Retrieve HAB Data From IOC-UNESCO Databases

IOC-UNESCO Databases

The Intergovernmental Oceanographic Commission (IOC) of UNESCO is the United Nations body dedicated to supporting global ocean science, services, and governance. The IOC-UNESCO Taxonomic Reference List of Harmful Microalgae (Lundholm et al., 2009) 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 accessed through APIs, as demonstrated in this tutorial using SHARK4R.

Getting Started

Installation

You can install the latest version of SHARK4R from CRAN using:

install.packages("SHARK4R")

Load the SHARK4R and dplyr libraries:

library(SHARK4R)

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
print(hab_list)
## # A tibble: 536 × 29
##    AphiaID ScientificName      Authority AphiaID_accepted ScientificName_accep…¹
##      <dbl> <chr>               <chr>                <dbl> <chr>                 
##  1  418135 Acanthogonyaulax s… (Murray …           418135 Acanthogonyaulax spin…
##  2  639809 Achomosphaera hype… (Defland…           110041 Gonyaulax spinifera   
##  3  841664 Aetokthonos hydril… S.B.Wild…           841664 Aetokthonos hydrillic…
##  4  232546 Akashiwo sanguinea  (K.Hiras…           232546 Akashiwo sanguinea    
##  5  233407 Alexandrium acaten… (Whedon …           231873 Alexandrium catenella 
##  6  109707 Alexandrium affine  (H.Inoue…           109707 Alexandrium affine    
##  7  231872 Alexandrium anders… Balech, …           246835 Alexandrium andersonii
##  8  246835 Alexandrium anders… Balech, …           246835 Alexandrium andersonii
##  9  233452 Alexandrium angust… F.J.R.Ta…           109711 Alexandrium minutum   
## 10  833063 Alexandrium austra… Sh.Murra…           833063 Alexandrium australie…
## # ℹ 526 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>, …

A separate list of harmful non-toxic species is also available (Zingone & Escalera, 2025). This compilation focuses on taxa for which no toxin production is known, yet which have been linked to negative impacts on marine organisms, including mortality and ecosystem disturbance. The list is designed to be used alongside the IOC-UNESCO Taxonomic Reference List of Harmful Microalgae and is mutually exclusive with it. As a result, any species known to produce toxins is omitted, even when reported harmful effects are attributed to non-toxic processes such as oxygen depletion.

# Retrieve complete Harmful non-toxic list
hab_non_toxic_list <- get_hab_list(harmful_non_toxic_only = TRUE,
                                   verbose = FALSE)

# Print result
print(hab_non_toxic_list)
## # A tibble: 67 × 24
##    AphiaID ScientificName      Authority AphiaID_accepted ScientificName_accep…¹
##      <int> <chr>               <chr>                <int> <chr>                 
##  1  109708 Alexandrium balech… (Steidin…           109708 Alexandrium balechii  
##  2  375699 Aureococcus anopha… Hargrave…           375699 Aureococcus anophagef…
##  3  375701 Aureoumbra lagunen… D.A.Stoc…           375701 Aureoumbra lagunensis 
##  4 1360848 Blixaea quinquecor… (T.H.Abé…          1360848 Blixaea quinquecornis 
##  5  149619 Cerataulina pelagi… (Cleve) …           149619 Cerataulina pelagica  
##  6  163013 Chaetoceros calcit… (Paulsen…           163015 Chaetoceros simplex v…
##  7  178180 Chaetoceros coarct… Lauder, …           178180 Chaetoceros coarctatus
##  8  156607 Chaetoceros concav… Mangin, …           156607 Chaetoceros concavico…
##  9  156611 Chaetoceros convol… Castraca…           156611 Chaetoceros convolutus
## 10  465389 Chaetoceros crioph… Castraca…           465389 Chaetoceros criophilus
## # ℹ 57 more rows
## # ℹ abbreviated name: ¹​ScientificName_accepted
## # ℹ 19 more variables: Authority_accepted <chr>, Fossil <int>, Kingdom <chr>,
## #   Phylum <chr>, Class <chr>, Order <chr>, Family <chr>, taxonRank <chr>,
## #   Genus <chr>, Marine <int>, Brackish <int>, Fresh <int>, Terrestrial <int>,
## #   taxonomicStatus <chr>, Unacceptreason <chr>, DateLastModified <dttm>,
## #   LSID <chr>, `Parent AphiaID` <int>, Citation <chr>

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
print(toxin_list)
## # A tibble: 536 × 55
##       id toxin_group recommended_name synonyms recommended_acronym acronyms
##    <int> <chr>       <chr>            <list>   <chr>               <list>  
##  1   624 Azaspiracid Azaspiracid-68   <NULL>   AZA-68              <NULL>  
##  2   623 Azaspiracid Azaspiracid-67   <NULL>   AZA-67              <NULL>  
##  3   622 Azaspiracid Azaspiracid-66   <NULL>   AZA-66              <NULL>  
##  4   621 Azaspiracid Azaspiracid-65   <NULL>   AZA-65              <NULL>  
##  5   620 Azaspiracid Azaspiracid-61   <NULL>   AZA-61              <NULL>  
##  6   619 Azaspiracid Azaspiracid-60   <NULL>   AZA-60              <NULL>  
##  7   618 Azaspiracid Azaspiracid-49   <NULL>   AZA-49              <NULL>  
##  8   617 Azaspiracid Azaspiracid-48   <NULL>   AZA-48              <NULL>  
##  9   616 Azaspiracid Azaspiracid-47   <NULL>   AZA-47              <NULL>  
## 10   615 Azaspiracid Azaspiracid-46   <NULL>   AZA-46              <NULL>  
## # ℹ 526 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>, …

On occasion the Toxins database TLS certificate may temporarily lapse. Should get_toxin_list() fail with a certificate error, the verification step can be bypassed by running get_toxin_list(insecure = TRUE). Only do this when the certificate issue is known and trusted, as it disables protection against tampering.

Citation

## To cite package 'SHARK4R' in publications use:
## 
##   Lindh, M. and Torstensson, A. (2026). SHARK4R: Accessing and
##   Validating Marine Environmental Data from 'SHARK' and Related
##   Databases. R package version 1.2.0.
##   https://CRAN.R-project.org/package=SHARK4R
## 
## 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 = {2026},
##     note = {R package version 1.2.0},
##     url = {https://CRAN.R-project.org/package=SHARK4R},
##   }

References