DOI: 10.5281/zenodo.18394735
title: Nomer Corpus of Taxonomic Resources hash://sha256/fb5933a0d18e62535dd34cc13fa0f22a4647759dc8dc93a0ea867cf2e15cdced hash://md5/64f564ecbd95239717e0ea6c193b3b5b

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], Encyclopedia of Life's Dynamic Hierarchy [17,18,20,21], Wikidata Taxon Items [19] and the Moure Neotropical Bees Cataogue [22].

Please follow academic citation guidelines when using this corpus.

To clone this archive:

preston clone --anchor hash://sha256/fb5933a0d18e62535dd34cc13fa0f22a4647759dc8dc93a0ea867cf2e15cdced --remote https://linker.bio,https://zenodo.org/records/18394735/files,https://zenodo.org/records/15596413/files,https://zenodo.org/records/12695629/files,https://zenodo.org/records/12536844/files,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/

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/fb5933a0d18e62535dd34cc13fa0f22a4647759dc8dc93a0ea867cf2e15cdced --remote https://linker.bio,https://zenodo.org/records/18394735/files,https://zenodo.org/records/15596413/files,https://zenodo.org/records/12695629/files,https://zenodo.org/records/12536844/files,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/

producing the following provenance graph -

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<hash://sha256/83617875e84bb8ae7ac2a257ad50eb8e82d8935d975f465b8ee8f3a803f72b48> .<hash://sha256/83617875e84bb8ae7ac2a257ad50eb8e82d8935d975f465b8ee8f3a803f72b48> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/d2903d0384a8b8193819b8061c8c4e6fec8cc2f7fe72dc0e91c90c07ba2fe15e> .<hash://sha256/d2903d0384a8b8193819b8061c8c4e6fec8cc2f7fe72dc0e91c90c07ba2fe15e> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/5d641367b570f7b3f3c3be4f778f9685f0f050a99f86d8b56475491a4810fc46> .<hash://sha256/5d641367b570f7b3f3c3be4f778f9685f0f050a99f86d8b56475491a4810fc46> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/e4dd19f14143b87497c126aa337a607838ea3766c70afb3a9ffcd978e7a9f7f3> .<hash://sha256/e4dd19f14143b87497c126aa337a607838ea3766c70afb3a9ffcd978e7a9f7f3> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/5a03c765d35a481908e87f518d2c6c801da42183c17002bea1888a8093a4f740> .<hash://sha256/5a03c765d35a481908e87f518d2c6c801da42183c17002bea1888a8093a4f740> 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.<hash://sha256/e7130fb557d9aee033ac7147f4d5c4c75f12223dd43e53c7cbb141372f9579cd> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/e7e1f2e470373b66719db5240947da5c1a76df5dc81ecf786b4173c6e51e89cb> .<hash://sha256/0e9bc57bc082b58a2c7a509bb73362b258ec8ddfc6664898e25c639786413fda> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/743e45b0c9fa29f5dffc3f46c45e4f62081e1857a213100887ecd9977a109333> .<hash://sha256/e7e1f2e470373b66719db5240947da5c1a76df5dc81ecf786b4173c6e51e89cb> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/8ba35deafc847f0d5d69d357241a431b7fd9b6f2735189575b2b7168d523caa9> .<hash://sha256/743e45b0c9fa29f5dffc3f46c45e4f62081e1857a213100887ecd9977a109333> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/6dc0ab2adbba30dd9bb430f317d0a050585e5c2ebb4e8a932331d3c9f0428d17> .<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/fb5933a0d18e62535dd34cc13fa0f22a4647759dc8dc93a0ea867cf2e15cdced --remote https://linker.bio,https://zenodo.org/records/18394735/files,https://zenodo.org/records/15596413/files,https://zenodo.org/records/12695629/files,https://zenodo.org/records/12536844/files,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.tsvcol:NameUsage.tsv.gzhttp://104.198.143.165/files/WFO_Backbone/_WFOCompleteBackbone/WFO_Backbone.ziphttps://download.catalogueoflife.org/col/latest_coldp.ziphttps://files.opentreeoflife.org/ott/ott3.3/ott3.3/taxonomy.tsvhttps://files.opentreeoflife.org/ott/ott3.4/ott3.4.tgzhttps://files.worldfloraonline.org/Files/WFO_Backbone/_WFOCompleteBackbone/WFO_Backbone.ziphttps://ftp.ncbi.nlm.nih.gov/pub/pmc/PMC-ids.csv.gzhttps://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gzhttps://github.com/bio-guoda/preston/releases/download/0.3.9/preston.jarhttps://github.com/bio-guoda/preston/releases/download/0.4.4/preston.jarhttps://github.com/globalbioticinteractions/globi-taxon-names/raw/main/non-taxon-words.txthttps://github.com/globalbioticinteractions/globi-taxon-names/raw/main/taxon-name-mapping.csvhttps://github.com/globalbioticinteractions/nomer/releases/download/0.2.5/nomer.jarhttps://github.com/mammaldiversity/mammaldiversity.github.io/raw/master/_data/mdd.csvhttps://github.com/plazi/treatments-rdf/archive/master.ziphttps://paleobiodb.org/data1.2/refs/list.tsv?all_recordshttps://paleobiodb.org/data1.2/taxa/list.tsv?all_recordshttps://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%7Dhttps://raw.githubusercontent.com/jhpoelen/zenodo-upload/master/zenodo_upload.shhttps://raw.githubusercontent.com/njdowdy/tpt-taxonomy/main/Acari/Acari-standardized-v2.csvhttps://raw.githubusercontent.com/njdowdy/tpt-taxonomy/main/host_files/Aves-standardized-v2.csvhttps://raw.githubusercontent.com/njdowdy/tpt-taxonomy/main/host_files/Mammalia-standardized-v2.csvhttps://raw.githubusercontent.com/njdowdy/tpt-taxonomy/main/Ixodida/Ixodida-standardized-v2.csvhttps://raw.githubusercontent.com/njdowdy/tpt-taxonomy/main/Phthiraptera/Phthiraptera-standardized-v2.csvhttps://raw.githubusercontent.com/njdowdy/tpt-taxonomy/main/Siphonaptera/Siphonaptera-standardized-v2.csvhttps://uofi.box.com/shared/static/54l3b7h4q4pwqq4fgqvx42h3d328fl1c.csvhttps://www.discoverlife.org/mp/20q/?act=x_checklisthttps://www.discoverlife.org/mp/20q/?act=x_checklist&guide=Apoidea_species&flags=HAShttps://www.discoverlife.org/nh/id/20q/Apoidea_species.xmlhttps://www.itis.gov/downloads/itisMSSql.ziphttps://www.nodc.noaa.gov/cgi-bin/OAS/prd/download/50418.1.1.tar.gzhttps://zenodo.org/record/10810438/files/gbif-backbone-by-id.tsv.gzhttps://zenodo.org/record/10810438/files/gbif-backbone-by-name.tsv.gzhttps://zenodo.org/record/3833105/files/synonym_links.gzhttps://zenodo.org/record/3833105/files/taxonomic_units.gzhttps://zenodo.org/record/3833105/files/taxon_unit_types.gzhttps://zenodo.org/record/3834881/files/taxon.tab.gzhttps://zenodo.org/record/5222044/files/gbif-backbone-by-id.tsv.gzhttps://zenodo.org/record/5222044/files/gbif-backbone-by-name.tsv.gzhttps://zenodo.org/record/5526782/files/taxonCache.tsv.gzhttps://zenodo.org/record/5526782/files/taxonMap.tsv.gzhttps://zenodo.org/record/5639794/fileshttps://zenodo.org/record/5719410/files/taxonCache.tsv.gzhttps://zenodo.org/record/5719410/files/taxonMap.tsv.gzhttps://zenodo.org/record/6127573/fileshttps://zenodo.org/record/6394935/files/taxonCache.tsv.gzhttps://zenodo.org/record/6394935/files/taxonMap.tsv.gzhttps://zenodo.org/record/6473194/fileshttps://zenodo.org/record/6707049/files/gbif-backbone-by-id.tsv.gzhttps://zenodo.org/record/6707049/files/gbif-backbone-by-name.tsv.gzhttps://zenodo.org/record/7405292/files/gbif-backbone-by-id.tsv.gzhttps://zenodo.org/record/7405292/files/gbif-backbone-by-name.tsv.gzhttps://zenodo.org/record/7761832/files/taxonCache.tsv.gzhttps://zenodo.org/record/7761832/files/taxonMap.tsv.gzhttps://zenodo.org/records/10037600/files/taxonCache.tsv.gzhttps://zenodo.org/records/10037600/files/taxonMap.tsv.gzhttps://zenodo.org/records/10044841/files/taxonMap.tsv.gzhttps://zenodo.org/records/10045192/files/taxonMap.tsv.gzhttps://zenodo.org/records/10045365/files/taxonMap.tsv.gzhttps://zenodo.org/records/12695294/files/dh21.ziphttps://zenodo.org/records/15399237/files/dh226.ziphttps://zenodo.org/records/18379586/files/moure.tgzurn:example:reverse-sort.shurn:uuid:964538e0-73f3-4091-a5f4-66b3a41bb814urn:uuid:d5675cd5-3edc-4dd0-8713-907cd5f910e3wikidata:wikidata.json.bz2worms: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

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[19] 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

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