Nomer Corpus of Taxonomic Resources hash://sha256/ed9f35887419d44ad294b4225fed0a9113ac68ca5314c4b6b009709fc1698898 hash://md5/cd316b81c3a6626cc9c9c07c8b8b3872

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/ed9f35887419d44ad294b4225fed0a9113ac68ca5314c4b6b009709fc1698898\
 https://zenodo.org/record/8290342/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\
 --remote https://zenodo.org/record/8290342/files/\
 --anchor hash://sha256/ed9f35887419d44ad294b4225fed0a9113ac68ca5314c4b6b009709fc1698898

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<hash://sha256/0e9bc57bc082b58a2c7a509bb73362b258ec8ddfc6664898e25c639786413fda> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/743e45b0c9fa29f5dffc3f46c45e4f62081e1857a213100887ecd9977a109333> .
<hash://sha256/743e45b0c9fa29f5dffc3f46c45e4f62081e1857a213100887ecd9977a109333> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/6dc0ab2adbba30dd9bb430f317d0a050585e5c2ebb4e8a932331d3c9f0428d17> .
<hash://sha256/6dc0ab2adbba30dd9bb430f317d0a050585e5c2ebb4e8a932331d3c9f0428d17> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/c7f53b23bbeb150dc3454839e25c806229e3414132071b391828bb06400360be> .
<hash://sha256/c7f53b23bbeb150dc3454839e25c806229e3414132071b391828bb06400360be> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/b42923293cebab084517099670cf0b50ad1cce3066286c959644d950b43d7e1b> .
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<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):

preston alias\
 -l tsv\
 --remote https://zenodo.org/record/8290342/files/\
 | cut -f1\
 | sort\
 | uniq

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

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. 2022. Discover Life bee species guide and world checklist (Hymenoptera: Apoidea: Anthophila). http://www.discoverlife.org/mp/20q?guide=Apoidea_species.