Retrieve Taxonomic Data From Dyntaxa
Source:vignettes/retrieve_dyntaxa_data.Rmd
retrieve_dyntaxa_data.RmdDyntaxa
Dyntaxa is a taxonomic database of Swedish organisms hosted at SLU Artdatabanken,
providing information on their names and relationships. The database
includes details such as the current classification, recommended names,
and commonly used synonymous or misapplied names. Dyntaxa is
continuously updated with new species for Sweden, new Swedish names,
synonymous scientific names, and new data on relationships. The data in
Dyntaxa serves as the foundation and framework for taxonomic information
in SHARK. It can be accessed via a
web interface or through the API, as demonstrated in
this tutorial using SHARK4R. Please note that the authors
of SHARK4R are not affiliated with Dyntaxa.
Getting Started
Installation
You can install the latest version of the package from GitHub using
the remotes package:
# install.packages("remotes")
remotes::install_github("sharksmhi/SHARK4R",
ref = remotes::github_release(),
dependencies = TRUE)Load the SHARK4R, tibble and
dplyr libraries:
Retrieve Taxonomy Table from SHARK
Taxon and data tables can be retrieved with the same filtering
options available in SHARK. To see
the available filtering options, please refer to
get_shark_options() and the Retrieve
Data From SHARK tutorial.
# Retrieve taxonomy reports for phytoplankton between 2019 and 2020
shark_taxon <- get_shark_data(tableView = "report_taxon",
fromYear = 2019,
toYear = 2020,
dataTypes = "Phytoplankton",
verbose = FALSE)
# Print data
print(shark_taxon)## # A tibble: 663 × 6
## reported_scientific_name scientific_name dyntaxa_id aphia_id taxon_hierarchy
## <chr> <chr> <dbl> <dbl> <chr>
## 1 Acanthoceras zachariasii Acanthoceras z… 264148 178990 Chromista - Sa…
## 2 Acanthoica quattrospina Acanthoica qua… 236952 235802 Chromista - Ha…
## 3 Acanthostomella Acanthostomella 1010638 NA Chromista - Sa…
## 4 Acanthostomella norvegica Acanthostomell… 238502 183556 Chromista - Sa…
## 5 Achnanthes Achnanthes 1010466 149191 Chromista - Sa…
## 6 Actinastrum hantzschii Actinastrum ha… 238839 160543 Plantae - Viri…
## 7 Actinocyclus Actinocyclus 1010407 148944 Chromista - Sa…
## 8 Actinocyclus normanii Actinocyclus n… 237433 148945 Chromista - Sa…
## 9 Actinocyclus octonarius Actinocyclus o… 237434 149164 Chromista - Sa…
## 10 Actinocyclus octonarius … Actinocyclus o… 248668 162770 Chromista - Sa…
## # ℹ 653 more rows
## # ℹ 1 more variable: counted_rows <dbl>
# Retrieve all phytoplankton data from July 2015
shark_data <- get_shark_data(tableView = "sharkdata_phytoplankton",
fromYear = 2015,
toYear = 2015,
months = 7,
dataTypes = c("Phytoplankton"),
verbose = FALSE)
# Print data
print(shark_data)## # A tibble: 1,627 × 114
## delivery_datatype check_status_sv data_checked_by_sv visit_year visit_month
## <chr> <chr> <chr> <dbl> <dbl>
## 1 Phytoplankton Klar Leverantör 2015 7
## 2 Phytoplankton Klar Leverantör 2015 7
## 3 Phytoplankton Klar Leverantör 2015 7
## 4 Phytoplankton Klar Leverantör 2015 7
## 5 Phytoplankton Klar Leverantör 2015 7
## 6 Phytoplankton Klar Leverantör 2015 7
## 7 Phytoplankton Klar Leverantör 2015 7
## 8 Phytoplankton Klar Leverantör 2015 7
## 9 Phytoplankton Klar Leverantör 2015 7
## 10 Phytoplankton Klar Leverantör 2015 7
## # ℹ 1,617 more rows
## # ℹ 109 more variables: station_name <chr>, reported_station_name <chr>,
## # sample_location_id <dbl>, station_id <dbl>, sample_project_name_sv <chr>,
## # sample_orderer_name_sv <chr>, platform_code <chr>, expedition_id <dbl>,
## # shark_sample_id_md5 <chr>, sample_date <date>, sample_time <time>,
## # sample_latitude_dm <chr>, sample_longitude_dm <chr>,
## # sample_latitude_dd <dbl>, sample_longitude_dd <dbl>, …Dyntaxa API Key
Dyntaxa requires a subscription key to access its API. To obtain your own key, sign up for the taxonomy product at the SLU Swedish Species Information Centre´s Developer Portal. In the example below, the key is retrieved from an environment variable.
# Retrieve the API key
dyntaxa_key <- Sys.getenv("DYNTAXA_KEY")Update SHARK Taxonomy Data
If the taxonomic data downloaded from SHARK are outdated, they can be
updated to the latest Dyntaxa information using SHARK4R.
Alternatively, data can be retrieved from WoRMS. For details, see the WoRMS
Tutorial.
# Update taxonomy information for the retrieved phytoplankton data
updated_taxonomy <- update_dyntaxa_taxonomy(
dyntaxa_ids = shark_data$dyntaxa_id,
subscription_key = dyntaxa_key,
verbose = FALSE)
# Print the updated taxonomy data
print(updated_taxonomy)## # A tibble: 1,627 × 10
## dyntaxa_id scientific_name taxon_kingdom taxon_phylum taxon_class taxon_order
## <dbl> <chr> <chr> <chr> <chr> <chr>
## 1 238225 Alexandrium ps… Chromista Miozoa Dinophyceae Gonyaulaca…
## 2 238302 Tripos fusus Chromista Miozoa Dinophyceae Gonyaulaca…
## 3 238302 Tripos fusus Chromista Miozoa Dinophyceae Gonyaulaca…
## 4 238307 Tripos lineatus Chromista Miozoa Dinophyceae Gonyaulaca…
## 5 238308 Tripos longipes Chromista Miozoa Dinophyceae Gonyaulaca…
## 6 238319 Tripos muelleri Chromista Miozoa Dinophyceae Gonyaulaca…
## 7 6018294 Chaetoceros so… Chromista Gyrista Mediophyce… Chaetocero…
## 8 5000054 Ciliophora Chromista Ciliophora NA NA
## 9 5000054 Ciliophora Chromista Ciliophora NA NA
## 10 4000164 Coscinodiscoph… Chromista Gyrista Coscinodis… NA
## # ℹ 1,617 more rows
## # ℹ 4 more variables: taxon_family <chr>, taxon_genus <chr>,
## # taxon_species <chr>, taxon_hierarchy <chr>Match Taxon Names
# Randomly select 10 phytoplankton taxa from shark_taxon
taxon_names <- sample(shark_taxon$scientific_name, size = 10)
# Match taxon_names with Dyntaxa API
matches <- match_taxon_name(taxon_names = taxon_names,
subscription_key = dyntaxa_key,
multiple_options = FALSE,
verbose = FALSE)
# Print the result
tibble(matches)## # A tibble: 10 × 5
## search_pattern taxon_id best_match author valid_name
## <chr> <int> <chr> <chr> <chr>
## 1 Cuspidothrix issatschenkoi 263645 Cuspidothrix issatsche… (Usač… Cuspidoth…
## 2 Oblea 1010594 Oblea Balec… Oblea
## 3 Chrysotila carterae 236939 Chrysotila carterae (Braa… Chrysotil…
## 4 Bacillaria paxillifera 237763 Bacillaria paxillifera (O.F.… Bacillari…
## 5 Protoperidinium conicoides 238248 Protoperidinium conico… (Paul… Protoperi…
## 6 Scrippsiella 1010578 Scrippsiella Balec… Scrippsie…
## 7 Binuclearia lauterbornii 238927 Binuclearia lauterborn… (Schm… Binuclear…
## 8 Dictyochales 3000573 Dictyochales Haeck… Dictyocha…
## 9 Diatoma vulgaris 238027 Diatoma vulgaris Bory Diatoma v…
## 10 Pseudopediastrum boryanum 257418 Pseudopediastrum borya… (Turp… Pseudoped…Retrieve Taxonomic information
Taxonomic records can be retrieved for individual taxa using the
get_dyntaxa_records() function.
# Get all Dyntaxa IDs
dyntaxa_id <- unique(matches$taxon_id)
# Remove potential NAs
dyntaxa_id <- dyntaxa_id[!is.na(dyntaxa_id)]
# Get Dyntaxa records
dyntaxa_records <- get_dyntaxa_records(taxon_ids = dyntaxa_id,
subscription_key = dyntaxa_key)
# Print records
tibble(dyntaxa_records)## # A tibble: 10 × 24
## taxonId parentId secondaryParents sortOrder isMicrospecies externalComment
## <int> <int> <list> <int> <lgl> <chr>
## 1 236939 6018284 <list [0]> 68774 FALSE NA
## 2 237763 1010465 <list [0]> 71256 FALSE "Illustration (LM…
## 3 238027 1010523 <list [0]> 73170 FALSE "Illustration (LM…
## 4 238248 1010596 <list [0]> 69719 FALSE NA
## 5 238927 1016130 <list [0]> 113140 FALSE NA
## 6 257418 6001140 <list [0]> 112275 FALSE NA
## 7 263645 1016291 <list [0]> 67476 FALSE "2005. Published …
## 8 1010578 2003230 <list [0]> 69660 FALSE NA
## 9 1010594 2003235 <list [0]> 69703 FALSE NA
## 10 3000573 4000161 <list [0]> 71016 FALSE NA
## # ℹ 18 more variables: redlistCategory <lgl>, excludeFromReportingSystem <lgl>,
## # nrOfChilds <int>, names <list>, typedRelations.parentRelations <list>,
## # typedRelations.childRelations <list>, status.id <int>, status.value <chr>,
## # status.name <chr>, statusReason.id <int>, statusReason.value <chr>,
## # statusReason.name <chr>, category.id <int>, category.value <chr>,
## # category.name <chr>, type.id <int>, type.value <chr>, type.name <chr>Retrieve Parent IDs
All parent taxa above the Dyntaxa ID can be retrieved using the
get_dyntaxa_parent_ids() function.
# Get all parents
parents_id <- get_dyntaxa_parent_ids(taxon_ids = dyntaxa_id,
subscription_key = dyntaxa_key,
verbose = FALSE)
# List the IDs
print(parents_id)## [[1]]
## [1] 5000052 5000053 4000147 6020337 3000511 6012635 1016291 263645
##
## [[2]]
## [1] 5000055 6011755 6011756 6011759 6011678 5000062 6011725 6011726 4000169
## [10] 3000850 2003235 1010594
##
## [[3]]
## [1] 5000055 6011754 5000056 4000153 6012363 3000558 2003122 6018284 236939
##
## [[4]]
## [1] 5000055 6011755 6011756 6011758 6322929 5000104 6323134 6323136 4000165
## [10] 3000830 3000599 2003196 1010465 237763
##
## [[5]]
## [1] 5000055 6011755 6011756 6011759 6011678 5000062 6011725 6011726 4000169
## [10] 3000850 2003235 1010596 238248
##
## [[6]]
## [1] 5000055 6011755 6011756 6011759 6011678 5000062 6011725 6011726 4000169
## [10] 3000850 2003230 1010578
##
## [[7]]
## [1] 5000045 6000581 6000582 5000046 4000178 3000405 2003796 1016130 238927
##
## [[8]]
## [1] 5000055 6011755 6011756 6011758 6322929 5000104 6323134 6323135 4000161
## [10] 3000573
##
## [[9]]
## [1] 5000055 6011755 6011756 6011758 6322929 5000104 6323134 6323136 4000165
## [10] 4000166 3000610 2003217 1010523 238027
##
## [[10]]
## [1] 5000045 6000581 6000582 5000046 4000128 3000412 2003286 6001140 257418Construct Complete Taxonomic Table
A comprehensive taxonomic table, including related taxa, can be
created with the construct_dyntaxa_table() function. Use
the add_synonyms parameter to include synonyms, and the
add_parents and add_descendants parameters to
include parent and descendant taxa, respectively. If Taxon IDs are
missing from the DwC-A export downloaded through
get_dyntaxa_dwca() (e.g. species complex and pseudotaxon),
they can be matched using the add_missing_taxa argument.
Additionally, complete hierarchy information can be added as a string of
parent taxa separated by “-” using the add_hierarchy
argument.
# Retrieve complete taxonomic table (including parents and descendants)
taxonomy_table <- construct_dyntaxa_table(taxon_ids = dyntaxa_id,
subscription_key = dyntaxa_key,
shark_output = FALSE,
add_parents = TRUE,
add_synonyms = TRUE,
add_descendants = TRUE,
add_descendants_rank = "genus",
add_missing_taxa = FALSE,
add_hierarchy = FALSE,
verbose = FALSE)
# Print the taxonomy table as a tibble
tibble(taxonomy_table)## # A tibble: 287 × 16
## taxonId acceptedNameUsageID parentNameUsageID scientificName taxonRank
## <chr> <chr> <chr> <chr> <chr>
## 1 urn:lsid:dynt… urn:lsid:dyntaxa.s… urn:lsid:dyntaxa… Pseudopediast… species
## 2 urn:lsid:dynt… urn:lsid:dyntaxa.s… urn:lsid:dyntaxa… Bacillaria pa… species
## 3 urn:lsid:dynt… urn:lsid:dyntaxa.s… urn:lsid:dyntaxa… Chrysotila ca… species
## 4 urn:lsid:dynt… urn:lsid:dyntaxa.s… urn:lsid:dyntaxa… Binuclearia l… species
## 5 urn:lsid:dynt… urn:lsid:dyntaxa.s… urn:lsid:dyntaxa… Oblea genus
## 6 urn:lsid:dynt… urn:lsid:dyntaxa.s… urn:lsid:dyntaxa… Scrippsiella genus
## 7 urn:lsid:dynt… urn:lsid:dyntaxa.s… urn:lsid:dyntaxa… Cuspidothrix … species
## 8 urn:lsid:dynt… urn:lsid:dyntaxa.s… urn:lsid:dyntaxa… Dictyochales order
## 9 urn:lsid:dynt… urn:lsid:dyntaxa.s… urn:lsid:dyntaxa… Diatoma vulga… species
## 10 urn:lsid:dynt… urn:lsid:dyntaxa.s… urn:lsid:dyntaxa… Protoperidini… species
## # ℹ 277 more rows
## # ℹ 11 more variables: scientificNameAuthorship <chr>, taxonomicStatus <chr>,
## # nomenclaturalStatus <chr>, taxonRemarks <chr>, kingdom <chr>, phylum <chr>,
## # class <chr>, order <chr>, family <chr>, genus <chr>, species <chr>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 0.1.7.9000.
## 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 0.1.7.9000},
## url = {https://doi.org/10.5281/zenodo.14169399},
## }