Retrieve HAB Data From IOC-UNESCO Databases

IOC-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

Installation

You can install the package from GitHub using the devtools package:

# install.packages("devtools")
devtools::install_github("sharksmhi/SHARK4R",
                         dependencies = TRUE)

Load the SHARK4R and dplyr libraries:

library(SHARK4R)
library(dplyr)

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: 599 × 29
##    AphiaID ScientificName      Authority AphiaID_accepted ScientificName_accep…¹
##      <dbl> <chr>               <chr>                <dbl> <chr>                 
##  1  231787 Akashiwo            G.Hansen…           231787 Akashiwo              
##  2  232546 Akashiwo sanguinea  (K.Hiras…           232546 Akashiwo sanguinea    
##  3  109470 Alexandrium         Halim, 1…           109470 Alexandrium           
##  4  109707 Alexandrium affine  (H.Inoue…           109707 Alexandrium affine    
##  5  231872 Alexandrium anders… Balech, …           246835 Alexandrium andersonii
##  6  246835 Alexandrium anders… Balech, …           246835 Alexandrium andersonii
##  7  233452 Alexandrium angust… F.J.R.Ta…           109711 Alexandrium minutum   
##  8  833063 Alexandrium austra… Sh.Murra…           833063 Alexandrium australie…
##  9  109708 Alexandrium balech… (Steidin…           109708 Alexandrium balechii  
## 10  231873 Alexandrium catene… (Whedon …           231873 Alexandrium catenella 
## # ℹ 589 more rows
## # ℹ abbreviated name: ¹​ScientificName_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: 457 × 55
##       id toxin_group recommended_name synonyms recommended_acronym acronyms
##    <int> <chr>       <chr>            <list>   <chr>               <list>  
##  1   541 Azaspiracid azaspiracid-27   <NULL>   AZA27               <NULL>  
##  2   540 Azaspiracid azaspiracid-26   <NULL>   AZA26               <NULL>  
##  3   539 Azaspiracid azaspiracid-23   <NULL>   AZA23               <NULL>  
##  4   538 Azaspiracid azaspiracid-21   <NULL>   AZA21               <NULL>  
##  5   537 Azaspiracid azaspriracid-19  <NULL>   AZA19               <NULL>  
##  6   536 Azaspiracid azaspriacid-18   <NULL>   AZA18               <NULL>  
##  7   535 Azaspiracid azaspiracid-17   <NULL>   AZA17               <NULL>  
##  8   534 Azaspiracid azaspiracid-16   <NULL>   AZA16               <NULL>  
##  9   533 Azaspiracid azaspriacid-15   <NULL>   AZA15               <NULL>  
## 10   532 Azaspiracid azaspiracid-14   <NULL>   AZA14               <NULL>  
## # ℹ 447 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 <lgl>, 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:
## 
##   Markus Lindh, Anders Torstensson (2025). SHARK4R: Retrieving,
##   Analyzing, and Validating Marine Data from SHARK and Nordic
##   Microalgae. R package version 0.1.7.
##   https://doi.org/10.5281/zenodo.14169399
## 
## A BibTeX entry for LaTeX users is
## 
##   @Manual{,
##     title = {SHARK4R: Retrieving, Analyzing, and Validating Marine Data from SHARK and Nordic Microalgae},
##     author = {Markus Lindh and Anders Torstensson},
##     year = {2025},
##     note = {R package version 0.1.7},
##     url = {https://doi.org/10.5281/zenodo.14169399},
##   }