DOI: 10.5281/zenodo.5639793
title: Nomer Corpus of Taxonomic Resources hash://sha256/f52b268bbabb342bb3e6312bc54e2f6ebe9ef6d2e745a42ee890e9d05537a77b hash://md5/f20ee16f88fa50ec2bc20660896376b6

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 [8,23], 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.
description: To clone this archive:

preston clone --anchor hash://sha256/f52b268bbabb342bb3e6312bc54e2f6ebe9ef6d2e745a42ee890e9d05537a77b --remote https://linker.bio,https://zenodo.org/records/18717269/files,https://zenodo.org/records/18705780/files,https://zenodo.org/records/18420075/files,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/f52b268bbabb342bb3e6312bc54e2f6ebe9ef6d2e745a42ee890e9d05537a77b --remote https://linker.bio,https://zenodo.org/records/18717269/files,https://zenodo.org/records/18705780/files,https://zenodo.org/records/18420075/files,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 starting with -

<hash://sha256/f52b268bbabb342bb3e6312bc54e2f6ebe9ef6d2e745a42ee890e9d05537a77b> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/bb066cdfa70a4c871fa33c3077d65debcfe1b515826a8d1c2d550afa72d419c1> .<hash://sha256/f52b268bbabb342bb3e6312bc54e2f6ebe9ef6d2e745a42ee890e9d05537a77b> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/79a897a43c52e78048adbc193b228341561a4bcd0502bf8033779fd0ba9b9c7e> .

and ending with

<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/f52b268bbabb342bb3e6312bc54e2f6ebe9ef6d2e745a42ee890e9d05537a77b --remote https://linker.bio,https://zenodo.org/records/18717269/files,https://zenodo.org/records/18705780/files,https://zenodo.org/records/18420075/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.tgzhttps://zenodo.org/records/18412318/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
description: 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

[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

[20] Encyclopedia of Life. (2024). Repackaged Encyclopedia of Life (EOL) Dynamic Hierarchy hash://sha256/f91877189f3cd14f4066b16b693a5f93105fd23b881b0825d6781be6ac674b88 hash://md5/18ca6625cf1d24093dc104851ab5722b (2.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.12695294

[21] Schulz, K. (2025). EOL Dynamic Hierarchy version 2.2.6 [Data set]. Zenodo. https://doi.org/10.5281/zenodo.15399237

[22] Salim, J. A. (2026). Moure Neotropical Bees Cataogue [Data set]. Zenodo. https://doi.org/10.5281/zenodo.18412318

[23] Poelen, J. H. (ed . ) . (2026). Catalogue of Life Repackaged and Sorted hash://sha256/35efd8089b3f86d6789ca75be70630e0e328f2c91b43c2636ecdc49f210b97bb hash://md5/c39e3cbe35f0ae86acf3e77baeb01bfb [Data set]. Zenodo. https://doi.org/10.5281/zenodo.18705780