DOI: 10.5281/zenodo.12117955
title: Nomer Corpus of Taxonomic Resources hash://sha256/3361f03229301a339b86779df0d74ed9ab564b1ef98dda4556ed0a0cafc28700 hash://md5/970d771ac2ff45e42a30b5cf88bf6a1b

description: This publication contains a Preston archive of resources used by Nomer, a biodiversity name and term translator.

This archive contains specific (repackaged) versions of:

NCBI Taxonomy [1,2], ITIS Taxonomy [3], GBIF Backbone Taxonomy [4,5], Index Fungorum [6], Plazi Treatment Bank [7], the Catalogue of Life [8], the Open Tree of Life Reference Taxonomy [9], the World of Flora Online [10], the Foundational Taxonomic Resources For The Terrestrial Parasite Tracker (TPT) Project [11], Paleobiology Database [12], Mammal Diversity Database [13], Discover Life bee species guide and world checklist [14],  the World Register of Marine Species [15,16], and Encyclopedia of Life's Dynamic Hierarchy [17,18].

Please follow academic citation guidelines when using this corpus.

To clone this archive:

preston clone --anchor hash://sha256/3361f03229301a339b86779df0d74ed9ab564b1ef98dda4556ed0a0cafc28700 --remote https://linker.bio,https://zenodo.org/records/12117955/files,https://zenodo.org/records/11105453/files/,https://zenodo.org/records/10045382/files/,https://zenodo.org/records/10037817/files/,https://zenodo.org/records/8327611/files/,https://zenodo.org/records/10044989/files/ 

After cloning this archive, you should be able to reproduce results below without the --remote https://zenodo.org... part.

This publication has history:

preston history --anchor hash://sha256/3361f03229301a339b86779df0d74ed9ab564b1ef98dda4556ed0a0cafc28700 --remote https://linker.bio,https://zenodo.org/records/12117955/files,https://zenodo.org/records/11105453/files/,https://zenodo.org/records/10045382/files/,https://zenodo.org/records/10037817/files/,https://zenodo.org/records/8327611/files/,https://zenodo.org/records/10044989/files/ 

producing the following provenance graph - 

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<hash://sha256/5a03c765d35a481908e87f518d2c6c801da42183c17002bea1888a8093a4f740> .<hash://sha256/5a03c765d35a481908e87f518d2c6c801da42183c17002bea1888a8093a4f740> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/05d79ed0c00e07032d053663a8cfdcf24ba7b5aed651721d5e99659e4db94131> .<hash://sha256/05d79ed0c00e07032d053663a8cfdcf24ba7b5aed651721d5e99659e4db94131> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/12051b8aa59930d6561a3ed46b7cf3f67a31a98445a457d78894f6b8a8e81641> .<hash://sha256/12051b8aa59930d6561a3ed46b7cf3f67a31a98445a457d78894f6b8a8e81641> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/ed9f35887419d44ad294b4225fed0a9113ac68ca5314c4b6b009709fc1698898> .<hash://sha256/12051b8aa59930d6561a3ed46b7cf3f67a31a98445a457d78894f6b8a8e81641> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/e7130fb557d9aee033ac7147f4d5c4c75f12223dd43e53c7cbb141372f9579cd> .<hash://sha256/ed9f35887419d44ad294b4225fed0a9113ac68ca5314c4b6b009709fc1698898> 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.<hash://sha256/8ba35deafc847f0d5d69d357241a431b7fd9b6f2735189575b2b7168d523caa9> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/f8e4e4d0ed105c6d1b933ddfbcf199dba732560e9dcfdb26569f3050980affa5> .<hash://sha256/6dc0ab2adbba30dd9bb430f317d0a050585e5c2ebb4e8a932331d3c9f0428d17> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/c7f53b23bbeb150dc3454839e25c806229e3414132071b391828bb06400360be> .<hash://sha256/f8e4e4d0ed105c6d1b933ddfbcf199dba732560e9dcfdb26569f3050980affa5> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/a9d3b1a8ca650d8ac8366cba306329e71eb40e6bdc10c594c1b13fd37311a3b8> .<hash://sha256/c7f53b23bbeb150dc3454839e25c806229e3414132071b391828bb06400360be> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/b42923293cebab084517099670cf0b50ad1cce3066286c959644d950b43d7e1b> .<hash://sha256/a9d3b1a8ca650d8ac8366cba306329e71eb40e6bdc10c594c1b13fd37311a3b8> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/b2a6462951bf8ae61cb4108bbab4bcec407bdab8cbe75b38400391930ff5e95b> .<hash://sha256/b42923293cebab084517099670cf0b50ad1cce3066286c959644d950b43d7e1b> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/cbb140a9f0736cba21c0438c3da7917ac4fce470c933e074ba96c838d98ebf4a> .<urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/b2a6462951bf8ae61cb4108bbab4bcec407bdab8cbe75b38400391930ff5e95b> .<hash://sha256/cbb140a9f0736cba21c0438c3da7917ac4fce470c933e074ba96c838d98ebf4a> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/dac5911a81fb605fab012e90c98b37e990a076d77f9264fdb38ec7f379d82108> .<hash://sha256/dac5911a81fb605fab012e90c98b37e990a076d77f9264fdb38ec7f379d82108> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/a0b5570204881a594cf0cca0d4b50c0ddca6f91c2086541516138a400620fb5b> .<hash://sha256/a0b5570204881a594cf0cca0d4b50c0ddca6f91c2086541516138a400620fb5b> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/b3742bf43d9da0a8ed5522659199f47d68d31aaf46c90381190f324c1ac143f2> .<hash://sha256/b3742bf43d9da0a8ed5522659199f47d68d31aaf46c90381190f324c1ac143f2> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/f4e2b9806440d0605f60b81feb9782655291aac2d000c74e4e8fdeb937e29b1d> .<hash://sha256/f4e2b9806440d0605f60b81feb9782655291aac2d000c74e4e8fdeb937e29b1d> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/06a0582443bec6aa00e8fcd78bdd17f821ee29c8c9ab1999577ca5d085b382a3> .<hash://sha256/06a0582443bec6aa00e8fcd78bdd17f821ee29c8c9ab1999577ca5d085b382a3> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/6224f259190590c7aed4784de2b27b3005eea0042ae02993ebf7a0fe30d87137> .<hash://sha256/6224f259190590c7aed4784de2b27b3005eea0042ae02993ebf7a0fe30d87137> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/d58ab1acf350f056a75bde7f4175d14c5e4dfaf0bf20e2eedbb2fb585bdf0822> .<hash://sha256/6224f259190590c7aed4784de2b27b3005eea0042ae02993ebf7a0fe30d87137> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/b7da22af4d24307f3c0c4f288243d5a32c88e7cf1e8cfbed054fd9bb7d777281> .<hash://sha256/d58ab1acf350f056a75bde7f4175d14c5e4dfaf0bf20e2eedbb2fb585bdf0822> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/df5b1b63af4c6e995eddfe6bf36b4ece5475574fd4e871ad1ec0a8b283091e08> .<hash://sha256/b7da22af4d24307f3c0c4f288243d5a32c88e7cf1e8cfbed054fd9bb7d777281> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/df5b1b63af4c6e995eddfe6bf36b4ece5475574fd4e871ad1ec0a8b283091e08> .<hash://sha256/df5b1b63af4c6e995eddfe6bf36b4ece5475574fd4e871ad1ec0a8b283091e08> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/bb6dac6461b66212c5b1826447d7765529ff5cbadeac1915f7c3be9748eda991> .<hash://sha256/df5b1b63af4c6e995eddfe6bf36b4ece5475574fd4e871ad1ec0a8b283091e08> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/bb6dac6461b66212c5b1826447d7765529ff5cbadeac1915f7c3be9748eda991> .<urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/bb6dac6461b66212c5b1826447d7765529ff5cbadeac1915f7c3be9748eda991> .<urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/bb6dac6461b66212c5b1826447d7765529ff5cbadeac1915f7c3be9748eda991> .


This publication contains versions for the following (internet) content aliases (aka URLs, URIs, URNs) as generated via:

preston alias -l tsv --anchor hash://sha256/3361f03229301a339b86779df0d74ed9ab564b1ef98dda4556ed0a0cafc28700 --remote https://linker.bio,https://zenodo.org/records/12117955/files,https://zenodo.org/records/11105453/files/,https://zenodo.org/records/10810821/files/,https://zenodo.org/records/10045382/files/,https://zenodo.org/records/10037817/files/,https://zenodo.org/records/8327611/files/ | cut -f1 | sort | uniq 

resulting in:

col:NameUsage.tsv
col:NameUsage.tsv.gz
http://104.198.143.165/files/WFO_Backbone/_WFOCompleteBackbone/WFO_Backbone.zip
https://download.catalogueoflife.org/col/latest_coldp.zip
https://files.opentreeoflife.org/ott/ott3.3/ott3.3/taxonomy.tsv
https://files.opentreeoflife.org/ott/ott3.4/ott3.4.tgz
https://files.worldfloraonline.org/Files/WFO_Backbone/_WFOCompleteBackbone/WFO_Backbone.zip
https://ftp.ncbi.nlm.nih.gov/pub/pmc/PMC-ids.csv.gz
https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
https://github.com/bio-guoda/preston/releases/download/0.3.9/preston.jar
https://github.com/bio-guoda/preston/releases/download/0.4.4/preston.jar
https://github.com/globalbioticinteractions/globi-taxon-names/raw/main/non-taxon-words.txt
https://github.com/globalbioticinteractions/globi-taxon-names/raw/main/taxon-name-mapping.csv
https://github.com/globalbioticinteractions/nomer/releases/download/0.2.5/nomer.jar
https://github.com/mammaldiversity/mammaldiversity.github.io/raw/master/_data/mdd.csv
https://github.com/plazi/treatments-rdf/archive/master.zip
https://paleobiodb.org/data1.2/refs/list.tsv?all_records
https://paleobiodb.org/data1.2/taxa/list.tsv?all_records
https://query.wikidata.org/sparql?format=json&query=PREFIX%20rdfs:%20%3Chttp://www.w3.org/2000/01/rdf-schema%23%3E%0APREFIX%20bd:%20%3Chttp://www.bigdata.com/rdf%23%3E%0APREFIX%20wd:%20%3Chttp://www.wikidata.org/entity/%3E%0APREFIX%20wikibase:%20%3Chttp://wikiba.se/ontology%23%3E%0APREFIX%20wdt:%20%3Chttp://www.wikidata.org/prop/direct/%3E%0ASELECT%20?i%20?l%20WHERE%20%7B%0A%20%20?i%20wdt:P31%20wd:Q427626.%0A%20%20?i%20rdfs:label%20?l%0A%7D
https://raw.githubusercontent.com/jhpoelen/zenodo-upload/master/zenodo_upload.sh
https://raw.githubusercontent.com/njdowdy/tpt-taxonomy/main/Acari/Acari-standardized-v2.csv
https://raw.githubusercontent.com/njdowdy/tpt-taxonomy/main/host_files/Aves-standardized-v2.csv
https://raw.githubusercontent.com/njdowdy/tpt-taxonomy/main/host_files/Mammalia-standardized-v2.csv
https://raw.githubusercontent.com/njdowdy/tpt-taxonomy/main/Ixodida/Ixodida-standardized-v2.csv
https://raw.githubusercontent.com/njdowdy/tpt-taxonomy/main/Phthiraptera/Phthiraptera-standardized-v2.csv
https://raw.githubusercontent.com/njdowdy/tpt-taxonomy/main/Siphonaptera/Siphonaptera-standardized-v2.csv
https://uofi.box.com/shared/static/54l3b7h4q4pwqq4fgqvx42h3d328fl1c.csv
https://www.discoverlife.org/mp/20q/?act=x_checklist
https://www.discoverlife.org/mp/20q/?act=x_checklist&guide=Apoidea_species&flags=HAS
https://www.discoverlife.org/nh/id/20q/Apoidea_species.xml
https://www.itis.gov/downloads/itisMSSql.zip
https://www.nodc.noaa.gov/cgi-bin/OAS/prd/download/50418.1.1.tar.gz
https://zenodo.org/record/10810438/files/gbif-backbone-by-id.tsv.gz
https://zenodo.org/record/10810438/files/gbif-backbone-by-name.tsv.gz
https://zenodo.org/record/3833105/files/synonym_links.gz
https://zenodo.org/record/3833105/files/taxonomic_units.gz
https://zenodo.org/record/3833105/files/taxon_unit_types.gz
https://zenodo.org/record/3834881/files/taxon.tab.gz
https://zenodo.org/record/5222044/files/gbif-backbone-by-id.tsv.gz
https://zenodo.org/record/5222044/files/gbif-backbone-by-name.tsv.gz
https://zenodo.org/record/5526782/files/taxonCache.tsv.gz
https://zenodo.org/record/5526782/files/taxonMap.tsv.gz
https://zenodo.org/record/5639794/files
https://zenodo.org/record/5719410/files/taxonCache.tsv.gz
https://zenodo.org/record/5719410/files/taxonMap.tsv.gz
https://zenodo.org/record/6127573/files
https://zenodo.org/record/6394935/files/taxonCache.tsv.gz
https://zenodo.org/record/6394935/files/taxonMap.tsv.gz
https://zenodo.org/record/6473194/files
https://zenodo.org/record/6707049/files/gbif-backbone-by-id.tsv.gz
https://zenodo.org/record/6707049/files/gbif-backbone-by-name.tsv.gz
https://zenodo.org/record/7405292/files/gbif-backbone-by-id.tsv.gz
https://zenodo.org/record/7405292/files/gbif-backbone-by-name.tsv.gz
https://zenodo.org/record/7761832/files/taxonCache.tsv.gz
https://zenodo.org/record/7761832/files/taxonMap.tsv.gz
https://zenodo.org/records/10037600/files/taxonCache.tsv.gz
https://zenodo.org/records/10037600/files/taxonMap.tsv.gz
https://zenodo.org/records/10044841/files/taxonMap.tsv.gz
https://zenodo.org/records/10045192/files/taxonMap.tsv.gz
https://zenodo.org/records/10045365/files/taxonMap.tsv.gz
urn:example:reverse-sort.sh
urn:uuid:964538e0-73f3-4091-a5f4-66b3a41bb814
urn:uuid:d5675cd5-3edc-4dd0-8713-907cd5f910e3
worms:worms.json.gz


References

[1] Schoch CL, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020: baaa062. doi: 10.1093/database/baaa062

[2] Sayers EW, et al. GenBank. Nucleic Acids Res. 2019. 47(D1):D94-D99. doi: 10.1093/nar/gky989.

[3]  Integrated Taxonomic Information System (ITIS), www.itis.gov, doi: 10.5066/F7KH0KBK

[4] Simplified GBIF Backbone Taxonomy. Accessed at https://hosted-datasets.gbif.org/datasets/backbone/ on 2021-08-18.

[5] GBIF Secretariat (2021). GBIF Backbone Taxonomy. Checklist dataset https://doi.org/10.15468/39omei accessed via GBIF.org on 2021-08-18.

[6] Index Fungorum: Species Fungorum (2021). http://www.speciesfungorum.org

[7] Plazi Treatment Bank (2021). https://github.com/plazi/treatments-rdf/ http://plazi.org/ .

[8] Bánki, O., Roskov, Y., Döring, M., Ower, G., Vandepitte, L., Hobern, D., Remsen, D., Schalk, P., DeWalt, R. E., Keping, M., Miller, J., Orrell, T., Aalbu, R., Adlard, R., Adriaenssens, E., Aedo, C., Aescht, E., Akkari, N., Alonso-Zarazaga, M. A., et al. (2022). Catalogue of Life Checklist (Version 2022-01-14). Catalogue of Life. https://doi.org/10.48580/d4tp

[9] OpenTree et al. 2022. "Open Tree of Life Taxonomy." Accessed on 2022-11-21 at https://files.opentreeoflife.org/ott/ott3.4/ .

[10] WFO (2022): World Flora Online. Published on the Internet; http://www.worldfloraonline.org. Accessed on: 09 Sep 2022

[11] Dr. Nicolas J. Dowdy, Dr. Erika M. Tucker, Jorrit Poelen, Dr. Vijay Barve, Teresa Mayfield-Meyer, Kathryn Sullivan, & Dr. Jennifer M. Zaspel. (2022). njdowdy/tpt-taxonomy: TPT Taxonomic Resource v2.0.0 (v2.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7215550 https://github.com/njdowdy/tpt-taxonomy/tree/d820e7e036483b48906deb5f3a62fc089f10d9e8

[12] The data were downloaded from the Paleobiology Database on 26 January, 2023

[13] Mammal Diversity Database. (2022). Mammal Diversity Database (1.10) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7394529

[14] Ascher, J. S. and J. Pickering. 2024. Discover Life bee species guide and world checklist (Hymenoptera: Apoidea: Anthophila). http://www.discoverlife.org/mp/20q?guide=Apoidea_species. 

[15]  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

[16] 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

[17] Encyclopedia of Life. 2022. Encyclopedia of Life Dynamic Hierarchy Data Sets. Available from https://opendata.eol.org/organization/about/dynamic-hierarchy

[18] Encyclopedia of Life. (2020). Repackaged Encyclopedia of Life (EOL) Dynamic Hierarchy (1.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.3834881