About jabotR

Open source tools to explore plant specimen collections from JABOT

Overview

jabotR is an R package for exploring plant specimen collections from the JABOT online herbarium collections, hosted by the Rio de Janeiro Botanical Garden. The package interacts with the JABOT Integrated Publishing Toolkit (IPT IPT) by readily downloading full specimen records in Darwin Core Format. It also provides functions to summarize and filter data by taxonomic or geographical criteria.

The JABOT

JABOT is an online system for managing scientific collections housed in herbaria, research laboratory networks at botanical institutions, and living collections in botanical gardens. From a management perspective, it offers curators, sub-curators, and herbarium staff a variety of tools for administration, productivity monitoring, and report generation. The platform allows users to input and publish specimen data and images, with built-in features for analyzing and improving data quality.

Package Description

Package: jabotR
Type: R Package
Version: 1.0.0

Authors: Domingos Cardoso (@DBOSlab ORCID), Carlos Calderón (@caldecid ORCID) and Luís Alexandre Estevão da Silva (@DBOSlab ORCID)

Maintainer: Domingos Cardoso (domingoscardoso@jbrj.gov.br)

Features

Retrieve specimen records by taxonomic/geographic filters
Summarize collections and data availability
Supports Darwin Core Archive (DwC-A) standards
Fully integrates with tidyverse workflows
Includes data visualization and mapping support

Contribute

You can contribute to jabotR by:

Opening issues for feedback or bug reports
Submitting pull requests for fixes or enhancements
Suggesting or developing new features (please open an issue for discussion first)

License

jabotR is open source software. Open tools empower science through reproducibility, accessibility, and equitable knowledge sharing.

Acknowledgements

Development of jabotR is led by the Rio de Janeiro Botanical Garden (JBRJ). We also gratefully acknowledge the financial support provided by CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil’s National Council for Scientific and Technological Development, and FINEP - Financiadora de Estudos e Projetos, Brazil’s Funding Authority for Studies and Projects.

--- title: "About jabotR" subtitle: "Open source tools to explore plant specimen collections from JABOT" format: html: toc: true --- <style> body { position: relative; } .watermark { position: fixed; bottom: 50px; right: 50px; opacity: 0.15; z-index: -1; width: 400px; } .background-overlay { position: fixed; top: 0; left: 0; width: 100%; height: 100%; background-color: rgba(255, 255, 255, 0.8); z-index: -1; } </style> <img src='/figures/jabot_original_logo.png' class='watermark' alt='jabot logo watermark'> ## Overview `jabotR` is an R package for exploring plant specimen collections from the [JABOT online herbarium collections](https://jabot.jbrj.gov.br/v3/consulta.php), hosted by the [Rio de Janeiro Botanical Garden](https://www.gov.br/jbrj/pt-br). The package interacts with the JABOT Integrated Publishing Toolkit ([IPT IPT](https://ipt.jbrj.gov.br/jabot)) by readily downloading full specimen records in Darwin Core Format. It also provides functions to summarize and filter data by taxonomic or geographical criteria. ## The JABOT JABOT is an online system for managing scientific collections housed in herbaria, research laboratory networks at botanical institutions, and living collections in botanical gardens. From a management perspective, it offers curators, sub-curators, and herbarium staff a variety of tools for administration, productivity monitoring, and report generation. The platform allows users to input and publish specimen data and images, with built-in features for analyzing and improving data quality. ## Package Description Package: `jabotR` Type: R Package Version: 1.0.0 Authors: Domingos Cardoso ([\@DBOSlab](https://github.com/DBOSlab) [ORCID](https://orcid.org/0000-0001-7072-2656)), Carlos Calderón ([\@caldecid](https://github.com/caldecid) [ORCID](https://orcid.org/0000-0002-3897-4615)) and Luís Alexandre Estevão da Silva ([\@DBOSlab](https://github.com/DBOSlab) [ORCID](https://orcid.org/0000-0002-7464-922X)) Maintainer: Domingos Cardoso (<domingoscardoso@jbrj.gov.br>) ### Features - Retrieve specimen records by taxonomic/geographic filters - Summarize collections and data availability - Supports Darwin Core Archive (DwC-A) standards - Fully integrates with tidyverse workflows - Includes data visualization and mapping support ## Contribute You can contribute to `jabotR` by: - Opening issues for feedback or bug reports - Submitting pull requests for fixes or enhancements - Suggesting or developing new features (please open an issue for discussion first) ## License `jabotR` is [open source software](/LICENSE.md). Open tools empower science through reproducibility, accessibility, and equitable knowledge sharing. ## Acknowledgements Development of `jabotR` is led by the [Rio de Janeiro Botanical Garden (JBRJ)](https://www.gov.br/jbrj). We also gratefully acknowledge the financial support provided by [CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico](https://www.gov.br/cnpq/pt-br), Brazil's National Council for Scientific and Technological Development, and [FINEP - Financiadora de Estudos e Projetos](https://www.gov.br/finep/pt-br), Brazil's Funding Authority for Studies and Projects.