Taxonomically validated and enriched Japan Octopodoidea records

The combined Japan Octopodoidea data set (museum) after full taxonomic cleaning, validation, synonym resolution, rank enrichment, authorship appending, and italic formatting. Represents the final stage of the datamuseum workflow and is intended for direct use in analysis and visualisation.

Usage

museum_taxon

Format

A data frame with 2,222 rows and 20 variables:

SciName: Validated scientific name in accepted nomenclature, canonical form without authorship.
Genus: Genus name, updated by taxon_validate where the primary name changed.
Family: Family name.
order: Taxonomic order, appended by taxon_add.
phylum: Taxonomic phylum, appended by taxon_add.
Year: Year of occurrence record.
Latitude: Decimal latitude, filtered to [25, 50].
Longitude: Decimal longitude, filtered to [125, 150].
Country: Country name or code as recorded in the source data set.
Prefecture: State, province, or region as recorded in the source data set.
Precise Location: Locality description as recorded in the source data set.
Source: Institution code or group abbreviation identifying the collecting institution.
Data Frame: Character. Identifies the source data set for each row. One of "GBIF", "InvBase", "BISMAL", "OBIS", or "NSMT".
catalogNumber: Museum lot identification code.
individualCount: Specimen count per lot.
Family_cite: Family name with authorship appended by taxon_cite. Enteroctopodidae authorship added manually as it could not be resolved automatically.
Genus_cite: Genus name with authorship appended by taxon_cite.
SciName_cite: Scientific name with authorship appended by taxon_cite.
Genus_cite_italic: Plotmath italic expression for Genus_cite, suitable for use in ggplot2 via italicize.
SciName_cite_italic: Plotmath italic expression for SciName_cite, suitable for use in ggplot2 via italicize.

Source

Derived from museum. Full source CSVs (raw, trimmed, and Japan-filtered) are available at https://github.com/btorgovitsky00/datamuseum.

Original sources:

Global Biodiversity Information Facility (GBIF). GBIF.org (30 March 2026) GBIF Occurrence Download. https://www.gbif.org doi:10.15468/dl.2379hj

Invert-E-Base. Downloaded 30 March 2026. https://invertebase.org

Biological Information System for Marine Life (BISMAL). Downloaded 30 March 2026. https://www.godac.jamstec.go.jp/bismal/e/

Ocean Biodiversity Information System (OBIS). Downloaded 30 March 2026. https://obis.org

National Museum of Nature and Science, Japan (NSMT). Data obtained directly from the museum, early 2024. https://www.kahaku.go.jp/english/

Details

Processing proceeds in the following steps from museum:

taxon_cleaner applied to SciName in place with drop_na = TRUE, removing uncertain names and reducing the data set from 2,633 to 2,222 observations.
Octopus vulgaris manually corrected to Octopus sinensis to reflect current accepted taxonomy for the Pacific form.
taxon_validate applied to SciName with update_related = TRUE to resolve synonyms and update related taxonomic columns.
taxon_spellcheck applied with update = TRUE using the pre-computed validation report.
Pinnoctopus manually corrected to Callistoctopus across all columns — a generic synonym not resolved automatically by taxon_validate.
taxon_add appends order and phylum with sort = TRUE.
taxon_cite appends authorship to Family, Genus, and SciName.
Muusoctopus small in mature removed as an informal morphospecies name not representing a valid taxon.
Enteroctopodidae authorship added manually as it could not be resolved by taxon_cite.
italicize applied to Genus_cite and SciName_cite.

Taxonomically validated and enriched Japan Octopodoidea records

Usage

Format

Source

Details

See also