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```{r setup, include=FALSE}
library(jabotR)

summary_df <- jabot_summary(verbose = FALSE,
                            save = FALSE,
                            dir = "jabot_summary")
```


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\
`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)](https://ipt.jbrj.gov.br/jabot) 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 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.\
\

## History

#### Version 1.0
The first version of the JABOT system (an acronym for Jardim Botânico) began development in 2002 and became operational in 2005. Its creation was preceded by a thorough requirements analysis process, based on interviews and meetings with a group of approximately 50 researchers from the Rio de Janeiro Botanical Garden Research Institute (IPJBRJ). The project also received significant input from the curators of Brazil’s largest herbarium and living collection (arboretum).

As a result of this collaborative design process, the system was tailored to the diverse workflows of botanical research laboratories, including molecular biology, structural botany, seed biology, algae, and fungi, among others. In its initial version, JABOT allowed users to search various scientific collections, such as preserved specimens (herbarium), living collections (arboretum), carpological collections (fruits), xylotheques (wood and wood laminates), and photo archives.

Over time, suggestions for new functionalities—driven by technological advances and the inclusion of new botanical collections—led to the development of updated versions.

#### Version 2.0
The second version incorporated both new modules and an updated user interface designed to be responsive across devices, including smartphones and tablets. The system was entirely developed in-house at IPJBRJ using open-source technologies, specifically the PHP programming language and PostgreSQL database.

#### Version 3.0
Development of Version 3 began in 2016, when partner herbaria started adopting JABOT to manage their own scientific collections. Since then, several new features have been added—many based on curator feedback—enabling integration across herbaria and fostering collaborative data use. This has facilitated curatorial work and improved user experience.

#### Version 4.0
Launched in 2024, Version 4 marked a major upgrade as the entire platform was migrated to Amazon’s cloud environment, resulting in improved system performance and availability. In addition to the platform migration, two new tools—Jabot Image and Jabot Transfer—were developed to streamline the transfer of images to the JABOT/REFLORA system.

Currently, the following **`r length(summary_df$collectionCode)`** collections are published on the JABOT platform, the majority of which from Brazilian herbaria and with digitized specimens:

```{r}
#| echo: false
knitr::asis_output(
  paste0(
    paste(
      mapply(
        function(code, url, holder) {
          sprintf("<a href='%s'><strong>%s</strong></a> (%s)", url, code, holder)
        },
        summary_df$collectionCode,
        summary_df$Jabot_URL,
        summary_df$rightsHolder
      ),
      collapse = ", "
    ),
    "."
  )
)
```

If you are an herbarium curator and wish to publish images and data from your collection in JABOT, send an email request to **Luís Alexandre Estevão da Silva <estevao@jbrj.gov.br>**.\
\
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### [Get Started](/get-started/index.qmd)

Welcome new users! Start learning how to install `jabotR`
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### [Articles](/articles/index.qmd)

"How-to" articles to help you learn how to use `jabotR`
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