DOI: 10.5281/zenodo.10044989
title: Nomer Corpus of Taxonomic Resources hash://sha256/5a03c765d35a481908e87f518d2c6c801da42183c17002bea1888a8093a4f740 hash://md5/b1b93da821959c605b4d7ea0ca361ded

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], and Discover Life bee species guide and world checklist [14].
Please follow academic citation guidelines when using this corpus.
To clone this archive:
preston clone --anchor hash://sha256/5a03c765d35a481908e87f518d2c6c801da42183c17002bea1888a8093a4f740  --remote https://zenodo.org/record/10044989/files/,https://zenodo.org/record/10037817/files/,https://zenodo.org/record/8327611/files/,https://linker.bio https://zenodo.org/record/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://sha256/5a03c765d35a481908e87f518d2c6c801da42183c17002bea1888a8093a4f740 --remote https://zenodo.org/record/10044989/files/,https://zenodo.org/record/10037817/files/,https://zenodo.org/record/8327611/files/,https://linker.bio
producing the following provenance graph - 
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<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):
preston alias -l tsv --anchor hash://sha256/5a03c765d35a481908e87f518d2c6c801da42183c17002bea1888a8093a4f740 --remote https://zenodo.org/record/10044989/files/,https://zenodo.org/record/10037817/files/,https://zenodo.org/record/8327611/files/,https://linker.bio | cut -f1 | sort | uniq 
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.itis.gov/downloads/itisMSSql.zip
https://www.nodc.noaa.gov/cgi-bin/OAS/prd/download/50418.1.1.tar.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
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urn:example:reverse-sort.sh
urn:uuid:964538e0-73f3-4091-a5f4-66b3a41bb814
urn:uuid:d5675cd5-3edc-4dd0-8713-907cd5f910e3
 
[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. 2022. Discover Life bee species guide and world checklist (Hymenoptera: Apoidea: Anthophila). http://www.discoverlife.org/mp/20q?guide=Apoidea_species.