolvedPath resolvedPathIds resolvedPathNames resolvedPathAuthorships resolvedExternalUrl Enhydra lutris HAS_ACCEPTED_NAME COL:39TWB Enhydra lutris species Eukaryota | Animalia | Chordata | Vertebrata | Gnathostomata | Osteichthyes | Tetrapoda | Mammalia | Theria | Eutheria | Carnivora | Caniformia | Mustelidae | Lutrinae | Enhydra | Enhydra lutris COL:CS5HF | 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 domain | kingdom | phylum | subphylum | infraphylum | parvphylum | megaclass | class | subclass | infraclass | order | suborder | family | subfamily | genus | species https://www.catalogueoflife.org/data/taxon/39TWB Enhydra lutris HAS_ACCEPTED_NAME ITIS:180547 Enhydra lutris species Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Carnivora | Caniformia | Mustelidae | Lutrinae | Enhydra | Enhydra lutris 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 kingdom | subkingdom | infrakingdom | phylum | subphylum | infraphylum | superclass | class | subclass | infraclass | order | suborder | family | subfamily | genus | species http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180547 Enhydra lutris HAS_ACCEPTED_NAME WORMS:242598 Enhydra lutris species Animalia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Carnivora | Caniformia | Mustelidae | Lutrinae | Enhydra | Enhydra lutris WORMS:2 | WORMS:1821 | WORMS:146419 | WORMS:1828 | WORMS:1831 | WORMS:1837 | WORMS:380416 | WORMS:2687 | WORMS:254957 | WORMS:136974 | WORMS:255009 | WORMS:242597 | WORMS:242598 kingdom | phylum | subphylum | infraphylum | megaclass | class | subclass | order | suborder | family | subfamily | genus | species https://www.marinespecies.org/aphia.php?p=taxdetails&id=242598 Enhydra lutris HAS_ACCEPTED_NAME PBDB:46078 Enhydra lutris https://paleobiodb.org/classic/checkTaxonInfo?taxon_no=46078 Enhydra lutris SAME_AS FBC:SLB:SpecCode:69195 Enhydra lutris Species Mammalia | Carnivora | Mustelidae | Enhydra | Enhydra lutris class | order | family | genus | Species https://sealifebase.org/summary/69195 Enhydra lutris HAS_ACCEPTED_NAME GBIF:2433670 Enhydra lutris species Animalia | Chordata | Mammalia | Carnivora | Mustelidae | Enhydra | Enhydra lutris GBIF:1 | GBIF:44 | GBIF:359 | GBIF:732 | GBIF:5307 | GBIF:2433669 | GBIF:2433670 kingdom | phylum | class | order | family | genus | species http://www.gbif.org/species/2433670 Enhydra lutris SAME_AS OTT:949676 Enhydra lutris species | | Eukaryota | Opisthokonta | Holozoa | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Caniformia | Mustelidae | Lutrinae | Enhydra | Enhydra lutris OTT:805080 | OTT:93302 | OTT:304358 | OTT:332573 | OTT:5246131 | OTT:691846 | OTT:641038 | OTT:117569 | OTT:147604 | OTT:125642 | OTT:947318 | OTT:801601 | OTT:278114 | OTT:114656 | OTT:114654 | OTT:458402 | OTT:4940726 | OTT:229562 | OTT:229560 | OTT:244265 | OTT:229558 | OTT:683263 | OTT:5334778 | OTT:392223 | OTT:44565 | OTT:827263 | OTT:348043 | OTT:306281 | OTT:949684 | OTT:949676 no rank | no rank | domain | no rank | no rank | kingdom | no rank | no rank | no rank | phylum | subphylum | subphylum | superclass | no rank | no rank | superclass | no rank | superclass | no rank | class | subclass | no rank | no rank | superorder | order | suborder | family | subfamily | genus | species https://tree.opentreeoflife.org/opentree/ottol@949676 Enhydra lutris SAME_AS WD:Q41407 Enhydra lutris https://www.wikidata.org/wiki/Q41407 Enhydra lutris SAME_AS NCBI:34882 Enhydra lutris species Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Caniformia | Musteloidea | Mustelidae | Lutrinae | Enhydra | Enhydra lutris NCBI:2759 | NCBI:33154 | NCBI:33208 | NCBI:6072 | NCBI:33213 | NCBI:33511 | NCBI:7711 | NCBI:89593 | NCBI:7742 | NCBI:7776 | NCBI:117570 | NCBI:117571 | NCBI:8287 | NCBI:1338369 | NCBI:32523 | NCBI:32524 | NCBI:40674 | NCBI:32525 | NCBI:9347 | NCBI:1437010 | NCBI:314145 | NCBI:33554 | NCBI:379584 | NCBI:3072906 | NCBI:9655 | NCBI:169417 | NCBI:34881 | NCBI:34882 superkingdom | unranked | kingdom | unranked | unranked | unranked | phylum | subphylum | unranked | unranked | unranked | unranked | superclass | unranked | unranked | unranked | class | unranked | unranked | unranked | superorder | order | suborder | superfamily | family | subfamily | genus | species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=34882 Enhydra lutris HAS_ACCEPTED_NAME IRMNG:10198728 Enhydra lutris species Animalia | Chordata | Mammalia | Carnivora | Mustelidae | Enhydra | Enhydra lutris IRMNG:11 | IRMNG:148 | IRMNG:1310 | IRMNG:12116 | IRMNG:104767 | IRMNG:1297077 | IRMNG:10198728 kingdom | phylum | class | order | family | genus | species https://www.irmng.org/aphia.php?p=taxdetails&id=10198728 Enhydra lutris SAME_AS INAT_TAXON:41860 Enhydra lutris species Animalia | Chordata | Vertebrata | Mammalia | Theria | Placentalia | Laurasiatheria | Carnivora | Mustelidae | Lutrinae | Enhydra | Enhydra lutris INAT_TAXON:1 | INAT_TAXON:2 | INAT_TAXON:355675 | INAT_TAXON:40151 | INAT_TAXON:848317 | INAT_TAXON:848320 | INAT_TAXON:848324 | INAT_TAXON:41573 | INAT_TAXON:41770 | INAT_TAXON:526556 | INAT_TAXON:41859 | INAT_TAXON:41860 kingdom | phylum | subphylum | class | subclass | infraclass | superorder | order | family | subfamily | genus | species https://inaturalist.org/taxa/41860 Bug Fixes fix regression (bug) preventing higher order matching; related to https://github.com/globalbioticinteractions/nomer/issues/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

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globalbioticinteractions/nomer: 0.5.15

globalbioticinteractions/nomer: 0.5.15

200 Research products, page 1 of 20

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