Describe the taxonomic name providers
Usage
taxadb_provider_info(provider = taxadb_providers())Value
a data.frame with one row per provider giving its title, url,
the source its data is taken from, its license and a citation.
Details
Providers are not interchangeable. col, gbif and ott are
synthesis projects that integrate other checklists, while itis, ncbi,
fb and slb are primary authorities; the synthesis column records
which is which. More importantly, providers disagree: the same name can
be accepted by one and a synonym of something else in another, so a name
resolved against one provider should not be mixed with names resolved
against another. See vignette("data-sources").
Redistribution terms differ too. fb and slb are CC BY-NC, so those
two tables may not be used commercially.
Examples
taxadb_provider_info()
#> provider title
#> 1 itis Integrated Taxonomic Information System
#> 2 ncbi NCBI Taxonomy
#> 3 col Catalogue of Life
#> 4 gbif GBIF Backbone Taxonomy
#> 5 ott Open Tree Taxonomy
#> 6 fb FishBase
#> 7 slb SeaLifeBase
#> url
#> 1 https://www.itis.gov
#> 2 https://www.ncbi.nlm.nih.gov/taxonomy
#> 3 https://www.catalogueoflife.org
#> 4 https://www.gbif.org
#> 5 https://tree.opentreeoflife.org
#> 6 https://fishbase.org
#> 7 https://www.sealifebase.org
#> source
#> 1 https://www.itis.gov/downloads/itisSqlite.zip
#> 2 https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
#> 3 https://download.checklistbank.org/col/latest_dwca.zip
#> 4 https://hosted-datasets.gbif.org/datasets/backbone/current/backbone.zip
#> 5 https://files.opentreeoflife.org/ott/
#> 6 s3://cboettig/fishbase/fb/
#> 7 s3://cboettig/fishbase/slb/
#> license license_url synthesis
#> 1 public domain https://www.itis.gov/what_itis.html FALSE
#> 2 public domain https://www.ncbi.nlm.nih.gov/home/about/policies/ FALSE
#> 3 CC BY 4.0 https://creativecommons.org/licenses/by/4.0/ TRUE
#> 4 CC BY 4.0 https://creativecommons.org/licenses/by/4.0/ TRUE
#> 5 CC0 1.0 https://creativecommons.org/publicdomain/zero/1.0/ TRUE
#> 6 CC BY-NC 4.0 https://creativecommons.org/licenses/by-nc/4.0/ FALSE
#> 7 CC BY-NC 4.0 https://creativecommons.org/licenses/by-nc/4.0/ FALSE
#> citation
#> 1 Retrieved from the Integrated Taxonomic Information System on-line database, https://www.itis.gov
#> 2 Schoch CL, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (2020). doi:10.1093/database/baaa062
#> 3 Bánki O, et al. Catalogue of Life. https://doi.org/10.48580/dfz8
#> 4 GBIF Secretariat. GBIF Backbone Taxonomy. https://doi.org/10.15468/39omei
#> 5 Rees JA, Cranston K. Automated assembly of a reference taxonomy for phylogenetic data synthesis. Biodiversity Data Journal (2017). doi:10.3897/BDJ.5.e12581
#> 6 Froese R, Pauly D (eds). FishBase. https://www.fishbase.org
#> 7 Palomares MLD, Pauly D (eds). SeaLifeBase. https://www.sealifebase.org
taxadb_provider_info("col")$citation
#> [1] "Bánki O, et al. Catalogue of Life. https://doi.org/10.48580/dfz8"