Retrieve HAB Data From IOC-UNESCO Databases
Source:vignettes/retrieve_hab_data.Rmd
retrieve_hab_data.RmdIOC-UNESCO Databases
The Intergovernmental Oceanographic Commission of UNESCO (IOC) is the United Nations body dedicated to supporting global ocean science, services, and governance. The IOC-UNESCO Taxonomic Reference List of Harmful Microalgae focuses on species known to produce toxins or exhibit toxic effects, along with a few species suspected of toxin production. All toxic species in the list are verified with WoRMS to ensure accurate taxonomy.
The IOC-UNESCO Toxins database complements this list by providing detailed reference information about toxins, some of which are associated with harmful algal events.
The information from these databases can be access through APIs, as
demonstrated in this tutorial using SHARK4R.
Getting Started
Retrieve HAB List From IOC Taxonomic List
The complete HAB list, including scientific names and AphiaIDs, can
be downloaded from the IOC-UNESCO Taxonomic Reference
List of Harmful Microalgae. The output fields are customizable
through function parameters—for example, setting
classification = FALSE excludes higher taxonomic
information from the results.
# Retrieve complete HAB list
hab_list <- get_hab_list()
# Print result as tibble
tibble(hab_list)## # A tibble: 704 × 29
## AphiaID ScientificName Authority AphiaID_accepted ScientificName_accep…¹
## <dbl> <chr> <chr> <dbl> <chr>
## 1 1653558 Aerosakkonemataceae Struneck… 1653558 Aerosakkonemataceae
## 2 836651 Aetokthonos S.B.Wild… 836651 Aetokthonos
## 3 841664 Aetokthonos hydril… S.B.Wild… 841664 Aetokthonos hydrillic…
## 4 231787 Akashiwo G.Hansen… 231787 Akashiwo
## 5 232546 Akashiwo sanguinea (K.Hiras… 232546 Akashiwo sanguinea
## 6 109470 Alexandrium Halim, 1… 109470 Alexandrium
## 7 109707 Alexandrium affine (H.Inoue… 109707 Alexandrium affine
## 8 231872 Alexandrium anders… Balech, … 246835 Alexandrium andersonii
## 9 246835 Alexandrium anders… Balech, … 246835 Alexandrium andersonii
## 10 233452 Alexandrium angust… F.J.R.Ta… 109711 Alexandrium minutum
## # ℹ 694 more rows
## # ℹ abbreviated name: ¹ScientificName_accepted
## # ℹ 24 more variables: Authority_accepted <chr>, Fossil <dbl>, Kingdom <chr>,
## # Phylum <chr>, Class <chr>, Order <chr>, Family <chr>, taxonRank <chr>,
## # Genus <chr>, Subgenus <lgl>, Species <chr>, Subspecies <lgl>, Marine <dbl>,
## # Brackish <dbl>, Fresh <dbl>, Terrestrial <dbl>, taxonomicStatus <chr>,
## # Qualitystatus <chr>, Unacceptreason <chr>, DateLastModified <date>, …Retrieve HAB Toxins From IOC Toxins Database
The complete Toxin list can be downloaded from the IOC-UNESCO Toxins
database using the get_toxin_list() function.
# Retrieve complete toxin list
toxin_list <- get_toxin_list()
# Print result as tibble
tibble(toxin_list)## # A tibble: 462 × 55
## id toxin_group recommended_name synonyms recommended_acronym acronyms
## <int> <chr> <chr> <list> <chr> <list>
## 1 546 Prymnesin Prymnesin-B2 <NULL> PRYM-B2 <chr [1]>
## 2 545 Prymnesin Prymnesin-B1 <NULL> PRYM-B1 <chr [1]>
## 3 544 Prymnesin Prymnesin-2 <NULL> PRYM-2 <chr [1]>
## 4 543 Prymnesin Prymnesin-1 <chr [1]> PRYM-1 <chr [1]>
## 5 542 None trial <NULL> NA <NULL>
## 6 541 Azaspiracid azaspiracid-27 <NULL> AZA27 <NULL>
## 7 540 Azaspiracid azaspiracid-26 <NULL> AZA26 <NULL>
## 8 539 Azaspiracid azaspiracid-23 <NULL> AZA23 <NULL>
## 9 538 Azaspiracid azaspiracid-21 <NULL> AZA21 <NULL>
## 10 537 Azaspiracid azaspriracid-19 <NULL> AZA19 <NULL>
## # ℹ 452 more rows
## # ℹ 49 more variables: cas_number <chr>, alternative_cas_numbers <list>,
## # formula <chr>, exact_mono_isotopic_mass <dbl>, molfile <chr>,
## # alternative_molfiles <lgl>, smiles <chr>, alternative_smiles <list>,
## # inchi_key <chr>, alternative_inchi_keys <list>, inchi <chr>,
## # alternative_inchies <lgl>, spectra_available <lgl>, certified <lgl>,
## # non_certified_reference_material <lgl>, chemical_analysis_research <lgl>, …Citation
## To cite package 'SHARK4R' in publications use:
##
## Lindh, M. and Torstensson, A. (2025). SHARK4R: Accessing and
## Validating Marine Environmental Data from SHARK and Related
## Databases. R package version 0.1.7.9000.
## https://doi.org/10.5281/zenodo.14169399
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {SHARK4R: Accessing and Validating Marine Environmental Data from SHARK and Related Databases},
## author = {Markus Lindh and Anders Torstensson},
## year = {2025},
## note = {R package version 0.1.7.9000},
## url = {https://doi.org/10.5281/zenodo.14169399},
## }