Treated and corrected occurrence data for plants in Brazil

Dataset Description and Intended Uses This dataset comprises plant occurrence records from Brazil, compiled from four biodiversity databases: the Global Biodiversity Information Facility (GBIF), Reflora – Virtual Herbarium, SpeciesLink, and JABOT. Records from these sources were integrated into a single, standardized dataset following the Darwin Core data standard. Geographic coordinates were added to records when missing, whenever possible, and geographic and taxonomic information was checked, corrected, and harmonized whenever possible to improve data consistency and reliability. The resulting dataset provides a more consistent and reliable resource for biodiversity research than the raw occurrence data available from the original repositories, as it incorporates data integration, standardization, and quality-control procedures. It can be used directly for a variety of applications, including the compilation of regional and national species checklists, biodiversity inventories, species distribution and climatic niche modelling, biogeographic analyses, assessments of species richness and distribution patterns, conservation planning, and studies of biodiversity responses to environmental change. The dataset may also serve as a baseline for future biodiversity assessments and ecological research in Brazil. Each file can be loaded into an R session with the function readRDS. Methods – Occurrence Data Compilation and Standardization Occurrence data were obtained from four biodiversity data repositories: the Global Biodiversity Information Facility (GBIF), Reflora – Virtual Herbarium, SpeciesLink, and JABOT. For Reflora and JABOT, all available records were downloaded through the Integrated Publishing Toolkit (IPT) on 31 July 2026. For SpeciesLink and GBIF, downloads were restricted to records from Brazil and the kingdom Plantae. The downloaded datasets were standardized and harmonized using the R package plantR. Scientific names were standardized against the Brazilian Flora Online whenever possible, and against the World Flora Online or the World Checklist of Vascular Plants when names were not available in the Brazilian reference. Records were filtered to retain only those containing at least one form of geographic information (municipality, locality, or geographic coordinates) and at least one taxonomic identification field (family, genus, or species). No additional filtering criteria were applied. Following standardization, records were organized according to their state-level geographic information, as extracted and processed by plantR. Records for which state information was unavailable were retained in a separate dataset (filename noStateInfo.rds). Data sources and citations GBIF: GBIF.org (24 June 2026). GBIF Occurrence Download. https://doi.org/10.15468/dl.bydy6e Reflora: Reflora – Virtual Herbarium. Available at: https://reflora.jbrj.gov.br/reflora/herbarioVirtual/. Accessed on 31 July 2026. SpeciesLink: SpeciesLink Network. Download performed on 3 August 2026, at 18:45. https://specieslink.net/search JABOT: Data downloaded through the IPT on 31 July 2026. No specific citation recommendation is provided by the repository. Note: The GBIF citation refers to the DOI associated with the occurrence download. The other repositories do not provide DOIs for the downloaded datasets. Field descriptions The following table describes the variables included in the standardized occurrence dataset. Field names follow Darwin Core terminology where applicable; additional fields were retained or generated during data integration, taxonomic standardization, geographic processing, and duplicate detection. Field Description numTombo Unique record identifier, containing the collection code and the number assigned to the specimen in the collection. This is equivalent to the barcode, except for formatting. country Country where the occurrence was recorded. stateProvince State or province where the occurrence was recorded. municipality Municipality where the occurrence was recorded. locality Textual description of the specific geographic location where the occurrence was recorded. basisOfRecord Nature of the record, indicating the type of evidence on which the occurrence is based (e.g., preserved specimen, human observation, or material sample). associatedMedia Links or references to media associated with the occurrence, such as specimen photographs or other digital images. typeStatus Nomenclatural type status of the specimen (e.g., holotype, isotype, or lectotype), when applicable. barcode Barcode or unique identifier associated with the specimen or its record. downloadedFrom Source database or repository from which the occurrence record was obtained. collectionCode Identifier or name of the collection within which the specimen is held. recordedBy Name of the person responsible for collecting or observing the specimen or occurrence. recordNumber Identifier assigned to the collection event by the collector, usually corresponding to the collector's field number. year Year in which the specimen was collected or the occurrence was observed. identifiedBy Name of the person responsible for identifying the specimen or occurrence. yearIdentified Year in which the specimen or occurrence was identified. recordedBy.aux Other people involved in the creation of this record. identifiedBy.aux Other people involved in identifying the specimen. latitude.gazetteer Latitude obtained or inferred through geographic matching with a gazetteer. longitude.gazetteer Longitude obtained or inferred through geographic matching with a gazetteer. resolution.gazetteer Geographic resolution or precision associated with the coordinates obtained through gazetteer matching. latitude Final latitude assigned to the occurrence record, in decimal degrees. longitude Final longitude assigned to the occurrence record, in decimal degrees. origin.coord Origin or provenance of the geographic coordinates, indicating whether they were originally provided or added or inferred through geographic matching with a gazetteer. virtualDuplicates Indicator or information identifying records considered virtual duplicates, provided by the original biodiversity databases. duplicates Indicator identifying records which are physical duplicates, provided by the original biodiversity databases. dup.ID Unique identifier (NumTombo) of records considered potential duplicates during data processing. scientificName Scientific name of the taxon associated with the occurrence, following taxonomic standardization. scientificNameAuthorship Authorship associated with the scientific name. scientificNameStatus Nomenclatural or taxonomic status of the scientific name, when available. scientificNameFull Complete scientific name, including authorship and other taxonomic information when available. taxon.rank Taxonomic rank of the identified organism (e.g., family, genus, or species). tax.notes Notes concerning taxonomic standardization, nomenclatural changes, or taxonomic decisions made during data processing. id Unique identifier assigned to the occurrence record in the standardized dataset. family Standardized family name of the taxon. genus Standardized genus name of the taxon. species Standardized specific epithet of the taxon. Notes on interpretation Some fields are original Darwin Core terms, while others are auxiliary variables created or retained during data processing. In particular: Geographic fields: latitude and longitude represent the final coordinates used in the dataset. The .gazetteer fields preserve geographic information obtained through gazetteer-based matching, while origin.coord documents coordinate provenance. Duplicate detection: virtualDuplicates, duplicates, and dup.ID provide information about virtual and physical duplicate records, as well as identifiers linking potential duplicates. These fields should be considered when selecting records for analyses that require independent occurrence observations. Taxonomic fields: scientificName, family, genus, and species contain the standardized taxonomic information. tax.notes provides additional context about taxonomic decisions. Auxiliary fields: recordedBy.aux and identifiedBy.aux document additional people involved in collecting or identifying specimens, respectively, apart from the principal collector or identifier.