Nomer Corpus of Taxonomic Resources hash://sha256/f4e2b9806440d0605f60b81feb9782655291aac2d000c74e4e8fdeb937e29b1d

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], and the World of Flora Online [10].

Please follow academic citation guidelines when using this corpus.

To clone this archive:

$ preston clone https://zenodo.org/record/7065661/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/7065661/files/

<urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/bb6dac6461b66212c5b1826447d7765529ff5cbadeac1915f7c3be9748eda991> .
<hash://sha256/df5b1b63af4c6e995eddfe6bf36b4ece5475574fd4e871ad1ec0a8b283091e08> <http://purl.org/pav/previousVersion> <hash://sha256/bb6dac6461b66212c5b1826447d7765529ff5cbadeac1915f7c3be9748eda991> .
<hash://sha256/d58ab1acf350f056a75bde7f4175d14c5e4dfaf0bf20e2eedbb2fb585bdf0822> <http://purl.org/pav/previousVersion> <hash://sha256/df5b1b63af4c6e995eddfe6bf36b4ece5475574fd4e871ad1ec0a8b283091e08> .
<hash://sha256/6224f259190590c7aed4784de2b27b3005eea0042ae02993ebf7a0fe30d87137> <http://purl.org/pav/previousVersion> <hash://sha256/d58ab1acf350f056a75bde7f4175d14c5e4dfaf0bf20e2eedbb2fb585bdf0822> .
<hash://sha256/06a0582443bec6aa00e8fcd78bdd17f821ee29c8c9ab1999577ca5d085b382a3> <http://purl.org/pav/previousVersion> <hash://sha256/6224f259190590c7aed4784de2b27b3005eea0042ae02993ebf7a0fe30d87137> .
<hash://sha256/f4e2b9806440d0605f60b81feb9782655291aac2d000c74e4e8fdeb937e29b1d> <http://purl.org/pav/previousVersion> <hash://sha256/06a0582443bec6aa00e8fcd78bdd17f821ee29c8c9ab1999577ca5d085b382a3> .

This publication contains versions for the following internet content aliases (aka URLs):

$ preston alias -l tsv --remote https://zenodo.org/record/7065661/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://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/plazi/treatments-rdf/archive/master.zip
https://raw.githubusercontent.com/jhpoelen/zenodo-upload/master/zenodo_upload.sh
https://uofi.box.com/shared/static/54l3b7h4q4pwqq4fgqvx42h3d328fl1c.csv
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
 

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. "Open Tree of Life Taxonomy" https://doi.org/10.5281/zenodo.3937750

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