DOI: 10.5281/zenodo.13363473
title: Remediating Toxic Elements with Sunflower, Hemp, Castor Bean, and Bamboo: An Open Dataset of Harmonized Variables

description: This archive contains a dataset collected from sunflower, hemp, castor bean, and bamboo studies for phytoremediation along with code used to parse and analyze the data entries. Data was collected between August 1, 2022, and March 15, 2023, through a comprehensive literature review of 587 studies on the uptake of elements from the soil by plants (i.e., phytoremediation). This dataset focuses on four commodity crops suitable for phytoremediation in semi-arid environments: sunflower, hemp, castor bean, and bamboo. Two hundred thirty-eight studies had data on soil types, elemental pollution, and plant components for calculating bioconcentration factors. We extracted data based on 22 harmonized variables from these studies to create this database to organize results for interpretation and enable consistent and further literature analysis. This archive contains all code and data needed to reproduce the results reported in Ha et al 2025. The database itself is stored in a single CSV file named raw_data/phytoremediation_database.csv and an analysis-ready version in data/bcfdb.csv. This archive also includes four scripts that generate data/bcfdb.csv, perform exploratory and statistical data analysis, and generate figures and summary tables found in the paper.
description: Code

Code is available under the [MIT License](License). 

The following scripts are found in the code/ directory.



01_data_munge.R is a data cleaning script with some exploratory analyses used to parse Excel file in the raw_data folder and generate the files in the data/ folder.

02_exploratory_data_analysis.R summarizes database contents in figures and tables

03_analysis.R script that performs statistical analyses and associated figures

04_figures.qmd report that generates manuscript figures 


Data

Data are available under CC-BY.

The raw_data/ directory contains the Phytoremediation Database and Supplementary Tables.



`phytoremediation_database.csv` is used to curate and manage the database.

`supplementary_table_1.xlsx` contains all citations for data sources used in this archive.


The data/ directory contains an analysis ready dataset in the file bcbdf.csv. This database is created from the phytoremediation_database.csv by the file 01_data_munge.R and includes the following fields:



doi: The Digital Object Identifier (DOI) for the study or source from which the data was obtained.

species: The common name of the crop tested in the study. One of "Sunflower", "Hemp", "Castorbean", "Bamboo"

plant_component: The part of the plant where the bioconcentration factor (BCF) was measured. One of "root", "aboveground", "stem", "whole_plant", "seed", "leaf", "petiole", "flower", "fiber", "fruit", "oil"

element: The type of pollutant element measured in the study. These are strings that represent the chemical symbol of the element, one of "Na", "Mg", "K", "Ca", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Li", "Zn", "As", "Se", "Mo", "Cd", "Sb", "Ba", "La", "Hg", "Tl", "Pb", "Bi", "Th", "U"

soil_type: The type of soil in which the plant is growing. One of "polluted", "spiked", "natural", "commercial", "amended", NA, "aqueous"

bcf: The Bioconcentration Factor (BCF) for the element in the specified organ of the plant. BCF is a measure of the accumulation of a chemical in an organism relative to its environment.

ph: The pH of the soil in which the plant was grown.


The file supplementary_table_1.csv The references are formatted as a single table in a text file for analysis. It is created in the file 01_data_munge.R.

Results

Thefigures/ folder contains figures.



data_collection.pdf shows the search process for collecting the research papers used for the database. Full figure caption: "Flowchart of data extraction from literature. Four commodity crops suitable for phytoremediation in semi-arid environments were included in this analysis. Relevant peer-reviewed studies were collected through Google Scholar, ASU Library Search, and Scopus. Papers meeting any of the following exclusion criteria—lack of data access, non-English language, or absence of relevant data (i.e., papers without obtainable BCF values)—were excluded from the analysis. Data were extracted for 22 harmonized variables from the selected studies. Among these, some studies directly reported BCF values, while others required BCF values to be calculated based on provided information."

fig1.pdf is a figure generated by 04_figures.qmd and shows the number of BCF observations for each plant component grouped by plant species. Full figure caption: "Number of bioconcentration factor (BCF) observations for bamboo, castor bean, hemp, and sunflower, organized by plant species and further categorized by specific plant components (e.g., roots, stems, leaves, and seeds). Sunflower has the highest number of BCF observations (3,732) in 283 analyzed studies, followed by hemp (1,483), castor bean (1,263), and bamboo (201). Among the plant components, stem had the most observations (2,273), followed by root (1,851), leaf (911), and whole plant (831)."

fig2.pdf is a figure generated by 04_figures.qmd and shows a box-plot of the BCF for each element observed in this dataset. Full figure caption: "The distribution of bioconcentration factor (BCF) observations by 27 elements, ranked by the median BCF of each element. A total of 6,679 BCF values obtained in 283 analyzed studies are shown on a log10 scale. The mean BCF values of the elements are ranked in a descending order and the boxes indicate the interquartile ranges. Selenium has the highest median BCF value (2.85) and thorium has the lowest (0.005)."

fig3.pdf is a figure generated by 04_figures.qmd and shows the number of observations for each element, additionally shaded based on the plant species it was observed in.

fig4.pdf is a figure generated by 04_figures.qmd and shows a violin plot for the BCF of three plant components, leaf, root, and stem in each of the four plant species. Full figure caption: "The distribution of bioconcentration factor (BCF) values on a log10 scale for root, stem, and leaf of bamboo, castor bean, hemp, and sunflower. The red line indicates the median BCF value. The medians for root are the highest in all four plants."


The results/ directory contains the file bcf_spiked_vs_polluted.csv that includes the table of results from an exploratory analysis looking at the differences in BCF for commonly studied elements in spiked compared to polluted soils.