refloraR hex sticker JBRJ logo

paubrasilia aechmea lobelia luetzelburgia luetzelburgia dipteryx aguiaria marcetia hypolepis aeschynomene bocoa ruellia staelia


refloraR is An R package for exploring plant specimen collections from Reflora Virtual Herbarium hosted by Rio de Janeiro Botanical Garden. The package interacts with the Reflora Integrated Publishing Toolkit (IPT) by readily downloading full specimen records for any herbarium in Darwin Core Format. Also, the package has specific functions to summarize information and filter specific information by taxonomic or geographical search.

The Reflora programme

The study of Brazil’s flora, renowned as the richest in the world (BFG 2022), has a long and storied history. During the 18th and 19th centuries, European naturalists, along with a few Brazilian botanists, collected plant specimens while in Brazil, sending them to herbaria in Europe. The primary aim during this period was to investigate the flora and its potential uses. Many of these collections laid the groundwork for the description of new species or genera (serving as nomenclatural types), and were integral to the monumental work Flora Brasiliensis (Martius, Eichler & Urban, 1840–1906), which described over 22,000 species.

In 2010, In 2010, the Brazilian government, through CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) launched the Reflora Programme, with the primary goal of retrieving and making accessible images and data related to Brazilian plant specimens stored primarily in overseas herbaria. These resources have been available since 2013 through the Reflora Virtual Herbarium. In 2014, this initiative was strengthened by the collaboration of SiBBr (Sistema de Informação sobre a Biodiversidade Brasileira) and the IFN (Inventário Florestal Nacional), which expanded the collections published by the Reflora project with the participation of Brazilian herbaria.

The Reflora Virtual Herbarium platform was developed through a partnership between the Rio de Janeiro Botanical Garden (JBRJ) and COPPE (Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering, UFRJ). JBRJ hosts the system, overseeing the reception, storage, and publication of the herbarium data and images.

Complementing the Reflora Virtual Herbarium is the “Flora platform”, first launched in 2008. This system has evolved through several stages — including the Lista de Espécies da Flora do Brasil, Flora do Brasil 2020, and now Flora e Funga do Brasil — and is also part of the broader Reflora Programme. Flora e Funga do Brasil serves as a critical validator for the nomenclature of the Reflora Virtual Herbarium’s images, which are continuously refined and enriched by taxonomists working collaboratively in an online system.

The Reflora Programme has played a crucial role in Brazil’s success in meeting the goals of the Global Strategy for Plant Conservation, part of the Convention on Biological Diversity, for 2010 and 2020. As the challenges of understanding and studying biodiversity persist, the Reflora systems will continue to provide unrestricted access to high-quality, accurate data on Brazil’s plants, algae, and fungi.

The Reflora Virtual Herbarium

The mission to build a virtual herbarium to display the images of Brazilian plants housed in foreign herbaria was presented by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) to the Rio de Janeiro Botanical Garden (JBRJ) in December 2010. The objective was to provide the capacity to store and display high-quality data regarding Brazil’s Flora within a public institution. The Reflora Virtual Herbarium is designed to allow taxonomists to perform procedures similar to those they are accustomed to doing within physical collections. On this site, they have access to high-quality images rather than physical specimens, which can be consulted, re-determined, and typified, among other functionalities. Curators also have access to specimen determination reports to help update their physical collections. This innovative system has been available for study and update by a group of over 900 taxonomists involved in the Lista de Espécies da Flora do Brasil and Flora do Brasil 2020 projects.

Initial partners of this initiative were the herbaria K (Royal Botanic Gardens, Kew), P (Muséum national d’histoire naturelle, Paris), and the RB (JBRJ) herbarium. From 2014 onwards, with the support of SiBBr (Sistema de Informação sobre a Biodiversidade Brasileira) and IFN (Inventário Florestal Nacional), other European, American, and Brazilian herbaria were included in this initiative, many of which received equipment and training to digitize their plant specimens.

Currently, 81 collections are published on the platform. Among them, 12 correspond to digitally repatriated collections, meaning sets of specimens collected in Brazil but physically housed in foreign herbaria, whose high-resolution images and associated metadata have been digitized by the holding institutions and made openly available through the Reflora Virtual Herbarium. This “digital repatriation” thereby supports taxonomic revision, curation, and national biodiversity assessments in Brazil. In this context, “repatriation” refers to the return of access to information (images, label data, determinations, and related metadata) to Brazil via a public national infrastructure, rather than the physical return of specimens.

B (Berlin Botanical Garden and Botanical Museum), E (Royal Botanic Garden Edinburgh), EBC (Economic Botany Collection), K (Royal Botanic Gardens, Kew), MOH ( Missouri Botanical Garden), NY (The New York Botanical Garden), P (Muséum national d’Histoire naturelle), PC (Cryptogamy Collection at the Muséum national d’Histoire naturelle), S (Naturhistoriska Riksmuseet), SOF (Swiss Orchid Foundation), US (Smithsonian Institution), W (Naturhistorisches Museum Wien).

The following 69 collections are from Brazilian herbaria with digitized specimens:

ACAM (Universidade Estadual da Paraíba), ALCB (Universidade Federal da Bahia), ASE (Universidade Federal de Sergipe), BRBA (Universidade Federal do Oeste da Bahia), CEN ( Embrapa Recursos Genéticos e Biotecnologia), CEPEC (Centro de Pesquisas do Cacau), CESJ (Universidade Federal de Juiz de Fora), CGMS (Universidade Federal de Mato Grosso do Sul), COR (Universidade Federal de Mato Grosso do Sul), CRI (Universidade do Extremo Sul Catarinense), DVPR (Universidade Tecnológica Federal do Paraná), EAC (Universidade Federal do Ceará), ECT (Embrapa Clima Temperado), ESA (Universidade de São Paulo), EVB (Universidade Federal da Integração Latino-Americana), FLOR (Universidade Federal de Santa Catarina), FURB (Universidade Regional de Blumenau), GH (Harvard University), HBR (Universidade Federal de Santa Catarina), HCF (Universidade Tecnológica Federal do Paraná), HDCF (Universidade Estadual da Paraíba), HEPH (Jardim Botânico de Brasília), HERBAM (Universidade do Estado de Mato Grosso), HJ (Universidade Federal de Jataí), HRCB (Universidade Estadual Paulista), HSTM (Universidade Federal do Oeste do Pará), HTO (Universidade Federal do Tocantins), HUCP (Pontífica Universidade Católica do Paraná), HUEFS (Universidade Estadual de Feira de Santana), HUEM (Universidade Estadual de Maringá), HUEMG (Universidade do Estado de Minas Gerais), HUENF (Universidade Estadual do Norte Fluminense), HUFU (Universidade Federal de Uberlândia), HUNI (Universidade Federal do Estado do Rio de Janeiro), HURB (Universidade do Recôncavo da Bahia), HVASF (Universidade Federal do Vale do São Francisco), HVAT (Universidade do Vale do Taquari), IAN (Embrapa Amazônia Oriental), IBGE (Herbário IBGE), ICN (Universidade Federal do Rio Grande do Sul), JOI (Universidade da Região de Joinville), LUSC (Universidade do Estado de Santa Catarina), MAC (Instituto do Meio Ambiente do Estado de Alagoas), MBM (Museu Botânico Municipal), MBML (Museu de Biologia Mello Leitão), MG (Museu Paraense Emílio Goeldi), MUFAL (Universidade Federal de Alagoas), PEL (Universidade Federal de Pelotas), PMSP (Prefeitura do Município de São Paulo), R (Museu Nacional), RB (Instituto de Pesquisas Jardim Botânico do Rio de Janeiro), RBR (Universidade Federal Rural do Rio de Janeiro), REAL (Universidade Federal da Fronteira Sul), RFA (Universidade Federal do Rio de Janeiro), RFFP (Universidade do Estado do Rio de Janeiro), RON (Universidade Federal de Rondônia), RSPF (Universidade de Passo Fundo), SAMES (Universidade Federal do Espírito Santo), SJRP (Universidade Estadual Paulista Júlio de Mesquita Filho), SLUI (Universidade Estadual do Maranhão), SPF (Universidade de são Paulo), TEPB (Universidade Federal do Piauí), UB (Universidade de Brasília), UFG (Universidade Federal de Goiás), UFRN (Universidade Federal do Rio Grande do Norte), UNIP (Universidade Paulista), UNOP (Universidade Estadual do Oeste do Paraná), UPCB (Universidade Federal de Paraná), VIES (Universidade Federal do Espírito Santo).

There are now more than 4,800,000 images of specimens available in the Reflora Virtual Herbarium. Among them, 157,652 are nomenclatural types and 1,985,843 are georeferenced records.

If you are an herbarium curator and wish to publish images and data from your collection in Reflora Virtual Herbarium, send a request to the contact email reflora@jbrj.gov.br.

Get Started

Welcome new users! Start learning how to install refloraR

Articles

“How-to” articles to help you learn how to use refloraR

:::